From 384e09fc59a634980f55e1d49ac86ce49c744afa Mon Sep 17 00:00:00 2001 From: Florian Engertsberger Date: Tue, 30 Nov 2021 13:06:30 +0100 Subject: [PATCH 01/38] add data-testid --- dist/common/forms.d.ts | 2 +- dist/menu/DatasetCard.js | 7 +++--- dist/menu/DatasetCard.js.map | 2 +- dist/menu/DatasetSearchBox.js | 4 +-- dist/menu/DatasetSearchBox.js.map | 2 +- dist/scores/forms.d.ts | 42 +++++++++++++++---------------- src/menu/DatasetCard.tsx | 7 +++--- src/menu/DatasetSearchBox.tsx | 4 +-- 8 files changed, 36 insertions(+), 34 deletions(-) diff --git a/dist/common/forms.d.ts b/dist/common/forms.d.ts index 7280ad5e..d9d379e5 100644 --- a/dist/common/forms.d.ts +++ b/dist/common/forms.d.ts @@ -149,7 +149,7 @@ export declare const FORM_GENE_FILTER: { return: string; optionsData: () => Promise<{ name: string; - value: string | number; + value: import("lineupjs").ICompareValue; }[]>; options: { placeholder: string; diff --git a/dist/menu/DatasetCard.js b/dist/menu/DatasetCard.js index 59315eb7..596b29e7 100644 --- a/dist/menu/DatasetCard.js +++ b/dist/menu/DatasetCard.js @@ -6,6 +6,7 @@ import { DatasetSearchBox } from './DatasetSearchBox'; import { Species, SpeciesUtils } from 'tdp_gene'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }) { var _a, _b; + const testId = `datasetcard-${cssClass}`; const { app } = React.useContext(OrdinoContext); const [dirtyNamedSets, setDirtyNamedSets] = React.useState(false); const loadPredefinedSet = React.useMemo(() => { @@ -74,7 +75,7 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, }; const id = React.useMemo(() => UniqueIdManager.getInstance().uniqueId(), []); const activeTabIndex = 0; - return (React.createElement("div", { className: `ordino-dataset ${cssClass || ''}` }, + return (React.createElement("div", { className: `ordino-dataset ${cssClass || ''}`, "data-testid": testId }, React.createElement("h4", { className: "text-start mb-3" }, React.createElement("i", { className: 'me-2 ordino-icon-2 ' + icon }), name), @@ -82,13 +83,13 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, React.createElement("div", { className: "card-body p-3" }, React.createElement("ul", { className: "nav nav-pills session-tab" }, tabs.map((tab, index) => { return (React.createElement("li", { key: tab.id, className: "nav-item", role: "presentation" }, - React.createElement("a", { className: `nav-link ${(index === activeTabIndex) ? 'active' : ''}`, id: `dataset-tab-${tab.id}-${id}`, "data-bs-toggle": "tab", href: `#dataset-panel-${tab.id}-${id}`, role: "tab", "aria-controls": `dataset-panel-${tab.id}-${id}`, "aria-selected": (index === activeTabIndex) }, + React.createElement("a", { className: `nav-link ${(index === activeTabIndex) ? 'active' : ''}`, "data-testid": `${tab.id}-link`, id: `dataset-tab-${tab.id}-${id}`, "data-bs-toggle": "tab", href: `#dataset-panel-${tab.id}-${id}`, role: "tab", "aria-controls": `dataset-panel-${tab.id}-${id}`, "aria-selected": (index === activeTabIndex) }, React.createElement("i", { className: 'me-2 ' + tab.icon }), tab.name))); })), React.createElement("div", { className: "tab-content" }, tabs.map((tab, index) => { const separators = tokenSeparators ? { tokenSeparators } : null; - return (React.createElement("div", { key: tab.id, className: `tab-pane fade mt-4 ${(index === activeTabIndex) ? 'show active' : ''}`, role: "tabpanel", id: `dataset-panel-${tab.id}-${id}`, "aria-labelledby": `dataset-tab-${tab.id}-${id}` }, + return (React.createElement("div", { key: tab.id, className: `tab-pane fade mt-4 ${(index === activeTabIndex) ? 'show active' : ''}`, "data-testid": `${tab.id}-tab`, role: "tabpanel", id: `dataset-panel-${tab.id}-${id}`, "aria-labelledby": `dataset-tab-${tab.id}-${id}` }, React.createElement(DatasetSearchBox, Object.assign({ placeholder: `Add ${name}`, dataSource: dataSource, params: { species: tab.id }, onSaveAsNamedSet: (items) => onSaveAsNamedSet(items, { key: Species.SPECIES_SESSION_KEY, value: tab.id }), onOpen: (event, searchResult) => { onOpenSearchResult(event, { searchResult, species: tab.id }); } }, separators)), React.createElement("div", { className: "row mt-4" }, React.createElement(NamedSetList, { headerIcon: "fas fa-database", headerText: "Predefined Sets", onOpen: (event, namedSet) => { onOpenNamedSet(event, { namedSet, species: tab.id }); }, status: predefinedNamedSets.status, value: filterValue(predefinedNamedSets.value, tab.id) }), diff --git a/dist/menu/DatasetCard.js.map b/dist/menu/DatasetCard.js.map index 6286b643..3af1cad3 100644 --- a/dist/menu/DatasetCard.js.map +++ b/dist/menu/DatasetCard.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/menu/DatasetSearchBox.js b/dist/menu/DatasetSearchBox.js index ec4127ff..88a667b0 100644 --- a/dist/menu/DatasetSearchBox.js +++ b/dist/menu/DatasetSearchBox.js @@ -103,8 +103,8 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName } }) } }), - React.createElement("button", { className: "btn btn-secondary", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: (event) => onOpen(event, searchResults) }, "Open"), - React.createElement("button", { className: "btn btn-outline-secondary", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: () => onSaveAsNamedSet(validItems) }, "Save as set"))); + React.createElement("button", { className: "btn btn-secondary", "data-testid": "open-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: (event) => onOpen(event, searchResults) }, "Open"), + React.createElement("button", { className: "btn btn-outline-secondary", "data-testid": "save-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: () => onSaveAsNamedSet(validItems) }, "Save as set"))); } function Input(props) { const { onPaste } = props.selectProps; diff --git a/dist/menu/DatasetSearchBox.js.map b/dist/menu/DatasetSearchBox.js.map index 03a42586..b1a1a6e4 100644 --- a/dist/menu/DatasetSearchBox.js.map +++ b/dist/menu/DatasetSearchBox.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/scores/forms.d.ts b/dist/scores/forms.d.ts index 34fd9e19..d8ea6ed3 100644 --- a/dist/scores/forms.d.ts +++ b/dist/scores/forms.d.ts @@ -137,22 +137,6 @@ export declare const FORM_SINGLE_SCORE: { useSession: boolean; }[]; export declare const FORM_AGGREGATED_SCORE_DEPLETION: ({ - type: FormElementType; - label: string; - id: string; - attributes: { - style: string; - }; - required: boolean; - options: { - placeholder: string; - data: { - id: string; - text: string; - }[]; - }; - useSession: boolean; -} | { type: FormElementType; label: string; id: string; @@ -199,8 +183,7 @@ export declare const FORM_AGGREGATED_SCORE_DEPLETION: ({ step: string; optionsData?: undefined; }; -})[]; -export declare const FORM_SINGLE_SCORE_DEPLETION: { +} | { type: FormElementType; label: string; id: string; @@ -216,8 +199,8 @@ export declare const FORM_SINGLE_SCORE_DEPLETION: { }[]; }; useSession: boolean; -}[]; -export declare const FORM_SINGLE_SCORE_DRUG: ({ +})[]; +export declare const FORM_SINGLE_SCORE_DEPLETION: { type: FormElementType; label: string; id: string; @@ -233,7 +216,8 @@ export declare const FORM_SINGLE_SCORE_DRUG: ({ }[]; }; useSession: boolean; -} | { +}[]; +export declare const FORM_SINGLE_SCORE_DRUG: ({ type: FormElementType; label: string; id: string; @@ -249,4 +233,20 @@ export declare const FORM_SINGLE_SCORE_DRUG: ({ format: typeof import("..").GeneUtils.formatDrugScreen; }; useSession: boolean; +} | { + type: FormElementType; + label: string; + id: string; + attributes: { + style: string; + }; + required: boolean; + options: { + placeholder: string; + data: { + id: string; + text: string; + }[]; + }; + useSession: boolean; })[]; diff --git a/src/menu/DatasetCard.tsx b/src/menu/DatasetCard.tsx index dd85b42f..a2387d83 100644 --- a/src/menu/DatasetCard.tsx +++ b/src/menu/DatasetCard.tsx @@ -7,6 +7,7 @@ import {Species, SpeciesUtils, IACommonListOptions} from 'tdp_gene'; import {IPublicDbStartMenuDatasetSectionDesc} from '../base/extensions'; export default function DatasetCard({name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators}: IPublicDbStartMenuDatasetSectionDesc) { + const testId = `datasetcard-${cssClass}`; const {app} = React.useContext(OrdinoContext); const [dirtyNamedSets, setDirtyNamedSets] = React.useState(false); @@ -90,7 +91,7 @@ export default function DatasetCard({name, icon, tabs, startViewId, dataSource, const activeTabIndex = 0; return ( -
+

{name}

@@ -98,7 +99,7 @@ export default function DatasetCard({name, icon, tabs, startViewId, dataSource, {tabs.map((tab, index) => { return (
  • - + {tab.name}
    • @@ -109,7 +110,7 @@ export default function DatasetCard({name, icon, tabs, startViewId, dataSource, {tabs.map((tab, index) => { const separators = tokenSeparators ? {tokenSeparators} : null; return ( -
    +
    - - + +
    ); } From e464ad309bcc81a61f9fd58b1a9b2ac23d3d0a39 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Mon, 13 Dec 2021 16:00:40 +0100 Subject: [PATCH 02/38] add id for dataset searchbox --- dist/common/forms.d.ts | 2 +- dist/menu/DatasetCard.d.ts | 1 - dist/menu/DatasetSearchBox.js | 6 +++-- dist/menu/DatasetSearchBox.js.map | 2 +- dist/scores/forms.d.ts | 42 +++++++++++++++---------------- src/menu/DatasetSearchBox.tsx | 6 +++-- 6 files changed, 31 insertions(+), 28 deletions(-) diff --git a/dist/common/forms.d.ts b/dist/common/forms.d.ts index d9d379e5..7280ad5e 100644 --- a/dist/common/forms.d.ts +++ b/dist/common/forms.d.ts @@ -149,7 +149,7 @@ export declare const FORM_GENE_FILTER: { return: string; optionsData: () => Promise<{ name: string; - value: import("lineupjs").ICompareValue; + value: string | number; }[]>; options: { placeholder: string; diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index efe4fcf9..238cd908 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,3 +1,2 @@ -/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; diff --git a/dist/menu/DatasetSearchBox.js b/dist/menu/DatasetSearchBox.js index 88a667b0..147fd600 100644 --- a/dist/menu/DatasetSearchBox.js +++ b/dist/menu/DatasetSearchBox.js @@ -54,7 +54,7 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName type: dataSource.tableName } }; - return (React.createElement("div", { className: "hstack gap-3 ordino-dataset-searchbox" }, + return (React.createElement("div", { className: "hstack gap-3 ordino-dataset-searchbox", "data-testid": "ordino-dataset-searchbox" }, React.createElement(AsyncPaginate, { className: "flex-fill", onPaste: onPaste, placeholder: placeholder, noOptionsMessage: () => 'No results found', isMulti: true, loadOptions: loadOptions, inputValue: inputValue, value: items, onChange: setItems, onInputChange: setInputValue, formatOptionLabel: formatOptionLabel, hideSelectedOptions: true, getOptionLabel: (option) => option.text, getOptionValue: (option) => option.id, captureMenuScroll: false, additional: { page: 0 // page starts from index 0 }, components: { Input }, styles: { @@ -108,6 +108,8 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName } function Input(props) { const { onPaste } = props.selectProps; - return (React.createElement(components.Input, Object.assign({ onPaste: onPaste }, props))); + const modifiedProps = Object.assign({ 'data-testid': 'async-paginate-input-component' }, props); + delete modifiedProps.popoverType; // remove the "illegal" prop from the copy + return (React.createElement(components.Input, Object.assign({ onPaste: onPaste }, modifiedProps))); } //# sourceMappingURL=DatasetSearchBox.js.map \ No newline at end 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\ No newline at end of file diff --git a/dist/scores/forms.d.ts b/dist/scores/forms.d.ts index d8ea6ed3..34fd9e19 100644 --- a/dist/scores/forms.d.ts +++ b/dist/scores/forms.d.ts @@ -137,6 +137,22 @@ export declare const FORM_SINGLE_SCORE: { useSession: boolean; }[]; export declare const FORM_AGGREGATED_SCORE_DEPLETION: ({ + type: FormElementType; + label: string; + id: string; + attributes: { + style: string; + }; + required: boolean; + options: { + placeholder: string; + data: { + id: string; + text: string; + }[]; + }; + useSession: boolean; +} | { type: FormElementType; label: string; id: string; @@ -183,7 +199,8 @@ export declare const FORM_AGGREGATED_SCORE_DEPLETION: ({ step: string; optionsData?: undefined; }; -} | { +})[]; +export declare const FORM_SINGLE_SCORE_DEPLETION: { type: FormElementType; label: string; id: string; @@ -199,8 +216,8 @@ export declare const FORM_AGGREGATED_SCORE_DEPLETION: ({ }[]; }; useSession: boolean; -})[]; -export declare const FORM_SINGLE_SCORE_DEPLETION: { +}[]; +export declare const FORM_SINGLE_SCORE_DRUG: ({ type: FormElementType; label: string; id: string; @@ -216,8 +233,7 @@ export declare const FORM_SINGLE_SCORE_DEPLETION: { }[]; }; useSession: boolean; -}[]; -export declare const FORM_SINGLE_SCORE_DRUG: ({ +} | { type: FormElementType; label: string; id: string; @@ -233,20 +249,4 @@ export declare const FORM_SINGLE_SCORE_DRUG: ({ format: typeof import("..").GeneUtils.formatDrugScreen; }; useSession: boolean; -} | { - type: FormElementType; - label: string; - id: string; - attributes: { - style: string; - }; - required: boolean; - options: { - placeholder: string; - data: { - id: string; - text: string; - }[]; - }; - useSession: boolean; })[]; diff --git a/src/menu/DatasetSearchBox.tsx b/src/menu/DatasetSearchBox.tsx index 68b75f5b..548e2eec 100644 --- a/src/menu/DatasetSearchBox.tsx +++ b/src/menu/DatasetSearchBox.tsx @@ -92,7 +92,7 @@ export function DatasetSearchBox({placeholder, dataSource, onOpen, onSaveAsNamed }; return ( -
    +
    ); + const modifiedProps = Object.assign({'data-testid': 'async-paginate-input-component'}, props); + delete modifiedProps.popoverType; // remove the "illegal" prop from the copy + return (); } From 5879b89ba2fbb426b72981f1166457df7757f2da Mon Sep 17 00:00:00 2001 From: Florian Engertsberger Date: Tue, 4 Jan 2022 10:27:25 +0100 Subject: [PATCH 03/38] add data-testid to react select components --- dist/menu/DatasetCard.d.ts | 1 + dist/menu/DatasetSearchBox.js | 16 ++- dist/menu/DatasetSearchBox.js.map | 2 +- src/menu/DatasetSearchBox.tsx | 192 ++++++++++++++++++------------ 4 files changed, 135 insertions(+), 76 deletions(-) diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index 238cd908..efe4fcf9 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,2 +1,3 @@ +/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; diff --git a/dist/menu/DatasetSearchBox.js b/dist/menu/DatasetSearchBox.js index 147fd600..7380b68b 100644 --- a/dist/menu/DatasetSearchBox.js +++ b/dist/menu/DatasetSearchBox.js @@ -57,7 +57,13 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName return (React.createElement("div", { className: "hstack gap-3 ordino-dataset-searchbox", "data-testid": "ordino-dataset-searchbox" }, React.createElement(AsyncPaginate, { className: "flex-fill", onPaste: onPaste, placeholder: placeholder, noOptionsMessage: () => 'No results found', isMulti: true, loadOptions: loadOptions, inputValue: inputValue, value: items, onChange: setItems, onInputChange: setInputValue, formatOptionLabel: formatOptionLabel, hideSelectedOptions: true, getOptionLabel: (option) => option.text, getOptionValue: (option) => option.id, captureMenuScroll: false, additional: { page: 0 // page starts from index 0 - }, components: { Input }, styles: { + }, components: { + Input, + Option: addDataTestId(Option, "async-paginate-option"), + MultiValueRemove: addDataTestId(MultiValueRemove, "async-paginate-multiselect-remove"), + ClearIndicator: addDataTestId(ClearIndicator, "async-paginate-clearindicator"), + DropdownIndicator: addDataTestId(DropdownIndicator, "async-paginate-dropdownindicator") + }, styles: { multiValue: (styles, { data }) => ({ ...styles, border: `1px solid #CCC`, @@ -106,10 +112,16 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName React.createElement("button", { className: "btn btn-secondary", "data-testid": "open-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: (event) => onOpen(event, searchResults) }, "Open"), React.createElement("button", { className: "btn btn-outline-secondary", "data-testid": "save-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: () => onSaveAsNamedSet(validItems) }, "Save as set"))); } +// functions to add data-testid attribute to react-select components +const addDataTestId = (Component, dataTestId) => (props => (React.createElement(Component, Object.assign({}, props, { innerProps: Object.assign({}, props.innerProps, { 'data-testid': `${dataTestId}${props.data ? "-" + props.data.id : ""}` }) })))); function Input(props) { const { onPaste } = props.selectProps; - const modifiedProps = Object.assign({ 'data-testid': 'async-paginate-input-component' }, props); + const modifiedProps = Object.assign({ 'data-testid': 'async-paginate-input' }, props); delete modifiedProps.popoverType; // remove the "illegal" prop from the copy return (React.createElement(components.Input, Object.assign({ onPaste: onPaste }, modifiedProps))); } +const ClearIndicator = props => (components.ClearIndicator && (React.createElement(components.ClearIndicator, Object.assign({}, props)))); +const DropdownIndicator = props => (components.DropdownIndicator && (React.createElement(components.DropdownIndicator, Object.assign({}, props)))); +const Option = props => (components.Option && (React.createElement(components.Option, Object.assign({}, props)))); +const MultiValueRemove = props => (components.MultiValueRemove && (React.createElement(components.MultiValueRemove, Object.assign({}, props)))); //# sourceMappingURL=DatasetSearchBox.js.map \ No newline at end of file diff --git a/dist/menu/DatasetSearchBox.js.map b/dist/menu/DatasetSearchBox.js.map index 7220e425..ae9e31b5 100644 --- a/dist/menu/DatasetSearchBox.js.map +++ b/dist/menu/DatasetSearchBox.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/menu/DatasetSearchBox.tsx b/src/menu/DatasetSearchBox.tsx index 548e2eec..2557ae49 100644 --- a/src/menu/DatasetSearchBox.tsx +++ b/src/menu/DatasetSearchBox.tsx @@ -93,84 +93,130 @@ export function DatasetSearchBox({placeholder, dataSource, onOpen, onSaveAsNamed return (
    - 'No results found'} - isMulti={true} - loadOptions={loadOptions} - inputValue={inputValue} - value={items} - onChange={setItems} - onInputChange={setInputValue} - formatOptionLabel={formatOptionLabel} - hideSelectedOptions - getOptionLabel={(option) => option.text} - getOptionValue={(option) => option.id} - captureMenuScroll={false} - additional={{ - page: 0 // page starts from index 0 - }} - components={{Input}} - styles={{ - - multiValue: (styles, {data}) => ({ - ...styles, - border: `1px solid #CCC`, - borderRadius: '3px' - }), - multiValueLabel: (styles, {data}) => ({ - ...styles, - textDecoration: data.invalid ? 'line-through' : 'none', - color: data.color, - backgroundColor: 'white', - order: 2, - paddingLeft: '0', - paddingRight: '6px' - }), - multiValueRemove: (styles, {data}) => ({ - ...styles, - color: data.invalid ? 'red' : '#999', - backgroundColor: 'white', - order: 1, - ':hover': { - color: '#333', - cursor: 'pointer' - }, - }), - - placeholder: (provided) => ({ - ...provided, - // disable placeholder mouse events - pointerEvents: 'none', - userSelect: 'none', - }), - input: (css) => ({ - ...css, - //expand the Input Component div - flex: '1 1 auto', - // expand the Input Component child div - '> div': { - width: '100%' - }, - // expand the Input Component input - input: { - width: '100% !important', - textAlign: 'left' - } - }) - }} - /> - - + 'No results found'} + isMulti={true} + loadOptions={loadOptions} + inputValue={inputValue} + value={items} + onChange={setItems} + onInputChange={setInputValue} + formatOptionLabel={formatOptionLabel} + hideSelectedOptions + getOptionLabel={(option) => option.text} + getOptionValue={(option) => option.id} + captureMenuScroll={false} + additional={{ + page: 0 // page starts from index 0 + }} + components={{ + Input, + Option: addDataTestId(Option, "async-paginate-option"), + MultiValueRemove: addDataTestId(MultiValueRemove, "async-paginate-multiselect-remove"), + ClearIndicator: addDataTestId(ClearIndicator, "async-paginate-clearindicator"), + DropdownIndicator: addDataTestId(DropdownIndicator, "async-paginate-dropdownindicator") + }} + styles={{ + + multiValue: (styles, {data}) => ({ + ...styles, + border: `1px solid #CCC`, + borderRadius: '3px' + }), + multiValueLabel: (styles, {data}) => ({ + ...styles, + textDecoration: data.invalid ? 'line-through' : 'none', + color: data.color, + backgroundColor: 'white', + order: 2, + paddingLeft: '0', + paddingRight: '6px' + }), + multiValueRemove: (styles, {data}) => ({ + ...styles, + color: data.invalid ? 'red' : '#999', + backgroundColor: 'white', + order: 1, + ':hover': { + color: '#333', + cursor: 'pointer' + }, + }), + + placeholder: (provided) => ({ + ...provided, + // disable placeholder mouse events + pointerEvents: 'none', + userSelect: 'none', + }), + input: (css) => ({ + ...css, + //expand the Input Component div + flex: '1 1 auto', + // expand the Input Component child div + '> div': { + width: '100%' + }, + // expand the Input Component input + input: { + width: '100% !important', + textAlign: 'left' + } + }) + }} + /> + +
    ); } +// functions to add data-testid attribute to react-select components +const addDataTestId = (Component, dataTestId) => ( + props => ( + + ) +); + function Input(props: any) { const {onPaste} = props.selectProps; - const modifiedProps = Object.assign({'data-testid': 'async-paginate-input-component'}, props); + const modifiedProps = Object.assign({'data-testid': 'async-paginate-input'}, props); delete modifiedProps.popoverType; // remove the "illegal" prop from the copy - return (); + return (); } + +const ClearIndicator = props => ( + components.ClearIndicator && ( + + + ) +); + +const DropdownIndicator = props => ( + components.DropdownIndicator && ( + + + ) +); + +const Option = props => ( + components.Option && ( + + + ) +); + +const MultiValueRemove = props => ( + components.MultiValueRemove && ( + + + ) +); + + From 452b83e12263d4f7c2b9e98d0f303d1163bfb8c7 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Mon, 17 Jan 2022 14:25:55 +0100 Subject: [PATCH 04/38] fix lint --- dist/menu/DatasetCard.d.ts | 1 - dist/menu/DatasetSearchBox.js | 33 ++++----- dist/menu/DatasetSearchBox.js.map | 2 +- dist/views/DependentGeneTable.d.ts | 2 +- dist/views/DependentSampleTable.d.ts | 2 +- src/menu/DatasetSearchBox.tsx | 102 +++++++++++++-------------- 6 files changed, 71 insertions(+), 71 deletions(-) diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index efe4fcf9..238cd908 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,3 +1,2 @@ -/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; diff --git a/dist/menu/DatasetSearchBox.js b/dist/menu/DatasetSearchBox.js index 7380b68b..ffada278 100644 --- a/dist/menu/DatasetSearchBox.js +++ b/dist/menu/DatasetSearchBox.js @@ -4,6 +4,19 @@ import { components } from 'react-select'; import { AsyncPaginate } from 'react-select-async-paginate'; import Highlighter from 'react-highlight-words'; import { GeneUtils } from '../common'; +// functions to add data-testid attribute to react-select components +/* tslint:disable-next-line:variable-name */ +const addDataTestId = (Component, dataTestId) => ((props) => (React.createElement(Component, Object.assign({}, props, { innerProps: Object.assign({}, props.innerProps, { 'data-testid': `${dataTestId}${props.data ? '-' + props.data.id : ''}` }) })))); +function Input(props) { + const { onPaste } = props.selectProps; + const modifiedProps = Object.assign({ 'data-testid': 'async-paginate-input' }, props); + delete modifiedProps.popoverType; // remove the "illegal" prop from the copy + return (React.createElement(components.Input, Object.assign({ onPaste: onPaste }, modifiedProps))); +} +const clearIndicator = (props) => (components.ClearIndicator && (React.createElement(components.ClearIndicator, Object.assign({}, props)))); +const dropdownIndicator = (props) => (components.DropdownIndicator && (React.createElement(components.DropdownIndicator, Object.assign({}, props)))); +const option = (props) => (components.Option && (React.createElement(components.Option, Object.assign({}, props)))); +const multiValueRemove = (props) => (components.MultiValueRemove && (React.createElement(components.MultiValueRemove, Object.assign({}, props)))); export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsNamedSet, params = {}, tokenSeparators = /[\s;,]+/gm }) { const [items, setItems] = React.useState([]); const [inputValue, setInputValue] = React.useState(''); @@ -59,10 +72,10 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName page: 0 // page starts from index 0 }, components: { Input, - Option: addDataTestId(Option, "async-paginate-option"), - MultiValueRemove: addDataTestId(MultiValueRemove, "async-paginate-multiselect-remove"), - ClearIndicator: addDataTestId(ClearIndicator, "async-paginate-clearindicator"), - DropdownIndicator: addDataTestId(DropdownIndicator, "async-paginate-dropdownindicator") + Option: addDataTestId(Option, 'async-paginate-option'), + MultiValueRemove: addDataTestId(multiValueRemove, 'async-paginate-multiselect-remove'), + ClearIndicator: addDataTestId(clearIndicator, 'async-paginate-clearindicator'), + DropdownIndicator: addDataTestId(dropdownIndicator, 'async-paginate-dropdownindicator') }, styles: { multiValue: (styles, { data }) => ({ ...styles, @@ -112,16 +125,4 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName React.createElement("button", { className: "btn btn-secondary", "data-testid": "open-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: (event) => onOpen(event, searchResults) }, "Open"), React.createElement("button", { className: "btn btn-outline-secondary", "data-testid": "save-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: () => onSaveAsNamedSet(validItems) }, "Save as set"))); } -// functions to add data-testid attribute to react-select components -const addDataTestId = (Component, dataTestId) => (props => (React.createElement(Component, Object.assign({}, props, { innerProps: Object.assign({}, props.innerProps, { 'data-testid': `${dataTestId}${props.data ? "-" + props.data.id : ""}` }) })))); -function Input(props) { - const { onPaste } = props.selectProps; - const modifiedProps = Object.assign({ 'data-testid': 'async-paginate-input' }, props); - delete modifiedProps.popoverType; // remove the "illegal" prop from the copy - return (React.createElement(components.Input, Object.assign({ onPaste: onPaste }, modifiedProps))); -} -const ClearIndicator = props => (components.ClearIndicator && (React.createElement(components.ClearIndicator, Object.assign({}, props)))); -const DropdownIndicator = props => (components.DropdownIndicator && (React.createElement(components.DropdownIndicator, Object.assign({}, props)))); -const Option = props => (components.Option && (React.createElement(components.Option, Object.assign({}, props)))); -const MultiValueRemove = props => (components.MultiValueRemove && (React.createElement(components.MultiValueRemove, Object.assign({}, props)))); //# sourceMappingURL=DatasetSearchBox.js.map \ No newline at end of file diff --git a/dist/menu/DatasetSearchBox.js.map b/dist/menu/DatasetSearchBox.js.map index ae9e31b5..b5f93945 100644 --- a/dist/menu/DatasetSearchBox.js.map +++ b/dist/menu/DatasetSearchBox.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/views/DependentGeneTable.d.ts b/dist/views/DependentGeneTable.d.ts index 89cf133c..2b63ecb2 100644 --- a/dist/views/DependentGeneTable.d.ts +++ b/dist/views/DependentGeneTable.d.ts @@ -10,7 +10,7 @@ export declare class DependentGeneTable extends ARankingView { private readonly dataSource; constructor(context: IViewContext, selection: ISelection, parent: HTMLElement, dataType: IDataTypeConfig, options?: Partial); protected getParameterFormDescs(): import("tdp_core").IFormElementDesc[]; - protected parameterChanged(name: string): void; + protected parameterChanged(name: string): Promise; protected loadColumnDesc(): Promise>; protected createSelectionAdapter(): import("tdp_core").ISelectionAdapter; protected getColumnDescs(columns: IServerColumn[]): import("tdp_core").IAdditionalColumnDesc[]; diff --git a/dist/views/DependentSampleTable.d.ts b/dist/views/DependentSampleTable.d.ts index 2ea0bc03..e5162f5d 100644 --- a/dist/views/DependentSampleTable.d.ts +++ b/dist/views/DependentSampleTable.d.ts @@ -12,7 +12,7 @@ export declare class DependentSampleTable extends ARankingView { get itemIDType(): import("tdp_core").IDType; private get dataSource(); private get dataSubType(); - protected parameterChanged(name: string): void; + protected parameterChanged(name: string): Promise; protected loadColumnDesc(): Promise>; protected createSelectionAdapter(): import("tdp_core").ISelectionAdapter; protected getColumnDescs(columns: IServerColumn[]): import("tdp_core").IAdditionalColumnDesc[]; diff --git a/src/menu/DatasetSearchBox.tsx b/src/menu/DatasetSearchBox.tsx index 2557ae49..0a4db205 100644 --- a/src/menu/DatasetSearchBox.tsx +++ b/src/menu/DatasetSearchBox.tsx @@ -28,6 +28,53 @@ interface IDatasetSearchBoxProps { tokenSeparators?: RegExp; } +// functions to add data-testid attribute to react-select components +/* tslint:disable-next-line:variable-name */ +const addDataTestId = (Component, dataTestId) => ( + (props) => ( + + ) +); + +function Input(props: any) { + const {onPaste} = props.selectProps; + const modifiedProps = Object.assign({'data-testid': 'async-paginate-input'}, props); + delete modifiedProps.popoverType; // remove the "illegal" prop from the copy + return (); +} + +const clearIndicator = (props) => ( + components.ClearIndicator && ( + + + ) +); + +const dropdownIndicator = (props) => ( + components.DropdownIndicator && ( + + + ) +); + +const option = (props) => ( + components.Option && ( + + + ) +); + +const multiValueRemove = (props) => ( + components.MultiValueRemove && ( + + + ) +); + + export function DatasetSearchBox({placeholder, dataSource, onOpen, onSaveAsNamedSet, params = {}, tokenSeparators = /[\s;,]+/gm}: IDatasetSearchBoxProps) { const [items, setItems] = React.useState([]); const [inputValue, setInputValue] = React.useState(''); @@ -114,10 +161,10 @@ export function DatasetSearchBox({placeholder, dataSource, onOpen, onSaveAsNamed }} components={{ Input, - Option: addDataTestId(Option, "async-paginate-option"), - MultiValueRemove: addDataTestId(MultiValueRemove, "async-paginate-multiselect-remove"), - ClearIndicator: addDataTestId(ClearIndicator, "async-paginate-clearindicator"), - DropdownIndicator: addDataTestId(DropdownIndicator, "async-paginate-dropdownindicator") + Option: addDataTestId(Option, 'async-paginate-option'), + MultiValueRemove: addDataTestId(multiValueRemove, 'async-paginate-multiselect-remove'), + ClearIndicator: addDataTestId(clearIndicator, 'async-paginate-clearindicator'), + DropdownIndicator: addDataTestId(dropdownIndicator, 'async-paginate-dropdownindicator') }} styles={{ @@ -173,50 +220,3 @@ export function DatasetSearchBox({placeholder, dataSource, onOpen, onSaveAsNamed
    ); } - -// functions to add data-testid attribute to react-select components -const addDataTestId = (Component, dataTestId) => ( - props => ( - - ) -); - -function Input(props: any) { - const {onPaste} = props.selectProps; - const modifiedProps = Object.assign({'data-testid': 'async-paginate-input'}, props); - delete modifiedProps.popoverType; // remove the "illegal" prop from the copy - return (); -} - -const ClearIndicator = props => ( - components.ClearIndicator && ( - - - ) -); - -const DropdownIndicator = props => ( - components.DropdownIndicator && ( - - - ) -); - -const Option = props => ( - components.Option && ( - - - ) -); - -const MultiValueRemove = props => ( - components.MultiValueRemove && ( - - - ) -); - - From d81f7a9acf0374de05e09d2a1abc8de7edb3ef1f Mon Sep 17 00:00:00 2001 From: Florian Engertsberger Date: Tue, 18 Jan 2022 08:23:45 +0100 Subject: [PATCH 05/38] fix react select error --- dist/menu/DatasetCard.d.ts | 1 + dist/menu/DatasetSearchBox.js | 2 +- src/menu/DatasetSearchBox.tsx | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index 238cd908..efe4fcf9 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,2 +1,3 @@ +/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; diff --git a/dist/menu/DatasetSearchBox.js b/dist/menu/DatasetSearchBox.js index ffada278..e0224028 100644 --- a/dist/menu/DatasetSearchBox.js +++ b/dist/menu/DatasetSearchBox.js @@ -72,7 +72,7 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName page: 0 // page starts from index 0 }, components: { Input, - Option: addDataTestId(Option, 'async-paginate-option'), + Option: addDataTestId(option, 'async-paginate-option'), MultiValueRemove: addDataTestId(multiValueRemove, 'async-paginate-multiselect-remove'), ClearIndicator: addDataTestId(clearIndicator, 'async-paginate-clearindicator'), DropdownIndicator: addDataTestId(dropdownIndicator, 'async-paginate-dropdownindicator') diff --git a/src/menu/DatasetSearchBox.tsx b/src/menu/DatasetSearchBox.tsx index 0a4db205..0d0a68fb 100644 --- a/src/menu/DatasetSearchBox.tsx +++ b/src/menu/DatasetSearchBox.tsx @@ -161,7 +161,7 @@ export function DatasetSearchBox({placeholder, dataSource, onOpen, onSaveAsNamed }} components={{ Input, - Option: addDataTestId(Option, 'async-paginate-option'), + Option: addDataTestId(option, 'async-paginate-option'), MultiValueRemove: addDataTestId(multiValueRemove, 'async-paginate-multiselect-remove'), ClearIndicator: addDataTestId(clearIndicator, 'async-paginate-clearindicator'), DropdownIndicator: addDataTestId(dropdownIndicator, 'async-paginate-dropdownindicator') From 761c42f655e36cfb5f003fc6f57cb301948b6f64 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 22 Mar 2022 13:31:03 +0100 Subject: [PATCH 06/38] update dist --- dist/menu/DatasetCard.d.ts | 1 - dist/menu/DatasetCard.d.ts.map | 2 +- dist/menu/DatasetCard.js | 81 ++++++++++++++++------------ dist/menu/DatasetCard.js.map | 2 +- dist/menu/DatasetSearchBox.d.ts.map | 2 +- dist/menu/DatasetSearchBox.js | 73 ++++++++++++++----------- dist/menu/DatasetSearchBox.js.map | 2 +- dist/views/DependentGeneTable.d.ts | 5 +- dist/views/DependentSampleTable.d.ts | 5 +- 9 files changed, 97 insertions(+), 76 deletions(-) diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index 2587b238..836b542b 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,4 +1,3 @@ -/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; //# sourceMappingURL=DatasetCard.d.ts.map \ No newline at end of file diff --git a/dist/menu/DatasetCard.d.ts.map b/dist/menu/DatasetCard.d.ts.map index b2fb68d6..2fd90cae 100644 --- a/dist/menu/DatasetCard.d.ts.map +++ b/dist/menu/DatasetCard.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":";AAiBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eAqLjJ"} \ No newline at end of file +{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":"AAiBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eAwLjJ"} \ No newline at end of file diff --git a/dist/menu/DatasetCard.js b/dist/menu/DatasetCard.js index 596b29e7..ad011a04 100644 --- a/dist/menu/DatasetCard.js +++ b/dist/menu/DatasetCard.js @@ -1,29 +1,34 @@ import React from 'react'; -import { ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils } from 'tdp_core'; +import { ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils, UserSession, UniqueIdManager, I18nextManager, IDTypeManager, useAsync, } from 'tdp_core'; import { NamedSetList, OrdinoContext } from 'ordino'; -import { UserSession, UniqueIdManager, I18nextManager, IDTypeManager, useAsync } from 'tdp_core'; +import { Species } from 'tdp_gene'; import { DatasetSearchBox } from './DatasetSearchBox'; -import { Species, SpeciesUtils } from 'tdp_gene'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }) { var _a, _b; const testId = `datasetcard-${cssClass}`; const { app } = React.useContext(OrdinoContext); const [dirtyNamedSets, setDirtyNamedSets] = React.useState(false); const loadPredefinedSet = React.useMemo(() => { - return () => RestBaseUtils.getTDPData(dataSource.db, `${dataSource.base}_panel`) - .then((panels) => { - return [{ - name: 'All', - type: ENamedSetType.CUSTOM, - subTypeKey: Species.SPECIES_SESSION_KEY, - subTypeFromSession: true, - subTypeValue: SpeciesUtils.getSelectedSpecies(), - description: '', - idType: '', - ids: '', - creator: '' - }, ...panels - .map(function panel2NamedSet({ id, description, species }) { + return async () => { + const panels = await RestBaseUtils.getTDPData(dataSource.db, `${dataSource.base}_panel`); + const uniqueSpecies = [...new Set(panels.map(({ species }) => species))]; + return [ + // first add an `All` named set for each species ... + ...uniqueSpecies.map((species) => { + return { + name: I18nextManager.getInstance().i18n.t(`tdp:datasetCard.predefinedSet.all.name`), + type: ENamedSetType.CUSTOM, + subTypeKey: Species.SPECIES_SESSION_KEY, + subTypeFromSession: true, + subTypeValue: species, + description: I18nextManager.getInstance().i18n.t(`tdp:datasetCard.predefinedSet.all.description`, { species }), + idType: '', + ids: '', + creator: '', + }; + }), + // ... then add all the predefined sets loaded from the backend + ...panels.map(({ id, description, species }) => { return { type: ENamedSetType.PANEL, id, @@ -32,13 +37,16 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, subTypeKey: Species.SPECIES_SESSION_KEY, subTypeFromSession: false, subTypeValue: species, - idType: '' + idType: '', }; - })]; - }); + }), + ]; + }; + // eslint-disable-next-line react-hooks/exhaustive-deps }, [dataSource.idType]); const loadNamedSets = React.useMemo(() => { return () => RestStorageUtils.listNamedSets(dataSource.idType); + // eslint-disable-next-line react-hooks/exhaustive-deps }, [dataSource.idType, dirtyNamedSets]); const predefinedNamedSets = useAsync(loadPredefinedSet, []); const me = UserSession.getInstance().currentUserNameOrAnonymous(); @@ -49,7 +57,7 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, const onOpenNamedSet = (event, { namedSet, species }) => { event.preventDefault(); const defaultSessionValues = { - [Species.SPECIES_SESSION_KEY]: species + [Species.SPECIES_SESSION_KEY]: species, }; // store the selected species/tab as it is necessary in the rankings UserSession.getInstance().store(Species.SPECIES_SESSION_KEY, species); @@ -58,18 +66,17 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, const onOpenSearchResult = (event, { searchResult, species }) => { event.preventDefault(); const defaultSessionValues = { - [Species.SPECIES_SESSION_KEY]: species + [Species.SPECIES_SESSION_KEY]: species, }; // store the selected species UserSession.getInstance().store(Species.SPECIES_SESSION_KEY, species); app.startNewSession(startViewId, searchResult, defaultSessionValues); }; const onSaveAsNamedSet = (items, subtype) => { - StoreUtils.editDialog(null, I18nextManager.getInstance().i18n.t(`tdp:core.editDialog.listOfEntities.default`), async (name, description, isPublic) => { + StoreUtils.editDialog(null, I18nextManager.getInstance().i18n.t(`tdp:core.editDialog.listOfEntities.default`), async (n, description, isPublic) => { const idStrings = items === null || items === void 0 ? void 0 : items.map((i) => i.id); const idType = IDTypeManager.getInstance().resolveIdType(dataSource.idType); - const ids = await idType.map(idStrings); - await RestStorageUtils.saveNamedSet(name, idType, ids, subtype, description, isPublic); + await RestStorageUtils.saveNamedSet(name, idType, idStrings, subtype, description, isPublic); setDirtyNamedSets((d) => !d); }); }; @@ -77,24 +84,32 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, const activeTabIndex = 0; return (React.createElement("div", { className: `ordino-dataset ${cssClass || ''}`, "data-testid": testId }, React.createElement("h4", { className: "text-start mb-3" }, - React.createElement("i", { className: 'me-2 ordino-icon-2 ' + icon }), + React.createElement("i", { className: `me-2 ordino-icon-2 ${icon}` }), name), React.createElement("div", { className: "card shadow-sm" }, React.createElement("div", { className: "card-body p-3" }, React.createElement("ul", { className: "nav nav-pills session-tab" }, tabs.map((tab, index) => { return (React.createElement("li", { key: tab.id, className: "nav-item", role: "presentation" }, - React.createElement("a", { className: `nav-link ${(index === activeTabIndex) ? 'active' : ''}`, "data-testid": `${tab.id}-link`, id: `dataset-tab-${tab.id}-${id}`, "data-bs-toggle": "tab", href: `#dataset-panel-${tab.id}-${id}`, role: "tab", "aria-controls": `dataset-panel-${tab.id}-${id}`, "aria-selected": (index === activeTabIndex) }, - React.createElement("i", { className: 'me-2 ' + tab.icon }), + React.createElement("a", { className: `nav-link ${index === activeTabIndex ? 'active' : ''}`, "data-testid": `${tab.id}-link`, id: `dataset-tab-${tab.id}-${id}`, "data-bs-toggle": "tab", href: `#dataset-panel-${tab.id}-${id}`, role: "tab", "aria-controls": `dataset-panel-${tab.id}-${id}`, "aria-selected": index === activeTabIndex }, + React.createElement("i", { className: `me-2 ${tab.icon}` }), tab.name))); })), React.createElement("div", { className: "tab-content" }, tabs.map((tab, index) => { const separators = tokenSeparators ? { tokenSeparators } : null; - return (React.createElement("div", { key: tab.id, className: `tab-pane fade mt-4 ${(index === activeTabIndex) ? 'show active' : ''}`, "data-testid": `${tab.id}-tab`, role: "tabpanel", id: `dataset-panel-${tab.id}-${id}`, "aria-labelledby": `dataset-tab-${tab.id}-${id}` }, - React.createElement(DatasetSearchBox, Object.assign({ placeholder: `Add ${name}`, dataSource: dataSource, params: { species: tab.id }, onSaveAsNamedSet: (items) => onSaveAsNamedSet(items, { key: Species.SPECIES_SESSION_KEY, value: tab.id }), onOpen: (event, searchResult) => { onOpenSearchResult(event, { searchResult, species: tab.id }); } }, separators)), + return (React.createElement("div", { key: tab.id, className: `tab-pane fade mt-4 ${index === activeTabIndex ? 'show active' : ''}`, "data-testid": `${tab.id}-tab`, role: "tabpanel", id: `dataset-panel-${tab.id}-${id}`, "aria-labelledby": `dataset-tab-${tab.id}-${id}` }, + React.createElement(DatasetSearchBox, { placeholder: `Add ${name}`, dataSource: dataSource, params: { species: tab.id }, onSaveAsNamedSet: (items) => onSaveAsNamedSet(items, { key: Species.SPECIES_SESSION_KEY, value: tab.id }), onOpen: (event, searchResult) => { + onOpenSearchResult(event, { searchResult, species: tab.id }); + }, ...separators }), React.createElement("div", { className: "row mt-4" }, - React.createElement(NamedSetList, { headerIcon: "fas fa-database", headerText: "Predefined Sets", onOpen: (event, namedSet) => { onOpenNamedSet(event, { namedSet, species: tab.id }); }, status: predefinedNamedSets.status, value: filterValue(predefinedNamedSets.value, tab.id) }), - React.createElement(NamedSetList, { headerIcon: "fas fa-user", headerText: "My Sets", onOpen: (event, namedSet) => { onOpenNamedSet(event, { namedSet, species: tab.id }); }, status: myNamedSets.status, value: filterValue(myNamedSets.value, tab.id) }), - React.createElement(NamedSetList, { headerIcon: "fas fa-users", headerText: "Other Sets", onOpen: (event, namedSet) => { onOpenNamedSet(event, { namedSet, species: tab.id }); }, status: publicNamedSets.status, value: filterValue(publicNamedSets.value, tab.id) })))); + React.createElement(NamedSetList, { headerIcon: "fas fa-database", headerText: "Predefined Sets", onOpen: (event, namedSet) => { + onOpenNamedSet(event, { namedSet, species: tab.id }); + }, status: predefinedNamedSets.status, value: filterValue(predefinedNamedSets.value, tab.id) }), + React.createElement(NamedSetList, { headerIcon: "fas fa-user", headerText: "My Sets", onOpen: (event, namedSet) => { + onOpenNamedSet(event, { namedSet, species: tab.id }); + }, status: myNamedSets.status, value: filterValue(myNamedSets.value, tab.id) }), + React.createElement(NamedSetList, { headerIcon: "fas fa-users", headerText: "Other Sets", onOpen: (event, namedSet) => { + onOpenNamedSet(event, { namedSet, species: tab.id }); + }, status: publicNamedSets.status, value: filterValue(publicNamedSets.value, tab.id) })))); })))))); } //# sourceMappingURL=DatasetCard.js.map \ No newline at end of file diff --git a/dist/menu/DatasetCard.js.map b/dist/menu/DatasetCard.js.map index 3af1cad3..a6f318a0 100644 --- a/dist/menu/DatasetCard.js.map +++ b/dist/menu/DatasetCard.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/menu/DatasetSearchBox.d.ts.map b/dist/menu/DatasetSearchBox.d.ts.map index 51d6774a..d19b6b47 100644 --- a/dist/menu/DatasetSearchBox.d.ts.map +++ b/dist/menu/DatasetSearchBox.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"DatasetSearchBox.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetSearchBox.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,EAAiB,UAAU,EAAgB,MAAM,UAAU,CAAC;AAInE,OAAO,EAAE,mBAAmB,EAAE,MAAM,UAAU,CAAC;AAC/C,OAAO,EAAa,iBAAiB,EAAE,MAAM,WAAW,CAAC;AAazD,UAAU,uBAAuB;IAC/B,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC;CACpB;AAED,UAAU,sBAAsB;IAC9B,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,iBAAiB,CAAC;IAC9B,gBAAgB,EAAE,CAAC,KAAK,EAAE,UAAU,EAAE,KAAK,IAAI,CAAC;IAChD,MAAM,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,mBAAmB,CAAC,KAAK,IAAI,CAAC;IAC7F;;OAEG;IACH,MAAM,CAAC,EAAE,uBAAuB,CAAC;IACjC,eAAe,CAAC,EAAE,MAAM,CAAC;CAC1B;AAED,wBAAgB,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAW,EAAE,eAA6B,EAAE,EAAE,sBAAsB,eA6IzJ"} \ No newline at end of file +{"version":3,"file":"DatasetSearchBox.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetSearchBox.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,EAAiB,UAAU,EAAgB,MAAM,UAAU,CAAC;AAInE,OAAO,EAAE,mBAAmB,EAAE,MAAM,UAAU,CAAC;AAC/C,OAAO,EAAa,iBAAiB,EAAE,MAAM,WAAW,CAAC;AAQzD,UAAU,uBAAuB;IAC/B,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC;CACpB;AAED,UAAU,sBAAsB;IAC9B,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,iBAAiB,CAAC;IAC9B,gBAAgB,EAAE,CAAC,KAAK,EAAE,UAAU,EAAE,KAAK,IAAI,CAAC;IAChD,MAAM,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,mBAAmB,CAAC,KAAK,IAAI,CAAC;IAC7F;;OAEG;IACH,MAAM,CAAC,EAAE,uBAAuB,CAAC;IACjC,eAAe,CAAC,EAAE,MAAM,CAAC;CAC1B;AA2BD,wBAAgB,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAW,EAAE,eAA6B,EAAE,EAAE,sBAAsB,eAgKzJ"} \ No newline at end of file diff --git a/dist/menu/DatasetSearchBox.js b/dist/menu/DatasetSearchBox.js index e0224028..34913c36 100644 --- a/dist/menu/DatasetSearchBox.js +++ b/dist/menu/DatasetSearchBox.js @@ -5,18 +5,24 @@ import { AsyncPaginate } from 'react-select-async-paginate'; import Highlighter from 'react-highlight-words'; import { GeneUtils } from '../common'; // functions to add data-testid attribute to react-select components -/* tslint:disable-next-line:variable-name */ -const addDataTestId = (Component, dataTestId) => ((props) => (React.createElement(Component, Object.assign({}, props, { innerProps: Object.assign({}, props.innerProps, { 'data-testid': `${dataTestId}${props.data ? '-' + props.data.id : ''}` }) })))); +// eslint-disable-next-line +const addDataTestId = (Component, dataTestId) => ( +// eslint-disable-next-line +(props) => ( +// eslint-disable-next-line +React.createElement(Component, { ...props, + // eslint-disable-next-line + innerProps: Object.assign({}, props.innerProps, { 'data-testid': `${dataTestId}${props.data ? '-' + props.data.id : ''}` }) }))); function Input(props) { const { onPaste } = props.selectProps; - const modifiedProps = Object.assign({ 'data-testid': 'async-paginate-input' }, props); + const modifiedProps = { 'data-testid': 'async-paginate-input', ...props }; delete modifiedProps.popoverType; // remove the "illegal" prop from the copy - return (React.createElement(components.Input, Object.assign({ onPaste: onPaste }, modifiedProps))); + return React.createElement(components.Input, { onPaste: onPaste, ...modifiedProps }); } -const clearIndicator = (props) => (components.ClearIndicator && (React.createElement(components.ClearIndicator, Object.assign({}, props)))); -const dropdownIndicator = (props) => (components.DropdownIndicator && (React.createElement(components.DropdownIndicator, Object.assign({}, props)))); -const option = (props) => (components.Option && (React.createElement(components.Option, Object.assign({}, props)))); -const multiValueRemove = (props) => (components.MultiValueRemove && (React.createElement(components.MultiValueRemove, Object.assign({}, props)))); +const clearIndicator = (props) => components.ClearIndicator && React.createElement(components.ClearIndicator, { ...props }); +const dropdownIndicator = (props) => components.DropdownIndicator && React.createElement(components.DropdownIndicator, { ...props }); +const option = (props) => components.Option && React.createElement(components.Option, { ...props }); +const multiValueRemove = (props) => components.MultiValueRemove && React.createElement(components.MultiValueRemove, { ...props }); export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsNamedSet, params = {}, tokenSeparators = /[\s;,]+/gm }) { const [items, setItems] = React.useState([]); const [inputValue, setInputValue] = React.useState(''); @@ -27,15 +33,16 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName ...params, query, page, - limit: 10 - }).then(({ items, more }) => ({ - options: items, + limit: 10, + }).then(({ items: elements, more }) => ({ + options: elements, hasMore: more, additional: { - page: page + 1 - } + page: page + 1, + }, })); }; + // eslint-disable-next-line @typescript-eslint/no-shadow const formatOptionLabel = (option, ctx) => { var _a; // do not highlight selected elements @@ -44,8 +51,7 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName } return (React.createElement(React.Fragment, null, React.createElement(Highlighter, { searchWords: [ctx.inputValue], autoEscape: true, textToHighlight: option.text }), - option.text !== option.id && - React.createElement("span", { className: "small text-muted ms-1" }, option.id))); + option.text !== option.id && React.createElement("span", { className: "small text-muted ms-1" }, option.id))); }; React.useEffect(() => { setInputValue(''); @@ -53,10 +59,13 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName const onPaste = async (event) => { var _a; const pastedData = (_a = event.clipboardData.getData('text')) === null || _a === void 0 ? void 0 : _a.toLocaleLowerCase(); - const splitData = Select3Utils.splitEscaped(pastedData, tokenSeparators, false).map((d) => d.trim()).filter((d) => d !== ''); + const splitData = Select3Utils.splitEscaped(pastedData, tokenSeparators, false) + .map((d) => d.trim()) + .filter((d) => d !== ''); const validData = await GeneUtils.validateGeneric(dataSource, splitData); const invalidData = splitData - .filter((s) => !validData.length || validData.every((o) => o.id.toLocaleLowerCase() !== s.toLocaleLowerCase() && o.text.toLocaleLowerCase() !== s.toLocaleLowerCase())) + .filter((s) => !validData.length || + validData.every((o) => o.id.toLocaleLowerCase() !== s.toLocaleLowerCase() && o.text.toLocaleLowerCase() !== s.toLocaleLowerCase())) .map((s) => ({ id: s, text: s, invalid: true })); setItems([...validData, ...invalidData]); }; @@ -64,23 +73,23 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName const searchResults = { search: { ids: validItems.map((i) => i.id), - type: dataSource.tableName - } + type: dataSource.tableName, + }, }; return (React.createElement("div", { className: "hstack gap-3 ordino-dataset-searchbox", "data-testid": "ordino-dataset-searchbox" }, - React.createElement(AsyncPaginate, { className: "flex-fill", onPaste: onPaste, placeholder: placeholder, noOptionsMessage: () => 'No results found', isMulti: true, loadOptions: loadOptions, inputValue: inputValue, value: items, onChange: setItems, onInputChange: setInputValue, formatOptionLabel: formatOptionLabel, hideSelectedOptions: true, getOptionLabel: (option) => option.text, getOptionValue: (option) => option.id, captureMenuScroll: false, additional: { - page: 0 // page starts from index 0 + React.createElement(AsyncPaginate, { className: "flex-fill", onPaste: onPaste, placeholder: placeholder, noOptionsMessage: () => 'No results found', isMulti: true, loadOptions: loadOptions, inputValue: inputValue, value: items, onChange: setItems, onInputChange: setInputValue, formatOptionLabel: formatOptionLabel, hideSelectedOptions: true, getOptionLabel: (opt) => opt.text, getOptionValue: (opt) => opt.id, captureMenuScroll: false, additional: { + page: 0, // page starts from index 0 }, components: { Input, Option: addDataTestId(option, 'async-paginate-option'), MultiValueRemove: addDataTestId(multiValueRemove, 'async-paginate-multiselect-remove'), ClearIndicator: addDataTestId(clearIndicator, 'async-paginate-clearindicator'), - DropdownIndicator: addDataTestId(dropdownIndicator, 'async-paginate-dropdownindicator') + DropdownIndicator: addDataTestId(dropdownIndicator, 'async-paginate-dropdownindicator'), }, styles: { multiValue: (styles, { data }) => ({ ...styles, border: `1px solid #CCC`, - borderRadius: '3px' + borderRadius: '3px', }), multiValueLabel: (styles, { data }) => ({ ...styles, @@ -89,7 +98,7 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName backgroundColor: 'white', order: 2, paddingLeft: '0', - paddingRight: '6px' + paddingRight: '6px', }), multiValueRemove: (styles, { data }) => ({ ...styles, @@ -98,7 +107,7 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName order: 1, ':hover': { color: '#333', - cursor: 'pointer' + cursor: 'pointer', }, }), placeholder: (provided) => ({ @@ -109,20 +118,20 @@ export function DatasetSearchBox({ placeholder, dataSource, onOpen, onSaveAsName }), input: (css) => ({ ...css, - //expand the Input Component div + // expand the Input Component div flex: '1 1 auto', // expand the Input Component child div '> div': { - width: '100%' + width: '100%', }, // expand the Input Component input input: { width: '100% !important', - textAlign: 'left' - } - }) + textAlign: 'left', + }, + }), } }), - React.createElement("button", { className: "btn btn-secondary", "data-testid": "open-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: (event) => onOpen(event, searchResults) }, "Open"), - React.createElement("button", { className: "btn btn-outline-secondary", "data-testid": "save-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: () => onSaveAsNamedSet(validItems) }, "Save as set"))); + React.createElement("button", { type: "button", className: "btn btn-secondary", "data-testid": "open-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: (event) => onOpen(event, searchResults) }, "Open"), + React.createElement("button", { type: "button", className: "btn btn-outline-secondary", "data-testid": "save-button", disabled: !(validItems === null || validItems === void 0 ? void 0 : validItems.length), onClick: () => onSaveAsNamedSet(validItems) }, "Save as set"))); } //# sourceMappingURL=DatasetSearchBox.js.map \ No newline at end of file diff --git a/dist/menu/DatasetSearchBox.js.map b/dist/menu/DatasetSearchBox.js.map index b5f93945..e903e9d9 100644 --- a/dist/menu/DatasetSearchBox.js.map +++ b/dist/menu/DatasetSearchBox.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/views/DependentGeneTable.d.ts b/dist/views/DependentGeneTable.d.ts index 2b63ecb2..959015cb 100644 --- a/dist/views/DependentGeneTable.d.ts +++ b/dist/views/DependentGeneTable.d.ts @@ -1,10 +1,8 @@ /** * Created by Marc Streit on 28.07.2016. */ -import { ARankingView, IARankingViewOptions } from 'tdp_core'; +import { ARankingView, IARankingViewOptions, ISelection, IViewContext, IServerColumn } from 'tdp_core'; import { IDataTypeConfig } from '../common/config'; -import { ISelection, IViewContext } from 'tdp_core'; -import { IServerColumn } from 'tdp_core'; export declare class DependentGeneTable extends ARankingView { private readonly dataType; private readonly dataSource; @@ -21,3 +19,4 @@ export declare class DependentGeneTable extends ARankingView { static createCopyNumberDependentGeneTable(context: IViewContext, selection: ISelection, parent: HTMLElement, options?: any): DependentGeneTable; static createMutationDependentGeneTable(context: IViewContext, selection: ISelection, parent: HTMLElement, options?: any): DependentGeneTable; } +//# sourceMappingURL=DependentGeneTable.d.ts.map \ No newline at end of file diff --git a/dist/views/DependentSampleTable.d.ts b/dist/views/DependentSampleTable.d.ts index e5162f5d..c46bd86a 100644 --- a/dist/views/DependentSampleTable.d.ts +++ b/dist/views/DependentSampleTable.d.ts @@ -1,10 +1,8 @@ /** * Created by Marc Streit on 26.07.2016. */ -import { ARankingView, IARankingViewOptions } from 'tdp_core'; +import { ARankingView, IARankingViewOptions, ISelection, IViewContext, IServerColumn } from 'tdp_core'; import { IDataTypeConfig } from '../common/config'; -import { ISelection, IViewContext } from 'tdp_core'; -import { IServerColumn } from 'tdp_core'; export declare class DependentSampleTable extends ARankingView { private readonly dataType; constructor(context: IViewContext, selection: ISelection, parent: HTMLElement, dataType: IDataTypeConfig, options?: Partial); @@ -22,3 +20,4 @@ export declare class DependentSampleTable extends ARankingView { static createCopyNumberDependentSampleTable(context: IViewContext, selection: ISelection, parent: HTMLElement, options?: any): DependentSampleTable; static createMutationDependentSampleTable(context: IViewContext, selection: ISelection, parent: HTMLElement, options?: any): DependentSampleTable; } +//# sourceMappingURL=DependentSampleTable.d.ts.map \ No newline at end of file From caec0d4d624c79ca80651d9209e8572ea322b830 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Mon, 30 May 2022 15:44:43 +0200 Subject: [PATCH 07/38] update dist --- dist/menu/DatasetCard.d.ts | 1 + dist/menu/DatasetCard.d.ts.map | 2 +- dist/menu/DatasetCard.js | 41 +++++++++++++++++++++------------- dist/menu/DatasetCard.js.map | 2 +- 4 files changed, 29 insertions(+), 17 deletions(-) diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index 836b542b..2587b238 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,3 +1,4 @@ +/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; //# sourceMappingURL=DatasetCard.d.ts.map \ No newline at end of file diff --git a/dist/menu/DatasetCard.d.ts.map b/dist/menu/DatasetCard.d.ts.map index 2fd90cae..d3463b7e 100644 --- a/dist/menu/DatasetCard.d.ts.map +++ b/dist/menu/DatasetCard.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":"AAiBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eAwLjJ"} \ No newline at end of file +{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":";AAmBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file diff --git a/dist/menu/DatasetCard.js b/dist/menu/DatasetCard.js index ad011a04..6bea9eb9 100644 --- a/dist/menu/DatasetCard.js +++ b/dist/menu/DatasetCard.js @@ -1,13 +1,13 @@ import React from 'react'; -import { ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils, UserSession, UniqueIdManager, I18nextManager, IDTypeManager, useAsync, } from 'tdp_core'; +import { ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils, UserSession, UniqueIdManager, I18nextManager, IDTypeManager, useAsync, GlobalEventHandler, AView, } from 'tdp_core'; import { NamedSetList, OrdinoContext } from 'ordino'; import { Species } from 'tdp_gene'; import { DatasetSearchBox } from './DatasetSearchBox'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }) { - var _a, _b; const testId = `datasetcard-${cssClass}`; const { app } = React.useContext(OrdinoContext); - const [dirtyNamedSets, setDirtyNamedSets] = React.useState(false); + const [namedSets, setNamedSets] = React.useState([]); + const [dirtyNamedSets, setDirtyNamedSets] = React.useState(true); const loadPredefinedSet = React.useMemo(() => { return async () => { const panels = await RestBaseUtils.getTDPData(dataSource.db, `${dataSource.base}_panel`); @@ -44,15 +44,26 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, }; // eslint-disable-next-line react-hooks/exhaustive-deps }, [dataSource.idType]); - const loadNamedSets = React.useMemo(() => { - return () => RestStorageUtils.listNamedSets(dataSource.idType); - // eslint-disable-next-line react-hooks/exhaustive-deps + const loadNamedSets = React.useCallback(async () => { + // if dirty is false do not reload data again + if (!dirtyNamedSets) { + return; + } + setNamedSets(await RestStorageUtils.listNamedSets(dataSource.idType)); + setDirtyNamedSets(false); }, [dataSource.idType, dirtyNamedSets]); + React.useEffect(() => { + const entryPointChanged = () => setDirtyNamedSets(true); + GlobalEventHandler.getInstance().on(AView.EVENT_UPDATE_ENTRY_POINT, entryPointChanged); + return () => { + GlobalEventHandler.getInstance().off(AView.EVENT_UPDATE_ENTRY_POINT, entryPointChanged); + }; + }, []); const predefinedNamedSets = useAsync(loadPredefinedSet, []); const me = UserSession.getInstance().currentUserNameOrAnonymous(); - const namedSets = useAsync(loadNamedSets, []); - const myNamedSets = { ...namedSets, ...{ value: (_a = namedSets.value) === null || _a === void 0 ? void 0 : _a.filter((d) => d.type === ENamedSetType.NAMEDSET && d.creator === me) } }; - const publicNamedSets = { ...namedSets, ...{ value: (_b = namedSets.value) === null || _b === void 0 ? void 0 : _b.filter((d) => d.type === ENamedSetType.NAMEDSET && d.creator !== me) } }; + const { status: namedSetsStatus } = useAsync(loadNamedSets, []); + const myNamedSets = { ...namedSets, ...{ value: namedSets === null || namedSets === void 0 ? void 0 : namedSets.filter((d) => d.type === ENamedSetType.NAMEDSET && d.creator === me) } }; + const publicNamedSets = { ...namedSets, ...{ value: namedSets === null || namedSets === void 0 ? void 0 : namedSets.filter((d) => d.type === ENamedSetType.NAMEDSET && d.creator !== me) } }; const filterValue = (value, tab) => value === null || value === void 0 ? void 0 : value.filter((entry) => entry.subTypeValue === tab); const onOpenNamedSet = (event, { namedSet, species }) => { event.preventDefault(); @@ -73,11 +84,11 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, app.startNewSession(startViewId, searchResult, defaultSessionValues); }; const onSaveAsNamedSet = (items, subtype) => { - StoreUtils.editDialog(null, I18nextManager.getInstance().i18n.t(`tdp:core.editDialog.listOfEntities.default`), async (n, description, isPublic) => { + StoreUtils.editDialog(null, I18nextManager.getInstance().i18n.t(`tdp:core.editDialog.listOfEntities.default`), async (datasetName, description, isPublic) => { const idStrings = items === null || items === void 0 ? void 0 : items.map((i) => i.id); const idType = IDTypeManager.getInstance().resolveIdType(dataSource.idType); - await RestStorageUtils.saveNamedSet(name, idType, idStrings, subtype, description, isPublic); - setDirtyNamedSets((d) => !d); + await RestStorageUtils.saveNamedSet(datasetName, idType, idStrings, subtype, description, isPublic); + setDirtyNamedSets(true); }); }; const id = React.useMemo(() => UniqueIdManager.getInstance().uniqueId(), []); @@ -103,13 +114,13 @@ export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, React.createElement("div", { className: "row mt-4" }, React.createElement(NamedSetList, { headerIcon: "fas fa-database", headerText: "Predefined Sets", onOpen: (event, namedSet) => { onOpenNamedSet(event, { namedSet, species: tab.id }); - }, status: predefinedNamedSets.status, value: filterValue(predefinedNamedSets.value, tab.id) }), + }, onEditNamedSet: () => setDirtyNamedSets(true), onDeleteNamedSet: () => setDirtyNamedSets(true), status: predefinedNamedSets.status, value: filterValue(predefinedNamedSets.value, tab.id) }), React.createElement(NamedSetList, { headerIcon: "fas fa-user", headerText: "My Sets", onOpen: (event, namedSet) => { onOpenNamedSet(event, { namedSet, species: tab.id }); - }, status: myNamedSets.status, value: filterValue(myNamedSets.value, tab.id) }), + }, onEditNamedSet: () => setDirtyNamedSets(true), onDeleteNamedSet: () => setDirtyNamedSets(true), status: namedSetsStatus, value: filterValue(myNamedSets.value, tab.id) }), React.createElement(NamedSetList, { headerIcon: "fas fa-users", headerText: "Other Sets", onOpen: (event, namedSet) => { onOpenNamedSet(event, { namedSet, species: tab.id }); - }, status: publicNamedSets.status, value: filterValue(publicNamedSets.value, tab.id) })))); + }, onEditNamedSet: () => setDirtyNamedSets(true), onDeleteNamedSet: () => setDirtyNamedSets(true), status: namedSetsStatus, value: filterValue(publicNamedSets.value, tab.id) })))); })))))); } //# sourceMappingURL=DatasetCard.js.map \ No newline at end of file diff --git a/dist/menu/DatasetCard.js.map b/dist/menu/DatasetCard.js.map index a6f318a0..ba8d89da 100644 --- a/dist/menu/DatasetCard.js.map +++ b/dist/menu/DatasetCard.js.map @@ -1 +1 @@ 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\ No newline at end of file From e71f24ed4b227cf8b349f18b4f1328f7301d8d42 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 7 Jun 2022 14:53:01 +0200 Subject: [PATCH 08/38] rename for constistency --- dist/menu/DatasetCard.js | 2 +- dist/menu/DatasetCard.js.map | 2 +- src/menu/DatasetCard.tsx | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/dist/menu/DatasetCard.js b/dist/menu/DatasetCard.js index 6bea9eb9..c1666290 100644 --- a/dist/menu/DatasetCard.js +++ b/dist/menu/DatasetCard.js @@ -4,7 +4,7 @@ import { NamedSetList, OrdinoContext } from 'ordino'; import { Species } from 'tdp_gene'; import { DatasetSearchBox } from './DatasetSearchBox'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }) { - const testId = `datasetcard-${cssClass}`; + const testId = `dataset-card-${cssClass}`; const { app } = React.useContext(OrdinoContext); const [namedSets, setNamedSets] = React.useState([]); const [dirtyNamedSets, setDirtyNamedSets] = React.useState(true); diff --git a/dist/menu/DatasetCard.js.map b/dist/menu/DatasetCard.js.map index ba8d89da..fdc2bfe7 100644 --- a/dist/menu/DatasetCard.js.map +++ b/dist/menu/DatasetCard.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/menu/DatasetCard.tsx b/src/menu/DatasetCard.tsx index 228380ad..ee81de24 100644 --- a/src/menu/DatasetCard.tsx +++ b/src/menu/DatasetCard.tsx @@ -20,7 +20,7 @@ import { DatasetSearchBox } from './DatasetSearchBox'; import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc) { - const testId = `datasetcard-${cssClass}`; + const testId = `dataset-card-${cssClass}`; const { app } = React.useContext(OrdinoContext); const [namedSets, setNamedSets] = React.useState([]); const [dirtyNamedSets, setDirtyNamedSets] = React.useState(true); From 3946d4ea4033aaed3420ed64d5746a71aadaaf1d Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 21 Jun 2022 10:46:46 +0200 Subject: [PATCH 09/38] update dist --- dist/menu/DatasetCard.d.ts | 1 - dist/menu/DatasetCard.d.ts.map | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index 2587b238..836b542b 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,4 +1,3 @@ -/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; //# sourceMappingURL=DatasetCard.d.ts.map \ No newline at end of file diff --git a/dist/menu/DatasetCard.d.ts.map b/dist/menu/DatasetCard.d.ts.map index d3463b7e..ce5bcc3d 100644 --- a/dist/menu/DatasetCard.d.ts.map +++ b/dist/menu/DatasetCard.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":";AAmBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file +{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":"AAmBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file From ee11bbc93de76527040dbcc31f5afa8b9f70f4f0 Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Thu, 30 Jun 2022 11:07:44 +0200 Subject: [PATCH 10/38] Fix typings Requires https://github.com/datavisyn/tdp_core/pull/749 --- dist/menu/DatasetCard.d.ts | 1 + dist/menu/DatasetCard.d.ts.map | 2 +- dist/scores/forms.d.ts | 42 +++++++++---------- dist/views/ACombinedDependentTable.d.ts | 2 +- dist/views/ACombinedDependentTable.d.ts.map | 2 +- dist/views/ACombinedDependentTable.js | 3 +- dist/views/ACombinedDependentTable.js.map | 2 +- dist/views/CombinedDependentSampleTable.d.ts | 2 +- .../CombinedDependentSampleTable.d.ts.map | 2 +- dist/views/CombinedDependentSampleTable.js | 5 +-- .../views/CombinedDependentSampleTable.js.map | 2 +- dist/views/DependentGeneTable.d.ts | 2 +- dist/views/DependentSampleTable.d.ts | 2 +- dist/views/SimilarityView.d.ts | 4 +- dist/views/SimilarityView.d.ts.map | 2 +- dist/views/SimilarityView.js | 8 ++-- dist/views/SimilarityView.js.map | 2 +- src/views/ACombinedDependentTable.ts | 5 ++- src/views/CombinedDependentSampleTable.ts | 5 +-- src/views/SimilarityView.ts | 9 ++-- 20 files changed, 52 insertions(+), 52 deletions(-) diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index 836b542b..2587b238 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,3 +1,4 @@ +/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; //# sourceMappingURL=DatasetCard.d.ts.map \ No newline at end of file diff --git a/dist/menu/DatasetCard.d.ts.map b/dist/menu/DatasetCard.d.ts.map index ce5bcc3d..d3463b7e 100644 --- a/dist/menu/DatasetCard.d.ts.map +++ b/dist/menu/DatasetCard.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":"AAmBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file +{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":";AAmBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file diff --git a/dist/scores/forms.d.ts b/dist/scores/forms.d.ts index 35ef6e91..26902869 100644 --- a/dist/scores/forms.d.ts +++ b/dist/scores/forms.d.ts @@ -134,6 +134,22 @@ export declare const FORM_SINGLE_SCORE: { useSession: boolean; }[]; export declare const FORM_AGGREGATED_SCORE_DEPLETION: ({ + type: FormElementType; + label: string; + id: string; + attributes: { + style: string; + }; + required: boolean; + options: { + placeholder: string; + data: { + id: string; + text: string; + }[]; + }; + useSession: boolean; +} | { type: FormElementType; label: string; id: string; @@ -180,7 +196,8 @@ export declare const FORM_AGGREGATED_SCORE_DEPLETION: ({ step: string; optionsData?: undefined; }; -} | { +})[]; +export declare const FORM_SINGLE_SCORE_DEPLETION: { type: FormElementType; label: string; id: string; @@ -196,8 +213,8 @@ export declare const FORM_AGGREGATED_SCORE_DEPLETION: ({ }[]; }; useSession: boolean; -})[]; -export declare const FORM_SINGLE_SCORE_DEPLETION: { +}[]; +export declare const FORM_SINGLE_SCORE_DRUG: ({ type: FormElementType; label: string; id: string; @@ -213,8 +230,7 @@ export declare const FORM_SINGLE_SCORE_DEPLETION: { }[]; }; useSession: boolean; -}[]; -export declare const FORM_SINGLE_SCORE_DRUG: ({ +} | { type: FormElementType; label: string; id: string; @@ -230,21 +246,5 @@ export declare const FORM_SINGLE_SCORE_DRUG: ({ format: typeof import("..").GeneUtils.formatDrugScreen; }; useSession: boolean; -} | { - type: FormElementType; - label: string; - id: string; - attributes: { - style: string; - }; - required: boolean; - options: { - placeholder: string; - data: { - id: string; - text: string; - }[]; - }; - useSession: boolean; })[]; //# sourceMappingURL=forms.d.ts.map \ No newline at end of file diff --git a/dist/views/ACombinedDependentTable.d.ts b/dist/views/ACombinedDependentTable.d.ts index 748b40a8..8eb1b95e 100644 --- a/dist/views/ACombinedDependentTable.d.ts +++ b/dist/views/ACombinedDependentTable.d.ts @@ -9,7 +9,7 @@ export declare abstract class ACombinedDependentTable extends ARankingView { protected getParameterFormDescs(): import("tdp_core").IFormElementDesc[]; private get subTypes(); protected createSelectionAdapter(): import("tdp_core").ISelectionAdapter; - protected parameterChanged(name: string): void; + protected parameterChanged(name: string): Promise; protected loadColumnDesc(): Promise>; protected getColumnDescs(columns: IServerColumn[]): IAdditionalColumnDesc[]; protected loadRows(): Promise; diff --git a/dist/views/ACombinedDependentTable.d.ts.map b/dist/views/ACombinedDependentTable.d.ts.map index 72d2f716..8994e547 100644 --- a/dist/views/ACombinedDependentTable.d.ts.map +++ b/dist/views/ACombinedDependentTable.d.ts.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/views/ACombinedDependentTable.js b/dist/views/ACombinedDependentTable.js index a4d1008e..ad6aae81 100644 --- a/dist/views/ACombinedDependentTable.js +++ b/dist/views/ACombinedDependentTable.js @@ -58,8 +58,9 @@ export class ACombinedDependentTable extends ARankingView { parameterChanged(name) { super.parameterChanged(name); if (name === 'filter') { - this.reloadData(); + return this.reloadData(); } + return Promise.resolve(); } loadColumnDesc() { return RestBaseUtils.getTDPDesc(this.dataSource.db, this.oppositeDataSource.base); diff --git a/dist/views/ACombinedDependentTable.js.map b/dist/views/ACombinedDependentTable.js.map index a163058b..680843a5 100644 --- a/dist/views/ACombinedDependentTable.js.map +++ b/dist/views/ACombinedDependentTable.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/views/CombinedDependentSampleTable.d.ts b/dist/views/CombinedDependentSampleTable.d.ts index 7d9538fb..3fb27d3b 100644 --- a/dist/views/CombinedDependentSampleTable.d.ts +++ b/dist/views/CombinedDependentSampleTable.d.ts @@ -5,7 +5,7 @@ export declare class CombinedDependentSampleTable extends ACombinedDependentTabl constructor(context: IViewContext, selection: ISelection, parent: HTMLElement, dataType: IDataTypeConfig[]); protected get oppositeDataSource(): IDataSourceConfig; protected getParameterFormDescs(): import("tdp_core").IFormElementDesc[]; - protected parameterChanged(name: string): void; + protected parameterChanged(name: string): Promise; protected getSelectionColumnLabel(ensg: string): Promise; static createCombinedDependentSampleTable(context: IViewContext, selection: ISelection, parent: HTMLElement): CombinedDependentSampleTable; } diff --git a/dist/views/CombinedDependentSampleTable.d.ts.map b/dist/views/CombinedDependentSampleTable.d.ts.map index 2ba92147..212ad41d 100644 --- a/dist/views/CombinedDependentSampleTable.d.ts.map +++ b/dist/views/CombinedDependentSampleTable.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"CombinedDependentSampleTable.d.ts","sourceRoot":"","sources":["../../src/views/CombinedDependentSampleTable.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,UAAU,CAAC;AACpD,OAAO,EAA0C,eAAe,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AAE9G,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAC;AAGpE,qBAAa,4BAA6B,SAAQ,uBAAuB;gBAC3D,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,eAAe,EAAE;IAM1G,SAAS,KAAK,kBAAkB,sBAE/B;IAED,SAAS,CAAC,qBAAqB;IAO/B,SAAS,CAAC,gBAAgB,CAAC,IAAI,EAAE,MAAM;IAQvC,SAAS,CAAC,uBAAuB,CAAC,IAAI,EAAE,MAAM;IAI9C,MAAM,CAAC,kCAAkC,CAAC,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW;CAG5G"} \ No newline at end of file +{"version":3,"file":"CombinedDependentSampleTable.d.ts","sourceRoot":"","sources":["../../src/views/CombinedDependentSampleTable.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,UAAU,CAAC;AACpD,OAAO,EAA0C,eAAe,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AAE9G,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAC;AAGpE,qBAAa,4BAA6B,SAAQ,uBAAuB;gBAC3D,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,eAAe,EAAE;IAM1G,SAAS,KAAK,kBAAkB,sBAE/B;IAED,SAAS,CAAC,qBAAqB;IAO/B,SAAS,CAAC,gBAAgB,CAAC,IAAI,EAAE,MAAM;IAOvC,SAAS,CAAC,uBAAuB,CAAC,IAAI,EAAE,MAAM;IAI9C,MAAM,CAAC,kCAAkC,CAAC,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW;CAG5G"} \ No newline at end of file diff --git a/dist/views/CombinedDependentSampleTable.js b/dist/views/CombinedDependentSampleTable.js index e11a336b..1ea5949f 100644 --- a/dist/views/CombinedDependentSampleTable.js +++ b/dist/views/CombinedDependentSampleTable.js @@ -18,10 +18,9 @@ export class CombinedDependentSampleTable extends ACombinedDependentTable { } parameterChanged(name) { if (name === FORM_DATA_SOURCE.id) { - this.rebuild(); - return; // early abort since there is nothing worse than building from scratch + return this.rebuild(); // early abort after rebuild since there is nothing worse than building from scratch } - super.parameterChanged(name); + return super.parameterChanged(name); } getSelectionColumnLabel(ensg) { return ViewUtils.loadFirstName(ensg); diff --git a/dist/views/CombinedDependentSampleTable.js.map b/dist/views/CombinedDependentSampleTable.js.map index bd7545e1..af86719a 100644 --- a/dist/views/CombinedDependentSampleTable.js.map +++ b/dist/views/CombinedDependentSampleTable.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/views/DependentGeneTable.d.ts b/dist/views/DependentGeneTable.d.ts index 959015cb..95d824d3 100644 --- a/dist/views/DependentGeneTable.d.ts +++ b/dist/views/DependentGeneTable.d.ts @@ -8,7 +8,7 @@ export declare class DependentGeneTable extends ARankingView { private readonly dataSource; constructor(context: IViewContext, selection: ISelection, parent: HTMLElement, dataType: IDataTypeConfig, options?: Partial); protected getParameterFormDescs(): import("tdp_core").IFormElementDesc[]; - protected parameterChanged(name: string): Promise; + protected parameterChanged(name: string): Promise; protected loadColumnDesc(): Promise>; protected createSelectionAdapter(): import("tdp_core").ISelectionAdapter; protected getColumnDescs(columns: IServerColumn[]): import("tdp_core").IAdditionalColumnDesc[]; diff --git a/dist/views/DependentSampleTable.d.ts b/dist/views/DependentSampleTable.d.ts index c46bd86a..feaeed55 100644 --- a/dist/views/DependentSampleTable.d.ts +++ b/dist/views/DependentSampleTable.d.ts @@ -10,7 +10,7 @@ export declare class DependentSampleTable extends ARankingView { get itemIDType(): import("tdp_core").IDType; private get dataSource(); private get dataSubType(); - protected parameterChanged(name: string): Promise; + protected parameterChanged(name: string): Promise; protected loadColumnDesc(): Promise>; protected createSelectionAdapter(): import("tdp_core").ISelectionAdapter; protected getColumnDescs(columns: IServerColumn[]): import("tdp_core").IAdditionalColumnDesc[]; diff --git a/dist/views/SimilarityView.d.ts b/dist/views/SimilarityView.d.ts index 09b6a2f3..2e980011 100644 --- a/dist/views/SimilarityView.d.ts +++ b/dist/views/SimilarityView.d.ts @@ -17,8 +17,8 @@ export declare class SimilarityView extends ARankingView { protected getColumnDescs(columns: any[]): IAdditionalColumnDesc[]; protected loadColumnDesc(): Promise; protected loadRows(): Promise; - protected parameterChanged(name: string): void; - protected selectionChanged(): void; + protected parameterChanged(name: string): Promise; + protected selectionChanged(): Promise; private updateImpl; protected createInitialRanking(provider: LocalDataProvider): void; } diff --git a/dist/views/SimilarityView.d.ts.map b/dist/views/SimilarityView.d.ts.map index bf260d43..6b412e9d 100644 --- a/dist/views/SimilarityView.d.ts.map +++ b/dist/views/SimilarityView.d.ts.map @@ -1 +1 @@ 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b/dist/views/SimilarityView.js @@ -92,16 +92,16 @@ export class SimilarityView extends ARankingView { } parameterChanged(name) { super.parameterChanged(name); - this.updateImpl(); + return this.updateImpl(); } selectionChanged() { super.selectionChanged(); - this.updateImpl(); + return this.updateImpl(); } updateImpl() { - this.updateOptionsData().then(() => { + return this.updateOptionsData().then(() => { this.loader = null; - this.rebuild(); + return this.rebuild(); }); } createInitialRanking(provider) { diff --git a/dist/views/SimilarityView.js.map b/dist/views/SimilarityView.js.map index 90ee81b4..454bf48e 100644 --- a/dist/views/SimilarityView.js.map +++ b/dist/views/SimilarityView.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/views/ACombinedDependentTable.ts b/src/views/ACombinedDependentTable.ts index 730253fe..b32f65bb 100644 --- a/src/views/ACombinedDependentTable.ts +++ b/src/views/ACombinedDependentTable.ts @@ -82,11 +82,12 @@ export abstract class ACombinedDependentTable extends ARankingView { }); } - protected parameterChanged(name: string) { + protected parameterChanged(name: string): Promise { super.parameterChanged(name); if (name === 'filter') { - this.reloadData(); + return this.reloadData(); } + return Promise.resolve(); } protected loadColumnDesc() { diff --git a/src/views/CombinedDependentSampleTable.ts b/src/views/CombinedDependentSampleTable.ts index ace183ed..8debe1f7 100644 --- a/src/views/CombinedDependentSampleTable.ts +++ b/src/views/CombinedDependentSampleTable.ts @@ -24,10 +24,9 @@ export class CombinedDependentSampleTable extends ACombinedDependentTable { protected parameterChanged(name: string) { if (name === FORM_DATA_SOURCE.id) { - this.rebuild(); - return; // early abort since there is nothing worse than building from scratch + return this.rebuild(); // early abort after rebuild since there is nothing worse than building from scratch } - super.parameterChanged(name); + return super.parameterChanged(name); } protected getSelectionColumnLabel(ensg: string) { diff --git a/src/views/SimilarityView.ts b/src/views/SimilarityView.ts index d1814523..e9079ac1 100644 --- a/src/views/SimilarityView.ts +++ b/src/views/SimilarityView.ts @@ -12,7 +12,6 @@ import { ColumnDescUtils, FormElementType, IFormSelectElement, - IDTypeManager, RestBaseUtils, } from 'tdp_core'; import { LocalDataProvider, createSelectionDesc, createStackDesc, StackColumn } from 'lineupjs'; @@ -127,18 +126,18 @@ export class SimilarityView extends ARankingView { protected parameterChanged(name: string) { super.parameterChanged(name); - this.updateImpl(); + return this.updateImpl(); } protected selectionChanged() { super.selectionChanged(); - this.updateImpl(); + return this.updateImpl(); } private updateImpl() { - this.updateOptionsData().then(() => { + return this.updateOptionsData().then(() => { this.loader = null; - this.rebuild(); + return this.rebuild(); }); } From fbc855a6eccf325182d2ee34df3a33181ca86d67 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 19 Jul 2022 07:58:42 +0200 Subject: [PATCH 11/38] add index.js --- cypress/integration/index.js | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 cypress/integration/index.js diff --git a/cypress/integration/index.js b/cypress/integration/index.js new file mode 100644 index 00000000..60357546 --- /dev/null +++ b/cypress/integration/index.js @@ -0,0 +1,4 @@ +export * from 'tdp_bi_bioinfodb/cypress/integration/long-running-score.spec'; +export * from './session_all_celllines.spec'; +export * from './session_all_genes.spec'; +export * from './session_all_tissues.spec'; From 2867237b4b72fe7f9cc47cd8af6e00e977bec824 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 19 Jul 2022 15:26:02 +0200 Subject: [PATCH 12/38] fix setup --- cypress/integration/index.js | 6 +- .../integration/long-running-score.spec.js | 46 ++++++ cypress/integration/ordino-video-test.spec.js | 156 ++++++++++++++++++ .../integration/session_all_celllines.spec.js | 27 +++ cypress/integration/session_all_genes.spec.js | 27 +++ .../integration/session_all_tissues.spec.js | 27 +++ 6 files changed, 287 insertions(+), 2 deletions(-) create mode 100644 cypress/integration/long-running-score.spec.js create mode 100644 cypress/integration/ordino-video-test.spec.js create mode 100644 cypress/integration/session_all_celllines.spec.js create mode 100644 cypress/integration/session_all_genes.spec.js create mode 100644 cypress/integration/session_all_tissues.spec.js diff --git a/cypress/integration/index.js b/cypress/integration/index.js index 60357546..34429a2b 100644 --- a/cypress/integration/index.js +++ b/cypress/integration/index.js @@ -1,4 +1,6 @@ -export * from 'tdp_bi_bioinfodb/cypress/integration/long-running-score.spec'; -export * from './session_all_celllines.spec'; +export * from './long-running-score.spec'; export * from './session_all_genes.spec'; +export * from './session_all_celllines.spec'; export * from './session_all_tissues.spec'; + +export * from './ordino-video-test.spec'; diff --git a/cypress/integration/long-running-score.spec.js b/cypress/integration/long-running-score.spec.js new file mode 100644 index 00000000..4da2592b --- /dev/null +++ b/cypress/integration/long-running-score.spec.js @@ -0,0 +1,46 @@ +import {scrollElementIntoCenter, formSelect, select2SingleSelect} from 'tdp_core/dist/cypress/utils'; +import {waitLineupReadyOrdino, checkScoreColLoadedOrdino} from 'ordino/dist/cypress/utils'; + +// https://www.youtube.com/watch?v=JZIIf-k852g&t=1s +it('Long Running Score', function() { + cy.visit(Cypress.env('host')); + // Login + cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); + + cy.login(); // use Cypress command registerd in Ordino app + + // Show you can select single genes if you wanted + scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + // wait intentionally a few seconds + cy.wait(2000) + cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click(); + + // Open Lineup ranking + // Define api calls to wait: + cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc'); + cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes'); + cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); + cy.wait('@gene_desc'); + cy.wait('@human_genes'); + waitLineupReadyOrdino(0) + + // Add column + cy.get('[data-testid=add-column-button]').click(); + cy.wait(2000); + cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); + select2SingleSelect("data-type", "Relative Copy Number") + formSelect("aggregation", "Boxplot") + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 9) + + // Add column + cy.get('[data-testid=add-column-button]').click(); + cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); + formSelect("aggregation", "Frequency") + formSelect("comparison-operator", "> greater than") + cy.get(':nth-child(5) > .form-control').clear(); + cy.get(':nth-child(5) > .form-control').type('4'); + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(0, ['Frequency > 4'], 10) +}) \ No newline at end of file diff --git a/cypress/integration/ordino-video-test.spec.js b/cypress/integration/ordino-video-test.spec.js new file mode 100644 index 00000000..2ce4b2c4 --- /dev/null +++ b/cypress/integration/ordino-video-test.spec.js @@ -0,0 +1,156 @@ +import { cy, it, Cypress } from 'local-cypress'; +import { waitLineupReadyOrdino, checkScoreColLoadedOrdino} from 'ordino/dist/cypress/utils'; +import { scrollElementIntoCenter, select2MultiSelect, formSelect, select2SingleSelect, waitTdpNotBusy} from 'tdp_core/dist/cypress/utils'; + +// https://www.youtube.com/watch?v=JZIIf-k852g&t=1s +it('ordino video', function() { + cy.visit(Cypress.env('host')); + + cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); + + cy.login(); // use Cypress command registerd in Ordino app + + // Show you can select single genes if you wanted + scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + // wait intentionally a few seconds + cy.wait(2000) + cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click(); + + // Open Lineup ranking + // Define api calls to wait: + cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc'); + cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes'); + cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); + cy.wait('@gene_desc'); + cy.wait('@human_genes'); + waitLineupReadyOrdino(0) + + // Add column + cy.get('[data-testid=add-column-button]').click(); + cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); + select2MultiSelect("cell-line", "HCC1954") + select2MultiSelect("data-type", "Relative Copy Number") + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(0, ['HCC1954', 'Relative Copy Number'], 9); + + // Sort by column + // cy.get('[data-draginfo="Merge"] > .lu-toolbar > .lu-action-sort').click(); + + // Show some information + cy.get('[data-testid="(un)collapse-button"] > .fas').click(); + // intentionally wait 1 second + cy.wait(1000) + // filter with histogram not possible + cy.get('[data-testid="(un)collapse-button"] > .fas').click(); + + // Add column + cy.get('[data-testid=add-column-button]').click(); + cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); + select2MultiSelect("cell-line", "HCC1954") + select2MultiSelect("data-type", "Normalized Gene Expression (TPM Values)") + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(0, ['HCC1954', 'Normalized Gene Expression (TPM Values)'], 10) + + // Add column + cy.get('[data-testid=add-column-button]').click(); + cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span').click(); + select2MultiSelect("cell-line", "HCC1954") + select2MultiSelect("data-type", "DRIVE RSA (ER McDonald III et al., Cell, 2017)") + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(0, ['HCC1954', 'DRIVE RSA (ER McDonald III et al., Cell, 2017)'], 11) + + // Invert column + // Here the title should be used. For some reason cypress has problmes, because there is a " character in the title. For now I use the data-id + cy.get('[data-id="col10"] > .lu-toolbar > .lu-action-more').click(); + cy.get('.lu-action-data-mapping > span').click(); + cy.get('.browser-default').select('linear_invert'); + cy.get('.lu-dialog-buttons > [type="submit"]').click(); + + // Add column + cy.get('[data-testid=add-column-button]').click(); + cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); + formSelect("row-1", "Tumor Type") + select2MultiSelect("row-1", "breast carcinoma") + select2SingleSelect("data-type", "Normalized Gene Expression (TPM Values)") + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(0, ['Tumor Type', 'breast carcinoma', 'Normalized Gene Expression (TPM Values)'], 12) + + // Add column + cy.get('[data-testid=add-column-button]').click(); + cy.wait(2000); + cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); + select2SingleSelect("data-type", "Relative Copy Number") + formSelect("aggregation", "Boxplot") + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 13) + + // Add column + cy.get('[data-testid=add-column-button]').click(); + cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); + formSelect("aggregation", "Frequency") + formSelect("comparison-operator", "> greater than") + cy.get(':nth-child(5) > .form-control').clear(); + cy.get(':nth-child(5) > .form-control').type('4'); + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(0, ['Frequency > 4'], 14) + + // Select elements and click on detail views + waitLineupReadyOrdino(0) + cy.get('[data-index="0"] > .lu-renderer-selection').click(); + cy.get('[data-testid=celllinedb_expression_vs_copynumber]').click(); + waitTdpNotBusy() + waitLineupReadyOrdino(0) + cy.wait(2000) + cy.get('[data-index="6"] > .lu-renderer-selection').click(); + waitTdpNotBusy() + waitLineupReadyOrdino(0) + cy.wait(2000) + cy.get('[data-index="6"] > .lu-renderer-selection').click(); + waitTdpNotBusy() + cy.wait(2000) + cy.get('[data-testid=targetvalidation]').click(); + waitTdpNotBusy() + cy.wait(2000) + cy.get('[data-testid=ensembl_org]').click(); + waitTdpNotBusy() + cy.wait(2000) + cy.get('[data-testid=copynumbertable]').click(); + waitTdpNotBusy() + cy.wait(2000) + + // Sort and filter columns + cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > [data-draginfo="Merge"] > .lu-toolbar > .lu-action-sort').click(); + cy.get('[title="Tumor Type"] > .lu-toolbar > .lu-action-filter').click(); + cy.get('.lu-dialog-table > :nth-child(1) > :nth-child(2) > div').click(); + cy.get('.lu-dialog-table > :nth-child(1) > input').uncheck(); + cy.get(':nth-child(6) > :nth-child(2) > .lu-dialog-filter-table-entry-label').click(); + cy.get('.lu-dialog-table > :nth-child(6) > input').check(); + cy.get('.lu-dialog-buttons > [type="submit"]').click(); + + // Add column + cy.get('[data-testid=viewWrapper-1] [data-testid=side-panel-wrapper] [data-testid=lu-adder-div] [data-testid=add-column-button]').click(); + cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > [data-testid=side-panel-wrapper] > .panel-header > :nth-child(2) > [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); + select2MultiSelect("gene-symbol", ["BRCA1", "BRCA2"]) + select2MultiSelect("data-type", "AA Mutated") + cy.get('[data-testid=primary-dialog-button]').click(); + checkScoreColLoadedOrdino(1, ['BRCA1', 'AA Mutated'], 10) + checkScoreColLoadedOrdino(1, ['BRCA2', 'AA Mutated'], 10) + + waitLineupReadyOrdino(1) + cy.get('[data-testid=viewWrapper-1] [data-index="0"] > .lu-renderer-selection').click(); + cy.get('[data-testid=viewWrapper-1] [data-index="1"] > .lu-renderer-selection').click(); + cy.get('[data-testid=cosmic]').click(); + // Intentionally wait 2 seconds + waitTdpNotBusy() + cy.wait(2000) + cy.get('[data-testid=show] [data-testid=form-select]').select('907046'); + // Intentionally wait 2 seconds + waitTdpNotBusy() + cy.wait(2000) + cy.get('[data-testid=ordino_sessions_shortcut-link]').click(); + cy.get('[data-testid=current-session-sessionscard] [data-testid=ordino0] [data-testid=save-button]').click(); + cy.get('[data-testid=agree-input]').check(); + cy.get('[data-testid=primary-dialog-button]').click(); + cy.get('[data-testid=ordino_sessions_tab] [data-testid=close-button]').click(); +}) \ No newline at end of file diff --git a/cypress/integration/session_all_celllines.spec.js b/cypress/integration/session_all_celllines.spec.js new file mode 100644 index 00000000..22f7d563 --- /dev/null +++ b/cypress/integration/session_all_celllines.spec.js @@ -0,0 +1,27 @@ +import {scrollElementIntoCenter} from 'tdp_core/dist/cypress/utils'; +import {waitLineupReadyOrdino} from 'ordino/dist/cypress/utils'; + +it('Load all Celllines', function() { + cy.visit(Cypress.env('host')); + + // Login + cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); + + cy.login(); // use Cypress command registerd in Ordino app + + // Show you can select single genes if you wanted + scrollElementIntoCenter('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + // wait intentionally a few seconds + cy.wait(2000) + cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-link]').click(); + + // Open Lineup ranking + // Define api calls to wait: + cy.intercept('/api/tdp/db/publicdb/cellline/desc').as('cellline_desc'); + cy.intercept('/api/tdp/db/publicdb/cellline/filter?filter_species=human&filter_panel=CCLE').as('human_cellline'); + cy.get('[data-testid=ccle-button]').click(); + cy.wait('@cellline_desc'); + cy.wait('@human_cellline'); + waitLineupReadyOrdino(0) +}); diff --git a/cypress/integration/session_all_genes.spec.js b/cypress/integration/session_all_genes.spec.js new file mode 100644 index 00000000..4f1f567f --- /dev/null +++ b/cypress/integration/session_all_genes.spec.js @@ -0,0 +1,27 @@ +import {scrollElementIntoCenter} from 'tdp_core/dist/cypress/utils'; +import {waitLineupReadyOrdino} from 'ordino/dist/cypress/utils'; + +it('Load all Genes', function() { + cy.visit(Cypress.env('host')); + + // Login + cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); + + cy.login(); // use Cypress command registerd in Ordino app + + // Show you can select single genes if you wanted + scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + // wait intentionally a few seconds + cy.wait(2000) + cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click(); + + // Open Lineup ranking + // Define api calls to wait: + cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc'); + cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes'); + cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); + cy.wait('@gene_desc'); + cy.wait('@human_genes'); + waitLineupReadyOrdino(0) +}); diff --git a/cypress/integration/session_all_tissues.spec.js b/cypress/integration/session_all_tissues.spec.js new file mode 100644 index 00000000..40b7bf9c --- /dev/null +++ b/cypress/integration/session_all_tissues.spec.js @@ -0,0 +1,27 @@ +import {scrollElementIntoCenter} from 'tdp_core/dist/cypress/utils'; +import {waitLineupReadyOrdino} from 'ordino/dist/cypress/utils'; + +it('Load all Tissues', function() { + cy.visit(Cypress.env('host')); + + // Login + cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); + + cy.login(); // use Cypress command registerd in Ordino app + + // Show you can select single genes if you wanted + scrollElementIntoCenter('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.get('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + // wait intentionally a few seconds + cy.wait(2000) + cy.get('[data-testid=dataset-card-tissue-dataset] [data-testid=human-link]').click(); + + // Open Lineup ranking + // Define api calls to wait: + cy.intercept('/api/tdp/db/publicdb/tissue/desc').as('tissue_desc'); + cy.intercept('/api/tdp/db/publicdb/tissue/filter?filter_species=human&filter_panel=TCGA+normals').as('human_tissue'); + cy.get('[data-testid=tcga-normals-button]').click(); + cy.wait('@tissue_desc'); + cy.wait('@human_tissue'); + waitLineupReadyOrdino(0) +}); From e0d7459193828255e477fce56e44655d4bf9c795 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Wed, 20 Jul 2022 07:54:43 +0200 Subject: [PATCH 13/38] update imports and function calls --- .../integration/long-running-score.spec.js | 19 ++--- cypress/integration/ordino-video-test.spec.js | 76 +++++++++---------- .../integration/session_all_celllines.spec.js | 7 +- cypress/integration/session_all_genes.spec.js | 7 +- .../integration/session_all_tissues.spec.js | 7 +- 5 files changed, 51 insertions(+), 65 deletions(-) diff --git a/cypress/integration/long-running-score.spec.js b/cypress/integration/long-running-score.spec.js index 4da2592b..0c738c7a 100644 --- a/cypress/integration/long-running-score.spec.js +++ b/cypress/integration/long-running-score.spec.js @@ -1,6 +1,3 @@ -import {scrollElementIntoCenter, formSelect, select2SingleSelect} from 'tdp_core/dist/cypress/utils'; -import {waitLineupReadyOrdino, checkScoreColLoadedOrdino} from 'ordino/dist/cypress/utils'; - // https://www.youtube.com/watch?v=JZIIf-k852g&t=1s it('Long Running Score', function() { cy.visit(Cypress.env('host')); @@ -10,7 +7,7 @@ it('Long Running Score', function() { cy.login(); // use Cypress command registerd in Ordino app // Show you can select single genes if you wanted - scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() // wait intentionally a few seconds cy.wait(2000) @@ -23,24 +20,24 @@ it('Long Running Score', function() { cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); cy.wait('@gene_desc'); cy.wait('@human_genes'); - waitLineupReadyOrdino(0) + cy.waitLineupReadyOrdino(0) // Add column cy.get('[data-testid=add-column-button]').click(); cy.wait(2000); cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - select2SingleSelect("data-type", "Relative Copy Number") - formSelect("aggregation", "Boxplot") + cy.select2SingleSelect("data-type", "Relative Copy Number") + cy.formSelect("aggregation", "Boxplot") cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 9) + cy.checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 9) // Add column cy.get('[data-testid=add-column-button]').click(); cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - formSelect("aggregation", "Frequency") - formSelect("comparison-operator", "> greater than") + cy.formSelect("aggregation", "Frequency") + cy.formSelect("comparison-operator", "> greater than") cy.get(':nth-child(5) > .form-control').clear(); cy.get(':nth-child(5) > .form-control').type('4'); cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(0, ['Frequency > 4'], 10) + cy.checkScoreColLoadedOrdino(0, ['Frequency > 4'], 10) }) \ No newline at end of file diff --git a/cypress/integration/ordino-video-test.spec.js b/cypress/integration/ordino-video-test.spec.js index 2ce4b2c4..c59ce185 100644 --- a/cypress/integration/ordino-video-test.spec.js +++ b/cypress/integration/ordino-video-test.spec.js @@ -1,6 +1,4 @@ import { cy, it, Cypress } from 'local-cypress'; -import { waitLineupReadyOrdino, checkScoreColLoadedOrdino} from 'ordino/dist/cypress/utils'; -import { scrollElementIntoCenter, select2MultiSelect, formSelect, select2SingleSelect, waitTdpNotBusy} from 'tdp_core/dist/cypress/utils'; // https://www.youtube.com/watch?v=JZIIf-k852g&t=1s it('ordino video', function() { @@ -11,7 +9,7 @@ it('ordino video', function() { cy.login(); // use Cypress command registerd in Ordino app // Show you can select single genes if you wanted - scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() // wait intentionally a few seconds cy.wait(2000) @@ -24,15 +22,15 @@ it('ordino video', function() { cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); cy.wait('@gene_desc'); cy.wait('@human_genes'); - waitLineupReadyOrdino(0) + cy.waitLineupReadyOrdino(0) // Add column cy.get('[data-testid=add-column-button]').click(); cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); - select2MultiSelect("cell-line", "HCC1954") - select2MultiSelect("data-type", "Relative Copy Number") + cy.select2MultiSelect("cell-line", "HCC1954") + cy.select2MultiSelect("data-type", "Relative Copy Number") cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(0, ['HCC1954', 'Relative Copy Number'], 9); + cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Relative Copy Number'], 9); // Sort by column // cy.get('[data-draginfo="Merge"] > .lu-toolbar > .lu-action-sort').click(); @@ -47,18 +45,18 @@ it('ordino video', function() { // Add column cy.get('[data-testid=add-column-button]').click(); cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); - select2MultiSelect("cell-line", "HCC1954") - select2MultiSelect("data-type", "Normalized Gene Expression (TPM Values)") + cy.select2MultiSelect("cell-line", "HCC1954") + cy.select2MultiSelect("data-type", "Normalized Gene Expression (TPM Values)") cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(0, ['HCC1954', 'Normalized Gene Expression (TPM Values)'], 10) + cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Normalized Gene Expression (TPM Values)'], 10) // Add column cy.get('[data-testid=add-column-button]').click(); cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span').click(); - select2MultiSelect("cell-line", "HCC1954") - select2MultiSelect("data-type", "DRIVE RSA (ER McDonald III et al., Cell, 2017)") + cy.select2MultiSelect("cell-line", "HCC1954") + cy.select2MultiSelect("data-type", "DRIVE RSA (ER McDonald III et al., Cell, 2017)") cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(0, ['HCC1954', 'DRIVE RSA (ER McDonald III et al., Cell, 2017)'], 11) + cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'DRIVE RSA (ER McDonald III et al., Cell, 2017)'], 11) // Invert column // Here the title should be used. For some reason cypress has problmes, because there is a " character in the title. For now I use the data-id @@ -70,53 +68,53 @@ it('ordino video', function() { // Add column cy.get('[data-testid=add-column-button]').click(); cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - formSelect("row-1", "Tumor Type") - select2MultiSelect("row-1", "breast carcinoma") - select2SingleSelect("data-type", "Normalized Gene Expression (TPM Values)") + cy.formSelect("row-1", "Tumor Type") + cy.select2MultiSelect("row-1", "breast carcinoma") + cy.select2SingleSelect("data-type", "Normalized Gene Expression (TPM Values)") cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(0, ['Tumor Type', 'breast carcinoma', 'Normalized Gene Expression (TPM Values)'], 12) + cy.checkScoreColLoadedOrdino(0, ['Tumor Type', 'breast carcinoma', 'Normalized Gene Expression (TPM Values)'], 12) // Add column cy.get('[data-testid=add-column-button]').click(); cy.wait(2000); cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - select2SingleSelect("data-type", "Relative Copy Number") - formSelect("aggregation", "Boxplot") + cy.select2SingleSelect("data-type", "Relative Copy Number") + cy.formSelect("aggregation", "Boxplot") cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 13) + cy.checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 13) // Add column cy.get('[data-testid=add-column-button]').click(); cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - formSelect("aggregation", "Frequency") - formSelect("comparison-operator", "> greater than") + cy.formSelect("aggregation", "Frequency") + cy.formSelect("comparison-operator", "> greater than") cy.get(':nth-child(5) > .form-control').clear(); cy.get(':nth-child(5) > .form-control').type('4'); cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(0, ['Frequency > 4'], 14) + cy.checkScoreColLoadedOrdino(0, ['Frequency > 4'], 14) // Select elements and click on detail views - waitLineupReadyOrdino(0) + cy.waitLineupReadyOrdino(0) cy.get('[data-index="0"] > .lu-renderer-selection').click(); cy.get('[data-testid=celllinedb_expression_vs_copynumber]').click(); - waitTdpNotBusy() - waitLineupReadyOrdino(0) + cy.waitTdpNotBusy() + cy.waitLineupReadyOrdino(0) cy.wait(2000) cy.get('[data-index="6"] > .lu-renderer-selection').click(); - waitTdpNotBusy() - waitLineupReadyOrdino(0) + cy.waitTdpNotBusy() + cy.waitLineupReadyOrdino(0) cy.wait(2000) cy.get('[data-index="6"] > .lu-renderer-selection').click(); - waitTdpNotBusy() + cy.waitTdpNotBusy() cy.wait(2000) cy.get('[data-testid=targetvalidation]').click(); - waitTdpNotBusy() + cy.waitTdpNotBusy() cy.wait(2000) cy.get('[data-testid=ensembl_org]').click(); - waitTdpNotBusy() + cy.waitTdpNotBusy() cy.wait(2000) cy.get('[data-testid=copynumbertable]').click(); - waitTdpNotBusy() + cy.waitTdpNotBusy() cy.wait(2000) // Sort and filter columns @@ -131,22 +129,22 @@ it('ordino video', function() { // Add column cy.get('[data-testid=viewWrapper-1] [data-testid=side-panel-wrapper] [data-testid=lu-adder-div] [data-testid=add-column-button]').click(); cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > [data-testid=side-panel-wrapper] > .panel-header > :nth-child(2) > [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); - select2MultiSelect("gene-symbol", ["BRCA1", "BRCA2"]) - select2MultiSelect("data-type", "AA Mutated") + cy.select2MultiSelect("gene-symbol", ["BRCA1", "BRCA2"]) + cy.select2MultiSelect("data-type", "AA Mutated") cy.get('[data-testid=primary-dialog-button]').click(); - checkScoreColLoadedOrdino(1, ['BRCA1', 'AA Mutated'], 10) - checkScoreColLoadedOrdino(1, ['BRCA2', 'AA Mutated'], 10) + cy.checkScoreColLoadedOrdino(1, ['BRCA1', 'AA Mutated'], 10) + cy.checkScoreColLoadedOrdino(1, ['BRCA2', 'AA Mutated'], 10) - waitLineupReadyOrdino(1) + cy.waitLineupReadyOrdino(1) cy.get('[data-testid=viewWrapper-1] [data-index="0"] > .lu-renderer-selection').click(); cy.get('[data-testid=viewWrapper-1] [data-index="1"] > .lu-renderer-selection').click(); cy.get('[data-testid=cosmic]').click(); // Intentionally wait 2 seconds - waitTdpNotBusy() + cy.waitTdpNotBusy() cy.wait(2000) cy.get('[data-testid=show] [data-testid=form-select]').select('907046'); // Intentionally wait 2 seconds - waitTdpNotBusy() + cy.waitTdpNotBusy() cy.wait(2000) cy.get('[data-testid=ordino_sessions_shortcut-link]').click(); cy.get('[data-testid=current-session-sessionscard] [data-testid=ordino0] [data-testid=save-button]').click(); diff --git a/cypress/integration/session_all_celllines.spec.js b/cypress/integration/session_all_celllines.spec.js index 22f7d563..266f8330 100644 --- a/cypress/integration/session_all_celllines.spec.js +++ b/cypress/integration/session_all_celllines.spec.js @@ -1,6 +1,3 @@ -import {scrollElementIntoCenter} from 'tdp_core/dist/cypress/utils'; -import {waitLineupReadyOrdino} from 'ordino/dist/cypress/utils'; - it('Load all Celllines', function() { cy.visit(Cypress.env('host')); @@ -10,7 +7,7 @@ it('Load all Celllines', function() { cy.login(); // use Cypress command registerd in Ordino app // Show you can select single genes if you wanted - scrollElementIntoCenter('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.scrollElementIntoCenter('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() // wait intentionally a few seconds cy.wait(2000) @@ -23,5 +20,5 @@ it('Load all Celllines', function() { cy.get('[data-testid=ccle-button]').click(); cy.wait('@cellline_desc'); cy.wait('@human_cellline'); - waitLineupReadyOrdino(0) + cy.waitLineupReadyOrdino(0) }); diff --git a/cypress/integration/session_all_genes.spec.js b/cypress/integration/session_all_genes.spec.js index 4f1f567f..68eabe85 100644 --- a/cypress/integration/session_all_genes.spec.js +++ b/cypress/integration/session_all_genes.spec.js @@ -1,6 +1,3 @@ -import {scrollElementIntoCenter} from 'tdp_core/dist/cypress/utils'; -import {waitLineupReadyOrdino} from 'ordino/dist/cypress/utils'; - it('Load all Genes', function() { cy.visit(Cypress.env('host')); @@ -10,7 +7,7 @@ it('Load all Genes', function() { cy.login(); // use Cypress command registerd in Ordino app // Show you can select single genes if you wanted - scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() // wait intentionally a few seconds cy.wait(2000) @@ -23,5 +20,5 @@ it('Load all Genes', function() { cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); cy.wait('@gene_desc'); cy.wait('@human_genes'); - waitLineupReadyOrdino(0) + cy.waitLineupReadyOrdino(0) }); diff --git a/cypress/integration/session_all_tissues.spec.js b/cypress/integration/session_all_tissues.spec.js index 40b7bf9c..3d430890 100644 --- a/cypress/integration/session_all_tissues.spec.js +++ b/cypress/integration/session_all_tissues.spec.js @@ -1,6 +1,3 @@ -import {scrollElementIntoCenter} from 'tdp_core/dist/cypress/utils'; -import {waitLineupReadyOrdino} from 'ordino/dist/cypress/utils'; - it('Load all Tissues', function() { cy.visit(Cypress.env('host')); @@ -10,7 +7,7 @@ it('Load all Tissues', function() { cy.login(); // use Cypress command registerd in Ordino app // Show you can select single genes if you wanted - scrollElementIntoCenter('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() + cy.scrollElementIntoCenter('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() cy.get('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() // wait intentionally a few seconds cy.wait(2000) @@ -23,5 +20,5 @@ it('Load all Tissues', function() { cy.get('[data-testid=tcga-normals-button]').click(); cy.wait('@tissue_desc'); cy.wait('@human_tissue'); - waitLineupReadyOrdino(0) + cy.waitLineupReadyOrdino(0) }); From 2fd228fa8ea2817ed7231051eb5744ddf026e436 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Fri, 22 Jul 2022 06:34:41 +0200 Subject: [PATCH 14/38] update video --- cypress/integration/ordino-video-test.spec.js | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/cypress/integration/ordino-video-test.spec.js b/cypress/integration/ordino-video-test.spec.js index c59ce185..b9d1fae5 100644 --- a/cypress/integration/ordino-video-test.spec.js +++ b/cypress/integration/ordino-video-test.spec.js @@ -33,7 +33,7 @@ it('ordino video', function() { cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Relative Copy Number'], 9); // Sort by column - // cy.get('[data-draginfo="Merge"] > .lu-toolbar > .lu-action-sort').click(); + cy.get('[data-testid=viewWrapper-0] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > section:nth-last-child(-n+1) > .lu-toolbar > .lu-action-sort').click(); // Show some information cy.get('[data-testid="(un)collapse-button"] > .fas').click(); @@ -100,13 +100,10 @@ it('ordino video', function() { cy.waitTdpNotBusy() cy.waitLineupReadyOrdino(0) cy.wait(2000) - cy.get('[data-index="6"] > .lu-renderer-selection').click(); - cy.waitTdpNotBusy() - cy.waitLineupReadyOrdino(0) - cy.wait(2000) - cy.get('[data-index="6"] > .lu-renderer-selection').click(); - cy.waitTdpNotBusy() - cy.wait(2000) + // cy.get('[data-index="6"] > .lu-renderer-selection').click(); + // cy.waitTdpNotBusy() + // cy.waitLineupReadyOrdino(0) + // cy.wait(2000) cy.get('[data-testid=targetvalidation]').click(); cy.waitTdpNotBusy() cy.wait(2000) @@ -118,7 +115,7 @@ it('ordino video', function() { cy.wait(2000) // Sort and filter columns - cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > [data-draginfo="Merge"] > .lu-toolbar > .lu-action-sort').click(); + cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > section:nth-last-child(-n+1) > .lu-toolbar > .lu-action-sort').click(); cy.get('[title="Tumor Type"] > .lu-toolbar > .lu-action-filter').click(); cy.get('.lu-dialog-table > :nth-child(1) > :nth-child(2) > div').click(); cy.get('.lu-dialog-table > :nth-child(1) > input').uncheck(); @@ -137,12 +134,12 @@ it('ordino video', function() { cy.waitLineupReadyOrdino(1) cy.get('[data-testid=viewWrapper-1] [data-index="0"] > .lu-renderer-selection').click(); - cy.get('[data-testid=viewWrapper-1] [data-index="1"] > .lu-renderer-selection').click(); + cy.get('[data-testid=viewWrapper-1] [data-index="12"] > .lu-renderer-selection').click(); cy.get('[data-testid=cosmic]').click(); // Intentionally wait 2 seconds cy.waitTdpNotBusy() cy.wait(2000) - cy.get('[data-testid=show] [data-testid=form-select]').select('907046'); + cy.get('[data-testid=show] [data-testid=form-select]').select('687455'); // Intentionally wait 2 seconds cy.waitTdpNotBusy() cy.wait(2000) From 1e07eb15809fc6790e788f93916005655e3c4dd2 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Tue, 9 Aug 2022 11:12:01 +0200 Subject: [PATCH 15/38] Refactored cy related files for Cypress v10 --- cypress.config.ts | 9 ++ cypress/fixtures/example.json | 5 + cypress/integration/index.js | 6 - .../integration/long-running-score.spec.js | 43 ----- cypress/integration/ordino-video-test.spec.js | 151 ------------------ .../integration/session_all_celllines.spec.js | 24 --- cypress/integration/session_all_genes.spec.js | 24 --- .../integration/session_all_tissues.spec.js | 24 --- cypress/support/commands.js | 37 +++++ cypress/support/e2e.js | 20 +++ package.json | 1 + 11 files changed, 72 insertions(+), 272 deletions(-) create mode 100644 cypress.config.ts create mode 100644 cypress/fixtures/example.json delete mode 100644 cypress/integration/index.js delete mode 100644 cypress/integration/long-running-score.spec.js delete mode 100644 cypress/integration/ordino-video-test.spec.js delete mode 100644 cypress/integration/session_all_celllines.spec.js delete mode 100644 cypress/integration/session_all_genes.spec.js delete mode 100644 cypress/integration/session_all_tissues.spec.js create mode 100644 cypress/support/commands.js create mode 100644 cypress/support/e2e.js diff --git a/cypress.config.ts b/cypress.config.ts new file mode 100644 index 00000000..17161e32 --- /dev/null +++ b/cypress.config.ts @@ -0,0 +1,9 @@ +import { defineConfig } from "cypress"; + +export default defineConfig({ + e2e: { + setupNodeEvents(on, config) { + // implement node event listeners here + }, + }, +}); diff --git a/cypress/fixtures/example.json b/cypress/fixtures/example.json new file mode 100644 index 00000000..02e42543 --- /dev/null +++ b/cypress/fixtures/example.json @@ -0,0 +1,5 @@ +{ + "name": "Using fixtures to represent data", + "email": "hello@cypress.io", + "body": "Fixtures are a great way to mock data for responses to routes" +} diff --git a/cypress/integration/index.js b/cypress/integration/index.js deleted file mode 100644 index 34429a2b..00000000 --- a/cypress/integration/index.js +++ /dev/null @@ -1,6 +0,0 @@ -export * from './long-running-score.spec'; -export * from './session_all_genes.spec'; -export * from './session_all_celllines.spec'; -export * from './session_all_tissues.spec'; - -export * from './ordino-video-test.spec'; diff --git a/cypress/integration/long-running-score.spec.js b/cypress/integration/long-running-score.spec.js deleted file mode 100644 index 0c738c7a..00000000 --- a/cypress/integration/long-running-score.spec.js +++ /dev/null @@ -1,43 +0,0 @@ -// https://www.youtube.com/watch?v=JZIIf-k852g&t=1s -it('Long Running Score', function() { - cy.visit(Cypress.env('host')); - // Login - cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); - - cy.login(); // use Cypress command registerd in Ordino app - - // Show you can select single genes if you wanted - cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - // wait intentionally a few seconds - cy.wait(2000) - cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click(); - - // Open Lineup ranking - // Define api calls to wait: - cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc'); - cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes'); - cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); - cy.wait('@gene_desc'); - cy.wait('@human_genes'); - cy.waitLineupReadyOrdino(0) - - // Add column - cy.get('[data-testid=add-column-button]').click(); - cy.wait(2000); - cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - cy.select2SingleSelect("data-type", "Relative Copy Number") - cy.formSelect("aggregation", "Boxplot") - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 9) - - // Add column - cy.get('[data-testid=add-column-button]').click(); - cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - cy.formSelect("aggregation", "Frequency") - cy.formSelect("comparison-operator", "> greater than") - cy.get(':nth-child(5) > .form-control').clear(); - cy.get(':nth-child(5) > .form-control').type('4'); - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(0, ['Frequency > 4'], 10) -}) \ No newline at end of file diff --git a/cypress/integration/ordino-video-test.spec.js b/cypress/integration/ordino-video-test.spec.js deleted file mode 100644 index b9d1fae5..00000000 --- a/cypress/integration/ordino-video-test.spec.js +++ /dev/null @@ -1,151 +0,0 @@ -import { cy, it, Cypress } from 'local-cypress'; - -// https://www.youtube.com/watch?v=JZIIf-k852g&t=1s -it('ordino video', function() { - cy.visit(Cypress.env('host')); - - cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); - - cy.login(); // use Cypress command registerd in Ordino app - - // Show you can select single genes if you wanted - cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - // wait intentionally a few seconds - cy.wait(2000) - cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click(); - - // Open Lineup ranking - // Define api calls to wait: - cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc'); - cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes'); - cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); - cy.wait('@gene_desc'); - cy.wait('@human_genes'); - cy.waitLineupReadyOrdino(0) - - // Add column - cy.get('[data-testid=add-column-button]').click(); - cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); - cy.select2MultiSelect("cell-line", "HCC1954") - cy.select2MultiSelect("data-type", "Relative Copy Number") - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Relative Copy Number'], 9); - - // Sort by column - cy.get('[data-testid=viewWrapper-0] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > section:nth-last-child(-n+1) > .lu-toolbar > .lu-action-sort').click(); - - // Show some information - cy.get('[data-testid="(un)collapse-button"] > .fas').click(); - // intentionally wait 1 second - cy.wait(1000) - // filter with histogram not possible - cy.get('[data-testid="(un)collapse-button"] > .fas').click(); - - // Add column - cy.get('[data-testid=add-column-button]').click(); - cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); - cy.select2MultiSelect("cell-line", "HCC1954") - cy.select2MultiSelect("data-type", "Normalized Gene Expression (TPM Values)") - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Normalized Gene Expression (TPM Values)'], 10) - - // Add column - cy.get('[data-testid=add-column-button]').click(); - cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span').click(); - cy.select2MultiSelect("cell-line", "HCC1954") - cy.select2MultiSelect("data-type", "DRIVE RSA (ER McDonald III et al., Cell, 2017)") - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'DRIVE RSA (ER McDonald III et al., Cell, 2017)'], 11) - - // Invert column - // Here the title should be used. For some reason cypress has problmes, because there is a " character in the title. For now I use the data-id - cy.get('[data-id="col10"] > .lu-toolbar > .lu-action-more').click(); - cy.get('.lu-action-data-mapping > span').click(); - cy.get('.browser-default').select('linear_invert'); - cy.get('.lu-dialog-buttons > [type="submit"]').click(); - - // Add column - cy.get('[data-testid=add-column-button]').click(); - cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - cy.formSelect("row-1", "Tumor Type") - cy.select2MultiSelect("row-1", "breast carcinoma") - cy.select2SingleSelect("data-type", "Normalized Gene Expression (TPM Values)") - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(0, ['Tumor Type', 'breast carcinoma', 'Normalized Gene Expression (TPM Values)'], 12) - - // Add column - cy.get('[data-testid=add-column-button]').click(); - cy.wait(2000); - cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - cy.select2SingleSelect("data-type", "Relative Copy Number") - cy.formSelect("aggregation", "Boxplot") - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 13) - - // Add column - cy.get('[data-testid=add-column-button]').click(); - cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click(); - cy.formSelect("aggregation", "Frequency") - cy.formSelect("comparison-operator", "> greater than") - cy.get(':nth-child(5) > .form-control').clear(); - cy.get(':nth-child(5) > .form-control').type('4'); - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(0, ['Frequency > 4'], 14) - - // Select elements and click on detail views - cy.waitLineupReadyOrdino(0) - cy.get('[data-index="0"] > .lu-renderer-selection').click(); - cy.get('[data-testid=celllinedb_expression_vs_copynumber]').click(); - cy.waitTdpNotBusy() - cy.waitLineupReadyOrdino(0) - cy.wait(2000) - // cy.get('[data-index="6"] > .lu-renderer-selection').click(); - // cy.waitTdpNotBusy() - // cy.waitLineupReadyOrdino(0) - // cy.wait(2000) - cy.get('[data-testid=targetvalidation]').click(); - cy.waitTdpNotBusy() - cy.wait(2000) - cy.get('[data-testid=ensembl_org]').click(); - cy.waitTdpNotBusy() - cy.wait(2000) - cy.get('[data-testid=copynumbertable]').click(); - cy.waitTdpNotBusy() - cy.wait(2000) - - // Sort and filter columns - cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > section:nth-last-child(-n+1) > .lu-toolbar > .lu-action-sort').click(); - cy.get('[title="Tumor Type"] > .lu-toolbar > .lu-action-filter').click(); - cy.get('.lu-dialog-table > :nth-child(1) > :nth-child(2) > div').click(); - cy.get('.lu-dialog-table > :nth-child(1) > input').uncheck(); - cy.get(':nth-child(6) > :nth-child(2) > .lu-dialog-filter-table-entry-label').click(); - cy.get('.lu-dialog-table > :nth-child(6) > input').check(); - cy.get('.lu-dialog-buttons > [type="submit"]').click(); - - // Add column - cy.get('[data-testid=viewWrapper-1] [data-testid=side-panel-wrapper] [data-testid=lu-adder-div] [data-testid=add-column-button]').click(); - cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > [data-testid=side-panel-wrapper] > .panel-header > :nth-child(2) > [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click(); - cy.select2MultiSelect("gene-symbol", ["BRCA1", "BRCA2"]) - cy.select2MultiSelect("data-type", "AA Mutated") - cy.get('[data-testid=primary-dialog-button]').click(); - cy.checkScoreColLoadedOrdino(1, ['BRCA1', 'AA Mutated'], 10) - cy.checkScoreColLoadedOrdino(1, ['BRCA2', 'AA Mutated'], 10) - - cy.waitLineupReadyOrdino(1) - cy.get('[data-testid=viewWrapper-1] [data-index="0"] > .lu-renderer-selection').click(); - cy.get('[data-testid=viewWrapper-1] [data-index="12"] > .lu-renderer-selection').click(); - cy.get('[data-testid=cosmic]').click(); - // Intentionally wait 2 seconds - cy.waitTdpNotBusy() - cy.wait(2000) - cy.get('[data-testid=show] [data-testid=form-select]').select('687455'); - // Intentionally wait 2 seconds - cy.waitTdpNotBusy() - cy.wait(2000) - cy.get('[data-testid=ordino_sessions_shortcut-link]').click(); - cy.get('[data-testid=current-session-sessionscard] [data-testid=ordino0] [data-testid=save-button]').click(); - cy.get('[data-testid=agree-input]').check(); - cy.get('[data-testid=primary-dialog-button]').click(); - cy.get('[data-testid=ordino_sessions_tab] [data-testid=close-button]').click(); -}) \ No newline at end of file diff --git a/cypress/integration/session_all_celllines.spec.js b/cypress/integration/session_all_celllines.spec.js deleted file mode 100644 index 266f8330..00000000 --- a/cypress/integration/session_all_celllines.spec.js +++ /dev/null @@ -1,24 +0,0 @@ -it('Load all Celllines', function() { - cy.visit(Cypress.env('host')); - - // Login - cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); - - cy.login(); // use Cypress command registerd in Ordino app - - // Show you can select single genes if you wanted - cy.scrollElementIntoCenter('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - // wait intentionally a few seconds - cy.wait(2000) - cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-link]').click(); - - // Open Lineup ranking - // Define api calls to wait: - cy.intercept('/api/tdp/db/publicdb/cellline/desc').as('cellline_desc'); - cy.intercept('/api/tdp/db/publicdb/cellline/filter?filter_species=human&filter_panel=CCLE').as('human_cellline'); - cy.get('[data-testid=ccle-button]').click(); - cy.wait('@cellline_desc'); - cy.wait('@human_cellline'); - cy.waitLineupReadyOrdino(0) -}); diff --git a/cypress/integration/session_all_genes.spec.js b/cypress/integration/session_all_genes.spec.js deleted file mode 100644 index 68eabe85..00000000 --- a/cypress/integration/session_all_genes.spec.js +++ /dev/null @@ -1,24 +0,0 @@ -it('Load all Genes', function() { - cy.visit(Cypress.env('host')); - - // Login - cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); - - cy.login(); // use Cypress command registerd in Ordino app - - // Show you can select single genes if you wanted - cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - // wait intentionally a few seconds - cy.wait(2000) - cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click(); - - // Open Lineup ranking - // Define api calls to wait: - cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc'); - cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes'); - cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click(); - cy.wait('@gene_desc'); - cy.wait('@human_genes'); - cy.waitLineupReadyOrdino(0) -}); diff --git a/cypress/integration/session_all_tissues.spec.js b/cypress/integration/session_all_tissues.spec.js deleted file mode 100644 index 3d430890..00000000 --- a/cypress/integration/session_all_tissues.spec.js +++ /dev/null @@ -1,24 +0,0 @@ -it('Load all Tissues', function() { - cy.visit(Cypress.env('host')); - - // Login - cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click(); - - cy.login(); // use Cypress command registerd in Ordino app - - // Show you can select single genes if you wanted - cy.scrollElementIntoCenter('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - cy.get('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click() - // wait intentionally a few seconds - cy.wait(2000) - cy.get('[data-testid=dataset-card-tissue-dataset] [data-testid=human-link]').click(); - - // Open Lineup ranking - // Define api calls to wait: - cy.intercept('/api/tdp/db/publicdb/tissue/desc').as('tissue_desc'); - cy.intercept('/api/tdp/db/publicdb/tissue/filter?filter_species=human&filter_panel=TCGA+normals').as('human_tissue'); - cy.get('[data-testid=tcga-normals-button]').click(); - cy.wait('@tissue_desc'); - cy.wait('@human_tissue'); - cy.waitLineupReadyOrdino(0) -}); diff --git a/cypress/support/commands.js b/cypress/support/commands.js new file mode 100644 index 00000000..698b01a4 --- /dev/null +++ b/cypress/support/commands.js @@ -0,0 +1,37 @@ +/// +// *********************************************** +// This example commands.ts shows you how to +// create various custom commands and overwrite +// existing commands. +// +// For more comprehensive examples of custom +// commands please read more here: +// https://on.cypress.io/custom-commands +// *********************************************** +// +// +// -- This is a parent command -- +// Cypress.Commands.add('login', (email, password) => { ... }) +// +// +// -- This is a child command -- +// Cypress.Commands.add('drag', { prevSubject: 'element'}, (subject, options) => { ... }) +// +// +// -- This is a dual command -- +// Cypress.Commands.add('dismiss', { prevSubject: 'optional'}, (subject, options) => { ... }) +// +// +// -- This will overwrite an existing command -- +// Cypress.Commands.overwrite('visit', (originalFn, url, options) => { ... }) +// +// declare global { +// namespace Cypress { +// interface Chainable { +// login(email: string, password: string): Chainable +// drag(subject: string, options?: Partial): Chainable +// dismiss(subject: string, options?: Partial): Chainable +// visit(originalFn: CommandOriginalFn, url: string, options: Partial): Chainable +// } +// } +// } \ No newline at end of file diff --git a/cypress/support/e2e.js b/cypress/support/e2e.js new file mode 100644 index 00000000..f80f74f8 --- /dev/null +++ b/cypress/support/e2e.js @@ -0,0 +1,20 @@ +// *********************************************************** +// This example support/e2e.ts is processed and +// loaded automatically before your test files. +// +// This is a great place to put global configuration and +// behavior that modifies Cypress. +// +// You can change the location of this file or turn off +// automatically serving support files with the +// 'supportFile' configuration option. +// +// You can read more here: +// https://on.cypress.io/configuration +// *********************************************************** + +// Import commands.js using ES2015 syntax: +import './commands' + +// Alternatively you can use CommonJS syntax: +// require('./commands') \ No newline at end of file diff --git a/package.json b/package.json index 063ffdea..899a7faf 100644 --- a/package.json +++ b/package.json @@ -36,6 +36,7 @@ "copy-assets": "if [ -d src/assets ]; then cp -rv src/assets/. dist/assets/; fi && if [ -d src/template ]; then shx --verbose cp -R src/template/. dist/template/; fi", "copy-styles": "if [ -d src/scss ]; then shx --verbose cp -R src/scss/. dist/scss/; fi", "copy": "npm run copy-assets && npm run copy-styles", + "cy:open": "cypress open", "delete-dependencies": "rimraf node_modules", "dist": "mkdir lib && cd dist && tar cvzf ../lib/tdp_publicdb.tar.gz *", "docs": "typedoc --options typedoc.json src/**.ts", From 992a58d33939a96c3f692981a53176b8eaade4b1 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Tue, 16 Aug 2022 15:15:11 +0200 Subject: [PATCH 16/38] Test Duplicant Tour --- src/phovea.ts | 19 ++++ src/tours/WelcomeTour2.ts | 179 ++++++++++++++++++++++++++++++++++++++ src/tours/index.ts | 1 + 3 files changed, 199 insertions(+) create mode 100644 src/tours/WelcomeTour2.ts diff --git a/src/phovea.ts b/src/phovea.ts index c4855cd7..c9fc9038 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1021,6 +1021,25 @@ export default function (registry) { }, ); + registry.push( + 'tdpTour', + 'ordinoWelcomeTour2', + function () { + return import('./tours').then((t) => t.WelcomeTour2); + }, + { + factory: 'createTour', + name: 'Ordino Welcome Tour 2', + description: 'Learn the basic features of Ordino in a short welcome tour again!!!!.', + preview() { + return import('./assets/previews/expression.jpg'); // TODO update preview image + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }, + ); + registry.push( 'tdpTour', 'ordinoStartMenuTour', diff --git a/src/tours/WelcomeTour2.ts b/src/tours/WelcomeTour2.ts new file mode 100644 index 00000000..ecae4ab4 --- /dev/null +++ b/src/tours/WelcomeTour2.ts @@ -0,0 +1,179 @@ +import { IStep, TourUtils } from 'tdp_core'; + +export class WelcomeTour2 { + static createTour(): IStep[] { + return [ + { + html: `

    W222elcome to this short tour showing the basic features of Ordino!

    +

    + Use the "Next" button to iterate through all the steps. You can use the + "Cancel" button at any time to stop the tour and to interact with Ordino. + Please note that the tour will load a new analysis session and the current + one will be discarded. +

    `, + }, + { + selector: 'ul[data-header="mainMenu"] > li:first-child > a', + html: `222222To start an analysis, click on the 'Datasets' tab. Subsequently, you can define the list of entities you want to work with`, + placement: 'centered', + preAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.add('hover'); + } + }, + postAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.remove('hover'); + datasetTab.querySelector('a').click(); + } + return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(3)')); + }, + pageBreak: 'manual', + }, + { + selector: '.ordino-dataset.genes-dataset > .card', + html: `

    222222222222You can choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

    In this example we will work with a list of genes

    `, + placement: 'centered', + preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), + postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), + }, + { + selector: '.ordino-dataset.genes-dataset .dataset-entry', + html: `Of the available predefined gene sets, we open a list of known cancer genes, called 'Cancer Gene Census'`, + placement: 'centered', + postAction: () => { + return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: Cancer Gene Census"]').then(TourUtils.click); + }, + pageBreak: 'manual', + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(600)), + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `Additional columns can be added using the plus sign.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-search .lu-search-item', + html: `First, we want to add a metadata column`, + placement: 'centered', + postAction: () => { + TourUtils.click('.lu-search .lu-search-item'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select2', + html: `Here we select 'Strand' …`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + postAction: () => TourUtils.setValueAndTrigger('.col > select', 'strand', 'change'), + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le header section[title=Strand]', + placement: 'centered', + html: `The strand information was added as a new column`, + preAction: TourUtils.waitForSelector, + }, + { + selector: '.lu-search .lu-search-group .lu-search-item', + placement: 'centered', + html: `Now, we want to add two columns containing the copy number information of two specific cell lines. To do so, we open the 'Cell Line Score' dialog`, + preAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + }, + postAction: () => { + TourUtils.click('.lu-search .lu-search-group .lu-search-item'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + html: `We select the cell lines 'HCC-827' and 'BT-20'.`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC-827;BT-20;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `As data type, we choose 'Relative Copy Number'`, + postAction: () => { + TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `Finally, click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: ['.le header section[title^=BT], .le header section[title^=HCC]'], + placement: 'centered', + preAction: () => TourUtils.waitFor('.le header section[title^=BT]', 10000), + html: `The copy number information for each selected cell line has been added as additional columns`, + }, + { + selector: '.le > header', + placement: 'centered', + html: `The column headers can be used to sort and filter the list of genes based on any of the available data`, + }, + { + selector: '.le header section[title^=HCC] i[title^=Sort]', + placement: 'centered', + html: `For example, you can use this icon to sort all genes by their copy number in the cell line 'HCC-827'`, + postAction: TourUtils.clickSelector, + }, + { + selector: '.le-tr[data-index="0"]', + placement: 'centered', + html: `In order to obtain additional information about one or more genes, click on the respective line or use the checkboxes`, + preAction: () => + TourUtils.waitFor(() => { + const r = document.querySelector('.le-tr[data-index="0"]'); + if (!r) { + return null; + } + // has a string renderered EGFR entry + if (!Array.from(r.querySelectorAll('div[data-renderer="string"]')).some((d) => d.textContent === 'EGFR')) { + return null; + } + return r; + }, Infinity).then(() => TourUtils.wait(500)), // wait for animation to complete + postAction: TourUtils.clickSelector, + }, + { + selector: '.viewWrapper .chooser:not(.hidden)', + placement: 'centered', + html: `Various 'Detail Views', providing additional information, are available.`, + preAction: TourUtils.waitForSelector, + }, + { + selector: '.viewWrapper .chooser button[data-viewid="celllinedb_expression_vs_copynumber"]', + placement: 'centered', + html: `For instance, clicking on 'Expression vs Copy Number' opens a scatter plot showing the relation of the two types of data`, + postAction: TourUtils.clickSelector, + }, + { + html: `

    Thanks for joining this tour demonstrating the basic features of Ordino.

    +

    There are many more features to discover. Enjoy!

    `, + }, + ]; + } +} diff --git a/src/tours/index.ts b/src/tours/index.ts index 62ba5110..8a5d7f76 100644 --- a/src/tours/index.ts +++ b/src/tours/index.ts @@ -1,3 +1,4 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; +export * from './WelcomeTour2'; From de915c9e41ea45aedd8572a932ae8cb318228296 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 22 Aug 2022 11:44:28 +0200 Subject: [PATCH 17/38] Halfway with AssessBCCellLines tour --- dist/phovea.d.ts.map | 2 +- dist/phovea.js | 13 + dist/phovea.js.map | 2 +- dist/tours/AssessBCCellLines.d.ts | 5 + dist/tours/AssessBCCellLines.d.ts.map | 1 + dist/tours/AssessBCCellLines.js | 253 ++++++++++++++++++ dist/tours/AssessBCCellLines.js.map | 1 + dist/tours/WelcomeTour2.d.ts | 5 + dist/tours/WelcomeTour2.d.ts.map | 1 + dist/tours/WelcomeTour2.js | 178 ++++++++++++ dist/tours/WelcomeTour2.js.map | 1 + dist/tours/index.d.ts | 1 + dist/tours/index.d.ts.map | 2 +- dist/tours/index.js | 1 + dist/tours/index.js.map | 2 +- src/phovea.ts | 24 +- .../{WelcomeTour2.ts => AssessBCCellLines.ts} | 137 +++++++--- src/tours/index.ts | 2 +- src/tours/tempNew.tempNew | 56 ++++ 19 files changed, 640 insertions(+), 47 deletions(-) create mode 100644 dist/tours/AssessBCCellLines.d.ts create mode 100644 dist/tours/AssessBCCellLines.d.ts.map create mode 100644 dist/tours/AssessBCCellLines.js create mode 100644 dist/tours/AssessBCCellLines.js.map create mode 100644 dist/tours/WelcomeTour2.d.ts create mode 100644 dist/tours/WelcomeTour2.d.ts.map create mode 100644 dist/tours/WelcomeTour2.js create mode 100644 dist/tours/WelcomeTour2.js.map rename src/tours/{WelcomeTour2.ts => AssessBCCellLines.ts} (52%) create mode 100644 src/tours/tempNew.tempNew diff --git a/dist/phovea.d.ts.map b/dist/phovea.d.ts.map index 84761458..1dc26488 100644 --- a/dist/phovea.d.ts.map +++ b/dist/phovea.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"phovea.d.ts","sourceRoot":"","sources":["../src/phovea.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,OAAO,WAAW,QAAQ,KAAA,QAqiChC"} \ No newline at end of file +{"version":3,"file":"phovea.d.ts","sourceRoot":"","sources":["../src/phovea.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,OAAO,WAAW,QAAQ,KAAA,QAwjChC"} \ No newline at end of file diff --git a/dist/phovea.js b/dist/phovea.js index 49676045..a5f71e59 100644 --- a/dist/phovea.js +++ b/dist/phovea.js @@ -733,6 +733,19 @@ export default function (registry) { level: 'beginner', canJumpAround: false, }); + registry.push('tdpTour', 'ordinoAssessBCCellLines', function () { + return import('./tours').then((t) => t.AssessBCCellLines); + }, { + factory: 'createTour', + name: 'Assessment and Selection of Breast Cancer Cell Lines', + description: 'This case study summarizes an analysis session carried out by a scientist working in a drug discovery team at a pharmaceutical company.', + preview() { + return import('./assets/previews/expression.jpg'); // TODO update preview image + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }); /// #endif registry.push(EP_PHOVEA_CORE_LOCALE, 'tdpPublicDBLocaleEN', function () { return import('./locales/en/tdp.json').then(PluginRegistry.getInstance().asResource); diff --git a/dist/phovea.js.map b/dist/phovea.js.map index 9dc0fba1..dbba2404 100644 --- a/dist/phovea.js.map +++ b/dist/phovea.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.d.ts b/dist/tours/AssessBCCellLines.d.ts new file mode 100644 index 00000000..552fa06d --- /dev/null +++ b/dist/tours/AssessBCCellLines.d.ts @@ -0,0 +1,5 @@ +import { IStep } from 'tdp_core'; +export declare class AssessBCCellLines { + static createTour(): IStep[]; +} +//# sourceMappingURL=AssessBCCellLines.d.ts.map \ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.d.ts.map b/dist/tours/AssessBCCellLines.d.ts.map new file mode 100644 index 00000000..978595fe --- /dev/null +++ b/dist/tours/AssessBCCellLines.d.ts.map @@ -0,0 +1 @@ +{"version":3,"file":"AssessBCCellLines.d.ts","sourceRoot":"","sources":["../../src/tours/AssessBCCellLines.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,iBAAiB;IAC5B,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CA4P7B"} \ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.js b/dist/tours/AssessBCCellLines.js new file mode 100644 index 00000000..dd821ca4 --- /dev/null +++ b/dist/tours/AssessBCCellLines.js @@ -0,0 +1,253 @@ +import { TourUtils } from 'tdp_core'; +export class AssessBCCellLines { + static createTour() { + return [ + { + html: `

    Welcome to this short tour showing the assessment of breast cancer cell lines!

    +

    + Use the "Next" button to iterate through all the steps. You can use the + "Cancel" button at any time to stop the tour and to interact with Ordino. + Please note that the tour will load a new analysis session and the current + one will be discarded. +

    `, + }, + { + selector: 'ul[data-header="mainMenu"] > li:first-child > a', + html: `To start an analysis, click on the 'Datasets' tab. Subsequently, you can define the list of entities you want to work with`, + placement: 'centered', + preAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)'); + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.add('hover'); + } + }, + postAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)'); + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.remove('hover'); + datasetTab.querySelector('a').click(); + } + return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(3)')); + }, + pageBreak: 'manual', + }, + { + selector: '.ordino-dataset.genes-dataset > .card', + html: `

    You can choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

    In this example we will work with a list of genes

    `, + placement: 'centered', + preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), + postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), + }, + { + selector: '[data-testid="normal-chromosome-protein-coding-human-genes-button"]', + html: `The scientist starts by loading the list of all protein coding genes.`, + placement: 'centered', + postAction: () => { + return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: normal chromosome protein coding human genes"]').then(TourUtils.click); + }, + pageBreak: 'manual', + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(600)), + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `Additional columns can be added using the plus sign.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + html: `First, we want to add a new column`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + html: `We select the Cell Line`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `and the data type`, + postAction: () => { + TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le header [data-col-id="col8"]', + placement: 'centered', + html: `The new column was added here`, + preAction: TourUtils.waitForSelector, + }, + { + selector: '.le [data-col-id="col8"] .lu-action-sort', + placement: 'centered', + html: `Now, we want to sort by this column`, + postAction: () => { + TourUtils.click('.le [data-col-id="col8"] .lu-action-sort'); + }, + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `Now everything was sorted!`, + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `After sorting by this column, the analyst observes + that about 15 genes on chromosome 17 are affected by a large genomic amplification.`, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `In order to identify the most relevant gene of these, the analyst adds a column with the gene expression (a measure of activity) in HCC1954`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + html: `We want to add a 2nd new column`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + html: `We select the 2nd Cell Line`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `and the 2nd data type`, + postAction: () => { + TourUtils.setValueAndTrigger('.col > select', 'expression-tpm', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `They also add a gene sensitivity score (a measure of importance for cell survival) for HCC1954 (RSA scores obtained from DRIVE data set [4]).`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span', + html: `We want to add a 3rd new column`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + html: `We select the 3rd Cell Line`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `and the 3rd data type`, + postAction: () => { + TourUtils.setValueAndTrigger('.col > select', 'depletion-rsa', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', + html: `We now want to invert the linear scaling of the depletion screen score to improve the scale's readability.`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-id="col10"] > .lu-toolbar > .lu-action-more'); + TourUtils.click('.lu-action-data-mapping > span'); + TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); + TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + }, + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `TOUR IS HERE SO FAR.`, + }, + { + selector: '.le header section[title^=HCC] i[title^=Sort]', + placement: 'centered', + html: `For example, you can use this icon to sort all genes by their copy number in the cell line 'HCC-827'`, + postAction: TourUtils.clickSelector, + }, + { + selector: '.le-tr[data-index="0"]', + placement: 'centered', + html: `In order to obtain additional information about one or more genes, click on the respective line or use the checkboxes`, + preAction: () => TourUtils.waitFor(() => { + const r = document.querySelector('.le-tr[data-index="0"]'); + if (!r) { + return null; + } + // has a string renderered EGFR entry + if (!Array.from(r.querySelectorAll('div[data-renderer="string"]')).some((d) => d.textContent === 'EGFR')) { + return null; + } + return r; + }, Infinity).then(() => TourUtils.wait(500)), + postAction: TourUtils.clickSelector, + }, + { + selector: '.viewWrapper .chooser:not(.hidden)', + placement: 'centered', + html: `Various 'Detail Views', providing additional information, are available.`, + preAction: TourUtils.waitForSelector, + }, + { + selector: '.viewWrapper .chooser button[data-viewid="celllinedb_expression_vs_copynumber"]', + placement: 'centered', + html: `For instance, clicking on 'Expression vs Copy Number' opens a scatter plot showing the relation of the two types of data`, + postAction: TourUtils.clickSelector, + }, + { + html: `

    Thanks for joining this tour demonstrating the basic features of Ordino.

    +

    There are many more features to discover. Enjoy!

    `, + }, + ]; + } +} +//# sourceMappingURL=AssessBCCellLines.js.map \ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.js.map b/dist/tours/AssessBCCellLines.js.map new file mode 100644 index 00000000..cf81111f --- /dev/null +++ b/dist/tours/AssessBCCellLines.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/dist/tours/WelcomeTour2.d.ts b/dist/tours/WelcomeTour2.d.ts new file mode 100644 index 00000000..cca36b85 --- /dev/null +++ b/dist/tours/WelcomeTour2.d.ts @@ -0,0 +1,5 @@ +import { IStep } from 'tdp_core'; +export declare class WelcomeTour2 { + static createTour(): IStep[]; +} +//# sourceMappingURL=WelcomeTour2.d.ts.map \ No newline at end of file diff --git a/dist/tours/WelcomeTour2.d.ts.map b/dist/tours/WelcomeTour2.d.ts.map new file mode 100644 index 00000000..415404a8 --- /dev/null +++ b/dist/tours/WelcomeTour2.d.ts.map @@ -0,0 +1 @@ +{"version":3,"file":"WelcomeTour2.d.ts","sourceRoot":"","sources":["../../src/tours/WelcomeTour2.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,YAAY;IACvB,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CA+K7B"} \ No newline at end of file diff --git a/dist/tours/WelcomeTour2.js b/dist/tours/WelcomeTour2.js new file mode 100644 index 00000000..326bc10a --- /dev/null +++ b/dist/tours/WelcomeTour2.js @@ -0,0 +1,178 @@ +import { TourUtils } from 'tdp_core'; +export class WelcomeTour2 { + static createTour() { + return [ + { + html: `

    W222elcome to this short tour showing the basic features of Ordino!

    +

    + Use the "Next" button to iterate through all the steps. You can use the + "Cancel" button at any time to stop the tour and to interact with Ordino. + Please note that the tour will load a new analysis session and the current + one will be discarded. +

    `, + }, + { + selector: 'ul[data-header="mainMenu"] > li:first-child > a', + html: `222222To start an analysis, click on the 'Datasets' tab. Subsequently, you can define the list of entities you want to work with`, + placement: 'centered', + preAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)'); + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.add('hover'); + } + }, + postAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)'); + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.remove('hover'); + datasetTab.querySelector('a').click(); + } + return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(3)')); + }, + pageBreak: 'manual', + }, + { + selector: '.ordino-dataset.genes-dataset > .card', + html: `

    222222222222You can choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

    In this example we will work with a list of genes

    `, + placement: 'centered', + preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), + postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), + }, + { + selector: '.ordino-dataset.genes-dataset .dataset-entry', + html: `Of the available predefined gene sets, we open a list of known cancer genes, called 'Cancer Gene Census'`, + placement: 'centered', + postAction: () => { + return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: Cancer Gene Census"]').then(TourUtils.click); + }, + pageBreak: 'manual', + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(600)), + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `Additional columns can be added using the plus sign.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-search .lu-search-item', + html: `First, we want to add a metadata column`, + placement: 'centered', + postAction: () => { + TourUtils.click('.lu-search .lu-search-item'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select2', + html: `Here we select 'Strand' …`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + postAction: () => TourUtils.setValueAndTrigger('.col > select', 'strand', 'change'), + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le header section[title=Strand]', + placement: 'centered', + html: `The strand information was added as a new column`, + preAction: TourUtils.waitForSelector, + }, + { + selector: '.lu-search .lu-search-group .lu-search-item', + placement: 'centered', + html: `Now, we want to add two columns containing the copy number information of two specific cell lines. To do so, we open the 'Cell Line Score' dialog`, + preAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + }, + postAction: () => { + TourUtils.click('.lu-search .lu-search-group .lu-search-item'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + html: `We select the cell lines 'HCC-827' and 'BT-20'.`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC-827;BT-20;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `As data type, we choose 'Relative Copy Number'`, + postAction: () => { + TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `Finally, click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: ['.le header section[title^=BT], .le header section[title^=HCC]'], + placement: 'centered', + preAction: () => TourUtils.waitFor('.le header section[title^=BT]', 10000), + html: `The copy number information for each selected cell line has been added as additional columns`, + }, + { + selector: '.le > header', + placement: 'centered', + html: `The column headers can be used to sort and filter the list of genes based on any of the available data`, + }, + { + selector: '.le header section[title^=HCC] i[title^=Sort]', + placement: 'centered', + html: `For example, you can use this icon to sort all genes by their copy number in the cell line 'HCC-827'`, + postAction: TourUtils.clickSelector, + }, + { + selector: '.le-tr[data-index="0"]', + placement: 'centered', + html: `In order to obtain additional information about one or more genes, click on the respective line or use the checkboxes`, + preAction: () => TourUtils.waitFor(() => { + const r = document.querySelector('.le-tr[data-index="0"]'); + if (!r) { + return null; + } + // has a string renderered EGFR entry + if (!Array.from(r.querySelectorAll('div[data-renderer="string"]')).some((d) => d.textContent === 'EGFR')) { + return null; + } + return r; + }, Infinity).then(() => TourUtils.wait(500)), + postAction: TourUtils.clickSelector, + }, + { + selector: '.viewWrapper .chooser:not(.hidden)', + placement: 'centered', + html: `Various 'Detail Views', providing additional information, are available.`, + preAction: TourUtils.waitForSelector, + }, + { + selector: '.viewWrapper .chooser button[data-viewid="celllinedb_expression_vs_copynumber"]', + placement: 'centered', + html: `For instance, clicking on 'Expression vs Copy Number' opens a scatter plot showing the relation of the two types of data`, + postAction: TourUtils.clickSelector, + }, + { + html: `

    Thanks for joining this tour demonstrating the basic features of Ordino.

    +

    There are many more features to discover. Enjoy!

    `, + }, + ]; + } +} +//# sourceMappingURL=WelcomeTour2.js.map \ No newline at end of file diff --git a/dist/tours/WelcomeTour2.js.map b/dist/tours/WelcomeTour2.js.map new file mode 100644 index 00000000..e438b1fb --- /dev/null +++ b/dist/tours/WelcomeTour2.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/dist/tours/index.d.ts b/dist/tours/index.d.ts index 7ef18030..87e8a782 100644 --- a/dist/tours/index.d.ts +++ b/dist/tours/index.d.ts @@ -1,4 +1,5 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; +export * from './AssessBCCellLines'; //# sourceMappingURL=index.d.ts.map \ No newline at end of file diff --git a/dist/tours/index.d.ts.map b/dist/tours/index.d.ts.map index 4d518b17..e8a4e0d6 100644 --- a/dist/tours/index.d.ts.map +++ b/dist/tours/index.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC"} \ No newline at end of file +{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,qBAAqB,CAAC"} \ No newline at end of file diff --git a/dist/tours/index.js b/dist/tours/index.js index 1d5ea8d4..1edb4faf 100644 --- a/dist/tours/index.js +++ b/dist/tours/index.js @@ -1,4 +1,5 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; +export * from './AssessBCCellLines'; //# sourceMappingURL=index.js.map \ No newline at end of file diff --git a/dist/tours/index.js.map b/dist/tours/index.js.map index b1d7eaa5..44a91c56 100644 --- a/dist/tours/index.js.map +++ b/dist/tours/index.js.map @@ -1 +1 @@ -{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC"} \ No newline at end of file +{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,qBAAqB,CAAC"} \ No newline at end of file diff --git a/src/phovea.ts b/src/phovea.ts index c9fc9038..75af4bb1 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1023,14 +1023,14 @@ export default function (registry) { registry.push( 'tdpTour', - 'ordinoWelcomeTour2', + 'ordinoStartMenuTour', function () { - return import('./tours').then((t) => t.WelcomeTour2); + return import('./tours').then((t) => t.StartMenuTour); }, { factory: 'createTour', - name: 'Ordino Welcome Tour 2', - description: 'Learn the basic features of Ordino in a short welcome tour again!!!!.', + name: 'Overview of Start Menu', + description: 'This tour provides an overview of the Ordino start menu.', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image }, @@ -1042,14 +1042,14 @@ export default function (registry) { registry.push( 'tdpTour', - 'ordinoStartMenuTour', + 'ordinoAddColumnToGeneListTour', function () { - return import('./tours').then((t) => t.StartMenuTour); + return import('./tours').then((t) => t.AddColumnToGeneListTour); }, { factory: 'createTour', - name: 'Overview of Start Menu', - description: 'This tour provides an overview of the Ordino start menu.', + name: 'Adding Data Columns', + description: 'Learn how to add data columns to rankings in Ordino.', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image }, @@ -1061,14 +1061,14 @@ export default function (registry) { registry.push( 'tdpTour', - 'ordinoAddColumnToGeneListTour', + 'ordinoAssessBCCellLines', function () { - return import('./tours').then((t) => t.AddColumnToGeneListTour); + return import('./tours').then((t) => t.AssessBCCellLines); }, { factory: 'createTour', - name: 'Adding Data Columns', - description: 'Learn how to add data columns to rankings in Ordino.', + name: 'Assessment and Selection of Breast Cancer Cell Lines', + description: 'This case study summarizes an analysis session carried out by a scientist working in a drug discovery team at a pharmaceutical company.', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image }, diff --git a/src/tours/WelcomeTour2.ts b/src/tours/AssessBCCellLines.ts similarity index 52% rename from src/tours/WelcomeTour2.ts rename to src/tours/AssessBCCellLines.ts index ecae4ab4..28efa1aa 100644 --- a/src/tours/WelcomeTour2.ts +++ b/src/tours/AssessBCCellLines.ts @@ -1,10 +1,10 @@ import { IStep, TourUtils } from 'tdp_core'; -export class WelcomeTour2 { +export class AssessBCCellLines { static createTour(): IStep[] { return [ { - html: `

    W222elcome to this short tour showing the basic features of Ordino!

    + html: `

    Welcome to this short tour showing the assessment of breast cancer cell lines!

    Use the "Next" button to iterate through all the steps. You can use the "Cancel" button at any time to stop the tour and to interact with Ordino. @@ -14,7 +14,7 @@ export class WelcomeTour2 { }, { selector: 'ul[data-header="mainMenu"] > li:first-child > a', - html: `222222To start an analysis, click on the 'Datasets' tab. Subsequently, you can define the list of entities you want to work with`, + html: `To start an analysis, click on the 'Datasets' tab. Subsequently, you can define the list of entities you want to work with`, placement: 'centered', preAction: () => { const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; @@ -34,17 +34,19 @@ export class WelcomeTour2 { }, { selector: '.ordino-dataset.genes-dataset > .card', - html: `

    222222222222You can choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

    In this example we will work with a list of genes

    `, + html: `

    You can choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

    In this example we will work with a list of genes

    `, placement: 'centered', preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), }, { - selector: '.ordino-dataset.genes-dataset .dataset-entry', - html: `Of the available predefined gene sets, we open a list of known cancer genes, called 'Cancer Gene Census'`, + selector: '[data-testid="normal-chromosome-protein-coding-human-genes-button"]', + html: `The scientist starts by loading the list of all protein coding genes.`, placement: 'centered', postAction: () => { - return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: Cancer Gene Census"]').then(TourUtils.click); + return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: normal chromosome protein coding human genes"]').then( + TourUtils.click, + ); }, pageBreak: 'manual', }, @@ -61,20 +63,30 @@ export class WelcomeTour2 { postAction: TourUtils.clickSelector, }, { - selector: '.lu-search .lu-search-item', - html: `First, we want to add a metadata column`, + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + html: `First, we want to add a new column`, placement: 'centered', postAction: () => { - TourUtils.click('.lu-search .lu-search-item'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); }, }, { - selector: '.modal.show .col > .select2', - html: `Here we select 'Strand' …`, + selector: '.modal.show .col > .select3', placement: 'centered', preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), - postAction: () => TourUtils.setValueAndTrigger('.col > select', 'strand', 'change'), + html: `We select the Cell Line`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `and the data type`, + postAction: () => { + TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + }, }, { selector: '.modal.show .modal-footer button[type=submit]', @@ -83,20 +95,42 @@ export class WelcomeTour2 { postAction: TourUtils.clickSelector, }, { - selector: '.le header section[title=Strand]', + selector: '.le header [data-col-id="col8"]', placement: 'centered', - html: `The strand information was added as a new column`, + html: `The new column was added here`, preAction: TourUtils.waitForSelector, }, { - selector: '.lu-search .lu-search-group .lu-search-item', + selector: '.le [data-col-id="col8"] .lu-action-sort', placement: 'centered', - html: `Now, we want to add two columns containing the copy number information of two specific cell lines. To do so, we open the 'Cell Line Score' dialog`, - preAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + html: `Now, we want to sort by this column`, + postAction: () => { + TourUtils.click('.le [data-col-id="col8"] .lu-action-sort'); }, + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `Now everything was sorted!`, + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `After sorting by this column, the analyst observes + that about 15 genes on chromosome 17 are affected by a large genomic amplification.`, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `In order to identify the most relevant gene of these, the analyst adds a column with the gene expression (a measure of activity) in HCC1954`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + html: `We want to add a 2nd new column`, + placement: 'centered', postAction: () => { - TourUtils.click('.lu-search .lu-search-group .lu-search-item'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); }, }, @@ -104,35 +138,78 @@ export class WelcomeTour2 { selector: '.modal.show .col > .select3', placement: 'centered', preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), - html: `We select the cell lines 'HCC-827' and 'BT-20'.`, + html: `We select the 2nd Cell Line`, postAction: () => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC-827;BT-20;', 'input'); + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); }, }, { selector: '.modal.show .col > .select2', placement: 'centered', - html: `As data type, we choose 'Relative Copy Number'`, + html: `and the 2nd data type`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.col > select', 'expression-tpm', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `They also add a gene sensitivity score (a measure of importance for cell survival) for HCC1954 (RSA scores obtained from DRIVE data set [4]).`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span', + html: `We want to add a 3rd new column`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + html: `We select the 3rd Cell Line`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `and the 3rd data type`, + postAction: () => { + TourUtils.setValueAndTrigger('.col > select', 'depletion-rsa', 'change'); }, }, { selector: '.modal.show .modal-footer button[type=submit]', - html: `Finally, click 'Add'`, + html: `… and click 'Add'`, placement: 'centered', postAction: TourUtils.clickSelector, }, { - selector: ['.le header section[title^=BT], .le header section[title^=HCC]'], + selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', + html: `We now want to invert the linear scaling of the depletion screen score to improve the scale's readability.`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le header section[title^=BT]', 10000), - html: `The copy number information for each selected cell line has been added as additional columns`, + postAction: () => { + TourUtils.click('[data-id="col10"] > .lu-toolbar > .lu-action-more'); + TourUtils.click('.lu-action-data-mapping > span'); + TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); + TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + }, }, { - selector: '.le > header', + selector: '.le.le-multi.lineup-engine', placement: 'centered', - html: `The column headers can be used to sort and filter the list of genes based on any of the available data`, + html: `TOUR IS HERE SO FAR.`, }, { selector: '.le header section[title^=HCC] i[title^=Sort]', diff --git a/src/tours/index.ts b/src/tours/index.ts index 8a5d7f76..7d9d1f5d 100644 --- a/src/tours/index.ts +++ b/src/tours/index.ts @@ -1,4 +1,4 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; -export * from './WelcomeTour2'; +export * from './AssessBCCellLines'; diff --git a/src/tours/tempNew.tempNew b/src/tours/tempNew.tempNew new file mode 100644 index 00000000..7837a792 --- /dev/null +++ b/src/tours/tempNew.tempNew @@ -0,0 +1,56 @@ +{ + html: `

    Welcome to this short tour showing the assessment of breast cancer cell lines!

    +

    + Use the "Next" button to iterate through all the steps. You can use the + "Cancel" button at any time to stop the tour and to interact with Ordino. + Please note that the tour will load a new analysis session and the current + one will be discarded. +

    `, + }, + { + selector: 'ul[data-header="mainMenu"] > li:first-child > a', + html: `Go to Datasets Tab`, + placement: 'centered', + preAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.add('hover'); + } + }, + postAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.remove('hover'); + datasetTab.querySelector('a').click(); + } + return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(3)')); + }, + }, + { + selector: '.ordino-dataset.genes-dataset > .card', + html: `Click on Genes > Human > Normal-chromosome-...`, + placement: 'centered', + preAction: () => { + TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)); + }, + postAction: () => { + TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'); + TourUtils.click('[data-testid=normal-chromosome-protein-coding-human-genes-button]'); + }, + pageBreak: 'manual', + }, + { + selector: '[data-testid=add-column-button]', + html: `Add a column`, + placement: 'centered', + preAction: () => { + TourUtils.waitFor('[data-testid=add-column-button]', Infinity); + }, + postAction: () => { + TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: Cancer Gene Census"]').then(TourUtils.click); + }, + }, + { + html: `

    Thanks for joining this tour demonstrating the basic features of Ordino.

    +

    There are many more features to discover. Enjoy!

    `, + }, \ No newline at end of file From 1443bdae3a76657d8c56a04f16b12727f6ad4038 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 22 Aug 2022 13:16:13 +0200 Subject: [PATCH 18/38] Almost done AssessBCCellLines tour --- dist/tours/AssessBCCellLines.d.ts.map | 2 +- dist/tours/AssessBCCellLines.js | 11 +++++++++ dist/tours/AssessBCCellLines.js.map | 2 +- src/tours/AssessBCCellLines.ts | 34 +++++++++++++++++++++++++++ 4 files changed, 47 insertions(+), 2 deletions(-) diff --git a/dist/tours/AssessBCCellLines.d.ts.map b/dist/tours/AssessBCCellLines.d.ts.map index 978595fe..304b78e3 100644 --- a/dist/tours/AssessBCCellLines.d.ts.map +++ b/dist/tours/AssessBCCellLines.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"AssessBCCellLines.d.ts","sourceRoot":"","sources":["../../src/tours/AssessBCCellLines.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,iBAAiB;IAC5B,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CA4P7B"} \ No newline at end of file +{"version":3,"file":"AssessBCCellLines.d.ts","sourceRoot":"","sources":["../../src/tours/AssessBCCellLines.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,iBAAiB;IAC5B,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CAuQ7B"} \ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.js b/dist/tours/AssessBCCellLines.js index dd821ca4..7c8d6400 100644 --- a/dist/tours/AssessBCCellLines.js +++ b/dist/tours/AssessBCCellLines.js @@ -203,6 +203,17 @@ export class AssessBCCellLines { TourUtils.click('.lu-dialog-buttons > [type="submit"]'); }, }, + { + selector: '[data-index="0"]', + placement: 'centered', + html: `Observe: Of the highly amplified genes, ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, + }, + { + selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', + html: `

    Combine both score columns to obtain stacked bars.

    +

    Observe: Combining the columns highlights the importance of ERBB2.

    `, + placement: 'centered', + }, { selector: '.le.le-multi.lineup-engine', placement: 'centered', diff --git a/dist/tours/AssessBCCellLines.js.map b/dist/tours/AssessBCCellLines.js.map index cf81111f..90c97a8a 100644 --- a/dist/tours/AssessBCCellLines.js.map +++ b/dist/tours/AssessBCCellLines.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/src/tours/AssessBCCellLines.ts b/src/tours/AssessBCCellLines.ts index 28efa1aa..ac7608f1 100644 --- a/src/tours/AssessBCCellLines.ts +++ b/src/tours/AssessBCCellLines.ts @@ -206,6 +206,40 @@ export class AssessBCCellLines { TourUtils.click('.lu-dialog-buttons > [type="submit"]'); }, }, + { + selector: '[data-index="0"]', + placement: 'centered', + html: `Observe: Of the highly amplified genes, ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, + }, + { + selector: '.le header [data-col-id="col10"]', + html: `

    Combine both score columns to obtain stacked bars.

    +

    Observe: Combining the columns highlights the importance of ERBB2.

    +

    It is therefore probably the most relevant gene within this amplified genomic region.

    `, + placement: 'centered', + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `

    This finding leads the scientist to the question whether ERBB2 is also highly expressed and frequently amplified in other breast cancer cell lines.

    +

    To investigate this, the analyst adds the following columns: +

      +
    • A column with the average gene expression
      • +
    • A column with the gene copy number distribution
      • +
    • a column with the gene amplification frequency across all breast cancer cell lines
      • +
    +

    `, + placement: 'centered', + postAction: () => { + // Add the average gene expression column + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + + + TourUtils.click('.lu-action-data-mapping > span'); + TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); + TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + }, + }, { selector: '.le.le-multi.lineup-engine', placement: 'centered', From f23554c793fd18333cac63237c7c007a26b4b7ea Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 22 Aug 2022 15:20:44 +0200 Subject: [PATCH 19/38] Update Dist --- dist/menu/DatasetCard.d.ts | 1 + dist/menu/DatasetCard.d.ts.map | 2 +- dist/menu/DatasetCard.js | 2 +- dist/menu/DatasetCard.js.map | 2 +- dist/menu/DatasetSearchBox.d.ts.map | 2 +- dist/menu/DatasetSearchBox.js | 4 +- dist/menu/DatasetSearchBox.js.map | 2 +- dist/phovea.d.ts.map | 2 +- dist/phovea.js | 162 +++++++++++++++- dist/phovea.js.map | 2 +- dist/tours/AssessBCCellLines.d.ts.map | 2 +- dist/tours/AssessBCCellLines.js | 25 ++- dist/tours/AssessBCCellLines.js.map | 2 +- dist/tours/WelcomeTour2.d.ts | 5 - dist/tours/WelcomeTour2.d.ts.map | 1 - dist/tours/WelcomeTour2.js | 178 ------------------ dist/tours/WelcomeTour2.js.map | 1 - dist/views/ACombinedDependentTable.d.ts.map | 2 +- dist/views/ACombinedDependentTable.js | 2 +- dist/views/ACombinedDependentTable.js.map | 2 +- .../CombinedDependentSampleTable.d.ts.map | 2 +- dist/views/CombinedDependentSampleTable.js | 2 +- .../views/CombinedDependentSampleTable.js.map | 2 +- dist/views/SimilarityView.d.ts.map | 2 +- dist/views/SimilarityView.js | 4 +- dist/views/SimilarityView.js.map | 2 +- 26 files changed, 203 insertions(+), 212 deletions(-) delete mode 100644 dist/tours/WelcomeTour2.d.ts delete mode 100644 dist/tours/WelcomeTour2.d.ts.map delete mode 100644 dist/tours/WelcomeTour2.js delete mode 100644 dist/tours/WelcomeTour2.js.map diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index 836b542b..2587b238 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,3 +1,4 @@ +/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; //# sourceMappingURL=DatasetCard.d.ts.map \ No newline at end of file diff --git a/dist/menu/DatasetCard.d.ts.map b/dist/menu/DatasetCard.d.ts.map index d3463b7e..b305a2a3 100644 --- a/dist/menu/DatasetCard.d.ts.map +++ b/dist/menu/DatasetCard.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":";AAmBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAE1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file +{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":";AAkBA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAI1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file diff --git a/dist/menu/DatasetCard.js b/dist/menu/DatasetCard.js index c1666290..43a28e9e 100644 --- a/dist/menu/DatasetCard.js +++ b/dist/menu/DatasetCard.js @@ -1,8 +1,8 @@ import React from 'react'; import { ENamedSetType, RestBaseUtils, RestStorageUtils, StoreUtils, UserSession, UniqueIdManager, I18nextManager, IDTypeManager, useAsync, GlobalEventHandler, AView, } from 'tdp_core'; import { NamedSetList, OrdinoContext } from 'ordino'; -import { Species } from 'tdp_gene'; import { DatasetSearchBox } from './DatasetSearchBox'; +import { Species } from '../common'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }) { const testId = `dataset-card-${cssClass}`; const { app } = React.useContext(OrdinoContext); diff --git a/dist/menu/DatasetCard.js.map b/dist/menu/DatasetCard.js.map index fdc2bfe7..b2b2b158 100644 --- a/dist/menu/DatasetCard.js.map +++ b/dist/menu/DatasetCard.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/menu/DatasetSearchBox.d.ts.map b/dist/menu/DatasetSearchBox.d.ts.map index d19b6b47..ea1ff397 100644 --- a/dist/menu/DatasetSearchBox.d.ts.map +++ b/dist/menu/DatasetSearchBox.d.ts.map @@ -1 +1 @@ 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+{"version":3,"file":"DatasetSearchBox.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetSearchBox.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,EAAiB,UAAU,EAAgB,MAAM,UAAU,CAAC;AAInE,OAAO,EAAE,mBAAmB,EAAE,MAAM,UAAU,CAAC;AAC/C,OAAO,EAAa,iBAAiB,EAAE,MAAM,WAAW,CAAC;AAQzD,UAAU,uBAAuB;IAC/B,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC;CACpB;AAED,UAAU,sBAAsB;IAC9B,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,iBAAiB,CAAC;IAC9B,gBAAgB,EAAE,CAAC,KAAK,EAAE,UAAU,EAAE,KAAK,IAAI,CAAC;IAChD,MAAM,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,mBAAmB,CAAC,KAAK,IAAI,CAAC;IAC7F;;OAEG;IACH,MAAM,CAAC,EAAE,uBAAuB,CAAC;IACjC,eAAe,CAAC,EAAE,MAAM,CAAC;CAC1B;AAgCD,wBAAgB,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAW,EAAE,eAA6B,EAAE,EAAE,sBAAsB,eAgKzJ"} \ No newline at end of file diff --git a/dist/menu/DatasetSearchBox.js b/dist/menu/DatasetSearchBox.js index 34913c36..fe71d903 100644 --- a/dist/menu/DatasetSearchBox.js +++ b/dist/menu/DatasetSearchBox.js @@ -6,13 +6,13 @@ import Highlighter from 'react-highlight-words'; import { GeneUtils } from '../common'; // functions to add data-testid attribute to react-select components // eslint-disable-next-line -const addDataTestId = (Component, dataTestId) => ( +const addDataTestId = (Component, dataTestId) => // eslint-disable-next-line (props) => ( // eslint-disable-next-line React.createElement(Component, { ...props, // eslint-disable-next-line - innerProps: Object.assign({}, props.innerProps, { 'data-testid': `${dataTestId}${props.data ? '-' + props.data.id : ''}` }) }))); + innerProps: Object.assign({}, props.innerProps, { 'data-testid': `${dataTestId}${props.data ? '-' + props.data.id : ''}` }) })); function Input(props) { const { onPaste } = props.selectProps; const modifiedProps = { 'data-testid': 'async-paginate-input', ...props }; diff --git a/dist/menu/DatasetSearchBox.js.map b/dist/menu/DatasetSearchBox.js.map index e903e9d9..238ddd6f 100644 --- a/dist/menu/DatasetSearchBox.js.map +++ b/dist/menu/DatasetSearchBox.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/phovea.d.ts.map b/dist/phovea.d.ts.map index 1dc26488..d05dfe17 100644 --- a/dist/phovea.d.ts.map +++ b/dist/phovea.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"phovea.d.ts","sourceRoot":"","sources":["../src/phovea.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,OAAO,WAAW,QAAQ,KAAA,QAwjChC"} \ No newline at end of file +{"version":3,"file":"phovea.d.ts","sourceRoot":"","sources":["../src/phovea.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,OAAO,WAAW,QAAQ,KAAA,QAqvChC"} \ No newline at end of file diff --git a/dist/phovea.js b/dist/phovea.js index a5f71e59..c985b3ee 100644 --- a/dist/phovea.js +++ b/dist/phovea.js @@ -239,7 +239,7 @@ export default function (registry) { /// #endif /// #if include('dTiles') registry.push('dTilesSearchProvider', 'gene', function () { - return import('./providers/SearchProvider').then((s) => s.GeneSearchProvider); + return import('./providers/GeneSearchProvider').then((s) => s.GeneSearchProvider); }, { factory: 'createGene', idType: 'Ensembl', @@ -384,7 +384,7 @@ export default function (registry) { }); /// #if include('dTiles') registry.push('dTilesSearchProvider', idType.toLowerCase(), function () { - return import('./providers/SearchProvider').then((s) => s.GeneSearchProvider); + return import('./providers/GeneSearchProvider').then((s) => s.GeneSearchProvider); }, { factory: `create${idType}`, idType, @@ -520,7 +520,7 @@ export default function (registry) { ], }); registry.push('tdpView', 'gene_details', function () { - return import('tdp_gene/dist/views/GeneProxyView'); + return import('./views/GeneProxyView'); }, { name: 'Genehopper', factory: 'new GeneProxyView', @@ -552,7 +552,7 @@ export default function (registry) { }, }); registry.push('tdpView', 'gene_similarity_external', function () { - return import('tdp_gene/dist/views/GeneProxyView'); + return import('./views/GeneProxyView'); }, { name: 'Gene Similarity', factory: 'new GeneProxyView', @@ -752,6 +752,160 @@ export default function (registry) { }, { ns: 'tdp', }); + function tdpView(id, loader, desc, ...descs) { + registry.push('tdpView', id, loader, Object.assign(desc, ...descs)); + } + // proxy pages + tdpView('ensembl_org', () => import('./views/GeneProxyView'), { + factory: 'new GeneProxyView', + name: 'Ensembl', + site: 'https://ensembl.org/{species}/Gene/Summary?g={gene}', + argument: 'gene', + idtype: 'Ensembl', + selection: 'chooser', + preview: () => import('./assets/previews/ensembl.jpg'), + group: { + name: 'External Resources', + // 'order: 0 + }, + description: 'Show information on your search from Ensembl.org', + topics: ['external'], + }); + // doesn't work properly + // tdpView('cansar', () => import('./views/UniProtProxyView'), { + // name: 'canSAR', + // site: 'https://cansar.icr.ac.uk/cansar/molecular-targets/{gene}/', + // argument: 'gene', + // idtype: 'Ensembl', + // selection: 'chooser', + // preview: () => import('./assets/previews/cansar.jpg'), + // group: { + // name: 'External Resources' + // // 'order: 60 + // }, + // filter: { + // species: 'human' + // }, + // description: 'Show information on your search from the canSAR page', + // topics: ['external'] + // }); + tdpView('uniprot', () => import('./views/UniProtProxyView'), { + factory: 'new UniProtProxyView', + name: 'UniProt', + site: 'https://www.uniprot.org/uniprot/{gene}/', + argument: 'gene', + idtype: 'Ensembl', + selection: 'chooser', + openExternally: true, + preview: () => import('./assets/previews/uniprot.jpg'), + group: { + name: 'External Resources', + // 'order: 70 + }, + description: 'Show information on your search from UniProt', + topics: ['uniprot', 'external'], + }); + tdpView('targetvalidation', () => import('./views/GeneProxyView'), { + factory: 'new GeneProxyView', + name: 'Open Targets', + site: 'https://www.targetvalidation.org/target/{gene}', + argument: 'gene', + idtype: 'Ensembl', + selection: 'chooser', + preview: () => import('./assets/previews/open_targets.jpg'), + group: { + name: 'External Resources', + // 'order: 40 + }, + filter: { + species: 'human', + }, + description: 'Show information on your search from Open Targets', + topics: ['external'], + }); + tdpView('proteinatlas_org', () => import('./views/GeneProxyView'), { + factory: 'new GeneProxyView', + name: 'Human Protein Atlas', + site: 'https://proteinatlas.org/{gene}', + argument: 'gene', + idtype: 'Ensembl', + selection: 'chooser', + openExternally: true, + preview: () => import('./assets/previews/human_protein_atlas.jpg'), + group: { + name: 'External Resources', + // 'order: 50 + }, + filter: { + species: 'human', + }, + description: 'Show information on your search from the Human Protein Atlas', + topics: ['protein', 'external'], + }); + const common = { + argument: 'gene', + idtype: 'GeneSymbol', + readableIDType: 'GeneSymbol', + selection: 'chooser', + group: { + name: 'External Resources', + // 'order: 60 + }, + filter: { + species: 'human', + }, + topics: ['external'], + }; + // tdpView('humanproteomemap', () => import('tdp_core/dist/views/ChooserProxyView'), { + // name: 'Human Proteome Map', + // site: 'http://www.humanproteomemap.org/protein.php?hpm_id={gene}', + // helpUrl: 'http://www.humanproteomemap.org/faqs.html', + // preview: () => import('./assets/previews/humanproteomemap.png'), + // description: 'Proteomics data from the human proteome map' + // }, common, { + // idtype: 'EntrezGene', + // readableIDType: 'GeneSymbol', + // topics: ['protein', 'external'] + // }); + tdpView('genenames', () => import('tdp_core/dist/views/ChooserProxyView'), { + factory: 'new ChooserProxyView', + name: 'Genenames', + site: 'https://www.genenames.org/cgi-bin/gene_symbol_report?match={gene}', + preview: () => import('./assets/previews/genenames.jpg'), + description: 'Reference for human gene symbols', + helpUrl: 'https://www.genenames.org/about/overview', + }, common); + tdpView('ClinVar', () => import('tdp_core/dist/views/ChooserProxyView'), { + factory: 'new ChooserProxyView', + name: 'ClinVar', + site: 'https://www.ncbi.nlm.nih.gov/clinvar/?term={gene}', + helpUrl: 'https://www.ncbi.nlm.nih.gov/clinvar/intro/', + preview: () => import('./assets/previews/clinvar.png'), + description: 'relationships among human variations and phenotypes, with supporting evidence', + }, common); + tdpView('cosmic_gene', () => import('tdp_core/dist/views/ChooserProxyView'), { + factory: 'new ChooserProxyView', + name: 'COSMIC', + site: 'https://cancer.sanger.ac.uk/cosmic/gene/analysis?genome=38&ln={gene}', + preview: () => import('./assets/previews/cosmic_banner.png'), + description: 'Catalogue Of Somatic Mutations In Cancer', + helpUrl: 'https://cancer.sanger.ac.uk/cosmic/about', + }, common, { + topics: ['cancer', 'external'], + }); + registry.push('importPostProcessor', 'GeneSymbol', () => import('./common/common').then((c) => c.SpeciesUtils), { + factory: 'convertGeneSymbolToEnsembl', + }); + registry.push('tdpListFilters', 'SpeciesFilter', () => import('./common/common').then((c) => c.SpeciesUtils), { + factory: 'filterSpecies', + }); + registry.push('idTypeDetector', 'gene_idtype_detector', () => { + return import('./providers/GeneIDTypeDetector').then((v) => v.GeneIDTypeDetector); + }, { + name: 'IDTypeDetector', + factory: 'geneIDTypeDetector', + idType: 'Ensembl', + }); // generator-phovea:end } //# sourceMappingURL=phovea.js.map \ No newline at end of file diff --git a/dist/phovea.js.map b/dist/phovea.js.map index dbba2404..f18fdd53 100644 --- a/dist/phovea.js.map +++ b/dist/phovea.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.d.ts.map b/dist/tours/AssessBCCellLines.d.ts.map index 304b78e3..f605442c 100644 --- a/dist/tours/AssessBCCellLines.d.ts.map +++ b/dist/tours/AssessBCCellLines.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"AssessBCCellLines.d.ts","sourceRoot":"","sources":["../../src/tours/AssessBCCellLines.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,iBAAiB;IAC5B,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CAuQ7B"} \ No newline at end of file +{"version":3,"file":"AssessBCCellLines.d.ts","sourceRoot":"","sources":["../../src/tours/AssessBCCellLines.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,iBAAiB;IAC5B,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CA8R7B"} \ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.js b/dist/tours/AssessBCCellLines.js index 7c8d6400..1b0c61db 100644 --- a/dist/tours/AssessBCCellLines.js +++ b/dist/tours/AssessBCCellLines.js @@ -209,10 +209,31 @@ export class AssessBCCellLines { html: `Observe: Of the highly amplified genes, ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, }, { - selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', + selector: '.le header [data-col-id="col10"]', html: `

    Combine both score columns to obtain stacked bars.

    -

    Observe: Combining the columns highlights the importance of ERBB2.

    `, +

    Observe: Combining the columns highlights the importance of ERBB2.

    +

    It is therefore probably the most relevant gene within this amplified genomic region.

    `, + placement: 'centered', + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `

    This finding leads the scientist to the question whether ERBB2 is also highly expressed and frequently amplified in other breast cancer cell lines.

    +

    To investigate this, the analyst adds the following columns: +

      +
    • A column with the average gene expression
      • +
    • A column with the gene copy number distribution
      • +
    • a column with the gene amplification frequency across all breast cancer cell lines
      • +
    +

    `, placement: 'centered', + postAction: () => { + // Add the average gene expression column + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.click('.lu-action-data-mapping > span'); + TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); + TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + }, }, { selector: '.le.le-multi.lineup-engine', diff --git a/dist/tours/AssessBCCellLines.js.map b/dist/tours/AssessBCCellLines.js.map index 90c97a8a..a17e4d52 100644 --- a/dist/tours/AssessBCCellLines.js.map +++ b/dist/tours/AssessBCCellLines.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/tours/WelcomeTour2.d.ts b/dist/tours/WelcomeTour2.d.ts deleted file mode 100644 index cca36b85..00000000 --- a/dist/tours/WelcomeTour2.d.ts +++ /dev/null @@ -1,5 +0,0 @@ -import { IStep } from 'tdp_core'; -export declare class WelcomeTour2 { - static createTour(): IStep[]; -} -//# sourceMappingURL=WelcomeTour2.d.ts.map \ No newline at end of file diff --git a/dist/tours/WelcomeTour2.d.ts.map b/dist/tours/WelcomeTour2.d.ts.map deleted file mode 100644 index 415404a8..00000000 --- a/dist/tours/WelcomeTour2.d.ts.map +++ /dev/null @@ -1 +0,0 @@ -{"version":3,"file":"WelcomeTour2.d.ts","sourceRoot":"","sources":["../../src/tours/WelcomeTour2.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,YAAY;IACvB,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CA+K7B"} \ No newline at end of file diff --git a/dist/tours/WelcomeTour2.js b/dist/tours/WelcomeTour2.js deleted file mode 100644 index 326bc10a..00000000 --- a/dist/tours/WelcomeTour2.js +++ /dev/null @@ -1,178 +0,0 @@ -import { TourUtils } from 'tdp_core'; -export class WelcomeTour2 { - static createTour() { - return [ - { - html: `

    W222elcome to this short tour showing the basic features of Ordino!

    -

    - Use the "Next" button to iterate through all the steps. You can use the - "Cancel" button at any time to stop the tour and to interact with Ordino. - Please note that the tour will load a new analysis session and the current - one will be discarded. -

    `, - }, - { - selector: 'ul[data-header="mainMenu"] > li:first-child > a', - html: `222222To start an analysis, click on the 'Datasets' tab. Subsequently, you can define the list of entities you want to work with`, - placement: 'centered', - preAction: () => { - const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)'); - if (!datasetTab.classList.contains('active')) { - datasetTab.querySelector('a').classList.add('hover'); - } - }, - postAction: () => { - const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)'); - if (!datasetTab.classList.contains('active')) { - datasetTab.querySelector('a').classList.remove('hover'); - datasetTab.querySelector('a').click(); - } - return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(3)')); - }, - pageBreak: 'manual', - }, - { - selector: '.ordino-dataset.genes-dataset > .card', - html: `

    222222222222You can choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

    In this example we will work with a list of genes

    `, - placement: 'centered', - preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), - postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), - }, - { - selector: '.ordino-dataset.genes-dataset .dataset-entry', - html: `Of the available predefined gene sets, we open a list of known cancer genes, called 'Cancer Gene Census'`, - placement: 'centered', - postAction: () => { - return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: Cancer Gene Census"]').then(TourUtils.click); - }, - pageBreak: 'manual', - }, - { - selector: '.le.le-multi.lineup-engine', - placement: 'centered', - html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, - preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(600)), - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `Additional columns can be added using the plus sign.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '.lu-search .lu-search-item', - html: `First, we want to add a metadata column`, - placement: 'centered', - postAction: () => { - TourUtils.click('.lu-search .lu-search-item'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - }, - }, - { - selector: '.modal.show .col > .select2', - html: `Here we select 'Strand' …`, - placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), - postAction: () => TourUtils.setValueAndTrigger('.col > select', 'strand', 'change'), - }, - { - selector: '.modal.show .modal-footer button[type=submit]', - html: `… and click 'Add'`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '.le header section[title=Strand]', - placement: 'centered', - html: `The strand information was added as a new column`, - preAction: TourUtils.waitForSelector, - }, - { - selector: '.lu-search .lu-search-group .lu-search-item', - placement: 'centered', - html: `Now, we want to add two columns containing the copy number information of two specific cell lines. To do so, we open the 'Cell Line Score' dialog`, - preAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - }, - postAction: () => { - TourUtils.click('.lu-search .lu-search-group .lu-search-item'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - }, - }, - { - selector: '.modal.show .col > .select3', - placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), - html: `We select the cell lines 'HCC-827' and 'BT-20'.`, - postAction: () => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC-827;BT-20;', 'input'); - }, - }, - { - selector: '.modal.show .col > .select2', - placement: 'centered', - html: `As data type, we choose 'Relative Copy Number'`, - postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); - }, - }, - { - selector: '.modal.show .modal-footer button[type=submit]', - html: `Finally, click 'Add'`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: ['.le header section[title^=BT], .le header section[title^=HCC]'], - placement: 'centered', - preAction: () => TourUtils.waitFor('.le header section[title^=BT]', 10000), - html: `The copy number information for each selected cell line has been added as additional columns`, - }, - { - selector: '.le > header', - placement: 'centered', - html: `The column headers can be used to sort and filter the list of genes based on any of the available data`, - }, - { - selector: '.le header section[title^=HCC] i[title^=Sort]', - placement: 'centered', - html: `For example, you can use this icon to sort all genes by their copy number in the cell line 'HCC-827'`, - postAction: TourUtils.clickSelector, - }, - { - selector: '.le-tr[data-index="0"]', - placement: 'centered', - html: `In order to obtain additional information about one or more genes, click on the respective line or use the checkboxes`, - preAction: () => TourUtils.waitFor(() => { - const r = document.querySelector('.le-tr[data-index="0"]'); - if (!r) { - return null; - } - // has a string renderered EGFR entry - if (!Array.from(r.querySelectorAll('div[data-renderer="string"]')).some((d) => d.textContent === 'EGFR')) { - return null; - } - return r; - }, Infinity).then(() => TourUtils.wait(500)), - postAction: TourUtils.clickSelector, - }, - { - selector: '.viewWrapper .chooser:not(.hidden)', - placement: 'centered', - html: `Various 'Detail Views', providing additional information, are available.`, - preAction: TourUtils.waitForSelector, - }, - { - selector: '.viewWrapper .chooser button[data-viewid="celllinedb_expression_vs_copynumber"]', - placement: 'centered', - html: `For instance, clicking on 'Expression vs Copy Number' opens a scatter plot showing the relation of the two types of data`, - postAction: TourUtils.clickSelector, - }, - { - html: `

    Thanks for joining this tour demonstrating the basic features of Ordino.

    -

    There are many more features to discover. Enjoy!

    `, - }, - ]; - } -} -//# sourceMappingURL=WelcomeTour2.js.map \ No newline at end of file diff --git a/dist/tours/WelcomeTour2.js.map b/dist/tours/WelcomeTour2.js.map deleted file mode 100644 index e438b1fb..00000000 --- a/dist/tours/WelcomeTour2.js.map +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/dist/views/ACombinedDependentTable.d.ts.map b/dist/views/ACombinedDependentTable.d.ts.map index 8994e547..aff82f60 100644 --- a/dist/views/ACombinedDependentTable.d.ts.map +++ b/dist/views/ACombinedDependentTable.d.ts.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/views/ACombinedDependentTable.js b/dist/views/ACombinedDependentTable.js index ad6aae81..908a783b 100644 --- a/dist/views/ACombinedDependentTable.js +++ b/dist/views/ACombinedDependentTable.js @@ -1,5 +1,5 @@ -import { SpeciesUtils } from 'tdp_gene'; import { ARankingView, RestBaseUtils, IDTypeManager, LineupUtils, AdapterUtils, } from 'tdp_core'; +import { SpeciesUtils } from '../common'; import { ParameterFormIds, FORM_DATA_HIERARCHICAL_SUBTYPE } from '../common/forms'; import { ViewUtils } from './ViewUtils'; import { splitTypes } from '../common/config'; diff --git a/dist/views/ACombinedDependentTable.js.map b/dist/views/ACombinedDependentTable.js.map index 680843a5..4253f8a7 100644 --- a/dist/views/ACombinedDependentTable.js.map +++ b/dist/views/ACombinedDependentTable.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/views/CombinedDependentSampleTable.d.ts.map b/dist/views/CombinedDependentSampleTable.d.ts.map index 212ad41d..3f492a8c 100644 --- a/dist/views/CombinedDependentSampleTable.d.ts.map +++ b/dist/views/CombinedDependentSampleTable.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"CombinedDependentSampleTable.d.ts","sourceRoot":"","sources":["../../src/views/CombinedDependentSampleTable.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,UAAU,CAAC;AACpD,OAAO,EAA0C,eAAe,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AAE9G,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAC;AAGpE,qBAAa,4BAA6B,SAAQ,uBAAuB;gBAC3D,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,eAAe,EAAE;IAM1G,SAAS,KAAK,kBAAkB,sBAE/B;IAED,SAAS,CAAC,qBAAqB;IAO/B,SAAS,CAAC,gBAAgB,CAAC,IAAI,EAAE,MAAM;IAOvC,SAAS,CAAC,uBAAuB,CAAC,IAAI,EAAE,MAAM;IAI9C,MAAM,CAAC,kCAAkC,CAAC,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW;CAG5G"} \ No newline at end of file +{"version":3,"file":"CombinedDependentSampleTable.d.ts","sourceRoot":"","sources":["../../src/views/CombinedDependentSampleTable.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,UAAU,CAAC;AACpD,OAAO,EAA0C,eAAe,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AAE9G,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAC;AAGpE,qBAAa,4BAA6B,SAAQ,uBAAuB;gBAC3D,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,eAAe,EAAE;IAM1G,SAAS,KAAK,kBAAkB,sBAE/B;IAED,SAAS,CAAC,qBAAqB;IAO/B,SAAS,CAAC,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAOvD,SAAS,CAAC,uBAAuB,CAAC,IAAI,EAAE,MAAM;IAI9C,MAAM,CAAC,kCAAkC,CAAC,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW;CAG5G"} \ No newline at end of file diff --git a/dist/views/CombinedDependentSampleTable.js b/dist/views/CombinedDependentSampleTable.js index 1ea5949f..78c7a2af 100644 --- a/dist/views/CombinedDependentSampleTable.js +++ b/dist/views/CombinedDependentSampleTable.js @@ -18,7 +18,7 @@ export class CombinedDependentSampleTable extends ACombinedDependentTable { } parameterChanged(name) { if (name === FORM_DATA_SOURCE.id) { - return this.rebuild(); // early abort after rebuild since there is nothing worse than building from scratch + return this.rebuild(); } return super.parameterChanged(name); } diff --git a/dist/views/CombinedDependentSampleTable.js.map b/dist/views/CombinedDependentSampleTable.js.map index af86719a..e7d33dee 100644 --- a/dist/views/CombinedDependentSampleTable.js.map +++ b/dist/views/CombinedDependentSampleTable.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/views/SimilarityView.d.ts.map b/dist/views/SimilarityView.d.ts.map index 6b412e9d..3c40c144 100644 --- a/dist/views/SimilarityView.d.ts.map +++ b/dist/views/SimilarityView.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"SimilarityView.d.ts","sourceRoot":"","sources":["../../src/views/SimilarityView.ts"],"names":[],"mappings":"AAAA;;GAEG;AAGH,OAAO,EACL,oBAAoB,EACpB,UAAU,EACV,YAAY,EACZ,YAAY,EACZ,qBAAqB,EAKtB,MAAM,UAAU,CAAC;AAClB,OAAO,EAAE,iBAAiB,EAAqD,MAAM,UAAU,CAAC;AAKhG,qBAAa,cAAe,SAAQ,YAAY;IAC9C,OAAO,CAAC,MAAM,CAAsB;gBAExB,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,GAAE,OAAO,CAAC,oBAAoB,CAAM;IAc1H,SAAS,CAAC,qBAAqB;IAa/B,IAAI,UAAU,8BAEb;YAEa,iBAAiB;IAgB/B,MAAM,CAAC,WAAW,CAAC,IAAI,EAAE,MAAM;;;YAajB,QAAQ;IAuBtB,OAAO,CAAC,IAAI;IAOZ,SAAS,CAAC,cAAc,CAAC,OAAO,EAAE,GAAG,EAAE,GAAG,qBAAqB,EAAE;IAIjE,SAAS,CAAC,cAAc;IAIxB,SAAS,CAAC,QAAQ;IAIlB,SAAS,CAAC,gBAAgB,CAAC,IAAI,EAAE,MAAM;IAKvC,SAAS,CAAC,gBAAgB;IAK1B,OAAO,CAAC,UAAU;IAOlB,SAAS,CAAC,oBAAoB,CAAC,QAAQ,EAAE,iBAAiB;CAe3D"} \ No newline at end of file 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b/dist/views/SimilarityView.js @@ -1,10 +1,10 @@ /** * Created by Samuel Gratzl on 29.01.2016. */ -import { tsv } from 'd3'; +import { tsv } from 'd3v3'; import { ARankingView, ColumnDescUtils, FormElementType, RestBaseUtils, } from 'tdp_core'; import { createSelectionDesc, createStackDesc } from 'lineupjs'; -import { SpeciesUtils } from 'tdp_gene'; +import { SpeciesUtils } from '../common'; const SELECT_ID = 'genehopper_selection'; export class SimilarityView extends ARankingView { constructor(context, selection, parent, options = {}) { diff --git a/dist/views/SimilarityView.js.map b/dist/views/SimilarityView.js.map index 454bf48e..2e75816c 100644 --- a/dist/views/SimilarityView.js.map +++ b/dist/views/SimilarityView.js.map @@ -1 +1 @@ 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\ No newline at end of file From 5eab43a74488bf17e631b627af7ddc4dc17531a0 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 29 Aug 2022 10:25:37 +0200 Subject: [PATCH 20/38] Fixed Hidden Modal Bug --- dist/tours/AddColumnToGeneListTour.js | 22 +++--- dist/tours/AddColumnToGeneListTour.js.map | 2 +- dist/tours/AssessBCCellLines.d.ts.map | 2 +- dist/tours/AssessBCCellLines.js | 79 ++++++++++++++++--- dist/tours/AssessBCCellLines.js.map | 2 +- src/tours/AddColumnToGeneListTour.ts | 22 +++--- src/tours/AssessBCCellLines.ts | 96 ++++++++++++++++++++--- 7 files changed, 179 insertions(+), 46 deletions(-) diff --git a/dist/tours/AddColumnToGeneListTour.js b/dist/tours/AddColumnToGeneListTour.js index 8aabad3b..2b93b3ed 100644 --- a/dist/tours/AddColumnToGeneListTour.js +++ b/dist/tours/AddColumnToGeneListTour.js @@ -87,7 +87,7 @@ export class AddColumnToGeneListTour {

    In this example, we select 'Strand' …

    `, placement: 'centered', preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), - postAction: () => TourUtils.setValueAndTrigger('.col > select', 'strand', 'change'), + postAction: () => TourUtils.setValueAndTrigger('.show .col > select', 'strand', 'change'), }, { selector: '.modal.show .modal-footer button[type=submit]', @@ -145,7 +145,7 @@ export class AddColumnToGeneListTour { placement: 'centered', html: `As data type, we choose 'Relative Copy Number'`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); }, }, { @@ -180,38 +180,38 @@ export class AddColumnToGeneListTour { preAction: () => TourUtils.waitFor('.modal.show .modal-content').then(() => TourUtils.wait(250)), }, { - selector: '.modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) div:nth-child(1) select', + selector: '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) div:nth-child(1) select', html: `

    First, we need to define the subset of cell lines which we want to aggregate.

    For the filter attribute we select 'Tumor Type' …

    `, placement: 'centered', postAction: () => { - TourUtils.setValueAndTrigger('.modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); }, }, { - selector: '.modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) .select2', + selector: '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) .select2', html: `… and for the filter value we select 'breast carcinoma'.`, placement: 'centered', - preAction: () => TourUtils.waitFor('.modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) .select2').then(() => TourUtils.wait(250)), + preAction: () => TourUtils.waitFor('.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) .select2').then(() => TourUtils.wait(250)), postAction: () => { - TourUtils.setValueAndTrigger('.modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', 'change'); }, }, { - selector: '.modal-body form > .col-sm-12:nth-child(2) .row:nth-child(1) .select2', + selector: '.show .modal-body form > .col-sm-12:nth-child(2) .row:nth-child(1) .select2', placement: 'centered', html: `As data type, we choose 'Relative Copy Number' …`, postAction: () => { - TourUtils.setValueAndTrigger('.modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); }, }, { - selector: '.modal-body form > .col-sm-12:nth-child(3) select', + selector: '.show .modal-body form > .col-sm-12:nth-child(3) select', placement: 'centered', html: `

    … and as type of aggregation we choose 'Average'

    FYI: other types of aggregation are, for instance, 'Min', 'Max', 'Median', 'Count', and 'Boxplot'.`, postAction: () => { - TourUtils.setValueAndTrigger('.modal-body form > .col-sm-12:nth-child(3) > select', 'avg', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(3) > select', 'avg', 'change'); }, }, { diff --git a/dist/tours/AddColumnToGeneListTour.js.map b/dist/tours/AddColumnToGeneListTour.js.map index a0074a21..5652a909 100644 --- a/dist/tours/AddColumnToGeneListTour.js.map +++ b/dist/tours/AddColumnToGeneListTour.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.d.ts.map b/dist/tours/AssessBCCellLines.d.ts.map index f605442c..b7d689e1 100644 --- a/dist/tours/AssessBCCellLines.d.ts.map +++ b/dist/tours/AssessBCCellLines.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"AssessBCCellLines.d.ts","sourceRoot":"","sources":["../../src/tours/AssessBCCellLines.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,iBAAiB;IAC5B,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CA8R7B"} \ No newline at end of file +{"version":3,"file":"AssessBCCellLines.d.ts","sourceRoot":"","sources":["../../src/tours/AssessBCCellLines.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,EAAmB,MAAM,UAAU,CAAC;AAElD,qBAAa,iBAAiB;IAC5B,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CAqW7B"} \ No newline at end of file diff --git a/dist/tours/AssessBCCellLines.js b/dist/tours/AssessBCCellLines.js index 1b0c61db..1b81b8d5 100644 --- a/dist/tours/AssessBCCellLines.js +++ b/dist/tours/AssessBCCellLines.js @@ -82,7 +82,7 @@ export class AssessBCCellLines { placement: 'centered', html: `and the data type`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); }, }, { @@ -145,7 +145,7 @@ export class AssessBCCellLines { placement: 'centered', html: `and the 2nd data type`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show .col > select', 'expression-tpm', 'change'); }, }, { @@ -183,7 +183,7 @@ export class AssessBCCellLines { placement: 'centered', html: `and the 3rd data type`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'depletion-rsa', 'change'); + TourUtils.setValueAndTrigger('.show .col > select', 'depletion-rsa', 'change'); }, }, { @@ -209,32 +209,93 @@ export class AssessBCCellLines { html: `Observe: Of the highly amplified genes, ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, }, { - selector: '.le header [data-col-id="col10"]', + selector: '.le header [data-col-id="col9"], .le header [data-col-id="col10"]', html: `

    Combine both score columns to obtain stacked bars.

    Observe: Combining the columns highlights the importance of ERBB2.

    It is therefore probably the most relevant gene within this amplified genomic region.

    `, placement: 'centered', }, { - selector: '.lu-side-panel-wrapper .lu-adder > button', + selector: '.le header [data-col-id="col10"]', html: `

    This finding leads the scientist to the question whether ERBB2 is also highly expressed and frequently amplified in other breast cancer cell lines.

    To investigate this, the analyst adds the following columns:

    • A column with the average gene expression
    • A column with the gene copy number distribution
      • -
    • a column with the gene amplification frequency across all breast cancer cell lines
      • +
    • A column with the gene amplification frequency across all breast cancer cell lines

    `, placement: 'centered', + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `1. A column with the average gene expression`, + placement: 'centered', postAction: () => { // Add the average gene expression column TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); - TourUtils.click('.lu-action-data-mapping > span'); - TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); - TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); }, }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `2. A column with the gene copy number distribution`, + placement: 'centered', + postAction: () => { + // Add the average gene expression column + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'boxplot', 'change'); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `3. A column with the gene amplification frequency across all breast cancer cell lines`, + placement: 'centered', + postAction: () => { + // Add the average gene expression column + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'frequency', 'change'); + TourUtils.waitFor('.show [data-testid="Comparison Operator"]').then(() => { + TourUtils.setValueAndTrigger('.show [data-testid="comparison-operator"] select', '>', 'change'); + TourUtils.setValueAndTrigger('.show [type="number"]', '4', 'input'); + }); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); + }, + }, + { + selector: '.le.le-multi.lineup-engine', + html: `Observe: ERBB2 is amplified in almost 25% of all assessed breast cancer cell lines. Further, it is highly expressed.`, + placement: 'centered', + }, + { + selector: '.le.le-multi.lineup-engine', + html: `

    The aim is now to get more information about ERBB2.

    +

    Select ERBB2 in the list.

    `, + placement: 'centered', + }, { selector: '.le.le-multi.lineup-engine', placement: 'centered', diff --git a/dist/tours/AssessBCCellLines.js.map b/dist/tours/AssessBCCellLines.js.map index a17e4d52..97a5da6e 100644 --- a/dist/tours/AssessBCCellLines.js.map +++ b/dist/tours/AssessBCCellLines.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/tours/AddColumnToGeneListTour.ts b/src/tours/AddColumnToGeneListTour.ts index 79c04473..59dc3031 100644 --- a/src/tours/AddColumnToGeneListTour.ts +++ b/src/tours/AddColumnToGeneListTour.ts @@ -93,7 +93,7 @@ export class AddColumnToGeneListTour {

    In this example, we select 'Strand' …

    `, placement: 'centered', preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), - postAction: () => TourUtils.setValueAndTrigger('.col > select', 'strand', 'change'), + postAction: () => TourUtils.setValueAndTrigger('.show .col > select', 'strand', 'change'), }, { @@ -157,7 +157,7 @@ export class AddColumnToGeneListTour { placement: 'centered', html: `As data type, we choose 'Relative Copy Number'`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); }, }, @@ -197,26 +197,26 @@ export class AddColumnToGeneListTour { }, { - selector: '.modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) div:nth-child(1) select', + selector: '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) div:nth-child(1) select', html: `

    First, we need to define the subset of cell lines which we want to aggregate.

    For the filter attribute we select 'Tumor Type' …

    `, placement: 'centered', postAction: () => { - TourUtils.setValueAndTrigger('.modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); }, }, { - selector: '.modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) .select2', + selector: '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) .select2', html: `… and for the filter value we select 'breast carcinoma'.`, placement: 'centered', preAction: () => - TourUtils.waitFor('.modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) .select2').then(() => + TourUtils.waitFor('.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) .select2').then(() => TourUtils.wait(250), ), postAction: () => { TourUtils.setValueAndTrigger( - '.modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', 'change', ); @@ -224,21 +224,21 @@ export class AddColumnToGeneListTour { }, { - selector: '.modal-body form > .col-sm-12:nth-child(2) .row:nth-child(1) .select2', + selector: '.show .modal-body form > .col-sm-12:nth-child(2) .row:nth-child(1) .select2', placement: 'centered', html: `As data type, we choose 'Relative Copy Number' …`, postAction: () => { - TourUtils.setValueAndTrigger('.modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); }, }, { - selector: '.modal-body form > .col-sm-12:nth-child(3) select', + selector: '.show .modal-body form > .col-sm-12:nth-child(3) select', placement: 'centered', html: `

    … and as type of aggregation we choose 'Average'

    FYI: other types of aggregation are, for instance, 'Min', 'Max', 'Median', 'Count', and 'Boxplot'.`, postAction: () => { - TourUtils.setValueAndTrigger('.modal-body form > .col-sm-12:nth-child(3) > select', 'avg', 'change'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(3) > select', 'avg', 'change'); }, }, diff --git a/src/tours/AssessBCCellLines.ts b/src/tours/AssessBCCellLines.ts index ac7608f1..a28221e9 100644 --- a/src/tours/AssessBCCellLines.ts +++ b/src/tours/AssessBCCellLines.ts @@ -1,4 +1,5 @@ -import { IStep, TourUtils } from 'tdp_core'; +import {ToursSection} from 'ordino'; +import { IStep, Tour, TourUtils } from 'tdp_core'; export class AssessBCCellLines { static createTour(): IStep[] { @@ -85,7 +86,7 @@ export class AssessBCCellLines { placement: 'centered', html: `and the data type`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); }, }, { @@ -148,7 +149,7 @@ export class AssessBCCellLines { placement: 'centered', html: `and the 2nd data type`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show .col > select', 'expression-tpm', 'change'); }, }, { @@ -186,7 +187,7 @@ export class AssessBCCellLines { placement: 'centered', html: `and the 3rd data type`, postAction: () => { - TourUtils.setValueAndTrigger('.col > select', 'depletion-rsa', 'change'); + TourUtils.setValueAndTrigger('.show .col > select', 'depletion-rsa', 'change'); }, }, { @@ -212,34 +213,105 @@ export class AssessBCCellLines { html: `Observe: Of the highly amplified genes, ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, }, { - selector: '.le header [data-col-id="col10"]', + selector: '.le header [data-col-id="col9"], .le header [data-col-id="col10"]', html: `

    Combine both score columns to obtain stacked bars.

    Observe: Combining the columns highlights the importance of ERBB2.

    It is therefore probably the most relevant gene within this amplified genomic region.

    `, placement: 'centered', }, { - selector: '.lu-side-panel-wrapper .lu-adder > button', + selector: '.le header [data-col-id="col10"]', html: `

    This finding leads the scientist to the question whether ERBB2 is also highly expressed and frequently amplified in other breast cancer cell lines.

    To investigate this, the analyst adds the following columns:

    • A column with the average gene expression
    • A column with the gene copy number distribution
      • -
    • a column with the gene amplification frequency across all breast cancer cell lines
      • +
    • A column with the gene amplification frequency across all breast cancer cell lines

    `, placement: 'centered', + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `1. A column with the average gene expression`, + placement: 'centered', postAction: () => { // Add the average gene expression column TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); - - - TourUtils.click('.lu-action-data-mapping > span'); - TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); - TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger( + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + 'breast carcinoma', + 'change', + ); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `2. A column with the gene copy number distribution`, + placement: 'centered', + postAction: () => { + // Add the average gene expression column + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger( + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + 'breast carcinoma', + 'change', + ); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'boxplot', 'change'); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `3. A column with the gene amplification frequency across all breast cancer cell lines`, + placement: 'centered', + postAction: () => { + // Add the average gene expression column + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger( + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + 'breast carcinoma', + 'change', + ); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'frequency', 'change'); + TourUtils.waitFor('.show [data-testid="Comparison Operator"]').then(() => { + TourUtils.setValueAndTrigger('.show [data-testid="comparison-operator"] select', '>', 'change'); + TourUtils.setValueAndTrigger('.show [type="number"]', '4', 'input'); + }); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); }, }, + { + selector: '.le.le-multi.lineup-engine', + html: `Observe: ERBB2 is amplified in almost 25% of all assessed breast cancer cell lines. Further, it is highly expressed.`, + placement: 'centered', + }, + { + selector: '.le.le-multi.lineup-engine', + html: `

    The aim is now to get more information about ERBB2.

    +

    Select ERBB2 in the list.

    `, + placement: 'centered', + }, { selector: '.le.le-multi.lineup-engine', placement: 'centered', From f52de57eeef84bacc94e77240f452163146deb96 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Tue, 30 Aug 2022 09:54:09 +0200 Subject: [PATCH 21/38] AssessBCCellLines Tour Complete (Unpolished) --- src/tours/AssessBCCellLines.ts | 201 +++++++++++++++++++++++++++------ 1 file changed, 164 insertions(+), 37 deletions(-) diff --git a/src/tours/AssessBCCellLines.ts b/src/tours/AssessBCCellLines.ts index a28221e9..0bff31c2 100644 --- a/src/tours/AssessBCCellLines.ts +++ b/src/tours/AssessBCCellLines.ts @@ -75,7 +75,7 @@ export class AssessBCCellLines { { selector: '.modal.show .col > .select3', placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), html: `We select the Cell Line`, postAction: () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); @@ -138,7 +138,7 @@ export class AssessBCCellLines { { selector: '.modal.show .col > .select3', placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), html: `We select the 2nd Cell Line`, postAction: () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); @@ -176,7 +176,7 @@ export class AssessBCCellLines { { selector: '.modal.show .col > .select3', placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(250)), + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), html: `We select the 3rd Cell Line`, postAction: () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); @@ -213,14 +213,14 @@ export class AssessBCCellLines { html: `Observe: Of the highly amplified genes, ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, }, { - selector: '.le header [data-col-id="col9"], .le header [data-col-id="col10"]', + selector: ['.le header [data-col-id="col9"], .le header [data-col-id="col10"]'], html: `

    Combine both score columns to obtain stacked bars.

    Observe: Combining the columns highlights the importance of ERBB2.

    It is therefore probably the most relevant gene within this amplified genomic region.

    `, placement: 'centered', }, { - selector: '.le header [data-col-id="col10"]', + selector: '[data-index="0"]', html: `

    This finding leads the scientist to the question whether ERBB2 is also highly expressed and frequently amplified in other breast cancer cell lines.

    To investigate this, the analyst adds the following columns:

      @@ -236,11 +236,10 @@ export class AssessBCCellLines { html: `1. A column with the average gene expression`, placement: 'centered', postAction: () => { - // Add the average gene expression column TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + return TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', @@ -257,12 +256,14 @@ export class AssessBCCellLines { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `2. A column with the gene copy number distribution`, placement: 'centered', + preAction: () => { + TourUtils.waitFor('.le header [data-col-id="col11"]'); + }, postAction: () => { - // Add the average gene expression column TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + return TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', @@ -279,12 +280,14 @@ export class AssessBCCellLines { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `3. A column with the gene amplification frequency across all breast cancer cell lines`, placement: 'centered', + preAction: () => { + TourUtils.waitFor('.le header [data-col-id="col12"]'); + }, postAction: () => { - // Add the average gene expression column TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + return TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', @@ -305,57 +308,181 @@ export class AssessBCCellLines { selector: '.le.le-multi.lineup-engine', html: `Observe: ERBB2 is amplified in almost 25% of all assessed breast cancer cell lines. Further, it is highly expressed.`, placement: 'centered', + preAction: () => { + TourUtils.waitFor('.le header [data-col-id="col13"]'); + }, }, { - selector: '.le.le-multi.lineup-engine', + selector: '[data-index="0"] .lu-renderer-selection', html: `

      The aim is now to get more information about ERBB2.

      Select ERBB2 in the list.

      `, placement: 'centered', + postAction: TourUtils.clickSelector, }, { - selector: '.le.le-multi.lineup-engine', + selector: '[data-viewid="celllinedb_expression_vs_copynumber"]', + html: `Open the Expression vs Copy Number detail view`, placement: 'centered', - html: `TOUR IS HERE SO FAR.`, + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, }, { - selector: '.le header section[title^=HCC] i[title^=Sort]', + selector: '.ids', + html: `Observe the direct correlation between copy number and expression of ERBB2`, + placement: 'centered', + preAction: () => { + return TourUtils.waitFor('.ids'); + }, + }, + { + selector: '[data-viewid="targetvalidation"]', + html: `Now open the Open Targets detail view...`, placement: 'centered', - html: `For example, you can use this icon to sort all genes by their copy number in the cell line 'HCC-827'`, postAction: TourUtils.clickSelector, }, { - selector: '.le-tr[data-index="0"]', - placement: 'centered', - html: `In order to obtain additional information about one or more genes, click on the respective line or use the checkboxes`, - preAction: () => - TourUtils.waitFor(() => { - const r = document.querySelector('.le-tr[data-index="0"]'); - if (!r) { - return null; - } - // has a string renderered EGFR entry - if (!Array.from(r.querySelectorAll('div[data-renderer="string"]')).some((d) => d.textContent === 'EGFR')) { - return null; - } - return r; - }, Infinity).then(() => TourUtils.wait(500)), // wait for animation to complete + selector: '[data-viewid="pubmed"]', + html: `...and the PubMed detail view.`, + placement: 'centered', postAction: TourUtils.clickSelector, }, { - selector: '.viewWrapper .chooser:not(.hidden)', + selector: '', + html: `Question: In what cell lines is ERBB2 amplified? Select cell lines with ERBB2 amplification that have mutation in BRCA1 or BRCA2`, + placement: 'centered', + }, + { + selector: '[data-viewid="copynumbertable"]', + html: `Start by opening the Copy Number detail view`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-id="col7"] .lu-action-sort', + html: `Now sort by the copy number`, placement: 'centered', - html: `Various 'Detail Views', providing additional information, are available.`, preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid="viewWrapper-1"] [data-id="col4"] .lu-action-filter', + html: `Filter for breast cancer via column menu of column tumor type (also filter out cell lines with unknown tumor type)`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-dialog .lu-dialog-table', + html: `First select only the "breast carcinoma" tumor type.`, + placement: 'centered', + postAction: () => { + TourUtils.wait(100) + .then(() => { + TourUtils.click('.lu-dialog-table .lu-checkbox:first-child'); + }) + .then(() => { + TourUtils.wait(500).then(() => { + TourUtils.click('input[type="checkbox"][data-cat="breast carcinoma"]'); + }); + }); + }, }, { - selector: '.viewWrapper .chooser button[data-viewid="celllinedb_expression_vs_copynumber"]', + selector: '.lu-dialog .lu-dialog-table', + html: `Then filter cell lines with unknown types and submit the filter.`, placement: 'centered', - html: `For instance, clicking on 'Expression vs Copy Number' opens a scatter plot showing the relation of the two types of data`, + postAction: () => { + TourUtils.wait(100) + .then(() => { + TourUtils.click('.lu-dialog > .lu-checkbox input'); + }) + .then(() => { + TourUtils.wait(500).then(() => { + TourUtils.click('.lu-dialog-button[type="submit"]'); + }); + }); + }, + }, + { + selector: '[data-testid="viewWrapper-1"] .lu-side-panel-wrapper .lu-adder > button', + html: `Let's now add the BRCA gene scores.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid="viewWrapper-1"] [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + html: `We want to add a new column`, + placement: 'centered', + postAction: () => { + TourUtils.click( + '[data-testid="viewWrapper-1"] [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + ); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), + html: `We select the BRCA1 and BRCA2 cell lines.`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'BRCA1;', 'input'); + TourUtils.wait(400).then(() => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'BRCA2;', 'input'); + }); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `Then set the data type to AA Mutated.`, + postAction: () => { + TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: ['[data-testid="viewWrapper-1"] [data-index="0"].le-tr, [data-testid="viewWrapper-1"] [data-index="2"].le-tr'], + html: `

      Observe:

      +

      HCC1954 has the highest ERBB2 amplification among BRCA1 mutated cell lines.

      +

      HCC1569 has the highest ERBB2 amplification among BRCA2 mutated cell lines.

      `, + placement: 'centered', + }, + { + selector: '', + html: `Aim: Show information provided by COSMIC about these two cell lines`, + placement: 'centered', + }, + { + selector: ['[data-testid="viewWrapper-1"] [data-index="0"].le-tr, [data-testid="viewWrapper-1"] [data-index="2"].le-tr'], + html: `Select HCC1954 and HCC1569`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid="viewWrapper-1"] [data-index="0"] .lu-renderer-selection'); + TourUtils.click('[data-testid="viewWrapper-1"] [data-index="2"] .lu-renderer-selection'); + }, + }, + { + selector: '[data-testid="viewWrapper-1"] [data-viewid="cosmic"]', + html: `Open the COSMIC detail view`, + placement: 'centered', + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid="viewWrapper-2"] select', + html: `Use the drop-down menu to switch between the two cell lines.`, + placement: 'centered', + preAction: TourUtils.waitForSelector, postAction: TourUtils.clickSelector, }, { - html: `

      Thanks for joining this tour demonstrating the basic features of Ordino.

      -

      There are many more features to discover. Enjoy!

      `, + html: `

      Thanks for joining this tour demonstrating the assessment of breast cancer cell lines.

      +

      There are still many more features to discover. Enjoy!

      `, }, ]; } From 38fbf9e229c09705e48e04c4c4ac06e98c10bfa7 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Fri, 2 Sep 2022 12:49:20 +0200 Subject: [PATCH 22/38] AssessBCCellLine Tour Complete (Polished) --- src/tours/AssessBCCellLines.ts | 217 ++++++++++++++------------------- 1 file changed, 91 insertions(+), 126 deletions(-) diff --git a/src/tours/AssessBCCellLines.ts b/src/tours/AssessBCCellLines.ts index 0bff31c2..69d3a31d 100644 --- a/src/tours/AssessBCCellLines.ts +++ b/src/tours/AssessBCCellLines.ts @@ -1,4 +1,4 @@ -import {ToursSection} from 'ordino'; +// import {ToursSection} from 'ordino'; import { IStep, Tour, TourUtils } from 'tdp_core'; export class AssessBCCellLines { @@ -6,6 +6,7 @@ export class AssessBCCellLines { return [ { html: `

      Welcome to this short tour showing the assessment of breast cancer cell lines!

      +

      This tour will follow an analysis session from the perspective of a drug discovery team at a pharmaceutical company.

      Use the "Next" button to iterate through all the steps. You can use the "Cancel" button at any time to stop the tour and to interact with Ordino. @@ -15,7 +16,7 @@ export class AssessBCCellLines { }, { selector: 'ul[data-header="mainMenu"] > li:first-child > a', - html: `To start an analysis, click on the 'Datasets' tab. Subsequently, you can define the list of entities you want to work with`, + html: `To start the analysis, the team clicks on the 'Datasets' tab.`, placement: 'centered', preAction: () => { const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; @@ -35,14 +36,15 @@ export class AssessBCCellLines { }, { selector: '.ordino-dataset.genes-dataset > .card', - html: `

      You can choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

      In this example we will work with a list of genes

      `, + html: `

      Here they choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

      +

      In this example they choose to work with a list of genes.

      `, placement: 'centered', preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), }, { selector: '[data-testid="normal-chromosome-protein-coding-human-genes-button"]', - html: `The scientist starts by loading the list of all protein coding genes.`, + html: `The scientists start by loading the list of all protein coding genes for humans.`, placement: 'centered', postAction: () => { return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: normal chromosome protein coding human genes"]').then( @@ -59,13 +61,13 @@ export class AssessBCCellLines { }, { selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `Additional columns can be added using the plus sign.`, + html: `They begin by adding an additional column, done so by clicking on the plus icon shown here.`, placement: 'centered', postAction: TourUtils.clickSelector, }, { selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', - html: `First, we want to add a new column`, + html: `They choose to add a column for a single cell line score.`, placement: 'centered', postAction: () => { TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); @@ -76,7 +78,7 @@ export class AssessBCCellLines { selector: '.modal.show .col > .select3', placement: 'centered', preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), - html: `We select the Cell Line`, + html: `Now they select the cell line 'HCC1954' …`, postAction: () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); }, @@ -84,125 +86,90 @@ export class AssessBCCellLines { { selector: '.modal.show .col > .select2', placement: 'centered', - html: `and the data type`, + html: `… and the data type as 'Relative Copy Number' …`, postAction: () => { TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); }, }, { selector: '.modal.show .modal-footer button[type=submit]', - html: `… and click 'Add'`, + html: `… and click 'Add'.`, placement: 'centered', postAction: TourUtils.clickSelector, }, - { - selector: '.le header [data-col-id="col8"]', - placement: 'centered', - html: `The new column was added here`, - preAction: TourUtils.waitForSelector, - }, { selector: '.le [data-col-id="col8"] .lu-action-sort', placement: 'centered', - html: `Now, we want to sort by this column`, + html: `They want to sort by this newly added column, so they click on the sort button in the column header.`, + preAction: () => TourUtils.waitFor('.le [data-col-id="col8"] .lu-action-sort'), postAction: () => { TourUtils.click('.le [data-col-id="col8"] .lu-action-sort'); }, }, { - selector: '.le.le-multi.lineup-engine', - placement: 'centered', - html: `Now everything was sorted!`, - }, - { - selector: '.le.le-multi.lineup-engine', + selector: ['[data-index="0"].le-tr, [data-index="14"].le-tr'], placement: 'centered', - html: `After sorting by this column, the analyst observes - that about 15 genes on chromosome 17 are affected by a large genomic amplification.`, + html: `After sorting by this column, the analyst observes that about 15 genes on chromosome 17 are affected by a large genomic amplification.`, }, { selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `In order to identify the most relevant gene of these, the analyst adds a column with the gene expression (a measure of activity) in HCC1954`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', - html: `We want to add a 2nd new column`, + html: `

      In order to identify the most relevant of these genes, the analyst adds a column with the Normalized Gene Expression (a measure of activity) for cell line HCC1954

      +

      Individual steps for adding a column have been skipped this time.

      `, placement: 'centered', postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(() => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'expression-tpm', 'change'); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); }, }, { - selector: '.modal.show .col > .select3', - placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), - html: `We select the 2nd Cell Line`, - postAction: () => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); - }, - }, - { - selector: '.modal.show .col > .select2', + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `They also add a column with a Gene Sensitivity Score (a measure of importance for cell survival) for HCC1954.`, placement: 'centered', - html: `and the 2nd data type`, + preAction: () => TourUtils.waitFor('.le header [data-col-id="col9"]').then(() => TourUtils.wait(500)), postAction: () => { - TourUtils.setValueAndTrigger('.show .col > select', 'expression-tpm', 'change'); + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); }, }, - { - selector: '.modal.show .modal-footer button[type=submit]', - html: `… and click 'Add'`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `They also add a gene sensitivity score (a measure of importance for cell survival) for HCC1954 (RSA scores obtained from DRIVE data set [4]).`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, { selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span', - html: `We want to add a 3rd new column`, + html: `

      To do so, they select to add a 'Depletion Screen Score (Single)' column.

      +

      Similarly, the specific steps for adding a column have been skipped this time.

      `, placement: 'centered', postAction: () => { TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(() => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'depletion-rsa', 'change'); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); }, }, { - selector: '.modal.show .col > .select3', - placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), - html: `We select the 3rd Cell Line`, - postAction: () => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); - }, - }, - { - selector: '.modal.show .col > .select2', + selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', + html: `

      In an effort to improve the depletion score's readability, they decide to invert the linear scaling.

      +

      To do this, they click on the three dots for more column options.

      `, placement: 'centered', - html: `and the 3rd data type`, - postAction: () => { - TourUtils.setValueAndTrigger('.show .col > select', 'depletion-rsa', 'change'); - }, + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, }, { - selector: '.modal.show .modal-footer button[type=submit]', - html: `… and click 'Add'`, + selector: '.lu-action-data-mapping > span', + html: `They now click on 'Data Mapping'.`, placement: 'centered', postAction: TourUtils.clickSelector, }, { - selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', - html: `We now want to invert the linear scaling of the depletion screen score to improve the scale's readability.`, + selector: ['.browser-default, .lu-dialog-buttons > [type="submit"]'], + html: `They select the 'Invert' option in the Normalization Scaling dropdown and then click on the tick at the bottom right to apply the new mapping.`, placement: 'centered', postAction: () => { - TourUtils.click('[data-id="col10"] > .lu-toolbar > .lu-action-more'); - TourUtils.click('.lu-action-data-mapping > span'); TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); TourUtils.click('.lu-dialog-buttons > [type="submit"]'); }, @@ -210,11 +177,11 @@ export class AssessBCCellLines { { selector: '[data-index="0"]', placement: 'centered', - html: `Observe: Of the highly amplified genes, ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, + html: `Observe: Of the highly amplified genes, they notice that ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, }, { selector: ['.le header [data-col-id="col9"], .le header [data-col-id="col10"]'], - html: `

      Combine both score columns to obtain stacked bars.

      + html: `

      They can combine both score columns by dragging them together to obtain stacked bars.

      Observe: Combining the columns highlights the importance of ERBB2.

      It is therefore probably the most relevant gene within this amplified genomic region.

      `, placement: 'centered', @@ -224,22 +191,22 @@ export class AssessBCCellLines { html: `

      This finding leads the scientist to the question whether ERBB2 is also highly expressed and frequently amplified in other breast cancer cell lines.

      To investigate this, the analyst adds the following columns:

        -
      • A column with the average gene expression
        • -
      • A column with the gene copy number distribution
        • -
      • A column with the gene amplification frequency across all breast cancer cell lines
        • +
      • A column with the average gene expression for breast cancer cell lines
        • +
      • A column with the gene copy number distribution for breast cancer cell lines in boxplot format
        • +
      • A column with the gene amplification frequency (>4) across all breast cancer cell lines

      `, placement: 'centered', }, { selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `1. A column with the average gene expression`, + html: `1. A column with the average gene expression for breast cancer cell lines`, placement: 'centered', postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - return TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', @@ -248,22 +215,22 @@ export class AssessBCCellLines { ); TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); - TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + TourUtils.wait(1000).then(() => { + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); }); }, }, { selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `2. A column with the gene copy number distribution`, + html: `2. A column with the gene copy number distribution for breast cancer cell lines in boxplot format`, placement: 'centered', - preAction: () => { - TourUtils.waitFor('.le header [data-col-id="col11"]'); - }, + preAction: () => TourUtils.waitFor('.le header [data-col-id="col11"]'), postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - return TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', @@ -272,22 +239,22 @@ export class AssessBCCellLines { ); TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'boxplot', 'change'); - TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + TourUtils.wait(1000).then(() => { + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); }); }, }, { selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `3. A column with the gene amplification frequency across all breast cancer cell lines`, + html: `3. A column with the gene amplification frequency (>4) across all breast cancer cell lines`, placement: 'centered', - preAction: () => { - TourUtils.waitFor('.le header [data-col-id="col12"]'); - }, + preAction: () => TourUtils.waitFor('.le header [data-col-id="col12"]'), postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - return TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', @@ -300,79 +267,77 @@ export class AssessBCCellLines { TourUtils.setValueAndTrigger('.show [data-testid="comparison-operator"] select', '>', 'change'); TourUtils.setValueAndTrigger('.show [type="number"]', '4', 'input'); }); - TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + TourUtils.wait(1000).then(() => { + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); }); }, }, { selector: '.le.le-multi.lineup-engine', - html: `Observe: ERBB2 is amplified in almost 25% of all assessed breast cancer cell lines. Further, it is highly expressed.`, + html: `Observe: They notice that ERBB2 is amplified in almost 25% of all assessed breast cancer cell lines. Further, it is highly expressed.`, placement: 'centered', - preAction: () => { - TourUtils.waitFor('.le header [data-col-id="col13"]'); - }, + preAction: () => TourUtils.waitFor('.le header [data-col-id="col13"]'), }, { selector: '[data-index="0"] .lu-renderer-selection', html: `

      The aim is now to get more information about ERBB2.

      -

      Select ERBB2 in the list.

      `, +

      They select ERBB2 in the list.

      `, placement: 'centered', postAction: TourUtils.clickSelector, }, { selector: '[data-viewid="celllinedb_expression_vs_copynumber"]', - html: `Open the Expression vs Copy Number detail view`, + html: `They open the Expression vs Copy Number detail view.`, placement: 'centered', preAction: TourUtils.waitForSelector, postAction: TourUtils.clickSelector, }, { selector: '.ids', - html: `Observe the direct correlation between copy number and expression of ERBB2`, + html: `Here they observe the direct correlation between copy number and expression of ERBB2.`, placement: 'centered', - preAction: () => { - return TourUtils.waitFor('.ids'); - }, + preAction: () => TourUtils.waitFor('.ids').then(() => TourUtils.wait(300)), }, { selector: '[data-viewid="targetvalidation"]', - html: `Now open the Open Targets detail view...`, + html: `To find more information, they open the 'Open Targets' detail view …`, placement: 'centered', postAction: TourUtils.clickSelector, }, { selector: '[data-viewid="pubmed"]', - html: `...and the PubMed detail view.`, + html: `… and then the 'PubMed' detail view.`, placement: 'centered', postAction: TourUtils.clickSelector, }, { selector: '', - html: `Question: In what cell lines is ERBB2 amplified? Select cell lines with ERBB2 amplification that have mutation in BRCA1 or BRCA2`, + html: `Their question is now: In what cell lines is ERBB2 amplified?`, placement: 'centered', }, { selector: '[data-viewid="copynumbertable"]', - html: `Start by opening the Copy Number detail view`, + html: `They continue by opening the Copy Number detail view …`, placement: 'centered', postAction: TourUtils.clickSelector, }, { selector: '[data-id="col7"] .lu-action-sort', - html: `Now sort by the copy number`, + html: `… and then sorting by the copy number.`, placement: 'centered', preAction: TourUtils.waitForSelector, postAction: TourUtils.clickSelector, }, { selector: '[data-testid="viewWrapper-1"] [data-id="col4"] .lu-action-filter', - html: `Filter for breast cancer via column menu of column tumor type (also filter out cell lines with unknown tumor type)`, + html: `They want to filter for breast cancer via the column menu of column 'Tumor Type', while also filtering out cell lines with unknown tumor types.`, placement: 'centered', postAction: TourUtils.clickSelector, }, { selector: '.lu-dialog .lu-dialog-table', - html: `First select only the "breast carcinoma" tumor type.`, + html: `First they select only the "breast carcinoma" tumor type.`, placement: 'centered', postAction: () => { TourUtils.wait(100) @@ -387,8 +352,8 @@ export class AssessBCCellLines { }, }, { - selector: '.lu-dialog .lu-dialog-table', - html: `Then filter cell lines with unknown types and submit the filter.`, + selector: ['.lu-dialog .lu-dialog-table, .lu-dialog-button[title="Apply"]'], + html: `Then they filter out cell lines with unknown types (the missing value rows) and submit the filter.`, placement: 'centered', postAction: () => { TourUtils.wait(100) @@ -404,13 +369,13 @@ export class AssessBCCellLines { }, { selector: '[data-testid="viewWrapper-1"] .lu-side-panel-wrapper .lu-adder > button', - html: `Let's now add the BRCA gene scores.`, + html: `They now want to add the BRCA gene score columns.`, placement: 'centered', postAction: TourUtils.clickSelector, }, { selector: '[data-testid="viewWrapper-1"] [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', - html: `We want to add a new column`, + html: `Once again, they use the plus icon to add a new column.`, placement: 'centered', postAction: () => { TourUtils.click( @@ -423,7 +388,7 @@ export class AssessBCCellLines { selector: '.modal.show .col > .select3', placement: 'centered', preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), - html: `We select the BRCA1 and BRCA2 cell lines.`, + html: `Here they select the BRCA1 and BRCA2 cell lines …`, postAction: () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'BRCA1;', 'input'); TourUtils.wait(400).then(() => { @@ -434,14 +399,14 @@ export class AssessBCCellLines { { selector: '.modal.show .col > .select2', placement: 'centered', - html: `Then set the data type to AA Mutated.`, + html: `… and then they set the data type to AA Mutated …`, postAction: () => { TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'change'); }, }, { selector: '.modal.show .modal-footer button[type=submit]', - html: `… and click 'Add'`, + html: `… and click 'Add'.`, placement: 'centered', postAction: TourUtils.clickSelector, }, @@ -451,15 +416,16 @@ export class AssessBCCellLines {

      HCC1954 has the highest ERBB2 amplification among BRCA1 mutated cell lines.

      HCC1569 has the highest ERBB2 amplification among BRCA2 mutated cell lines.

      `, placement: 'centered', + preAction: () => TourUtils.waitFor('[data-testid="viewWrapper-1"] .le header [data-col-id="col8"]'), }, { selector: '', - html: `Aim: Show information provided by COSMIC about these two cell lines`, + html: `Finally, their aim is to find information provided by COSMIC about these two cell lines.`, placement: 'centered', }, { selector: ['[data-testid="viewWrapper-1"] [data-index="0"].le-tr, [data-testid="viewWrapper-1"] [data-index="2"].le-tr'], - html: `Select HCC1954 and HCC1569`, + html: `They select HCC1954 and HCC1569 …`, placement: 'centered', postAction: () => { TourUtils.click('[data-testid="viewWrapper-1"] [data-index="0"] .lu-renderer-selection'); @@ -468,17 +434,16 @@ export class AssessBCCellLines { }, { selector: '[data-testid="viewWrapper-1"] [data-viewid="cosmic"]', - html: `Open the COSMIC detail view`, + html: `… and open the COSMIC detail view.`, placement: 'centered', preAction: TourUtils.waitForSelector, postAction: TourUtils.clickSelector, }, { selector: '[data-testid="viewWrapper-2"] select', - html: `Use the drop-down menu to switch between the two cell lines.`, + html: `Here they can use the drop-down menu to switch between the two cell lines.`, placement: 'centered', - preAction: TourUtils.waitForSelector, - postAction: TourUtils.clickSelector, + preAction: () => TourUtils.waitFor('[data-testid="viewWrapper-2"] select').then(() => TourUtils.wait(1000)), }, { html: `

      Thanks for joining this tour demonstrating the assessment of breast cancer cell lines.

      From cbfdd78f265fb1626d98a1752af08a3a9e1b11f8 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Fri, 2 Sep 2022 13:17:39 +0200 Subject: [PATCH 23/38] Prep PredictionTP53Tour and slight refactoring --- src/phovea.ts | 23 +- ...CCellLines.ts => AssessBCCellLinesTour.ts} | 4 +- src/tours/PredictionTP53Tour.ts | 459 ++++++++++++++++++ src/tours/index.ts | 3 +- src/tours/tempNew.tempNew | 56 --- 5 files changed, 484 insertions(+), 61 deletions(-) rename src/tours/{AssessBCCellLines.ts => AssessBCCellLinesTour.ts} (99%) create mode 100644 src/tours/PredictionTP53Tour.ts delete mode 100644 src/tours/tempNew.tempNew diff --git a/src/phovea.ts b/src/phovea.ts index 37ace83e..1465d36f 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1061,9 +1061,9 @@ export default function (registry) { registry.push( 'tdpTour', - 'ordinoAssessBCCellLines', + 'ordinoAssessBCCellLinesTour', function () { - return import('./tours').then((t) => t.AssessBCCellLines); + return import('./tours').then((t) => t.AssessBCCellLinesTour); }, { factory: 'createTour', @@ -1077,6 +1077,25 @@ export default function (registry) { canJumpAround: false, }, ); + + registry.push( + 'tdpTour', + 'ordinoPredictionTP53Tour', + function () { + return import('./tours').then((t) => t.PredictionTP53Tour); + }, + { + factory: 'createTour', + name: 'Something about TP53 Mutation', + description: 'Add description here.', + preview() { + return import('./assets/previews/expression.jpg'); // TODO update preview image + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }, + ); /// #endif registry.push( diff --git a/src/tours/AssessBCCellLines.ts b/src/tours/AssessBCCellLinesTour.ts similarity index 99% rename from src/tours/AssessBCCellLines.ts rename to src/tours/AssessBCCellLinesTour.ts index 69d3a31d..555d5d39 100644 --- a/src/tours/AssessBCCellLines.ts +++ b/src/tours/AssessBCCellLinesTour.ts @@ -1,7 +1,7 @@ // import {ToursSection} from 'ordino'; import { IStep, Tour, TourUtils } from 'tdp_core'; -export class AssessBCCellLines { +export class AssessBCCellLinesTour { static createTour(): IStep[] { return [ { @@ -57,7 +57,7 @@ export class AssessBCCellLines { selector: '.le.le-multi.lineup-engine', placement: 'centered', html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, - preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(600)), + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), }, { selector: '.lu-side-panel-wrapper .lu-adder > button', diff --git a/src/tours/PredictionTP53Tour.ts b/src/tours/PredictionTP53Tour.ts new file mode 100644 index 00000000..3cd40e88 --- /dev/null +++ b/src/tours/PredictionTP53Tour.ts @@ -0,0 +1,459 @@ +// import {ToursSection} from 'ordino'; +import { IStep, Tour, TourUtils } from 'tdp_core'; + +export class PredictionTP53Tour { + static createTour(): IStep[] { + return [ + { + html: `

      Welcome to this short tour showing the assessment of breast cancer cell lines!

      +

      This tour will follow an analysis session from the perspective of a drug discovery team at a pharmaceutical company.

      +

      + Use the "Next" button to iterate through all the steps. You can use the + "Cancel" button at any time to stop the tour and to interact with Ordino. + Please note that the tour will load a new analysis session and the current + one will be discarded. +

      `, + }, + { + selector: 'ul[data-header="mainMenu"] > li:first-child > a', + html: `To start the analysis, the team clicks on the 'Datasets' tab.`, + placement: 'centered', + preAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.add('hover'); + } + }, + postAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.remove('hover'); + datasetTab.querySelector('a').click(); + } + return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(3)')); + }, + pageBreak: 'manual', + }, + { + selector: '.le.le-multi.lineup-engine', + html: `TOUR IS HERE SO FAR`, + placement: 'centered', + }, + { + selector: '.ordino-dataset.genes-dataset > .card', + html: `

      Here they choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

      +

      In this example they choose to work with a list of genes.

      `, + placement: 'centered', + preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), + postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), + }, + { + selector: '[data-testid="normal-chromosome-protein-coding-human-genes-button"]', + html: `The scientists start by loading the list of all protein coding genes for humans.`, + placement: 'centered', + postAction: () => { + return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: normal chromosome protein coding human genes"]').then( + TourUtils.click, + ); + }, + pageBreak: 'manual', + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(600)), + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `They begin by adding an additional column, done so by clicking on the plus icon shown here.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + html: `They choose to add a column for a single cell line score.`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), + html: `Now they select the cell line 'HCC1954' …`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `… and the data type as 'Relative Copy Number' …`, + postAction: () => { + TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le [data-col-id="col8"] .lu-action-sort', + placement: 'centered', + html: `They want to sort by this newly added column, so they click on the sort button in the column header.`, + preAction: () => TourUtils.waitFor('.le [data-col-id="col8"] .lu-action-sort'), + postAction: () => { + TourUtils.click('.le [data-col-id="col8"] .lu-action-sort'); + }, + }, + { + selector: ['[data-index="0"].le-tr, [data-index="14"].le-tr'], + placement: 'centered', + html: `After sorting by this column, the analyst observes that about 15 genes on chromosome 17 are affected by a large genomic amplification.`, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `

      In order to identify the most relevant of these genes, the analyst adds a column with the Normalized Gene Expression (a measure of activity) for cell line HCC1954

      +

      Individual steps for adding a column have been skipped this time.

      `, + placement: 'centered', + postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(() => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'expression-tpm', 'change'); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `They also add a column with a Gene Sensitivity Score (a measure of importance for cell survival) for HCC1954.`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le header [data-col-id="col9"]').then(() => TourUtils.wait(500)), + postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + }, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span', + html: `

      To do so, they select to add a 'Depletion Screen Score (Single)' column.

      +

      Similarly, the specific steps for adding a column have been skipped this time.

      `, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(() => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'depletion-rsa', 'change'); + TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); + }, + }, + { + selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', + html: `

      In an effort to improve the depletion score's readability, they decide to invert the linear scaling.

      +

      To do this, they click on the three dots for more column options.

      `, + placement: 'centered', + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-action-data-mapping > span', + html: `They now click on 'Data Mapping'.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: ['.browser-default, .lu-dialog-buttons > [type="submit"]'], + html: `They select the 'Invert' option in the Normalization Scaling dropdown and then click on the tick at the bottom right to apply the new mapping.`, + placement: 'centered', + postAction: () => { + TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); + TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + }, + }, + { + selector: '[data-index="0"]', + placement: 'centered', + html: `Observe: Of the highly amplified genes, they notice that ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, + }, + { + selector: ['.le header [data-col-id="col9"], .le header [data-col-id="col10"]'], + html: `

      They can combine both score columns by dragging them together to obtain stacked bars.

      +

      Observe: Combining the columns highlights the importance of ERBB2.

      +

      It is therefore probably the most relevant gene within this amplified genomic region.

      `, + placement: 'centered', + }, + { + selector: '[data-index="0"]', + html: `

      This finding leads the scientist to the question whether ERBB2 is also highly expressed and frequently amplified in other breast cancer cell lines.

      +

      To investigate this, the analyst adds the following columns: +

        +
      • A column with the average gene expression for breast cancer cell lines
        • +
      • A column with the gene copy number distribution for breast cancer cell lines in boxplot format
        • +
      • A column with the gene amplification frequency (>4) across all breast cancer cell lines
        • +
      +

      `, + placement: 'centered', + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `1. A column with the average gene expression for breast cancer cell lines`, + placement: 'centered', + postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger( + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + 'breast carcinoma', + 'change', + ); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); + TourUtils.wait(1000).then(() => { + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); + }); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `2. A column with the gene copy number distribution for breast cancer cell lines in boxplot format`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le header [data-col-id="col11"]'), + postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger( + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + 'breast carcinoma', + 'change', + ); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'boxplot', 'change'); + TourUtils.wait(1000).then(() => { + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); + }); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `3. A column with the gene amplification frequency (>4) across all breast cancer cell lines`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le header [data-col-id="col12"]'), + postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + TourUtils.setValueAndTrigger( + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + 'breast carcinoma', + 'change', + ); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'frequency', 'change'); + TourUtils.waitFor('.show [data-testid="Comparison Operator"]').then(() => { + TourUtils.setValueAndTrigger('.show [data-testid="comparison-operator"] select', '>', 'change'); + TourUtils.setValueAndTrigger('.show [type="number"]', '4', 'input'); + }); + TourUtils.wait(1000).then(() => { + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); + }); + }, + }, + { + selector: '.le.le-multi.lineup-engine', + html: `Observe: They notice that ERBB2 is amplified in almost 25% of all assessed breast cancer cell lines. Further, it is highly expressed.`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le header [data-col-id="col13"]'), + }, + { + selector: '[data-index="0"] .lu-renderer-selection', + html: `

      The aim is now to get more information about ERBB2.

      +

      They select ERBB2 in the list.

      `, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-viewid="celllinedb_expression_vs_copynumber"]', + html: `They open the Expression vs Copy Number detail view.`, + placement: 'centered', + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, + }, + { + selector: '.ids', + html: `Here they observe the direct correlation between copy number and expression of ERBB2.`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.ids').then(() => TourUtils.wait(300)), + }, + { + selector: '[data-viewid="targetvalidation"]', + html: `To find more information, they open the 'Open Targets' detail view …`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-viewid="pubmed"]', + html: `… and then the 'PubMed' detail view.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '', + html: `Their question is now: In what cell lines is ERBB2 amplified?`, + placement: 'centered', + }, + { + selector: '[data-viewid="copynumbertable"]', + html: `They continue by opening the Copy Number detail view …`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-id="col7"] .lu-action-sort', + html: `… and then sorting by the copy number.`, + placement: 'centered', + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid="viewWrapper-1"] [data-id="col4"] .lu-action-filter', + html: `They want to filter for breast cancer via the column menu of column 'Tumor Type', while also filtering out cell lines with unknown tumor types.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-dialog .lu-dialog-table', + html: `First they select only the "breast carcinoma" tumor type.`, + placement: 'centered', + postAction: () => { + TourUtils.wait(100) + .then(() => { + TourUtils.click('.lu-dialog-table .lu-checkbox:first-child'); + }) + .then(() => { + TourUtils.wait(500).then(() => { + TourUtils.click('input[type="checkbox"][data-cat="breast carcinoma"]'); + }); + }); + }, + }, + { + selector: ['.lu-dialog .lu-dialog-table, .lu-dialog-button[title="Apply"]'], + html: `Then they filter out cell lines with unknown types (the missing value rows) and submit the filter.`, + placement: 'centered', + postAction: () => { + TourUtils.wait(100) + .then(() => { + TourUtils.click('.lu-dialog > .lu-checkbox input'); + }) + .then(() => { + TourUtils.wait(500).then(() => { + TourUtils.click('.lu-dialog-button[type="submit"]'); + }); + }); + }, + }, + { + selector: '[data-testid="viewWrapper-1"] .lu-side-panel-wrapper .lu-adder > button', + html: `They now want to add the BRCA gene score columns.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid="viewWrapper-1"] [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + html: `Once again, they use the plus icon to add a new column.`, + placement: 'centered', + postAction: () => { + TourUtils.click( + '[data-testid="viewWrapper-1"] [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + ); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), + html: `Here they select the BRCA1 and BRCA2 cell lines …`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'BRCA1;', 'input'); + TourUtils.wait(400).then(() => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'BRCA2;', 'input'); + }); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `… and then they set the data type to AA Mutated …`, + postAction: () => { + TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: ['[data-testid="viewWrapper-1"] [data-index="0"].le-tr, [data-testid="viewWrapper-1"] [data-index="2"].le-tr'], + html: `

      Observe:

      +

      HCC1954 has the highest ERBB2 amplification among BRCA1 mutated cell lines.

      +

      HCC1569 has the highest ERBB2 amplification among BRCA2 mutated cell lines.

      `, + placement: 'centered', + preAction: () => TourUtils.waitFor('[data-testid="viewWrapper-1"] .le header [data-col-id="col8"]'), + }, + { + selector: '', + html: `Finally, their aim is to find information provided by COSMIC about these two cell lines.`, + placement: 'centered', + }, + { + selector: ['[data-testid="viewWrapper-1"] [data-index="0"].le-tr, [data-testid="viewWrapper-1"] [data-index="2"].le-tr'], + html: `They select HCC1954 and HCC1569 …`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid="viewWrapper-1"] [data-index="0"] .lu-renderer-selection'); + TourUtils.click('[data-testid="viewWrapper-1"] [data-index="2"] .lu-renderer-selection'); + }, + }, + { + selector: '[data-testid="viewWrapper-1"] [data-viewid="cosmic"]', + html: `… and open the COSMIC detail view.`, + placement: 'centered', + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid="viewWrapper-2"] select', + html: `Here they can use the drop-down menu to switch between the two cell lines.`, + placement: 'centered', + preAction: () => TourUtils.waitFor('[data-testid="viewWrapper-2"] select').then(() => TourUtils.wait(1000)), + }, + { + html: `

      Thanks for joining this tour demonstrating the assessment of breast cancer cell lines.

      +

      There are still many more features to discover. Enjoy!

      `, + }, + ]; + } +} diff --git a/src/tours/index.ts b/src/tours/index.ts index 7d9d1f5d..a0d72ccf 100644 --- a/src/tours/index.ts +++ b/src/tours/index.ts @@ -1,4 +1,5 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; -export * from './AssessBCCellLines'; +export * from './AssessBCCellLinesTour'; +export * from './PredictionTP53Tour'; diff --git a/src/tours/tempNew.tempNew b/src/tours/tempNew.tempNew deleted file mode 100644 index 7837a792..00000000 --- a/src/tours/tempNew.tempNew +++ /dev/null @@ -1,56 +0,0 @@ -{ - html: `

      Welcome to this short tour showing the assessment of breast cancer cell lines!

      -

      - Use the "Next" button to iterate through all the steps. You can use the - "Cancel" button at any time to stop the tour and to interact with Ordino. - Please note that the tour will load a new analysis session and the current - one will be discarded. -

      `, - }, - { - selector: 'ul[data-header="mainMenu"] > li:first-child > a', - html: `Go to Datasets Tab`, - placement: 'centered', - preAction: () => { - const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; - if (!datasetTab.classList.contains('active')) { - datasetTab.querySelector('a').classList.add('hover'); - } - }, - postAction: () => { - const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; - if (!datasetTab.classList.contains('active')) { - datasetTab.querySelector('a').classList.remove('hover'); - datasetTab.querySelector('a').click(); - } - return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(3)')); - }, - }, - { - selector: '.ordino-dataset.genes-dataset > .card', - html: `Click on Genes > Human > Normal-chromosome-...`, - placement: 'centered', - preAction: () => { - TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)); - }, - postAction: () => { - TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'); - TourUtils.click('[data-testid=normal-chromosome-protein-coding-human-genes-button]'); - }, - pageBreak: 'manual', - }, - { - selector: '[data-testid=add-column-button]', - html: `Add a column`, - placement: 'centered', - preAction: () => { - TourUtils.waitFor('[data-testid=add-column-button]', Infinity); - }, - postAction: () => { - TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: Cancer Gene Census"]').then(TourUtils.click); - }, - }, - { - html: `

      Thanks for joining this tour demonstrating the basic features of Ordino.

      -

      There are many more features to discover. Enjoy!

      `, - }, \ No newline at end of file From 9efaeffcad0f502901dca37ec9cb57c24eecc8c9 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 5 Sep 2022 13:16:22 +0200 Subject: [PATCH 24/38] Updated Tour2 --- src/tours/PredictionTP53Tour.ts | 46 ++++++++++++++++++++++++++++----- 1 file changed, 40 insertions(+), 6 deletions(-) diff --git a/src/tours/PredictionTP53Tour.ts b/src/tours/PredictionTP53Tour.ts index 3cd40e88..f866b97a 100644 --- a/src/tours/PredictionTP53Tour.ts +++ b/src/tours/PredictionTP53Tour.ts @@ -34,19 +34,53 @@ export class PredictionTP53Tour { }, pageBreak: 'manual', }, - { - selector: '.le.le-multi.lineup-engine', - html: `TOUR IS HERE SO FAR`, - placement: 'centered', - }, { selector: '.ordino-dataset.genes-dataset > .card', html: `

      Here they choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

      -

      In this example they choose to work with a list of genes.

      `, +

      In this example they choose to work with a list of 13 specific genes.

      `, placement: 'centered', preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), }, + { + selector: '.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox', + html: `

      12To create a set with these specific genes, they add each gene into the highlighted field.

      `, + placement: 'centered', + postAction: () => { + // TourUtils.click('.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox input'); + // TourUtils.setValueAndTrigger('.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox input', 'AEN;', 'input'); + // TourUtils.keyDownEnter('.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox input'); + }, + }, + { + selector: '.ordino-dataset.genes-dataset .show [data-testid="save-button"]', + html: `Once the genes have been added, they choose to save these genes as a custom set.`, + placement: 'centered', + postAction: () => TourUtils.clickSelector, + }, + { + selector: '.ordino-dataset.tissue-dataset', + html: `Next they aim to test the applicability of gene signature using TCGA tumor samples.`, + placement: 'centered', + }, + { + selector: '.ordino-dataset.tissue-dataset [data-testid="tcga-tumors-button"]', + html: `They start by opening a list of all TCGA tumors.`, + placement: 'centered', + postAction: () => TourUtils.clickSelector, + pageBreak: 'manual', + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `///The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), + }, + { + selector: '', + html: `THE TOUR IS HERE SO FAR`, + placement: 'centered', + }, { selector: '[data-testid="normal-chromosome-protein-coding-human-genes-button"]', html: `The scientists start by loading the list of all protein coding genes for humans.`, From d4184c1f71a4f1988f4ae22487858da565287a18 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 5 Sep 2022 13:55:17 +0200 Subject: [PATCH 25/38] Updated Tour2 --- src/tours/PredictionTP53Tour.ts | 409 +------------------------------- 1 file changed, 4 insertions(+), 405 deletions(-) diff --git a/src/tours/PredictionTP53Tour.ts b/src/tours/PredictionTP53Tour.ts index f866b97a..3a2506b9 100644 --- a/src/tours/PredictionTP53Tour.ts +++ b/src/tours/PredictionTP53Tour.ts @@ -70,423 +70,22 @@ export class PredictionTP53Tour { postAction: () => TourUtils.clickSelector, pageBreak: 'manual', }, - { - selector: '.le.le-multi.lineup-engine', - placement: 'centered', - html: `///The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, - preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), - }, - { - selector: '', - html: `THE TOUR IS HERE SO FAR`, - placement: 'centered', - }, - { - selector: '[data-testid="normal-chromosome-protein-coding-human-genes-button"]', - html: `The scientists start by loading the list of all protein coding genes for humans.`, - placement: 'centered', - postAction: () => { - return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: normal chromosome protein coding human genes"]').then( - TourUtils.click, - ); - }, - pageBreak: 'manual', - }, { selector: '.le.le-multi.lineup-engine', placement: 'centered', html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, - preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(600)), - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `They begin by adding an additional column, done so by clicking on the plus icon shown here.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', - html: `They choose to add a column for a single cell line score.`, - placement: 'centered', - postAction: () => { - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - }, - }, - { - selector: '.modal.show .col > .select3', - placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), - html: `Now they select the cell line 'HCC1954' …`, - postAction: () => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); - }, - }, - { - selector: '.modal.show .col > .select2', - placement: 'centered', - html: `… and the data type as 'Relative Copy Number' …`, - postAction: () => { - TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); - }, - }, - { - selector: '.modal.show .modal-footer button[type=submit]', - html: `… and click 'Add'.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '.le [data-col-id="col8"] .lu-action-sort', - placement: 'centered', - html: `They want to sort by this newly added column, so they click on the sort button in the column header.`, - preAction: () => TourUtils.waitFor('.le [data-col-id="col8"] .lu-action-sort'), - postAction: () => { - TourUtils.click('.le [data-col-id="col8"] .lu-action-sort'); - }, - }, - { - selector: ['[data-index="0"].le-tr, [data-index="14"].le-tr'], - placement: 'centered', - html: `After sorting by this column, the analyst observes that about 15 genes on chromosome 17 are affected by a large genomic amplification.`, - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `

      In order to identify the most relevant of these genes, the analyst adds a column with the Normalized Gene Expression (a measure of activity) for cell line HCC1954

      -

      Individual steps for adding a column have been skipped this time.

      `, - placement: 'centered', - postAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.modal.show').then(() => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); - TourUtils.setValueAndTrigger('.show .col > select', 'expression-tpm', 'change'); - TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); - }); - }, - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `They also add a column with a Gene Sensitivity Score (a measure of importance for cell survival) for HCC1954.`, - placement: 'centered', - preAction: () => TourUtils.waitFor('.le header [data-col-id="col9"]').then(() => TourUtils.wait(500)), - postAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - }, - }, - { - selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span', - html: `

      To do so, they select to add a 'Depletion Screen Score (Single)' column.

      -

      Similarly, the specific steps for adding a column have been skipped this time.

      `, - placement: 'centered', - postAction: () => { - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.modal.show').then(() => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); - TourUtils.setValueAndTrigger('.show .col > select', 'depletion-rsa', 'change'); - TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); - }); - }, - }, - { - selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', - html: `

      In an effort to improve the depletion score's readability, they decide to invert the linear scaling.

      -

      To do this, they click on the three dots for more column options.

      `, - placement: 'centered', - preAction: TourUtils.waitForSelector, - postAction: TourUtils.clickSelector, - }, - { - selector: '.lu-action-data-mapping > span', - html: `They now click on 'Data Mapping'.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: ['.browser-default, .lu-dialog-buttons > [type="submit"]'], - html: `They select the 'Invert' option in the Normalization Scaling dropdown and then click on the tick at the bottom right to apply the new mapping.`, - placement: 'centered', - postAction: () => { - TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); - TourUtils.click('.lu-dialog-buttons > [type="submit"]'); - }, - }, - { - selector: '[data-index="0"]', - placement: 'centered', - html: `Observe: Of the highly amplified genes, they notice that ERBB2 (HER2) has the highest expression and the lowest sensitivity score. Therefore, it is probably the most relevant gene of this amplicon.`, - }, - { - selector: ['.le header [data-col-id="col9"], .le header [data-col-id="col10"]'], - html: `

      They can combine both score columns by dragging them together to obtain stacked bars.

      -

      Observe: Combining the columns highlights the importance of ERBB2.

      -

      It is therefore probably the most relevant gene within this amplified genomic region.

      `, - placement: 'centered', - }, - { - selector: '[data-index="0"]', - html: `

      This finding leads the scientist to the question whether ERBB2 is also highly expressed and frequently amplified in other breast cancer cell lines.

      -

      To investigate this, the analyst adds the following columns: -

        -
      • A column with the average gene expression for breast cancer cell lines
        • -
      • A column with the gene copy number distribution for breast cancer cell lines in boxplot format
        • -
      • A column with the gene amplification frequency (>4) across all breast cancer cell lines
        • -
      -

      `, - placement: 'centered', - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `1. A column with the average gene expression for breast cancer cell lines`, - placement: 'centered', - postAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { - TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); - TourUtils.setValueAndTrigger( - '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', - 'breast carcinoma', - 'change', - ); - TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); - TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); - TourUtils.wait(1000).then(() => { - TourUtils.click('.modal.show .modal-footer button[type=submit]'); - }); - }); - }, - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `2. A column with the gene copy number distribution for breast cancer cell lines in boxplot format`, - placement: 'centered', - preAction: () => TourUtils.waitFor('.le header [data-col-id="col11"]'), - postAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { - TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); - TourUtils.setValueAndTrigger( - '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', - 'breast carcinoma', - 'change', - ); - TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); - TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'boxplot', 'change'); - TourUtils.wait(1000).then(() => { - TourUtils.click('.modal.show .modal-footer button[type=submit]'); - }); - }); - }, - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `3. A column with the gene amplification frequency (>4) across all breast cancer cell lines`, - placement: 'centered', - preAction: () => TourUtils.waitFor('.le header [data-col-id="col12"]'), - postAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { - TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); - TourUtils.setValueAndTrigger( - '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', - 'breast carcinoma', - 'change', - ); - TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'copy_number-relativecopynumber', 'change'); - TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'frequency', 'change'); - TourUtils.waitFor('.show [data-testid="Comparison Operator"]').then(() => { - TourUtils.setValueAndTrigger('.show [data-testid="comparison-operator"] select', '>', 'change'); - TourUtils.setValueAndTrigger('.show [type="number"]', '4', 'input'); - }); - TourUtils.wait(1000).then(() => { - TourUtils.click('.modal.show .modal-footer button[type=submit]'); - }); - }); - }, + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), }, { selector: '.le.le-multi.lineup-engine', - html: `Observe: They notice that ERBB2 is amplified in almost 25% of all assessed breast cancer cell lines. Further, it is highly expressed.`, - placement: 'centered', - preAction: () => TourUtils.waitFor('.le header [data-col-id="col13"]'), - }, - { - selector: '[data-index="0"] .lu-renderer-selection', - html: `

      The aim is now to get more information about ERBB2.

      -

      They select ERBB2 in the list.

      `, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '[data-viewid="celllinedb_expression_vs_copynumber"]', - html: `They open the Expression vs Copy Number detail view.`, - placement: 'centered', - preAction: TourUtils.waitForSelector, - postAction: TourUtils.clickSelector, - }, - { - selector: '.ids', - html: `Here they observe the direct correlation between copy number and expression of ERBB2.`, - placement: 'centered', - preAction: () => TourUtils.waitFor('.ids').then(() => TourUtils.wait(300)), - }, - { - selector: '[data-viewid="targetvalidation"]', - html: `To find more information, they open the 'Open Targets' detail view …`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '[data-viewid="pubmed"]', - html: `… and then the 'PubMed' detail view.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '', - html: `Their question is now: In what cell lines is ERBB2 amplified?`, - placement: 'centered', - }, - { - selector: '[data-viewid="copynumbertable"]', - html: `They continue by opening the Copy Number detail view …`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '[data-id="col7"] .lu-action-sort', - html: `… and then sorting by the copy number.`, - placement: 'centered', - preAction: TourUtils.waitForSelector, - postAction: TourUtils.clickSelector, - }, - { - selector: '[data-testid="viewWrapper-1"] [data-id="col4"] .lu-action-filter', - html: `They want to filter for breast cancer via the column menu of column 'Tumor Type', while also filtering out cell lines with unknown tumor types.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '.lu-dialog .lu-dialog-table', - html: `First they select only the "breast carcinoma" tumor type.`, - placement: 'centered', - postAction: () => { - TourUtils.wait(100) - .then(() => { - TourUtils.click('.lu-dialog-table .lu-checkbox:first-child'); - }) - .then(() => { - TourUtils.wait(500).then(() => { - TourUtils.click('input[type="checkbox"][data-cat="breast carcinoma"]'); - }); - }); - }, - }, - { - selector: ['.lu-dialog .lu-dialog-table, .lu-dialog-button[title="Apply"]'], - html: `Then they filter out cell lines with unknown types (the missing value rows) and submit the filter.`, - placement: 'centered', - postAction: () => { - TourUtils.wait(100) - .then(() => { - TourUtils.click('.lu-dialog > .lu-checkbox input'); - }) - .then(() => { - TourUtils.wait(500).then(() => { - TourUtils.click('.lu-dialog-button[type="submit"]'); - }); - }); - }, - }, - { - selector: '[data-testid="viewWrapper-1"] .lu-side-panel-wrapper .lu-adder > button', - html: `They now want to add the BRCA gene score columns.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: '[data-testid="viewWrapper-1"] [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', - html: `Once again, they use the plus icon to add a new column.`, - placement: 'centered', - postAction: () => { - TourUtils.click( - '[data-testid="viewWrapper-1"] [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', - ); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - }, - }, - { - selector: '.modal.show .col > .select3', - placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), - html: `Here they select the BRCA1 and BRCA2 cell lines …`, - postAction: () => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'BRCA1;', 'input'); - TourUtils.wait(400).then(() => { - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'BRCA2;', 'input'); - }); - }, - }, - { - selector: '.modal.show .col > .select2', - placement: 'centered', - html: `… and then they set the data type to AA Mutated …`, - postAction: () => { - TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'change'); - }, - }, - { - selector: '.modal.show .modal-footer button[type=submit]', - html: `… and click 'Add'.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - }, - { - selector: ['[data-testid="viewWrapper-1"] [data-index="0"].le-tr, [data-testid="viewWrapper-1"] [data-index="2"].le-tr'], - html: `

      Observe:

      -

      HCC1954 has the highest ERBB2 amplification among BRCA1 mutated cell lines.

      -

      HCC1569 has the highest ERBB2 amplification among BRCA2 mutated cell lines.

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('[data-testid="viewWrapper-1"] .le header [data-col-id="col8"]'), + html: `///The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), }, { selector: '', - html: `Finally, their aim is to find information provided by COSMIC about these two cell lines.`, - placement: 'centered', - }, - { - selector: ['[data-testid="viewWrapper-1"] [data-index="0"].le-tr, [data-testid="viewWrapper-1"] [data-index="2"].le-tr'], - html: `They select HCC1954 and HCC1569 …`, - placement: 'centered', - postAction: () => { - TourUtils.click('[data-testid="viewWrapper-1"] [data-index="0"] .lu-renderer-selection'); - TourUtils.click('[data-testid="viewWrapper-1"] [data-index="2"] .lu-renderer-selection'); - }, - }, - { - selector: '[data-testid="viewWrapper-1"] [data-viewid="cosmic"]', - html: `… and open the COSMIC detail view.`, - placement: 'centered', - preAction: TourUtils.waitForSelector, - postAction: TourUtils.clickSelector, - }, - { - selector: '[data-testid="viewWrapper-2"] select', - html: `Here they can use the drop-down menu to switch between the two cell lines.`, + html: `THE TOUR IS HERE SO FAR`, placement: 'centered', - preAction: () => TourUtils.waitFor('[data-testid="viewWrapper-2"] select').then(() => TourUtils.wait(1000)), - }, - { - html: `

      Thanks for joining this tour demonstrating the assessment of breast cancer cell lines.

      -

      There are still many more features to discover. Enjoy!

      `, }, ]; } From 01a3229137fe798b0b61ea221248a74da5d4d3cf Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Tue, 27 Sep 2022 10:13:49 +0200 Subject: [PATCH 26/38] Nearly complete DrugTargetDiscoveryTour --- src/phovea.ts | 6 +- src/tours/DrugTargetDiscoveryTour.ts | 395 +++++++++++++++++++++++++++ src/tours/index.ts | 2 +- 3 files changed, 399 insertions(+), 4 deletions(-) create mode 100644 src/tours/DrugTargetDiscoveryTour.ts diff --git a/src/phovea.ts b/src/phovea.ts index 1465d36f..de89c630 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1080,13 +1080,13 @@ export default function (registry) { registry.push( 'tdpTour', - 'ordinoPredictionTP53Tour', + 'ordinoDrugTargetDiscoveryTour', function () { - return import('./tours').then((t) => t.PredictionTP53Tour); + return import('./tours').then((t) => t.DrugTargetDiscoveryTour); }, { factory: 'createTour', - name: 'Something about TP53 Mutation', + name: '???Drug Target Discovery', description: 'Add description here.', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image diff --git a/src/tours/DrugTargetDiscoveryTour.ts b/src/tours/DrugTargetDiscoveryTour.ts new file mode 100644 index 00000000..58f62a8a --- /dev/null +++ b/src/tours/DrugTargetDiscoveryTour.ts @@ -0,0 +1,395 @@ +// import {ToursSection} from 'ordino'; +import { IStep, Tour, TourManager, TourUtils } from 'tdp_core'; + +export class DrugTargetDiscoveryTour { + static createTour(): IStep[] { + return [ + { + html: `

      Welcome to this short tour showing the assessment of breast cancer cell lines!

      +

      This tour will follow an analysis session from the perspective of a drug discovery team at a pharmaceutical company.

      +

      + Use the "Next" button to iterate through all the steps. You can use the + "Cancel" button at any time to stop the tour and to interact with Ordino. + Please note that the tour will load a new analysis session and the current + one will be discarded. +

      `, + }, + { + selector: 'ul[data-header="mainMenu"] > li:first-child > a', + html: `To start the analysis, the team clicks on the 'Datasets' tab.`, + placement: 'centered', + preAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.add('hover'); + } + }, + postAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.remove('hover'); + datasetTab.querySelector('a').click(); + } + return TourUtils.waitFor('.ordino-dataset.cellline-dataset').then(() => + TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(1)'), + ); + }, + pageBreak: 'manual', + }, + { + selector: '.ordino-dataset.cellline-dataset > .card [data-testid="ccle-button"]', + html: `The analyst begins by loading a list of 1009 cell lines from the public CCLE dataset.`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.ordino-dataset.cellline-dataset > .card [data-testid="ccle-button"]').then(() => TourUtils.wait(600)), + postAction: TourUtils.clickSelector, + pageBreak: 'manual', + }, + { + selector: '.le.le-multi.lineup-engine', + placement: 'centered', + html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), + }, + { + selector: '[data-id="col4"] .lu-action-filter', + placement: 'centered', + html: `Since only a subset of tumor types is of interest, the analyst decides to filter the data.`, + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-dialog .lu-dialog-table', + html: `Here they select only the following filters: astrocytoma/glioblastoma (type of cancer of the brain), bone sarcoma, melanoma, and non-small-cell lung cancer (NSCLC).`, + placement: 'centered', + postAction: () => { + TourUtils.wait(100) + .then(() => { + TourUtils.click('.lu-dialog-table .lu-checkbox:first-child'); + }) + .then(() => { + TourUtils.wait(500).then(() => { + TourUtils.click('input[type="checkbox"][data-cat="astrocytoma/glioblastoma"]'); + TourUtils.click('input[type="checkbox"][data-cat="bone sarcoma"]'); + TourUtils.click('input[type="checkbox"][data-cat="melanoma"]'); + TourUtils.click('input[type="checkbox"][data-cat="NSCLC"]'); + TourUtils.click('.lu-dialog > .lu-checkbox input'); + }); + }); + }, + }, + { + selector: ['.lu-dialog .lu-dialog-table, .lu-dialog-button[title="Apply"]'], + html: `They now apply the filter, after which only 255 cell lines remain.`, + placement: 'centered', + postAction: () => { + TourUtils.click('.lu-dialog-button[type="submit"]'); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `As the analyst wants to investigate the TP53 gene, he decides to add a categorical column with the mutation status (mutated vs non mutated).`, + placement: 'centered', + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + html: `They do this by adding a column for a single cell line score.`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: '.modal.show .col > .select3', + placement: 'centered', + preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), + html: `Now they select the cell line 'TP53' …`, + postAction: () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); + }, + }, + { + selector: '.modal.show .col > .select2', + placement: 'centered', + html: `… and the data type as 'AA Mutated' …`, + postAction: () => { + TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and click 'Add'.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `

      Additionally, they decide to add a textual column that provides further details about the mutation (if present).

      +

      This is done by repeating the same steps to add a column, but choosing "AA Mutation" as the data type this time instead.

      +

      Individual steps for adding a column have been skipped this time.

      `, + placement: 'centered', + postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(() => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aamutation', 'change'); + TourUtils.wait(2000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `To investigate the effectiveness of the 13 genes in predicting the TP53 status, the analyst loads the average expression of these genes together with a matrix column containing the individual expression values.`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le [data-col-id="col8"]').then(() => TourUtils.wait(600)), + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `They begin by adding a new column.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span', + html: `Firstly the column with the average expression is added. This is done by adding a 'Gene Score (Aggregated)' column`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + }, + }, + { + selector: [ + '.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select, .show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + ], + html: `They select 'My Named Sets' in the drop down and then enter 'TP53 Predictor' as the specific set …`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select'), + postAction: () => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'namedset4ensg', 'change'); + TourUtils.wait(1500).then(() => { + TourUtils.setValueAndTrigger( + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + '0Qd2E6S4R9', + 'change', + ); + }); + }, + }, + { + selector: '.show .modal-body form > .col-sm-12:nth-child(2) select', + html: `… then set the 'Data Type' to 'Normalized Gene Expression (TPM Values)' …`, + placement: 'centered', + postAction: () => { + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + }, + }, + { + selector: '.show [data-testid="aggregation"] select', + html: `… and set the 'Aggregation' to 'Average' …`, + placement: 'centered', + postAction: () => { + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); + }, + }, + { + selector: '.modal.show .modal-footer button[type=submit]', + html: `… and finally click 'Add'.`, + placement: 'centered', + postAction: () => { + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `Similarly, they add a matrix column with all of the individual expression values.`, + placement: 'centered', + postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'namedset4ensg', 'change'); + TourUtils.setValueAndTrigger( + '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', + '0Qd2E6S4R9', + 'change', + ); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'numbers', 'change'); + TourUtils.wait(1000).then(() => { + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); + }); + }, + }, + { + selector: '[data-id="col7"] .lu-action-filter', + html: `Furthermore, they decide to hide all cell lines with unknown mutation status.`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-id="col7"] .lu-action-filter'); + TourUtils.waitFor('.lu-dialog > .lu-checkbox input').then(() => { + TourUtils.click('.lu-dialog > .lu-checkbox input'); + TourUtils.click('.lu-dialog-button[type="submit"]'); + }); + }, + }, + { + selector: '.le [data-col-id="col9"] .lu-action-sort', + html: `Next, they sort the list in descending order based on the average gene expression column that was added …`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[data-testid="en/disable-overview-button"]', + html: `… and then swap to the overview.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le.le-multi.lineup-engine', + html: `Looking at the overview, the analyst observes the overall good correlation between expression and mutation status: there is a clear enrichment of TP53 mutants among the cell lines with a low score.`, + placement: 'centered', + }, + { + selector: '.le [data-col-id="col4"] .lu-action-group', + html: `In order to test whether the correlation is present for all selected tumor types, the analyst groups the table by tumor type.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le.le-multi.lineup-engine', + html: `They observe that the prediction seems to work particularly well for the astrocytoma/glioblastoma cell lines (almost perfect separation between mutated and non mutated).`, + placement: 'centered', + }, + { + selector: '.le [data-col-id="col7"] .lu-action-more', + html: `They further investigate this observation by also stratifying by mutation status and aggregating all groups.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-dialog.lu-more-options .lu-action-group', + html: `To do so, they click 'Group By' …`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-dialog input[value="true"]', + html: `… then select 'Enabled' …`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.lu-dialog-buttons > [type="submit"]', + html: `… and then hit apply.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '[title="Collapse All Groups"]:nth-child(2)', + html: `Lastly, they aggregate all of the groups.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le.le-multi.lineup-engine', + html: `

      The expression box plots show good separation for astrocytoma/glioblastoma and melanoma, whereas the expression ranges are overlapping for NSCLC.

      +

      Having confirmed that the prediction of the TP53 mutation status works reasonably well in several tumor types, the analyst wants to select a set of cell lines for a wet-lab experiment. He is interested in melanoma cell lines that have no TP53 mutation. Furthermore, the activity of CDKN2A, another important tumor suppressor gene, should be impaired due to a reduced number of CDKN2A gene copies in the genome.

      `, + placement: 'centered', + }, + { + selector: '.le [data-col-id="col7"] .lu-action-group', + html: `The analyst now removes the mutation status grouping, …`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le [data-col-id="col7"] .lu-action-filter', + html: `… includes cell lines for which it is unclear whether TP53 is mutated, …`, + placement: 'centered', + postAction: () => { + TourUtils.click('.le [data-col-id="col7"] .lu-action-filter'); + TourUtils.click('.lu-dialog > .lu-checkbox input'); + TourUtils.wait(1000).then(() => TourUtils.click('.lu-dialog-buttons > [type="submit"]')); + }, + }, + { + selector: '', + html: `… and unfolds the melanoma cell lines group.`, + placement: 'centered', + postAction: () => { + TourUtils.click('[data-testid="en/disable-overview-button"]'); + TourUtils.click('[title="Collapse All Groups"]:nth-child(1)'); + TourUtils.click('.le-tr[data-index="2"] .lu-agg-expand'); + }, + }, + { + selector: '.le.le-multi.lineup-engine', + html: `Based on the ranking, he decides to consider all cell lines with unknown TP53 mutation status and a TP53 predictor score greater than 110 as non mutated.`, + placement: 'centered', + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `He adds a column with the CDKN2A relative copy number, …`, + placement: 'centered', + postAction: () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(() => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'CDKN2A;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); + TourUtils.wait(2000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + }); + }, + }, + { + selector: '.le [data-col-id="col11"] .lu-action-sort', + html: `… sorts by it in ascending order, …`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le [data-col-id="col11"] .lu-action-sort').then(() => TourUtils.wait(600)), + postAction: () => { + TourUtils.click('.le [data-col-id="col11"] .lu-action-sort'); + TourUtils.click('.le [data-col-id="col11"] .lu-action-sort'); + }, + }, + { + selector: '.le [data-col-id="col11"] .lu-action-filter', + html: `… and filters out missing data.`, + placement: 'centered', + postAction: () => { + TourUtils.click('.le [data-col-id="col11"] .lu-action-filter'); + TourUtils.click('.lu-dialog > .lu-summary .lu-checkbox input'); + TourUtils.wait(1000).then(() => TourUtils.click('.lu-dialog-buttons > [type="submit"]')); + }, + }, + { + selector: ['.le-tr[data-index="2"] .lu-renderer-selection, .le-tr[data-index="20"] .lu-renderer-selection'], + html: `Finally, he selects the top hits of the resulting list (see Figure 11). All these cell lines fulfill the analyst's requirements.`, + placement: 'centered', + postAction: () => { + TourUtils.click('.le-tr[data-index="2"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="3"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="4"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="5"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="6"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="7"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="8"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="9"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="10"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="11"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="12"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="13"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="14"] .lu-renderer-selection'); + TourUtils.click('.le-tr[data-index="15"] .lu-renderer-selection'); + }, + }, + ]; + } +} diff --git a/src/tours/index.ts b/src/tours/index.ts index a0d72ccf..265816af 100644 --- a/src/tours/index.ts +++ b/src/tours/index.ts @@ -2,4 +2,4 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; export * from './AssessBCCellLinesTour'; -export * from './PredictionTP53Tour'; +export * from './DrugTargetDiscoveryTour'; From 3ad9fe0ac66f9bfc674e1413fd41813513176560 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Wed, 15 Feb 2023 12:46:08 +0100 Subject: [PATCH 27/38] Update gitignore --- .gitignore | 1 + src/phovea.ts | 23 +++++++++++++++++++++-- src/tours/index.ts | 1 + 3 files changed, 23 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 72b6d40b..0362f23d 100644 --- a/.gitignore +++ b/.gitignore @@ -16,6 +16,7 @@ __pycache__/ *.pyc *.swp *.lock +/dist/ # due to using tox and pytest .tox .cache diff --git a/src/phovea.ts b/src/phovea.ts index de89c630..f9639b8f 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1078,6 +1078,25 @@ export default function (registry) { }, ); + registry.push( + 'tdpTour', + 'ordinoPredictionTP53Tour', + function () { + return import('./tours').then((t) => t.PredictionTP53Tour); + }, + { + factory: 'createTour', + name: 'Prediction of TP53 Mutation Status', + description: 'This case study summarizes another analysis session, this time involving the prediction of the mutation status for TP53.', + preview() { + return import('./assets/previews/expression.jpg'); // TODO update preview image + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }, + ); + registry.push( 'tdpTour', 'ordinoDrugTargetDiscoveryTour', @@ -1086,8 +1105,8 @@ export default function (registry) { }, { factory: 'createTour', - name: '???Drug Target Discovery', - description: 'Add description here.', + name: 'Drug Target Discovery', + description: '??? Add description here.', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image }, diff --git a/src/tours/index.ts b/src/tours/index.ts index 265816af..bcaa86c0 100644 --- a/src/tours/index.ts +++ b/src/tours/index.ts @@ -2,4 +2,5 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; export * from './AssessBCCellLinesTour'; +export * from './PredictionTP53Tour'; export * from './DrugTargetDiscoveryTour'; From c97bf0816fdfdea71940ef838e9c8cce60bcdd32 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 13 Mar 2023 11:38:35 +0100 Subject: [PATCH 28/38] Stash Tour Testing --- dist/menu/DatasetCard.d.ts | 1 + dist/menu/DatasetCard.d.ts.map | 2 +- dist/phovea.d.ts.map | 2 +- dist/phovea.js | 30 +++++++++++- dist/phovea.js.map | 2 +- dist/tours/index.d.ts | 4 +- dist/tours/index.d.ts.map | 2 +- dist/tours/index.js | 4 +- dist/tours/index.js.map | 2 +- src/tours/PredictionTP53Tour.ts | 83 ++++++++++++++++++++++++++++++--- 10 files changed, 117 insertions(+), 15 deletions(-) diff --git a/dist/menu/DatasetCard.d.ts b/dist/menu/DatasetCard.d.ts index 836b542b..2587b238 100644 --- a/dist/menu/DatasetCard.d.ts +++ b/dist/menu/DatasetCard.d.ts @@ -1,3 +1,4 @@ +/// import { IPublicDbStartMenuDatasetSectionDesc } from '../base/extensions'; export default function DatasetCard({ name, icon, tabs, startViewId, dataSource, cssClass, tokenSeparators }: IPublicDbStartMenuDatasetSectionDesc): JSX.Element; //# sourceMappingURL=DatasetCard.d.ts.map \ No newline at end of file diff --git a/dist/menu/DatasetCard.d.ts.map b/dist/menu/DatasetCard.d.ts.map index ca009ec8..1a52e87c 100644 --- a/dist/menu/DatasetCard.d.ts.map +++ b/dist/menu/DatasetCard.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":"AAKA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAI1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file +{"version":3,"file":"DatasetCard.d.ts","sourceRoot":"","sources":["../../src/menu/DatasetCard.tsx"],"names":[],"mappings":";AAKA,OAAO,EAAE,oCAAoC,EAAE,MAAM,oBAAoB,CAAC;AAI1E,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,eAAe,EAAE,EAAE,oCAAoC,eA+MjJ"} \ No newline at end of file diff --git a/dist/phovea.d.ts.map b/dist/phovea.d.ts.map index d05dfe17..b3839088 100644 --- a/dist/phovea.d.ts.map +++ b/dist/phovea.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"phovea.d.ts","sourceRoot":"","sources":["../src/phovea.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,OAAO,WAAW,QAAQ,KAAA,QAqvChC"} \ No newline at end of file +{"version":3,"file":"phovea.d.ts","sourceRoot":"","sources":["../src/phovea.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,OAAO,WAAW,QAAQ,KAAA,QAiyChC"} \ No newline at end of file diff --git a/dist/phovea.js b/dist/phovea.js index 7fd82b98..f1b24df9 100644 --- a/dist/phovea.js +++ b/dist/phovea.js @@ -733,8 +733,8 @@ export default function (registry) { level: 'beginner', canJumpAround: false, }); - registry.push('tdpTour', 'ordinoAssessBCCellLines', function () { - return import('./tours').then((t) => t.AssessBCCellLines); + registry.push('tdpTour', 'ordinoAssessBCCellLinesTour', function () { + return import('./tours').then((t) => t.AssessBCCellLinesTour); }, { factory: 'createTour', name: 'Assessment and Selection of Breast Cancer Cell Lines', @@ -746,6 +746,32 @@ export default function (registry) { level: 'beginner', canJumpAround: false, }); + registry.push('tdpTour', 'ordinoPredictionTP53Tour', function () { + return import('./tours').then((t) => t.PredictionTP53Tour); + }, { + factory: 'createTour', + name: 'Prediction of TP53 Mutation Status', + description: 'This case study summarizes another analysis session, this time involving the prediction of the mutation status for TP53.', + preview() { + return import('./assets/previews/expression.jpg'); // TODO update preview image + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }); + registry.push('tdpTour', 'ordinoDrugTargetDiscoveryTour', function () { + return import('./tours').then((t) => t.DrugTargetDiscoveryTour); + }, { + factory: 'createTour', + name: 'Drug Target Discovery', + description: '??? Add description here.', + preview() { + return import('./assets/previews/expression.jpg'); // TODO update preview image + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }); /// #endif registry.push(EP_PHOVEA_CORE_LOCALE, 'tdpPublicDBLocaleEN', function () { return import('./locales/en/tdp.json').then(PluginRegistry.getInstance().asResource); diff --git a/dist/phovea.js.map b/dist/phovea.js.map index f18fdd53..a9ea3d13 100644 --- a/dist/phovea.js.map +++ b/dist/phovea.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/tours/index.d.ts b/dist/tours/index.d.ts index 87e8a782..b6553e9f 100644 --- a/dist/tours/index.d.ts +++ b/dist/tours/index.d.ts @@ -1,5 +1,7 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; -export * from './AssessBCCellLines'; +export * from './AssessBCCellLinesTour'; +export * from './PredictionTP53Tour'; +export * from './DrugTargetDiscoveryTour'; //# sourceMappingURL=index.d.ts.map \ No newline at end of file diff --git a/dist/tours/index.d.ts.map b/dist/tours/index.d.ts.map index e8a4e0d6..f6317ad8 100644 --- a/dist/tours/index.d.ts.map +++ b/dist/tours/index.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,qBAAqB,CAAC"} \ No newline at end of file +{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,yBAAyB,CAAC;AACxC,cAAc,sBAAsB,CAAC;AACrC,cAAc,2BAA2B,CAAC"} \ No newline at end of file diff --git a/dist/tours/index.js b/dist/tours/index.js index 1edb4faf..6a76d982 100644 --- a/dist/tours/index.js +++ b/dist/tours/index.js @@ -1,5 +1,7 @@ export * from './WelcomeTour'; export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; -export * from './AssessBCCellLines'; +export * from './AssessBCCellLinesTour'; +export * from './PredictionTP53Tour'; +export * from './DrugTargetDiscoveryTour'; //# sourceMappingURL=index.js.map \ No newline at end of file diff --git a/dist/tours/index.js.map b/dist/tours/index.js.map index 44a91c56..460884b2 100644 --- a/dist/tours/index.js.map +++ b/dist/tours/index.js.map @@ -1 +1 @@ -{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,qBAAqB,CAAC"} \ No newline at end of file +{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,yBAAyB,CAAC;AACxC,cAAc,sBAAsB,CAAC;AACrC,cAAc,2BAA2B,CAAC"} \ No newline at end of file diff --git a/src/tours/PredictionTP53Tour.ts b/src/tours/PredictionTP53Tour.ts index 3a2506b9..0d0abed9 100644 --- a/src/tours/PredictionTP53Tour.ts +++ b/src/tours/PredictionTP53Tour.ts @@ -1,12 +1,30 @@ // import {ToursSection} from 'ordino'; -import { IStep, Tour, TourUtils } from 'tdp_core'; +import { IStep, Tour } from 'tdp_core'; +import { TourUtils } from 'tdp_core/src/tour/TourUtils'; +// import selectEvent from 'react-select-event'; export class PredictionTP53Tour { static createTour(): IStep[] { return [ { - html: `

      Welcome to this short tour showing the assessment of breast cancer cell lines!

      -

      This tour will follow an analysis session from the perspective of a drug discovery team at a pharmaceutical company.

      + html: ` +

      + This case study summarizes another analysis session carried out by a + research scientist working in a drug discovery team at a pharmaceutical company. +

      + +

      + In order to identify potential drug targets in a set of tumor + types, the analyst performs experiments with cancer cell lines—cultured cells that are derived from + tumors and that can proliferate indefinitely in the laboratory. +

      + +

      + These cell lines are characterized by various properties, such as tumor type (lung cancer, prostate cancer, etc.) + and the set of genes that are mutated. One very important gene in the context of cancer is TP53. It encodes the + p53 protein, whose presence is known to suppress the uncontrolled division of cells. +

      +

      Use the "Next" button to iterate through all the steps. You can use the "Cancel" button at any time to stop the tour and to interact with Ordino. @@ -44,11 +62,64 @@ export class PredictionTP53Tour { }, { selector: '.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox', - html: `

      12To create a set with these specific genes, they add each gene into the highlighted field.

      `, + html: `

      123To create a set with these specific genes, they add each gene into the highlighted field.

      `, placement: 'centered', + allowUserInteraction: true, + preAction: () => { + // TourUtils.click('#dataset-panel-human-5 [data-testid="async-paginate-dropdownindicator"]'); + // -------- + // const backdrop = document.querySelector('div.tdp-tour-back-disabled') as HTMLElement; + // backdrop.style.display = 'none'; + // const backdropblocker = document.querySelector('div.tdp-tour-backdrop-blocker') as HTMLElement; + // backdropblocker.style.display = 'none'; + // TourUtils.removeBlocker('div.tdp-tour-back-disabled'); + // TourUtils.removeBlocker('div.tdp-tour-backdrop-blocker'); + // ------------- + // TourUtils.setValueAndTrigger('div.css-1pahdxg-control', 'AEN', 'change'); + // -------------------- + // selectEvent.openMenu(document.querySelector('[id="react-select-6-input"]')); + // // eslint-disable-next-line @typescript-eslint/no-unused-expressions + // TourUtils.waitFor('[id="react-select-6-option-0"]').then(() => { + // TourUtils.wait(3000) + // // .then(() => TourUtils.fireMouseDown('div.css-1pahdxg-control')) + // // .then(() => TourUtils.wait(3000)) + // .then(() => { + // TourUtils.focus('div.css-1pahdxg-control'); + // TourUtils.fireKeyPress('div.css-1pahdxg-control', 'a'); + // }); + // }); + }, postAction: () => { - // TourUtils.click('.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox input'); - // TourUtils.setValueAndTrigger('.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox input', 'AEN;', 'input'); + // TourUtils.focus(document.querySelector('[id="react-select-6-input"]')); + // TourUtils.fireMouseDown(document.querySelector('[id="react-select-6-input"]')); + // TourUtils.fireKeyPress(document.querySelector('[id="react-select-6-input"]'), 'A'); + // --------------- + // selectEvent.select(document.querySelector('[id="react-select-6-input"]'), "AEN"); + // selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['A1BG']); + // --------------- + // selectEvent.openMenu(document.querySelector('[id="react-select-6-input"]')); + // // eslint-disable-next-line @typescript-eslint/no-unused-expressions + // TourUtils.waitFor('[id="react-select-6-option-0"]').then(() => { + // TourUtils.wait(3000) + // .then(() => TourUtils.fireMouseDown('[id="react-select-6-input"]')) + // .then(() => TourUtils.wait(3000)) + // .then(() => TourUtils.fireKeyPress('[id="react-select-6-input"]', 'a')); + // }); + // ------------------------- + // TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000121410"]').then(() => TourUtils.wait(1000)); + // TourUtils.removeBlocker('div.tdp-tour-back-disabled'); + // TourUtils.removeBlocker('div.tdp-tour-backdrop-blocker'); + // TourUtils.click('#dataset-panel-human-5 [data-testid="async-paginate-dropdownindicator"]'); + // ------------------ + // .then(() => TourUtils.click('[id="react-select-6-option-0"]'));"react-select-6-option-0"]').then(() => { + // TourUtils.wait(1000).then(() => { + // TourUtils.setValueAndTrigger('[id="react-select-6-input"]', 'AEN', 'change'); + // }); + // }); + // TourUtils.setValueWithoutTrigger('[id="react-select-6-input"]', 'AEN'); + // TourUtils.click('[id="react-select-6-option-0"]'); + // div[class$="-MenuList"] #react-select-3-option-1 + // TourUtils.setValueAndTrigger('[id="react-select-6-input"]', 'AEN', 'input'); // TourUtils.keyDownEnter('.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox input'); }, }, From e2efaf68010e340c54230cb03d2727236c8a2b27 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Thu, 23 Mar 2023 10:00:28 +0100 Subject: [PATCH 29/38] Updated tours --- src/tours/PredictionTP53Tour.ts | 333 +++++++++++++++++++++++++------- 1 file changed, 268 insertions(+), 65 deletions(-) diff --git a/src/tours/PredictionTP53Tour.ts b/src/tours/PredictionTP53Tour.ts index 0d0abed9..c05a5f3b 100644 --- a/src/tours/PredictionTP53Tour.ts +++ b/src/tours/PredictionTP53Tour.ts @@ -1,7 +1,8 @@ // import {ToursSection} from 'ordino'; import { IStep, Tour } from 'tdp_core'; import { TourUtils } from 'tdp_core/src/tour/TourUtils'; -// import selectEvent from 'react-select-event'; +import selectEvent from 'react-select-event'; +import { wideEnoughCat } from 'lineupjs/build/src/renderer/utils'; export class PredictionTP53Tour { static createTour(): IStep[] { @@ -62,83 +63,96 @@ export class PredictionTP53Tour { }, { selector: '.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox', - html: `

      123To create a set with these specific genes, they add each gene into the highlighted field.

      `, + html: `

      To create a set with these specific genes, they add each gene into the highlighted field.

      `, placement: 'centered', allowUserInteraction: true, - preAction: () => { - // TourUtils.click('#dataset-panel-human-5 [data-testid="async-paginate-dropdownindicator"]'); - // -------- - // const backdrop = document.querySelector('div.tdp-tour-back-disabled') as HTMLElement; - // backdrop.style.display = 'none'; - // const backdropblocker = document.querySelector('div.tdp-tour-backdrop-blocker') as HTMLElement; - // backdropblocker.style.display = 'none'; - // TourUtils.removeBlocker('div.tdp-tour-back-disabled'); - // TourUtils.removeBlocker('div.tdp-tour-backdrop-blocker'); - // ------------- - // TourUtils.setValueAndTrigger('div.css-1pahdxg-control', 'AEN', 'change'); - // -------------------- - // selectEvent.openMenu(document.querySelector('[id="react-select-6-input"]')); - // // eslint-disable-next-line @typescript-eslint/no-unused-expressions - // TourUtils.waitFor('[id="react-select-6-option-0"]').then(() => { - // TourUtils.wait(3000) - // // .then(() => TourUtils.fireMouseDown('div.css-1pahdxg-control')) - // // .then(() => TourUtils.wait(3000)) - // .then(() => { - // TourUtils.focus('div.css-1pahdxg-control'); - // TourUtils.fireKeyPress('div.css-1pahdxg-control', 'a'); - // }); - // }); - }, - postAction: () => { - // TourUtils.focus(document.querySelector('[id="react-select-6-input"]')); - // TourUtils.fireMouseDown(document.querySelector('[id="react-select-6-input"]')); - // TourUtils.fireKeyPress(document.querySelector('[id="react-select-6-input"]'), 'A'); - // --------------- - // selectEvent.select(document.querySelector('[id="react-select-6-input"]'), "AEN"); - // selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['A1BG']); - // --------------- - // selectEvent.openMenu(document.querySelector('[id="react-select-6-input"]')); - // // eslint-disable-next-line @typescript-eslint/no-unused-expressions - // TourUtils.waitFor('[id="react-select-6-option-0"]').then(() => { - // TourUtils.wait(3000) - // .then(() => TourUtils.fireMouseDown('[id="react-select-6-input"]')) - // .then(() => TourUtils.wait(3000)) - // .then(() => TourUtils.fireKeyPress('[id="react-select-6-input"]', 'a')); - // }); - // ------------------------- - // TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000121410"]').then(() => TourUtils.wait(1000)); - // TourUtils.removeBlocker('div.tdp-tour-back-disabled'); - // TourUtils.removeBlocker('div.tdp-tour-backdrop-blocker'); - // TourUtils.click('#dataset-panel-human-5 [data-testid="async-paginate-dropdownindicator"]'); - // ------------------ - // .then(() => TourUtils.click('[id="react-select-6-option-0"]'));"react-select-6-option-0"]').then(() => { - // TourUtils.wait(1000).then(() => { - // TourUtils.setValueAndTrigger('[id="react-select-6-input"]', 'AEN', 'change'); - // }); - // }); - // TourUtils.setValueWithoutTrigger('[id="react-select-6-input"]', 'AEN'); - // TourUtils.click('[id="react-select-6-option-0"]'); - // div[class$="-MenuList"] #react-select-3-option-1 - // TourUtils.setValueAndTrigger('[id="react-select-6-input"]', 'AEN', 'input'); - // TourUtils.keyDownEnter('.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox input'); + postAction: async () => { + selectEvent.openMenu(document.querySelector('[id="react-select-6-input"]')); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'AEN'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['AEN']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000181026"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'BAX'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['BAX']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000087088"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'CCNG1'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['CCNG1']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000218991"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'CDKN1A'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['CDKN1A']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000124762"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'DDB2'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['DDB2']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000134574"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'FDXR'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['FDXR']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000161513"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'MDM2'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['MDM2']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000135679"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'RPS27L'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['RPS27L']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000185088"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'RRM2B'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['RRM2B']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000048392"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'SESN1'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['SESN1']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000080546"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'TNFRSF10B'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['TNFRSF10B']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000120889"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'XPC'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['XPC']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000154767"]'); + + selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'ZMAT3'); + selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['ZMAT3']); + await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000172667"]'); }, }, { selector: '.ordino-dataset.genes-dataset .show [data-testid="save-button"]', - html: `Once the genes have been added, they choose to save these genes as a custom set.`, + html: `Once the genes have been added, they choose to save these genes as a custom set called 'TP53 Predictor'.`, placement: 'centered', - postAction: () => TourUtils.clickSelector, + postAction: async () => { + // Checks for an existing set called 'TP53 Predictor' + // If this named set already exists but with different genes, then the tour will erroneously continue + if (document.querySelector('[data-testid="tp53-predictor-button"]') !== null) { + TourUtils.click('[data-testid="async-paginate-clearindicator"]'); + } else { + TourUtils.click('#dataset-panel-human-5 [data-testid="save-button"]'); + await TourUtils.wait(1000); // + TourUtils.setValueAndTrigger('[data-testid="name-input"]', 'TP53 Predictor', 'input'); + TourUtils.click('[data-testid="primary-dialog-button"]'); + // TourUtils.click('[data-testid="save-list-of-entities"] [data-testid="close-button"]') + } + }, }, { - selector: '.ordino-dataset.tissue-dataset', + // BUGGED: Doesn't scroll up + selector: '.ordino-dataset.tissue-dataset > .card', html: `Next they aim to test the applicability of gene signature using TCGA tumor samples.`, placement: 'centered', + preAction: () => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(2)'), }, { selector: '.ordino-dataset.tissue-dataset [data-testid="tcga-tumors-button"]', html: `They start by opening a list of all TCGA tumors.`, placement: 'centered', - postAction: () => TourUtils.clickSelector, + // preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .tissue-dataset > .card').then(() => TourUtils.wait(600)), + postAction: TourUtils.clickSelector, pageBreak: 'manual', }, { @@ -148,10 +162,199 @@ export class PredictionTP53Tour { preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), }, { - selector: '.le.le-multi.lineup-engine', + selector: '[data-testid="viewWrapper-0"] [data-id="col4"] .lu-action-filter', + html: `First, they choose to filter the tumor type by colon adenocarcinoma`, placement: 'centered', - html: `///The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, - preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), + postAction: async () => { + TourUtils.click('[data-testid="viewWrapper-0"] [data-id="col4"] .lu-action-filter'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-table .lu-checkbox:first-child'); + await TourUtils.wait(500); + TourUtils.click('input[type="checkbox"][data-cat="colon adenocarcinoma"]'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-button[type="submit"]'); + }, + }, + { + selector: '[data-testid="add-column-button"]', + html: `

      Now they add a single gene score for the following:

      +

      Gene: TP53

      +

      Data Type: AA Mutated

      `, + placement: 'centered', + postAction: async () => { + TourUtils.click('[data-testid="add-column-button"]'); + await TourUtils.wait(500); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + // await TourUtils.wait(500); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(async () => { + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'change'); + await TourUtils.wait(500); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); + }, + }, + { + selector: '[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter', + html: `They filter out the samples with an unknown TP53 mutation status.`, + placement: 'centered', + postAction: async () => { + TourUtils.click('[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog > .lu-checkbox input'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-button[type="submit"]'); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `

      Next they add an aggregated gene score with the following criteria:

      +

      Filter: My Named Sets = TP53 Predictor

      +

      Data Type: Expression (TPM)

      +

      Aggregation: Average

      +

      Compute score only for current sample subset

      `, + placement: 'centered', + postAction: async () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + await TourUtils.wait(500); + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'namedset4ensg', 'change'); + await TourUtils.wait(1000); + // TourUtils.click('.modal-dialog [data-testid="row-1"] .select2 input'); + // selectEvent.create(document.querySelector('.modal-dialog [data-testid="row-1"] .select2 input'), 'TP53 Predictor'); + TourUtils.setValueAndTrigger('.modal-dialog [data-testid="row-1"] .select2 input', 'TP53 Predictor', 'input'); + TourUtils.keyDownEnter('.modal-dialog [data-testid="row-1"] .select2 input'); + // selectEvent.select(document.querySelector('.modal-dialog [data-testid="row-1"] .select2 input'), ['TP53 Predictor']); + // TourUtils.click('.select2-results__options li:first-child'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); + TourUtils.click('[data-testid="form-checkbox"]'); + await TourUtils.wait(500); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }, + }, + { + selector: '[data-id="col8"] .lu-action-sort', + html: `They sort by this newly-added gene expression column.`, + placement: 'centered', + preAction: TourUtils.waitForSelector, + postAction: TourUtils.clickSelector, + }, + { + selector: ['[data-id="col7"], [data-id="col8"]'], + html: `

      Observe: There is a clear correlation between gene expression signature and mutation status of + TP53: Of the 50 samples with the highest expression only 3 are TP53 mutated, whereas of the 50 + samples with the lowest expression 35 are TP53 mutated.

      `, + placement: 'centered', + }, // Comment out til here to remove first section + { + selector: 'ul[data-header="mainMenu"] > li:first-child > a', + html: `Next, they aim to test the applicability of gene signature and MDM2 sensitivity using all cell lines.`, + placement: 'centered', + preAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.add('hover'); + } + }, + postAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.remove('hover'); + datasetTab.querySelector('a').click(); + } + return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(1)')); + }, + }, + { + selector: '.ordino-dataset.cellline-dataset [data-testid="all-button"]', + html: `They open the list of ALL cell lines.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + pageBreak: 'manual', + }, + { + selector: '[data-testid="add-column-button"]', + html: `

      They add a single gene score for the following:

      +

      Gene: TP53

      +

      Data Type: AA Mutated and AA Mutation

      `, + placement: 'centered', + postAction: async () => { + TourUtils.click('[data-testid="add-column-button"]'); + await TourUtils.wait(500); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(async () => { + if (document.querySelector('[data-testid="data-type"] .select2-selection__clear') !== null) { + TourUtils.click('[data-testid="data-type"] .select2-selection__clear'); + TourUtils.click('label[data-testid="Data Type"]'); // Just click anywhere safe to get rid of dropdown + } + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'input'); + await TourUtils.wait(500); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); + await TourUtils.wait(1500); + // Repeat again for the AA Mutation Column + TourUtils.click('[data-testid="add-column-button"]'); + await TourUtils.wait(500); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + TourUtils.waitFor('.modal.show').then(async () => { + if (document.querySelector('[data-testid="data-type"] .select2-selection__clear') !== null) { + TourUtils.click('[data-testid="data-type"] .select2-selection__clear'); + TourUtils.click('label[data-testid="Data Type"]'); + } + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aamutation', 'input'); + + await TourUtils.wait(500); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }); + }, + }, + { + selector: '[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter', + html: `They once again filter out the samples with an unknown TP53 mutation status.`, + placement: 'centered', + postAction: async () => { + TourUtils.click('[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog > .lu-checkbox input'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-button[type="submit"]'); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `

      Next they add the aggregated gene score with the following criteria again:

      +

      Filter: My Named Sets = TP53 Predictor

      +

      Data Type: Expression (TPM)

      +

      Aggregation: Average

      +

      Compute score for all cell lines

      `, + placement: 'centered', + postAction: async () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + await TourUtils.wait(500); + if (document.querySelector('[data-testid="row-1"] [data-testid="close-button"]') !== null) { + TourUtils.click('[data-testid="row-1"] [data-testid="close-button"]'); + } + await TourUtils.wait(500); + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'namedset4ensg', 'change'); + await TourUtils.wait(1000); + TourUtils.setValueAndTrigger('.modal-dialog [data-testid="row-1"] .select2 input', 'TP53 Predictor', 'input'); + TourUtils.keyDownEnter('.modal-dialog [data-testid="row-1"] .select2 input'); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); + /// ??? Uncomment the following line when the test is ready + // TourUtils.click('[data-testid="form-checkbox"]'); // This is very risky, as we are assuming it was checked previously, which should be remembered by the cookies and thus clicking again would deselect (as desired) + await TourUtils.wait(500); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }, }, { selector: '', From ebb9ddbf2e861927a5e74f1c09f40242b7bbe571 Mon Sep 17 00:00:00 2001 From: oltionchampari Date: Thu, 23 Mar 2023 10:03:33 +0100 Subject: [PATCH 30/38] Add dependency --- package.json | 1 + 1 file changed, 1 insertion(+) diff --git a/package.json b/package.json index d95b899b..30ce7f20 100644 --- a/package.json +++ b/package.json @@ -57,6 +57,7 @@ "dependencies": { "jquery-ui": "1.12.1", "jstat": "^1.9.4", + "react-select-event": "^5.5.1", "react-highlight-words": "^0.17.0", "react-select": "^4.1.0", "react-select-async-paginate": "^0.5.3", From 5fbb05d7796f9359cdff8f88603b6fe294a56d47 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Thu, 23 Mar 2023 12:18:29 +0100 Subject: [PATCH 31/38] Added blockers to stabilize tour --- src/phovea.ts | 38 ++++++++++++++--------------- src/tours/AssessBCCellLinesTour.ts | 39 ++++++++++++++++++------------ src/tours/index.ts | 2 +- 3 files changed, 43 insertions(+), 36 deletions(-) diff --git a/src/phovea.ts b/src/phovea.ts index 7740c8b3..6eb1e24c 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1092,7 +1092,7 @@ export default function (registry) { }, { factory: 'createTour', - name: 'Prediction of TP53 Mutation Status', + name: 'Prediction of TP53 Mutation Status (WIP)', description: 'This case study summarizes another analysis session, this time involving the prediction of the mutation status for TP53.', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image @@ -1103,24 +1103,24 @@ export default function (registry) { }, ); - registry.push( - 'tdpTour', - 'ordinoDrugTargetDiscoveryTour', - function () { - return import('./tours').then((t) => t.DrugTargetDiscoveryTour); - }, - { - factory: 'createTour', - name: 'Drug Target Discovery', - description: '??? Add description here.', - preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image - }, - multiPage: true, - level: 'beginner', - canJumpAround: false, - }, - ); + // registry.push( + // 'tdpTour', + // 'ordinoDrugTargetDiscoveryTour', + // function () { + // return import('./tours').then((t) => t.DrugTargetDiscoveryTour); + // }, + // { + // factory: 'createTour', + // name: 'Drug Target Discovery', + // description: '??? Add description here.', + // preview() { + // return import('./assets/previews/expression.jpg'); // TODO update preview image + // }, + // multiPage: true, + // level: 'beginner', + // canJumpAround: false, + // }, + // ); /// #endif registry.push( diff --git a/src/tours/AssessBCCellLinesTour.ts b/src/tours/AssessBCCellLinesTour.ts index 555d5d39..1dd268b5 100644 --- a/src/tours/AssessBCCellLinesTour.ts +++ b/src/tours/AssessBCCellLinesTour.ts @@ -1,4 +1,5 @@ // import {ToursSection} from 'ordino'; +import selectEvent from 'react-select-event'; import { IStep, Tour, TourUtils } from 'tdp_core'; export class AssessBCCellLinesTour { @@ -39,7 +40,7 @@ export class AssessBCCellLinesTour { html: `

      Here they choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

      In this example they choose to work with a list of genes.

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), + preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(1000)), postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), }, { @@ -57,7 +58,7 @@ export class AssessBCCellLinesTour { selector: '.le.le-multi.lineup-engine', placement: 'centered', html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, - preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1)', Infinity), }, { selector: '.lu-side-panel-wrapper .lu-adder > button', @@ -77,7 +78,7 @@ export class AssessBCCellLinesTour { { selector: '.modal.show .col > .select3', placement: 'centered', - preAction: () => TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(150)), + preAction: () => TourUtils.waitFor('.modal.show', Infinity).then(() => TourUtils.wait(150)), html: `Now they select the cell line 'HCC1954' …`, postAction: () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); @@ -101,15 +102,16 @@ export class AssessBCCellLinesTour { selector: '.le [data-col-id="col8"] .lu-action-sort', placement: 'centered', html: `They want to sort by this newly added column, so they click on the sort button in the column header.`, - preAction: () => TourUtils.waitFor('.le [data-col-id="col8"] .lu-action-sort'), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="1.83"]', Infinity), postAction: () => { TourUtils.click('.le [data-col-id="col8"] .lu-action-sort'); }, }, { - selector: ['[data-index="0"].le-tr, [data-index="14"].le-tr'], + // selector: ['[data-index="0"].le-tr, [data-index="14"].le-tr'], // Bug: It highlights the selectors before waiting for the preAction placement: 'centered', html: `After sorting by this column, the analyst observes that about 15 genes on chromosome 17 are affected by a large genomic amplification.`, + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="8.00"]', Infinity), }, { selector: '.lu-side-panel-wrapper .lu-adder > button', @@ -120,10 +122,11 @@ export class AssessBCCellLinesTour { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.modal.show').then(() => { + TourUtils.waitFor('.modal.show').then(async () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); TourUtils.setValueAndTrigger('.show .col > select', 'expression-tpm', 'change'); - TourUtils.wait(1000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); + await TourUtils.wait(1000); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); }); }, }, @@ -131,7 +134,7 @@ export class AssessBCCellLinesTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `They also add a column with a Gene Sensitivity Score (a measure of importance for cell survival) for HCC1954.`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le header [data-col-id="col9"]').then(() => TourUtils.wait(500)), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="5324.86"]', Infinity), postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); }, @@ -156,7 +159,7 @@ export class AssessBCCellLinesTour { html: `

      In an effort to improve the depletion score's readability, they decide to invert the linear scaling.

      To do this, they click on the three dots for more column options.

      `, placement: 'centered', - preAction: TourUtils.waitForSelector, + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="−2.75"]', Infinity), postAction: TourUtils.clickSelector, }, { @@ -185,6 +188,7 @@ export class AssessBCCellLinesTour {

      Observe: Combining the columns highlights the importance of ERBB2.

      It is therefore probably the most relevant gene within this amplified genomic region.

      `, placement: 'centered', + allowUserInteraction: true, }, { selector: '[data-index="0"]', @@ -206,8 +210,9 @@ export class AssessBCCellLinesTour { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(async () => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + await TourUtils.wait(500); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', @@ -225,13 +230,14 @@ export class AssessBCCellLinesTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `2. A column with the gene copy number distribution for breast cancer cell lines in boxplot format`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le header [data-col-id="col11"]'), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="890.37"]', Infinity), postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(async () => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + await TourUtils.wait(500); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', @@ -249,13 +255,14 @@ export class AssessBCCellLinesTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `3. A column with the gene amplification frequency (>4) across all breast cancer cell lines`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le header [data-col-id="col12"]'), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) .lu-renderer-boxplot', Infinity), postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { + TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(async () => { TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'tumortype', 'change'); + await TourUtils.wait(500); TourUtils.setValueAndTrigger( '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', 'breast carcinoma', @@ -277,7 +284,7 @@ export class AssessBCCellLinesTour { selector: '.le.le-multi.lineup-engine', html: `Observe: They notice that ERBB2 is amplified in almost 25% of all assessed breast cancer cell lines. Further, it is highly expressed.`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le header [data-col-id="col13"]'), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="0.25"]', Infinity), }, { selector: '[data-index="0"] .lu-renderer-selection', @@ -416,7 +423,7 @@ export class AssessBCCellLinesTour {

      HCC1954 has the highest ERBB2 amplification among BRCA1 mutated cell lines.

      HCC1569 has the highest ERBB2 amplification among BRCA2 mutated cell lines.

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('[data-testid="viewWrapper-1"] .le header [data-col-id="col8"]'), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col8"][data-renderer="categorical"]'), }, { selector: '', diff --git a/src/tours/index.ts b/src/tours/index.ts index bcaa86c0..d52e5a44 100644 --- a/src/tours/index.ts +++ b/src/tours/index.ts @@ -3,4 +3,4 @@ export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; export * from './AssessBCCellLinesTour'; export * from './PredictionTP53Tour'; -export * from './DrugTargetDiscoveryTour'; +// export * from './DrugTargetDiscoveryTour'; From fb08f9f1aa91c5254fc4c97387d87508c949d1d6 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Thu, 30 Mar 2023 10:06:45 +0200 Subject: [PATCH 32/38] Functional completion of the new tours --- src/phovea.ts | 59 ++++-- src/tours/DrugTargetDiscoveryTour.ts | 87 ++++++--- src/tours/PredictionTP53Tour.ts | 248 ++++--------------------- src/tours/PredictionTP53Tour2.ts | 259 +++++++++++++++++++++++++++ src/tours/index.ts | 3 +- 5 files changed, 394 insertions(+), 262 deletions(-) create mode 100644 src/tours/PredictionTP53Tour2.ts diff --git a/src/phovea.ts b/src/phovea.ts index 6eb1e24c..f75ac7dc 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1092,7 +1092,7 @@ export default function (registry) { }, { factory: 'createTour', - name: 'Prediction of TP53 Mutation Status (WIP)', + name: 'Prediction of TP53 Mutation Status', description: 'This case study summarizes another analysis session, this time involving the prediction of the mutation status for TP53.', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image @@ -1103,24 +1103,45 @@ export default function (registry) { }, ); - // registry.push( - // 'tdpTour', - // 'ordinoDrugTargetDiscoveryTour', - // function () { - // return import('./tours').then((t) => t.DrugTargetDiscoveryTour); - // }, - // { - // factory: 'createTour', - // name: 'Drug Target Discovery', - // description: '??? Add description here.', - // preview() { - // return import('./assets/previews/expression.jpg'); // TODO update preview image - // }, - // multiPage: true, - // level: 'beginner', - // canJumpAround: false, - // }, - // ); + registry.push( + 'tdpTour', + 'ordinoPredictionTP53Tour2', + function () { + return import('./tours').then((t) => t.PredictionTP53Tour2); + }, + { + factory: 'createTour', + name: 'Prediction of TP53 Mutation Status: Continued', + description: + 'This case study serves as a continuation of the initial tour "Prediction of TP53 Mutation Status". It takes a deeper look into the efficacy of the TP53 Predictor Score, in combination with the MDM2 sensitivity score.', + preview() { + return import('./assets/previews/expression.jpg'); // TODO update preview image + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }, + ); + + registry.push( + 'tdpTour', + 'ordinoDrugTargetDiscoveryTour', + function () { + return import('./tours').then((t) => t.DrugTargetDiscoveryTour); + }, + { + factory: 'createTour', + name: 'Drug Target Discovery', + description: + 'A demonstration of Taggle (integrated into the Ordino Target Discovery Platform) by means of a case study conducted on complex genomics data for the purpose of drug target discovery.', + preview() { + return import('./assets/previews/expression.jpg'); // TODO update preview image + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }, + ); /// #endif registry.push( diff --git a/src/tours/DrugTargetDiscoveryTour.ts b/src/tours/DrugTargetDiscoveryTour.ts index 58f62a8a..2eaf76d6 100644 --- a/src/tours/DrugTargetDiscoveryTour.ts +++ b/src/tours/DrugTargetDiscoveryTour.ts @@ -162,21 +162,32 @@ export class DrugTargetDiscoveryTour { }, }, { - selector: [ - '.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select, .show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', - ], - html: `They select 'My Named Sets' in the drop down and then enter 'TP53 Predictor' as the specific set …`, + selector: '[data-testid="Filter"] [data-testid="row-1"] .form-select', + html: `They select 'Gene Symbol' in the drop down and then enter the list of genes used for the TP53 Predictor …`, placement: 'centered', preAction: () => TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select'), - postAction: () => { - TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'namedset4ensg', 'change'); - TourUtils.wait(1500).then(() => { - TourUtils.setValueAndTrigger( - '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', - '0Qd2E6S4R9', - 'change', - ); - }); + postAction: async () => { + // Ensure that the list of inputs is empty first + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'ensg', 'change'); + await TourUtils.wait(1500); + TourUtils.click('[data-testid="Filter"] [data-testid="close-button"]'); + await TourUtils.wait(1500); + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'ensg', 'change'); + await TourUtils.wait(1500); + + // Now add the list of 13 genes here instead + TourUtils.setValueAndTrigger( + '.modal-dialog [data-testid="row-2"] .select2 input', + 'AEN,BAX,CCNG1,CDKN1A,DDB2,FDXR,MDM2,RPS27L,RRM2B,SESN1,TNFRSF10B,XPC,ZMAT3', + 'input', + ); + await TourUtils.wait(1020); + + // Inspect if the checkbox is checked, if so then uncheck it + const checkboxTest = document.querySelector('.modal-dialog [data-testid="form-checkbox"]') as HTMLInputElement; + if (!checkboxTest.checked) { + TourUtils.click('.modal-dialog [data-testid="form-checkbox"]'); + } }, }, { @@ -207,30 +218,46 @@ export class DrugTargetDiscoveryTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `Similarly, they add a matrix column with all of the individual expression values.`, placement: 'centered', - postAction: () => { + postAction: async () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select').then(() => { - TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'namedset4ensg', 'change'); - TourUtils.setValueAndTrigger( - '.show .modal-body form > .col-sm-12:nth-child(1) .row:nth-child(1) .row:nth-child(1) > div:nth-child(2) select', - '0Qd2E6S4R9', - 'change', - ); - TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); - TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'numbers', 'change'); - TourUtils.wait(1000).then(() => { - TourUtils.click('.modal.show .modal-footer button[type=submit]'); - TourUtils.click('.modal.show .modal-footer button[type=submit]'); - }); - }); + await TourUtils.wait(500); + + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'ensg', 'change'); + await TourUtils.wait(1500); + TourUtils.click('[data-testid="Filter"] [data-testid="close-button"]'); + await TourUtils.wait(1500); + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'ensg', 'change'); + await TourUtils.wait(1500); + + // Now add the list of 13 genes here instead + TourUtils.setValueAndTrigger( + '.modal-dialog [data-testid="row-2"] .select2 input', + 'AEN,BAX,CCNG1,CDKN1A,DDB2,FDXR,MDM2,RPS27L,RRM2B,SESN1,TNFRSF10B,XPC,ZMAT3', + 'input', + ); + await TourUtils.wait(1020); + + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'numbers', 'change'); + + // Inspect if the checkbox is checked, if so then uncheck it + const checkboxTest = document.querySelector('.modal-dialog [data-testid="form-checkbox"]') as HTMLInputElement; + if (!checkboxTest.checked) { + TourUtils.click('.modal-dialog [data-testid="form-checkbox"]'); + } + await TourUtils.wait(1000); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + await TourUtils.wait(1000); // Button must be pressed twice because of the warning that is thrown + TourUtils.click('.modal.show .modal-footer button[type=submit]'); }, }, { selector: '[data-id="col7"] .lu-action-filter', html: `Furthermore, they decide to hide all cell lines with unknown mutation status.`, placement: 'centered', + // preAction: // ??? Wait for the matrix load postAction: () => { TourUtils.click('[data-id="col7"] .lu-action-filter'); TourUtils.waitFor('.lu-dialog > .lu-checkbox input').then(() => { @@ -390,6 +417,10 @@ export class DrugTargetDiscoveryTour { TourUtils.click('.le-tr[data-index="15"] .lu-renderer-selection'); }, }, + { + html: `

      Thanks for joining this tour demonstrating a typical analysis session by a drug discovery team at a pharmaceutical company.

      +

      There are still many more features to discover. Enjoy!

      `, + }, ]; } } diff --git a/src/tours/PredictionTP53Tour.ts b/src/tours/PredictionTP53Tour.ts index c05a5f3b..3de6bc0c 100644 --- a/src/tours/PredictionTP53Tour.ts +++ b/src/tours/PredictionTP53Tour.ts @@ -3,6 +3,7 @@ import { IStep, Tour } from 'tdp_core'; import { TourUtils } from 'tdp_core/src/tour/TourUtils'; import selectEvent from 'react-select-event'; import { wideEnoughCat } from 'lineupjs/build/src/renderer/utils'; +import { select } from 'lineupjs'; export class PredictionTP53Tour { static createTour(): IStep[] { @@ -49,109 +50,22 @@ export class PredictionTP53Tour { datasetTab.querySelector('a').classList.remove('hover'); datasetTab.querySelector('a').click(); } - return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(3)')); + return TourUtils.waitFor('.ordino-dataset.tissue-dataset').then(() => + TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(2)'), + ); }, pageBreak: 'manual', }, { - selector: '.ordino-dataset.genes-dataset > .card', - html: `

      Here they choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

      -

      In this example they choose to work with a list of 13 specific genes.

      `, - placement: 'centered', - preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .genes-dataset > .card').then(() => TourUtils.wait(600)), - postAction: () => TourUtils.click('.ordino-dataset.genes-dataset .session-tab > li:first-child'), - }, - { - selector: '.ordino-dataset.genes-dataset .show .ordino-dataset-searchbox', - html: `

      To create a set with these specific genes, they add each gene into the highlighted field.

      `, - placement: 'centered', - allowUserInteraction: true, - postAction: async () => { - selectEvent.openMenu(document.querySelector('[id="react-select-6-input"]')); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'AEN'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['AEN']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000181026"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'BAX'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['BAX']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000087088"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'CCNG1'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['CCNG1']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000218991"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'CDKN1A'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['CDKN1A']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000124762"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'DDB2'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['DDB2']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000134574"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'FDXR'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['FDXR']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000161513"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'MDM2'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['MDM2']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000135679"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'RPS27L'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['RPS27L']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000185088"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'RRM2B'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['RRM2B']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000048392"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'SESN1'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['SESN1']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000080546"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'TNFRSF10B'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['TNFRSF10B']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000120889"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'XPC'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['XPC']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000154767"]'); - - selectEvent.create(document.querySelector('[id="react-select-6-input"]'), 'ZMAT3'); - selectEvent.select(document.querySelector('[id="react-select-6-input"]'), ['ZMAT3']); - await TourUtils.waitFor('[data-testid="async-paginate-multiselect-remove-ENSG00000172667"]'); - }, - }, - { - selector: '.ordino-dataset.genes-dataset .show [data-testid="save-button"]', - html: `Once the genes have been added, they choose to save these genes as a custom set called 'TP53 Predictor'.`, - placement: 'centered', - postAction: async () => { - // Checks for an existing set called 'TP53 Predictor' - // If this named set already exists but with different genes, then the tour will erroneously continue - if (document.querySelector('[data-testid="tp53-predictor-button"]') !== null) { - TourUtils.click('[data-testid="async-paginate-clearindicator"]'); - } else { - TourUtils.click('#dataset-panel-human-5 [data-testid="save-button"]'); - await TourUtils.wait(1000); // - TourUtils.setValueAndTrigger('[data-testid="name-input"]', 'TP53 Predictor', 'input'); - TourUtils.click('[data-testid="primary-dialog-button"]'); - // TourUtils.click('[data-testid="save-list-of-entities"] [data-testid="close-button"]') - } - }, - }, - { - // BUGGED: Doesn't scroll up selector: '.ordino-dataset.tissue-dataset > .card', - html: `Next they aim to test the applicability of gene signature using TCGA tumor samples.`, + html: `

      Here they can choose between the three entity types 'Cell Lines', 'Tissue Samples', and 'Genes'.

      +

      They aim to test the applicability of the gene signature using TCGA tumor samples.

      `, placement: 'centered', - preAction: () => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(2)'), }, { selector: '.ordino-dataset.tissue-dataset [data-testid="tcga-tumors-button"]', html: `They start by opening a list of all TCGA tumors.`, placement: 'centered', - // preAction: () => TourUtils.waitFor('#ordino_dataset_tab > .ordino-scrollspy-container .tissue-dataset > .card').then(() => TourUtils.wait(600)), postAction: TourUtils.clickSelector, pageBreak: 'manual', }, @@ -159,7 +73,7 @@ export class PredictionTP53Tour { selector: '.le.le-multi.lineup-engine', placement: 'centered', html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, - preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(1500)), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1)', Infinity).then(() => TourUtils.wait(1500)), }, { selector: '[data-testid="viewWrapper-0"] [data-id="col4"] .lu-action-filter', @@ -185,7 +99,6 @@ export class PredictionTP53Tour { TourUtils.click('[data-testid="add-column-button"]'); await TourUtils.wait(500); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); - // await TourUtils.wait(500); TourUtils.toggleClass('.lu-adder.once', 'once', false); TourUtils.waitFor('.modal.show').then(async () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); @@ -199,6 +112,7 @@ export class PredictionTP53Tour { selector: '[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter', html: `They filter out the samples with an unknown TP53 mutation status.`, placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col7"].lu-missing', Infinity), postAction: async () => { TourUtils.click('[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter'); await TourUtils.wait(500); @@ -215,23 +129,37 @@ export class PredictionTP53Tour {

      Aggregation: Average

      Compute score only for current sample subset

      `, placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col7"] [style="background-color: rgb(170, 170, 170);"]', Infinity), postAction: async () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); await TourUtils.wait(500); - TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'namedset4ensg', 'change'); - await TourUtils.wait(1000); - // TourUtils.click('.modal-dialog [data-testid="row-1"] .select2 input'); - // selectEvent.create(document.querySelector('.modal-dialog [data-testid="row-1"] .select2 input'), 'TP53 Predictor'); - TourUtils.setValueAndTrigger('.modal-dialog [data-testid="row-1"] .select2 input', 'TP53 Predictor', 'input'); - TourUtils.keyDownEnter('.modal-dialog [data-testid="row-1"] .select2 input'); - // selectEvent.select(document.querySelector('.modal-dialog [data-testid="row-1"] .select2 input'), ['TP53 Predictor']); - // TourUtils.click('.select2-results__options li:first-child'); + + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'ensg', 'change'); + await TourUtils.wait(1500); + TourUtils.click('[data-testid="Filter"] [data-testid="close-button"]'); + await TourUtils.wait(1500); + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'ensg', 'change'); + await TourUtils.wait(1500); + + // Now add the list of 13 genes here instead + TourUtils.setValueAndTrigger( + '.modal-dialog [data-testid="row-2"] .select2 input', + 'AEN,BAX,CCNG1,CDKN1A,DDB2,FDXR,MDM2,RPS27L,RRM2B,SESN1,TNFRSF10B,XPC,ZMAT3', + 'input', + ); + await TourUtils.wait(1020); + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); - TourUtils.click('[data-testid="form-checkbox"]'); - await TourUtils.wait(500); + + const checkboxTest = document.querySelector('.modal-dialog [data-testid="form-checkbox"]') as HTMLInputElement; + if (!checkboxTest.checked) { + TourUtils.click('.modal-dialog [data-testid="form-checkbox"]'); + } + + await TourUtils.wait(1000); TourUtils.click('.modal.show .modal-footer button[type=submit]'); }, }, @@ -248,118 +176,10 @@ export class PredictionTP53Tour { TP53: Of the 50 samples with the highest expression only 3 are TP53 mutated, whereas of the 50 samples with the lowest expression 35 are TP53 mutated.

      `, placement: 'centered', - }, // Comment out til here to remove first section - { - selector: 'ul[data-header="mainMenu"] > li:first-child > a', - html: `Next, they aim to test the applicability of gene signature and MDM2 sensitivity using all cell lines.`, - placement: 'centered', - preAction: () => { - const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; - if (!datasetTab.classList.contains('active')) { - datasetTab.querySelector('a').classList.add('hover'); - } - }, - postAction: () => { - const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; - if (!datasetTab.classList.contains('active')) { - datasetTab.querySelector('a').classList.remove('hover'); - datasetTab.querySelector('a').click(); - } - return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(1)')); - }, - }, - { - selector: '.ordino-dataset.cellline-dataset [data-testid="all-button"]', - html: `They open the list of ALL cell lines.`, - placement: 'centered', - postAction: TourUtils.clickSelector, - pageBreak: 'manual', }, { - selector: '[data-testid="add-column-button"]', - html: `

      They add a single gene score for the following:

      -

      Gene: TP53

      -

      Data Type: AA Mutated and AA Mutation

      `, - placement: 'centered', - postAction: async () => { - TourUtils.click('[data-testid="add-column-button"]'); - await TourUtils.wait(500); - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.modal.show').then(async () => { - if (document.querySelector('[data-testid="data-type"] .select2-selection__clear') !== null) { - TourUtils.click('[data-testid="data-type"] .select2-selection__clear'); - TourUtils.click('label[data-testid="Data Type"]'); // Just click anywhere safe to get rid of dropdown - } - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); - TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'input'); - await TourUtils.wait(500); - TourUtils.click('.modal.show .modal-footer button[type=submit]'); - }); - await TourUtils.wait(1500); - // Repeat again for the AA Mutation Column - TourUtils.click('[data-testid="add-column-button"]'); - await TourUtils.wait(500); - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.modal.show').then(async () => { - if (document.querySelector('[data-testid="data-type"] .select2-selection__clear') !== null) { - TourUtils.click('[data-testid="data-type"] .select2-selection__clear'); - TourUtils.click('label[data-testid="Data Type"]'); - } - TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); - TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aamutation', 'input'); - - await TourUtils.wait(500); - TourUtils.click('.modal.show .modal-footer button[type=submit]'); - }); - }, - }, - { - selector: '[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter', - html: `They once again filter out the samples with an unknown TP53 mutation status.`, - placement: 'centered', - postAction: async () => { - TourUtils.click('[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter'); - await TourUtils.wait(500); - TourUtils.click('.lu-dialog > .lu-checkbox input'); - await TourUtils.wait(500); - TourUtils.click('.lu-dialog-button[type="submit"]'); - }, - }, - { - selector: '.lu-side-panel-wrapper .lu-adder > button', - html: `

      Next they add the aggregated gene score with the following criteria again:

      -

      Filter: My Named Sets = TP53 Predictor

      -

      Data Type: Expression (TPM)

      -

      Aggregation: Average

      -

      Compute score for all cell lines

      `, - placement: 'centered', - postAction: async () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); - TourUtils.toggleClass('.lu-adder.once', 'once', false); - await TourUtils.wait(500); - if (document.querySelector('[data-testid="row-1"] [data-testid="close-button"]') !== null) { - TourUtils.click('[data-testid="row-1"] [data-testid="close-button"]'); - } - await TourUtils.wait(500); - TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'namedset4ensg', 'change'); - await TourUtils.wait(1000); - TourUtils.setValueAndTrigger('.modal-dialog [data-testid="row-1"] .select2 input', 'TP53 Predictor', 'input'); - TourUtils.keyDownEnter('.modal-dialog [data-testid="row-1"] .select2 input'); - TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); - TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); - /// ??? Uncomment the following line when the test is ready - // TourUtils.click('[data-testid="form-checkbox"]'); // This is very risky, as we are assuming it was checked previously, which should be remembered by the cookies and thus clicking again would deselect (as desired) - await TourUtils.wait(500); - TourUtils.click('.modal.show .modal-footer button[type=submit]'); - }, - }, - { - selector: '', - html: `THE TOUR IS HERE SO FAR`, - placement: 'centered', + html: `

      Thanks for joining this tour demonstrating the creation and basic testing of the TP53 Predictor Score.

      +

      There are still many more features to discover. Enjoy!

      `, }, ]; } diff --git a/src/tours/PredictionTP53Tour2.ts b/src/tours/PredictionTP53Tour2.ts new file mode 100644 index 00000000..38ee76b6 --- /dev/null +++ b/src/tours/PredictionTP53Tour2.ts @@ -0,0 +1,259 @@ +// import {ToursSection} from 'ordino'; +import { IStep, Tour } from 'tdp_core'; +import { TourUtils } from 'tdp_core/src/tour/TourUtils'; +import selectEvent from 'react-select-event'; +import { wideEnoughCat } from 'lineupjs/build/src/renderer/utils'; +import { select } from 'lineupjs'; + +export class PredictionTP53Tour2 { + static createTour(): IStep[] { + return [ + { + html: ` +

      + The following is a continuation of the tour investigating the TP53 Predictor Score, this + time in conjunction with the MDM2 sensitivity score, compared against all cell lines. +

      +

      + Use the "Next" button to iterate through all the steps. You can use the + "Cancel" button at any time to stop the tour and to interact with Ordino. + Please note that the tour will load a new analysis session and the current + one will be discarded. +

      + `, + }, + { + selector: 'ul[data-header="mainMenu"] > li:first-child > a', + html: `They start by opening the dataset tab, in order to find the relevant dataset to begin working with.`, + placement: 'centered', + preAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.add('hover'); + } + }, + postAction: () => { + const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; + if (!datasetTab.classList.contains('active')) { + datasetTab.querySelector('a').classList.remove('hover'); + datasetTab.querySelector('a').click(); + } + return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(1)')); + }, + }, + { + selector: '.ordino-dataset.cellline-dataset [data-testid="all-button"]', + html: `They open the list of ALL cell lines.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + pageBreak: 'manual', + }, + { + selector: '[data-testid="add-column-button"]', + html: `

      They add a single gene score for the following:

      +

      Gene: TP53

      +

      Data Type: AA Mutated and AA Mutation

      `, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1)', Infinity).then(() => TourUtils.wait(1500)), + postAction: async () => { + TourUtils.click('[data-testid="add-column-button"]'); + await TourUtils.wait(500); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + await TourUtils.waitFor('.modal.show'); + + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); + await TourUtils.wait(500); + + // Check if data types were remembered and remove + while (document.querySelector('[data-testid="Data Type"] span.select2-selection__choice__remove') !== null) { + TourUtils.click('[data-testid="Data Type"] span.select2-selection__choice__remove:nth-of-type(1)'); + } + + // Now check if the pesky dropdown menu has shown up, and remove + if (document.querySelector('span.select2-dropdown') !== null) { + TourUtils.click('[data-testid="Data Type"] .select2-search--inline > input.select2-search__field'); + } + await TourUtils.wait(200); + + // KNOWN BUG: (Sometimes) If either of the following options were selected the last time a single gene score column was added, they won't be + // selected when running this tour the first time around. This can be fixed by simply restarting the tour. + + const selection1 = document.querySelector('option[value="mutation-aa_mutated"]'); + selection1.setAttribute('selected', 'selected'); + + const selection2 = document.querySelector('option[value="mutation-aamutation"]'); + selection2.setAttribute('selected', 'selected'); + + await TourUtils.wait(1500); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }, + }, + { + selector: '[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter', + html: `They once again filter out the samples with an unknown TP53 mutation status.`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col8"].lu-missing', Infinity), + postAction: async () => { + TourUtils.click('[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog > .lu-checkbox input'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-button[type="submit"]'); + }, + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `

      Next they add an aggregated gene score with the following criteria:

      +

      Filter: Gene Symbol = AEN, BAX, CCNG1, CDKN1A, DDB2, FDXR, MDM2, RPS27L, RRM2B, SESN1, TNFRSF10B, XPC, + ZMAT3

      +

      Data Type: Expression (TPM)

      +

      Aggregation: Average

      +

      Compute score for all cell lines, not only the selected subset

      `, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col7"] [style="background-color: rgb(27, 166, 78);"]', Infinity), + postAction: async () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + await TourUtils.wait(500); + + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'ensg', 'change'); + await TourUtils.wait(1500); + TourUtils.click('[data-testid="Filter"] [data-testid="close-button"]'); + await TourUtils.wait(1500); + TourUtils.setValueAndTrigger('.show .modal-body form > div:nth-child(1) .row:nth-child(1) div:nth-child(1) select', 'ensg', 'change'); + await TourUtils.wait(1500); + + // Now add the list of 13 genes here instead + TourUtils.setValueAndTrigger( + '.modal-dialog [data-testid="row-2"] .select2 input', + 'AEN,BAX,CCNG1,CDKN1A,DDB2,FDXR,MDM2,RPS27L,RRM2B,SESN1,TNFRSF10B,XPC,ZMAT3', + 'input', + ); + await TourUtils.wait(1020); + + TourUtils.setValueAndTrigger('.show .modal-body form > .col-sm-12:nth-child(2) select', 'expression-tpm', 'change'); + TourUtils.setValueAndTrigger('.show [data-testid="aggregation"] select', 'avg', 'change'); + + // Inspect if the checkbox is checked, if so then uncheck it + const checkboxTest = document.querySelector('.modal-dialog [data-testid="form-checkbox"]') as HTMLInputElement; + if (checkboxTest.checked) { + TourUtils.click('.modal-dialog [data-testid="form-checkbox"]'); + } + await TourUtils.wait(1000); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }, + }, + { + selector: '[data-id="col9"] > .lu-toolbar > .lu-action-more', + html: `

      They decide to rename the new column to "TP53 Predictor Score".

      `, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="54.56"]', Infinity), + postAction: async () => { + TourUtils.click('[data-id="col9"] > .lu-toolbar > .lu-action-more'); + await TourUtils.wait(500); + TourUtils.click('.lu-action-rename > span'); + await TourUtils.waitFor('.lu-dialog-rename input[placeholder="name"]'); + TourUtils.setValueAndTrigger('.lu-dialog-rename input[placeholder="name"]', 'TP53 Predictor Score', 'change'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + }, + }, + { + selector: '[data-id="col9"] .lu-action-filter', + html: `They now filter out the samples with an unknown TP53 Predictor Score …`, + placement: 'centered', + postAction: async () => { + TourUtils.click('[data-id="col9"] .lu-action-filter'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog .lu-checkbox input'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-button[type="submit"]'); + }, + }, + { + selector: '[data-id="col9"] .lu-action-sort', + html: `… and sort by this column.`, + placement: 'centered', + postAction: TourUtils.clickSelector, + }, + { + selector: '.le.le-multi.lineup-engine', + html: `

      Observe: There is a clear enrichment of TP53 non-mutated among the cell lines with high score.

      `, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="209.10"]', Infinity), + }, + { + selector: '.lu-side-panel-wrapper .lu-adder > button', + html: `

      Next, they choose to add a 'Depletion Screen Score (Single)' using the following:

      +

      Gene: MDM2

      +

      Data type: DRIVE RSA (NB: the lower this value, the more sensitive a cell line is to the depletion of the gene of interest)

      `, + placement: 'centered', + postAction: async () => { + TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); + TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(4) > span'); + TourUtils.toggleClass('.lu-adder.once', 'once', false); + await TourUtils.waitFor('.modal.show').then(() => TourUtils.wait(500)); + TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'MDM2;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', 'depletion-rsa', 'change'); + const checkboxTest = document.querySelector('.modal-dialog [data-testid="form-checkbox"]') as HTMLInputElement; + if (!checkboxTest.checked) { + TourUtils.click('.modal-dialog [data-testid="form-checkbox"]'); + } + await TourUtils.wait(1000); + TourUtils.click('.modal.show .modal-footer button[type=submit]'); + }, + }, + { + selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', + html: `

      To amplify the visibility of the added depletion score's significance, they decide to invert the scaling via the data mapping.

      `, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col10"].lu-missing', Infinity), + postAction: async () => { + TourUtils.click('[data-id="col10"] > .lu-toolbar > .lu-action-more'); + await TourUtils.wait(500); + TourUtils.click('.lu-action-data-mapping > span'); + TourUtils.setValueAndTrigger('.browser-default', 'linear_invert', 'change'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-buttons > [type="submit"]'); + }, + }, + { + selector: '[data-id="col10"] .lu-action-filter', + html: `They filter out this MDM2 column's missing values …`, + placement: 'centered', + postAction: async () => { + TourUtils.click('[data-id="col10"] .lu-action-filter'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog .lu-checkbox input'); + await TourUtils.wait(500); + TourUtils.click('.lu-dialog-button[type="submit"]'); + }, + }, + { + selector: '[data-id="col10"] .lu-action-sort', + html: `… and sort by this column.`, + placement: 'centered', + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="−1.00"]', Infinity), + postAction: TourUtils.clickSelector, + }, + { + selector: '.le.le-multi.lineup-engine', + html: `

      Observe: Small MDM2 RSA values (large bars) are correlated to the expression score (TP53 predictor score) and the TP53 mutation status

      `, + placement: 'centered', + allowUserInteraction: true, + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="−7.14"]', Infinity), + }, + // Can't do the drag operation for this final step in the aim + // Remaining two aims are also primarily just observations, but rely on the combined score column; What to do? + { + selector: '', + html: `

      Conclusion: When combining the TP53 Predictor Score column and the MDM2 Gene Sensitivity Score, the new weighted sum column serves as an even more accurate predictor.

      +

      Thanks for joining this tour taking a deeper look into the TP53 Predictor Score.

      +

      There are still many more features to discover. Enjoy!

      `, + placement: 'centered', + }, + ]; + } +} diff --git a/src/tours/index.ts b/src/tours/index.ts index d52e5a44..49afb11a 100644 --- a/src/tours/index.ts +++ b/src/tours/index.ts @@ -3,4 +3,5 @@ export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; export * from './AssessBCCellLinesTour'; export * from './PredictionTP53Tour'; -// export * from './DrugTargetDiscoveryTour'; +export * from './PredictionTP53Tour2'; +export * from './DrugTargetDiscoveryTour'; From f3329a991aded90f904986697b9a6122f788a8ad Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 3 Apr 2023 10:38:22 +0200 Subject: [PATCH 33/38] Shortened names and descriptions for spacing --- src/phovea.ts | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/phovea.ts b/src/phovea.ts index f75ac7dc..4f13c9a3 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1073,7 +1073,7 @@ export default function (registry) { }, { factory: 'createTour', - name: 'Assessment and Selection of Breast Cancer Cell Lines', + name: 'Assessment of Breast Cancer Cell Lines', description: 'This case study summarizes an analysis session carried out by a scientist working in a drug discovery team at a pharmaceutical company.', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image @@ -1112,8 +1112,7 @@ export default function (registry) { { factory: 'createTour', name: 'Prediction of TP53 Mutation Status: Continued', - description: - 'This case study serves as a continuation of the initial tour "Prediction of TP53 Mutation Status". It takes a deeper look into the efficacy of the TP53 Predictor Score, in combination with the MDM2 sensitivity score.', + description: 'This case study serves as a continuation of the initial tour "Prediction of TP53 Mutation Status".', preview() { return import('./assets/previews/expression.jpg'); // TODO update preview image }, From 787e1c0b3e325ce40832ec04e4216aa39bdad049 Mon Sep 17 00:00:00 2001 From: Michael Peterseil Date: Mon, 3 Apr 2023 14:20:23 +0200 Subject: [PATCH 34/38] Updated tour preview images --- src/assets/previews/tourAddColumn.png | Bin 0 -> 7770 bytes src/assets/previews/tourBreastCancerCL.png | Bin 0 -> 11358 bytes src/assets/previews/tourDrugDiscovery.png | Bin 0 -> 22449 bytes src/assets/previews/tourOrdinoWelcome.png | Bin 0 -> 5809 bytes src/assets/previews/tourStartMenu.png | Bin 0 -> 8664 bytes src/assets/previews/tourTP53Predictor.png | Bin 0 -> 10594 bytes src/phovea.ts | 14 +++++++------- 7 files changed, 7 insertions(+), 7 deletions(-) create mode 100644 src/assets/previews/tourAddColumn.png create mode 100644 src/assets/previews/tourBreastCancerCL.png create mode 100644 src/assets/previews/tourDrugDiscovery.png create mode 100644 src/assets/previews/tourOrdinoWelcome.png create mode 100644 src/assets/previews/tourStartMenu.png create mode 100644 src/assets/previews/tourTP53Predictor.png diff --git a/src/assets/previews/tourAddColumn.png b/src/assets/previews/tourAddColumn.png new file mode 100644 index 0000000000000000000000000000000000000000..5a67cc5f8d9fb24f215175ab4203170ca13cf9ec GIT binary patch literal 7770 zcmbW6WmHseyT%7W8bLuiM5Ls1XcQ2X7*doDfuV=)Qd*cnK{^#FNu|3%a>${(JBN<5 z{lDw1_g!cC;hZxcVA!+QX3w+l`?`PE^@OWI6o~Mt@j)OE(W{qo8XyqHGvIw0E;jIU zWf^@R_=V*x^GXXBc=_O(g#mw4xx9Gmq6xEbaW`=?2SM#&cII5p@0`rd?VT-QE_;}b zQou>fe@>EhGBjc-JoyPzw+kW;VKo03#XxCV|eO}rVMzL{m-^Q%ixnlLnztyPcX}!%A%GG+R8GlEs88ot0 z)|)IIs&2xhV(^h2^%I1EKs~(Pxb=unA z-acXua>8N@Qsc#Y#u#M!3WU!{rgTRQ_v_mS0W!Gl(I7Gzwm7T|5}BV*K*1y*Uvu4Y zxQgHzUdf|hX-G>HGvl}3#?tk^94e9p9j)>_D;|s4S9pArTBD(* z-zc;o5F&A@`u1`U5$Tw(pjP(99Pz0BQOBu@F|n&k2NOuV+8&pPm7 zYvYaE*vV)3itvaCf3~fZn_bSsqoaumb5bR8p5-l=@Btc} zY&ly;#ZU((wXxX>9a8ly)8%@{S|@kuW_Ny2yAz2=)3pU_XwMslJ}oy2AZ1nM_gmy3 z#N9=n6ee%b4t(ZYVs%1qjw0jy!R};?Brx6wySus?lsLK=?$;0|EpJc z!*hwjV@q}$(`YL<-_yXst@HD-uAZJu^Bx7O@eB-E>`?yGz|)e7ip2}`mU7|+OH}1G zg+cl~)7$q(pz+FE(2VzS$5yyor2m1rtg-9fVDbQCtL4s)lC?E;=)GG-W297wo2RFz zyf19BE?7ZN5W2n2o8;ladmbCVKAp$3)}Nk}n;QnsRsoODmHR3r`hwAYm7eB@HXvH@ z8&;L1%EugA4+LgY+cO3jC5HV$vki1_f4NY>l#?Me=_eB4v%80fhhfvy!Tvc#brPQV zhN@*uw!I#rKMG7QPWO-qbCphazqS#H{?dlxN=`WLmdkE9Cm$og zCoCTOvC`Crx0G;lA|6S9`gqRw786tEVrh4^<5w7uh~E{Kx?ThG@x*iGB>vdxX?>Q4 z!>7RKKW)69-1c>wo=l&Ip!2kzqKYm)OqSd5nJjWdQc6YU{)Scitl)FJDHi&{B_ssT zR!OGL7NRCnBKKFe;o*t%Z}`yKc-`^mUL-b{vz1fjofH+@XW1TY4Kb7VruQVMn{eVA zeaL}o3ft);yEJpgtGB#mlcnmtf7+w*O;2`MPv*bk7aM6wL7`9?S=osyM(v2{vBO!&js{bjyqS^0~;>-^=|OFrA5zdRUTcb$q#9g zyFLa^$XQAR!)?s0uWZ6iKj+7f5wBEL!PWxiha7S*{32@gWM|X(V%D&UGpni+0z>_> zplXkHckP4VlpXOl+K1ly5@W?iP?zzS)6~LdzvtCVPxinCTN}Ho3rp8norv46@@?DM zOXGWzm&a>SZA>W=u9LZQweU8&Qkb;w<#D!E3`@}QUT8$AKx3P>M24;)Og>_@Z-Z=} zxG4jpxy*8w77Pae;x@R`)I6I;uj<~}d5LE&D&lZ{7z-@jl|V{r>c&tO!RODPT{ec= zZCi#7&frCnW|w?23Kl7*IL zs9;Ak{dR4vPaM|wi>IZctFp3~Rgyi7?d;%+S^R_ohPt{RAvrvix8uIvXGfNISfiMK z9ml+oFRm7{eb#NK;Hp~~_ewL{NpORb8s1?kQK_LgxCK{LXK=|qI{fg)9cpm%j#s!DCe>{Zz%6p+<(^r=WI z|4LtD`{ZPjN^&Ky_pDE}rp8M#w-lg^jiFGzuSt^^9;D^ItT~YMg-Zs%x_8Nl8$a8K zNr+DiLmTT=vr>$qPz}o5%Brg~LYi?g;$e!of7+a1glzGcW~qhB-itBsATv*BI*9RU+5`^MGNHd0keNNArBR-Z6vX>swDlG575b4<&T->LHO>5Z{U zVqsz7?eU)x2k$!7D(wx#uv|+XBAxpORO0Tw zs;BhziAM`Q*^OvysaaKClW9ubGD}FhALiR~FFGU6+ekoC4kn@fFt+3g`Z-lb{bX>9xT*p$lE zdd$LQ92Z!ACNniQXKDSWl+#<4VHTChI0o7aPV4dzscY;nqV?pfJpBAa>q&EkHXned zU@6*e&b8=I(aGxPDT2fjn;A$nK zg}2lJ&*#Vdrd?gzk|>_4-B}3~(sinipo1&()l%>SKN&6c2LZ%7new|n^?p0`H293l z{kFvz_>66H%oqTaaH_n%ghL?^M4l3fjMlf56k1zbTV(@mP?DJIW&%JnKokCpW@u?? 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a/src/phovea.ts b/src/phovea.ts index 4f13c9a3..636d0211 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1019,7 +1019,7 @@ export default function (registry) { name: 'Ordino Welcome Tour', description: 'Learn the basic features of Ordino in a short welcome tour.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourOrdinoWelcome.png'); }, multiPage: true, level: 'beginner', @@ -1038,7 +1038,7 @@ export default function (registry) { name: 'Overview of Start Menu', description: 'This tour provides an overview of the Ordino start menu.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourStartMenu.png'); }, multiPage: true, level: 'beginner', @@ -1057,7 +1057,7 @@ export default function (registry) { name: 'Adding Data Columns', description: 'Learn how to add data columns to rankings in Ordino.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourAddColumn.png'); }, multiPage: true, level: 'beginner', @@ -1076,7 +1076,7 @@ export default function (registry) { name: 'Assessment of Breast Cancer Cell Lines', description: 'This case study summarizes an analysis session carried out by a scientist working in a drug discovery team at a pharmaceutical company.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourBreastCancerCL.png'); }, multiPage: true, level: 'beginner', @@ -1095,7 +1095,7 @@ export default function (registry) { name: 'Prediction of TP53 Mutation Status', description: 'This case study summarizes another analysis session, this time involving the prediction of the mutation status for TP53.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourTP53Predictor.png'); }, multiPage: true, level: 'beginner', @@ -1114,7 +1114,7 @@ export default function (registry) { name: 'Prediction of TP53 Mutation Status: Continued', description: 'This case study serves as a continuation of the initial tour "Prediction of TP53 Mutation Status".', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourTP53Predictor.png'); }, multiPage: true, level: 'beginner', @@ -1134,7 +1134,7 @@ export default function (registry) { description: 'A demonstration of Taggle (integrated into the Ordino Target Discovery Platform) by means of a case study conducted on complex genomics data for the purpose of drug target discovery.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourDrugDiscovery.png'); }, multiPage: true, level: 'beginner', From 2fad12f388628ff3e94c0a94efc94f0982be93b0 Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Thu, 6 Apr 2023 12:13:04 +0200 Subject: [PATCH 35/38] chore: add missing dist files --- dist/phovea.d.ts.map | 2 +- dist/phovea.js | 29 +++++++++++++++++++++-------- dist/phovea.js.map | 2 +- dist/tours/index.d.ts | 1 + dist/tours/index.d.ts.map | 2 +- dist/tours/index.js | 1 + dist/tours/index.js.map | 2 +- 7 files changed, 27 insertions(+), 12 deletions(-) diff --git a/dist/phovea.d.ts.map b/dist/phovea.d.ts.map index b3839088..af44ac3c 100644 --- a/dist/phovea.d.ts.map +++ b/dist/phovea.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"phovea.d.ts","sourceRoot":"","sources":["../src/phovea.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,OAAO,WAAW,QAAQ,KAAA,QAiyChC"} \ No newline at end of file +{"version":3,"file":"phovea.d.ts","sourceRoot":"","sources":["../src/phovea.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,OAAO,WAAW,QAAQ,KAAA,QAqzChC"} \ No newline at end of file diff --git a/dist/phovea.js b/dist/phovea.js index f1b24df9..bd78f5a5 100644 --- a/dist/phovea.js +++ b/dist/phovea.js @@ -701,7 +701,7 @@ export default function (registry) { name: 'Ordino Welcome Tour', description: 'Learn the basic features of Ordino in a short welcome tour.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourOrdinoWelcome.png'); }, multiPage: true, level: 'beginner', @@ -714,7 +714,7 @@ export default function (registry) { name: 'Overview of Start Menu', description: 'This tour provides an overview of the Ordino start menu.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourStartMenu.png'); }, multiPage: true, level: 'beginner', @@ -727,7 +727,7 @@ export default function (registry) { name: 'Adding Data Columns', description: 'Learn how to add data columns to rankings in Ordino.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourAddColumn.png'); }, multiPage: true, level: 'beginner', @@ -737,10 +737,10 @@ export default function (registry) { return import('./tours').then((t) => t.AssessBCCellLinesTour); }, { factory: 'createTour', - name: 'Assessment and Selection of Breast Cancer Cell Lines', + name: 'Assessment of Breast Cancer Cell Lines', description: 'This case study summarizes an analysis session carried out by a scientist working in a drug discovery team at a pharmaceutical company.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourBreastCancerCL.png'); }, multiPage: true, level: 'beginner', @@ -753,7 +753,20 @@ export default function (registry) { name: 'Prediction of TP53 Mutation Status', description: 'This case study summarizes another analysis session, this time involving the prediction of the mutation status for TP53.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourTP53Predictor.png'); + }, + multiPage: true, + level: 'beginner', + canJumpAround: false, + }); + registry.push('tdpTour', 'ordinoPredictionTP53Tour2', function () { + return import('./tours').then((t) => t.PredictionTP53Tour2); + }, { + factory: 'createTour', + name: 'Prediction of TP53 Mutation Status: Continued', + description: 'This case study serves as a continuation of the initial tour "Prediction of TP53 Mutation Status".', + preview() { + return import('./assets/previews/tourTP53Predictor.png'); }, multiPage: true, level: 'beginner', @@ -764,9 +777,9 @@ export default function (registry) { }, { factory: 'createTour', name: 'Drug Target Discovery', - description: '??? Add description here.', + description: 'A demonstration of Taggle (integrated into the Ordino Target Discovery Platform) by means of a case study conducted on complex genomics data for the purpose of drug target discovery.', preview() { - return import('./assets/previews/expression.jpg'); // TODO update preview image + return import('./assets/previews/tourDrugDiscovery.png'); }, multiPage: true, level: 'beginner', diff --git a/dist/phovea.js.map b/dist/phovea.js.map index a9ea3d13..b9c4c5d0 100644 --- a/dist/phovea.js.map +++ b/dist/phovea.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/tours/index.d.ts b/dist/tours/index.d.ts index b6553e9f..7f2f9116 100644 --- a/dist/tours/index.d.ts +++ b/dist/tours/index.d.ts @@ -3,5 +3,6 @@ export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; export * from './AssessBCCellLinesTour'; export * from './PredictionTP53Tour'; +export * from './PredictionTP53Tour2'; export * from './DrugTargetDiscoveryTour'; //# sourceMappingURL=index.d.ts.map \ No newline at end of file diff --git a/dist/tours/index.d.ts.map b/dist/tours/index.d.ts.map index f6317ad8..878fdb0f 100644 --- a/dist/tours/index.d.ts.map +++ b/dist/tours/index.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,yBAAyB,CAAC;AACxC,cAAc,sBAAsB,CAAC;AACrC,cAAc,2BAA2B,CAAC"} \ No newline at end of file +{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,yBAAyB,CAAC;AACxC,cAAc,sBAAsB,CAAC;AACrC,cAAc,uBAAuB,CAAC;AACtC,cAAc,2BAA2B,CAAC"} \ No newline at end of file diff --git a/dist/tours/index.js b/dist/tours/index.js index 6a76d982..c91f02b2 100644 --- a/dist/tours/index.js +++ b/dist/tours/index.js @@ -3,5 +3,6 @@ export * from './AddColumnToGeneListTour'; export * from './StartMenuTour'; export * from './AssessBCCellLinesTour'; export * from './PredictionTP53Tour'; +export * from './PredictionTP53Tour2'; export * from './DrugTargetDiscoveryTour'; //# sourceMappingURL=index.js.map \ No newline at end of file diff --git a/dist/tours/index.js.map b/dist/tours/index.js.map index 460884b2..a2cb0eff 100644 --- a/dist/tours/index.js.map +++ b/dist/tours/index.js.map @@ -1 +1 @@ -{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,yBAAyB,CAAC;AACxC,cAAc,sBAAsB,CAAC;AACrC,cAAc,2BAA2B,CAAC"} \ No newline at end of file +{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/tours/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAC;AAC9B,cAAc,2BAA2B,CAAC;AAC1C,cAAc,iBAAiB,CAAC;AAChC,cAAc,yBAAyB,CAAC;AACxC,cAAc,sBAAsB,CAAC;AACrC,cAAc,uBAAuB,CAAC;AACtC,cAAc,2BAA2B,CAAC"} \ No newline at end of file From edbcfc191ae98b3e3dbcc9cd5b3abba25e7c058d Mon Sep 17 00:00:00 2001 From: oltionchampari Date: Fri, 7 Apr 2023 09:59:03 +0200 Subject: [PATCH 36/38] Minor fixes and improvments --- src/tours/AddColumnToGeneListTour.ts | 11 +++--- src/tours/AssessBCCellLinesTour.ts | 50 +++++++++++++++------------- src/tours/DrugTargetDiscoveryTour.ts | 17 ++++++---- src/tours/PredictionTP53Tour.ts | 30 +++++++++-------- src/tours/PredictionTP53Tour2.ts | 46 +++++++++++++++---------- src/tours/WelcomeTour.ts | 3 +- src/tours/utils.ts | 16 +++++++++ 7 files changed, 104 insertions(+), 69 deletions(-) create mode 100644 src/tours/utils.ts diff --git a/src/tours/AddColumnToGeneListTour.ts b/src/tours/AddColumnToGeneListTour.ts index 59dc3031..fdcf0a1b 100644 --- a/src/tours/AddColumnToGeneListTour.ts +++ b/src/tours/AddColumnToGeneListTour.ts @@ -1,4 +1,5 @@ import { IStep, TourUtils } from 'tdp_core'; +import { openAddColumPanel } from './utils'; export class AddColumnToGeneListTour { static createTour(): IStep[] { @@ -64,7 +65,7 @@ export class AddColumnToGeneListTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `Additional columns can be added using the plus sign.`, placement: 'centered', - postAction: TourUtils.clickSelector, + postAction: openAddColumPanel, }, { @@ -133,9 +134,7 @@ export class AddColumnToGeneListTour { selector: '.lu-search .lu-search-group .lu-search-item', placement: 'centered', html: `Now, we want to add two columns containing the copy number information of two specific cell lines. To do so, we open the 'Cell Line Score (Single)' dialog`, - preAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - }, + preAction: openAddColumPanel, postAction: () => { TourUtils.click('.lu-search .lu-search-group .lu-search-item'); TourUtils.toggleClass('.lu-adder.once', 'once', false); @@ -180,9 +179,7 @@ export class AddColumnToGeneListTour { placement: 'centered', html: `Finally, we want to add an aggregated column containing the mean/average copy number values of all breast cancer cell lines. To do so, we open the 'Cell Line Score (Aggregated)' dialog`, - preAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - }, + preAction: openAddColumPanel, postAction: () => { TourUtils.click('.lu-search .lu-search-group .lu-search-item:nth-child(2)'); TourUtils.toggleClass('.lu-adder.once', 'once', false); diff --git a/src/tours/AssessBCCellLinesTour.ts b/src/tours/AssessBCCellLinesTour.ts index 1dd268b5..cd25c628 100644 --- a/src/tours/AssessBCCellLinesTour.ts +++ b/src/tours/AssessBCCellLinesTour.ts @@ -1,6 +1,5 @@ -// import {ToursSection} from 'ordino'; -import selectEvent from 'react-select-event'; -import { IStep, Tour, TourUtils } from 'tdp_core'; +import { IStep, TourUtils } from 'tdp_core'; +import { openAddColumPanel, setNextActive } from './utils'; export class AssessBCCellLinesTour { static createTour(): IStep[] { @@ -25,7 +24,7 @@ export class AssessBCCellLinesTour { datasetTab.querySelector('a').classList.add('hover'); } }, - postAction: () => { + postAction: async () => { const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; if (!datasetTab.classList.contains('active')) { datasetTab.querySelector('a').classList.remove('hover'); @@ -47,7 +46,7 @@ export class AssessBCCellLinesTour { selector: '[data-testid="normal-chromosome-protein-coding-human-genes-button"]', html: `The scientists start by loading the list of all protein coding genes for humans.`, placement: 'centered', - postAction: () => { + postAction: async () => { return TourUtils.waitFor('.ordino-dataset.genes-dataset .dataset-entry button[title^="Name: normal chromosome protein coding human genes"]').then( TourUtils.click, ); @@ -57,22 +56,23 @@ export class AssessBCCellLinesTour { { selector: '.le.le-multi.lineup-engine', placement: 'centered', + preAction: () => TourUtils.waitFor('.le.le-multi.lineup-engine', Infinity).then(() => TourUtils.wait(2000)), html: `The information is presented in a tabular format. Additionally to the gene ID, a set of columns containing some basic information is shown by default.`, - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1)', Infinity), }, { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `They begin by adding an additional column, done so by clicking on the plus icon shown here.`, placement: 'centered', - postAction: TourUtils.clickSelector, + postAction: openAddColumPanel, }, { - selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', + selector: '[data-testid="lu-adder-div"] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', html: `They choose to add a column for a single cell line score.`, placement: 'centered', - postAction: () => { - TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); + postAction: async () => { + TourUtils.click('[data-testid="lu-adder-div"] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); + return Promise.resolve(); }, }, { @@ -102,27 +102,27 @@ export class AssessBCCellLinesTour { selector: '.le [data-col-id="col8"] .lu-action-sort', placement: 'centered', html: `They want to sort by this newly added column, so they click on the sort button in the column header.`, - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="1.83"]', Infinity), + preAction: () => TourUtils.waitFor('.le-tr[data-index="0"] [data-id="col8"].lu-renderer-number', Infinity), postAction: () => { TourUtils.click('.le [data-col-id="col8"] .lu-action-sort'); }, }, { - // selector: ['[data-index="0"].le-tr, [data-index="14"].le-tr'], // Bug: It highlights the selectors before waiting for the preAction + selector: ['[data-index="0"].le-tr, [data-index="14"].le-tr'], placement: 'centered', html: `After sorting by this column, the analyst observes that about 15 genes on chromosome 17 are affected by a large genomic amplification.`, - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="8.00"]', Infinity), + preAction: () => TourUtils.waitFor('[data-index="0"].le-tr', Infinity).then(() => TourUtils.wait(2000)), }, { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `

      In order to identify the most relevant of these genes, the analyst adds a column with the Normalized Gene Expression (a measure of activity) for cell line HCC1954

      Individual steps for adding a column have been skipped this time.

      `, placement: 'centered', - postAction: () => { + postAction: async () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.modal.show').then(async () => { + await TourUtils.waitFor('.modal.show').then(async () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'HCC1954;', 'input'); TourUtils.setValueAndTrigger('.show .col > select', 'expression-tpm', 'change'); await TourUtils.wait(1000); @@ -134,7 +134,7 @@ export class AssessBCCellLinesTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `They also add a column with a Gene Sensitivity Score (a measure of importance for cell survival) for HCC1954.`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="5324.86"]', Infinity), + preAction: () => TourUtils.waitFor('.le-tr[data-index="0"] [data-id="col9"].lu-renderer-number', Infinity), postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); }, @@ -159,7 +159,7 @@ export class AssessBCCellLinesTour { html: `

      In an effort to improve the depletion score's readability, they decide to invert the linear scaling.

      To do this, they click on the three dots for more column options.

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="−2.75"]', Infinity), + preAction: () => TourUtils.waitFor('.le-tr[data-index="0"] [data-id="col10"].lu-renderer-number', Infinity), postAction: TourUtils.clickSelector, }, { @@ -230,7 +230,7 @@ export class AssessBCCellLinesTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `2. A column with the gene copy number distribution for breast cancer cell lines in boxplot format`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="890.37"]', Infinity), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col11"].lu-renderer-number', Infinity), postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); @@ -255,7 +255,7 @@ export class AssessBCCellLinesTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `3. A column with the gene amplification frequency (>4) across all breast cancer cell lines`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) .lu-renderer-boxplot', Infinity), + preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col12"].lu-renderer-boxplot', Infinity), postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); @@ -301,22 +301,24 @@ export class AssessBCCellLinesTour { postAction: TourUtils.clickSelector, }, { - selector: '.ids', + selector: '.tdp-view.expressionVsCopyNumber .ids', html: `Here they observe the direct correlation between copy number and expression of ERBB2.`, placement: 'centered', - preAction: () => TourUtils.waitFor('.ids').then(() => TourUtils.wait(300)), + preAction: () => TourUtils.waitFor('.tdp-view.expressionVsCopyNumber .ids').then(() => TourUtils.wait(300)), }, { selector: '[data-viewid="targetvalidation"]', + preAction: TourUtils.clickSelector, html: `To find more information, they open the 'Open Targets' detail view …`, placement: 'centered', - postAction: TourUtils.clickSelector, + waitFor: () => TourUtils.waitFor('iframe [title="ERBB2"]').then(setNextActive), }, { selector: '[data-viewid="pubmed"]', html: `… and then the 'PubMed' detail view.`, placement: 'centered', - postAction: TourUtils.clickSelector, + preAction: TourUtils.clickSelector, + waitFor: () => TourUtils.waitFor('.tdp-view.proxy_view ').then(setNextActive), }, { selector: '', @@ -378,7 +380,7 @@ export class AssessBCCellLinesTour { selector: '[data-testid="viewWrapper-1"] .lu-side-panel-wrapper .lu-adder > button', html: `They now want to add the BRCA gene score columns.`, placement: 'centered', - postAction: TourUtils.clickSelector, + postAction: openAddColumPanel, }, { selector: '[data-testid="viewWrapper-1"] [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', diff --git a/src/tours/DrugTargetDiscoveryTour.ts b/src/tours/DrugTargetDiscoveryTour.ts index 2eaf76d6..231e5a30 100644 --- a/src/tours/DrugTargetDiscoveryTour.ts +++ b/src/tours/DrugTargetDiscoveryTour.ts @@ -1,5 +1,6 @@ // import {ToursSection} from 'ordino'; -import { IStep, Tour, TourManager, TourUtils } from 'tdp_core'; +import { IStep, TourUtils } from 'tdp_core'; +import { openAddColumPanel } from './utils'; export class DrugTargetDiscoveryTour { static createTour(): IStep[] { @@ -89,7 +90,7 @@ export class DrugTargetDiscoveryTour { html: `As the analyst wants to investigate the TP53 gene, he decides to add a categorical column with the mutation status (mutated vs non mutated).`, placement: 'centered', preAction: TourUtils.waitForSelector, - postAction: TourUtils.clickSelector, + postAction: openAddColumPanel, }, { selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', @@ -124,11 +125,12 @@ export class DrugTargetDiscoveryTour { postAction: TourUtils.clickSelector, }, { - selector: '.lu-side-panel-wrapper .lu-adder > button', + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', html: `

      Additionally, they decide to add a textual column that provides further details about the mutation (if present).

      This is done by repeating the same steps to add a column, but choosing "AA Mutation" as the data type this time instead.

      Individual steps for adding a column have been skipped this time.

      `, placement: 'centered', + preAction: openAddColumPanel, postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); @@ -150,7 +152,7 @@ export class DrugTargetDiscoveryTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `They begin by adding a new column.`, placement: 'centered', - postAction: TourUtils.clickSelector, + postAction: openAddColumPanel, }, { selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span', @@ -215,9 +217,10 @@ export class DrugTargetDiscoveryTour { }, }, { - selector: '.lu-side-panel-wrapper .lu-adder > button', + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span', html: `Similarly, they add a matrix column with all of the individual expression values.`, placement: 'centered', + preAction: openAddColumPanel, postAction: async () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); @@ -362,15 +365,17 @@ export class DrugTargetDiscoveryTour { placement: 'centered', }, { - selector: '.lu-side-panel-wrapper .lu-adder > button', + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', html: `He adds a column with the CDKN2A relative copy number, …`, placement: 'centered', + preAction: openAddColumPanel, postAction: () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); TourUtils.waitFor('.modal.show').then(() => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'CDKN2A;', 'input'); + TourUtils.setValueAndTrigger('.show .col > select', null, 'change'); // clear previous value TourUtils.setValueAndTrigger('.show .col > select', 'copy_number-relativecopynumber', 'change'); TourUtils.wait(2000).then(() => TourUtils.click('.modal.show .modal-footer button[type=submit]')); }); diff --git a/src/tours/PredictionTP53Tour.ts b/src/tours/PredictionTP53Tour.ts index 3de6bc0c..7d4d99e0 100644 --- a/src/tours/PredictionTP53Tour.ts +++ b/src/tours/PredictionTP53Tour.ts @@ -1,9 +1,7 @@ // import {ToursSection} from 'ordino'; -import { IStep, Tour } from 'tdp_core'; +import { IStep } from 'tdp_core'; import { TourUtils } from 'tdp_core/src/tour/TourUtils'; -import selectEvent from 'react-select-event'; -import { wideEnoughCat } from 'lineupjs/build/src/renderer/utils'; -import { select } from 'lineupjs'; +import { openAddColumPanel } from './utils'; export class PredictionTP53Tour { static createTour(): IStep[] { @@ -44,15 +42,17 @@ export class PredictionTP53Tour { datasetTab.querySelector('a').classList.add('hover'); } }, - postAction: () => { + postAction: async () => { const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; if (!datasetTab.classList.contains('active')) { datasetTab.querySelector('a').classList.remove('hover'); datasetTab.querySelector('a').click(); } - return TourUtils.waitFor('.ordino-dataset.tissue-dataset').then(() => - TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(2)'), - ); + + await TourUtils.waitFor('.ordino-dataset.tissue-dataset').then(async () => { + TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(2)'); + await TourUtils.wait(1000); + }); }, pageBreak: 'manual', }, @@ -90,17 +90,18 @@ export class PredictionTP53Tour { }, }, { - selector: '[data-testid="add-column-button"]', + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', html: `

      Now they add a single gene score for the following:

      Gene: TP53

      Data Type: AA Mutated

      `, placement: 'centered', + preAction: openAddColumPanel, postAction: async () => { TourUtils.click('[data-testid="add-column-button"]'); await TourUtils.wait(500); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span'); TourUtils.toggleClass('.lu-adder.once', 'once', false); - TourUtils.waitFor('.modal.show').then(async () => { + await TourUtils.waitFor('.modal.show').then(async () => { TourUtils.setValueAndTrigger('.modal.show .select3 input.select2-search__field', 'TP53;', 'input'); TourUtils.setValueAndTrigger('.show .col > select', 'mutation-aa_mutated', 'change'); await TourUtils.wait(500); @@ -112,7 +113,7 @@ export class PredictionTP53Tour { selector: '[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter', html: `They filter out the samples with an unknown TP53 mutation status.`, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col7"].lu-missing', Infinity), + preAction: TourUtils.waitForSelector, postAction: async () => { TourUtils.click('[data-testid="viewWrapper-0"] [data-id="col7"] .lu-action-filter'); await TourUtils.wait(500); @@ -122,14 +123,17 @@ export class PredictionTP53Tour { }, }, { - selector: '.lu-side-panel-wrapper .lu-adder > button', + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span', html: `

      Next they add an aggregated gene score with the following criteria:

      Filter: My Named Sets = TP53 Predictor

      Data Type: Expression (TPM)

      Aggregation: Average

      Compute score only for current sample subset

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col7"] [style="background-color: rgb(170, 170, 170);"]', Infinity), + preAction: async () => { + await TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col7"] [style="background-color: rgb(170, 170, 170);"]', Infinity); + openAddColumPanel(); + }, postAction: async () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); diff --git a/src/tours/PredictionTP53Tour2.ts b/src/tours/PredictionTP53Tour2.ts index 38ee76b6..264f1c7f 100644 --- a/src/tours/PredictionTP53Tour2.ts +++ b/src/tours/PredictionTP53Tour2.ts @@ -1,9 +1,7 @@ // import {ToursSection} from 'ordino'; -import { IStep, Tour } from 'tdp_core'; +import { IStep } from 'tdp_core'; import { TourUtils } from 'tdp_core/src/tour/TourUtils'; -import selectEvent from 'react-select-event'; -import { wideEnoughCat } from 'lineupjs/build/src/renderer/utils'; -import { select } from 'lineupjs'; +import { openAddColumPanel } from './utils'; export class PredictionTP53Tour2 { static createTour(): IStep[] { @@ -32,13 +30,16 @@ export class PredictionTP53Tour2 { datasetTab.querySelector('a').classList.add('hover'); } }, - postAction: () => { + postAction: async () => { const datasetTab = document.querySelector('ul[data-header="mainMenu"] > li:nth-child(1)') as HTMLElement; if (!datasetTab.classList.contains('active')) { datasetTab.querySelector('a').classList.remove('hover'); datasetTab.querySelector('a').click(); } - return TourUtils.waitFor('.ordino-dataset.genes-dataset').then(() => TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(1)')); + await TourUtils.waitFor('.ordino-dataset.genes-dataset').then(async () => { + TourUtils.click('#ordino_dataset_tab > .ordino-scrollspy-nav > a:nth-child(1)'); + await TourUtils.wait(1000); + }); }, }, { @@ -49,12 +50,15 @@ export class PredictionTP53Tour2 { pageBreak: 'manual', }, { - selector: '[data-testid="add-column-button"]', + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span', html: `

      They add a single gene score for the following:

      Gene: TP53

      Data Type: AA Mutated and AA Mutation

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1)', Infinity).then(() => TourUtils.wait(1500)), + preAction: async () => { + await TourUtils.waitFor('.le-tr:nth-of-type(1)', Infinity).then(() => TourUtils.wait(1500)); + openAddColumPanel(); + }, postAction: async () => { TourUtils.click('[data-testid="add-column-button"]'); await TourUtils.wait(500); @@ -103,7 +107,7 @@ export class PredictionTP53Tour2 { }, }, { - selector: '.lu-side-panel-wrapper .lu-adder > button', + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span', html: `

      Next they add an aggregated gene score with the following criteria:

      Filter: Gene Symbol = AEN, BAX, CCNG1, CDKN1A, DDB2, FDXR, MDM2, RPS27L, RRM2B, SESN1, TNFRSF10B, XPC, ZMAT3

      @@ -111,7 +115,10 @@ export class PredictionTP53Tour2 {

      Aggregation: Average

      Compute score for all cell lines, not only the selected subset

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col7"] [style="background-color: rgb(27, 166, 78);"]', Infinity), + preAction: async () => { + await TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col7"] [style="background-color: rgb(27, 166, 78);"]', Infinity); + openAddColumPanel(); + }, postAction: async () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span'); @@ -138,7 +145,7 @@ export class PredictionTP53Tour2 { // Inspect if the checkbox is checked, if so then uncheck it const checkboxTest = document.querySelector('.modal-dialog [data-testid="form-checkbox"]') as HTMLInputElement; - if (checkboxTest.checked) { + if (checkboxTest?.checked) { TourUtils.click('.modal-dialog [data-testid="form-checkbox"]'); } await TourUtils.wait(1000); @@ -149,7 +156,6 @@ export class PredictionTP53Tour2 { selector: '[data-id="col9"] > .lu-toolbar > .lu-action-more', html: `

      They decide to rename the new column to "TP53 Predictor Score".

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="54.56"]', Infinity), postAction: async () => { TourUtils.click('[data-id="col9"] > .lu-toolbar > .lu-action-more'); await TourUtils.wait(500); @@ -179,17 +185,21 @@ export class PredictionTP53Tour2 { postAction: TourUtils.clickSelector, }, { - selector: '.le.le-multi.lineup-engine', + selector: '.le-tbody.le-tbody', html: `

      Observe: There is a clear enrichment of TP53 non-mutated among the cell lines with high score.

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="209.10"]', Infinity), + preAction: () => TourUtils.waitFor('[data-id="col9"].lu-renderer-number', Infinity), + postAction: async () => { + await TourUtils.wait(500); + }, }, { - selector: '.lu-side-panel-wrapper .lu-adder > button', + selector: '[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(4) > span', html: `

      Next, they choose to add a 'Depletion Screen Score (Single)' using the following:

      Gene: MDM2

      Data type: DRIVE RSA (NB: the lower this value, the more sensitive a cell line is to the depletion of the gene of interest)

      `, placement: 'centered', + preAction: openAddColumPanel, postAction: async () => { TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); TourUtils.click('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(4) > span'); @@ -209,7 +219,7 @@ export class PredictionTP53Tour2 { selector: '[data-id="col10"] > .lu-toolbar > .lu-action-more', html: `

      To amplify the visibility of the added depletion score's significance, they decide to invert the scaling via the data mapping.

      `, placement: 'centered', - preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [data-id="col10"].lu-missing', Infinity), + preAction: () => TourUtils.waitFor('.le-tr [data-id="col10"].lu-renderer-number', Infinity), postAction: async () => { TourUtils.click('[data-id="col10"] > .lu-toolbar > .lu-action-more'); await TourUtils.wait(500); @@ -242,13 +252,13 @@ export class PredictionTP53Tour2 { selector: '.le.le-multi.lineup-engine', html: `

      Observe: Small MDM2 RSA values (large bars) are correlated to the expression score (TP53 predictor score) and the TP53 mutation status

      `, placement: 'centered', - allowUserInteraction: true, preAction: () => TourUtils.waitFor('.le-tr:nth-of-type(1) [title="−7.14"]', Infinity), + postAction: () => TourUtils.wait(500), }, // Can't do the drag operation for this final step in the aim // Remaining two aims are also primarily just observations, but rely on the combined score column; What to do? { - selector: '', + selector: ['section[data-col-id="col9"]', 'section[data-col-id="col10"]'], html: `

      Conclusion: When combining the TP53 Predictor Score column and the MDM2 Gene Sensitivity Score, the new weighted sum column serves as an even more accurate predictor.

      Thanks for joining this tour taking a deeper look into the TP53 Predictor Score.

      There are still many more features to discover. Enjoy!

      `, diff --git a/src/tours/WelcomeTour.ts b/src/tours/WelcomeTour.ts index 57ed70f0..49d0eafd 100644 --- a/src/tours/WelcomeTour.ts +++ b/src/tours/WelcomeTour.ts @@ -1,4 +1,5 @@ import { IStep, TourUtils } from 'tdp_core'; +import { openAddColumPanel } from './utils'; export class WelcomeTour { static createTour(): IStep[] { @@ -58,7 +59,7 @@ export class WelcomeTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `Additional columns can be added using the plus sign.`, placement: 'centered', - postAction: TourUtils.clickSelector, + postAction: openAddColumPanel, }, { selector: '.lu-search .lu-search-item', diff --git a/src/tours/utils.ts b/src/tours/utils.ts new file mode 100644 index 00000000..12585de7 --- /dev/null +++ b/src/tours/utils.ts @@ -0,0 +1,16 @@ +import { TourUtils } from 'tdp_core'; + +/** + * Set the next button to active after the promise is resolved + * @example + * waitFor: ()=> TourUtils.wait(500).then(setNextActive) + */ +export const setNextActive = async (): Promise<'enable'> => 'enable'; + +/** + * Clicks the add column button and prevents the score list from closing + */ +export function openAddColumPanel() { + TourUtils.click('.viewWrapper.t-focus .lu-side-panel-wrapper .lu-adder > button'); + (document.querySelector('.viewWrapper.t-focus .lu-search-input') as HTMLInputElement).onblur = (ev) => ev.preventDefault(); +} From ba09b7c1bdee7e2ff495f8d3948de8206fed2a47 Mon Sep 17 00:00:00 2001 From: oltionchampari Date: Fri, 7 Apr 2023 10:25:56 +0200 Subject: [PATCH 37/38] Dist --- dist/tours/AddColumnToGeneListTour.d.ts.map | 2 +- dist/tours/AddColumnToGeneListTour.js | 11 ++++------- dist/tours/AddColumnToGeneListTour.js.map | 2 +- dist/tours/WelcomeTour.d.ts.map | 2 +- dist/tours/WelcomeTour.js | 3 ++- dist/tours/WelcomeTour.js.map | 2 +- 6 files changed, 10 insertions(+), 12 deletions(-) diff --git a/dist/tours/AddColumnToGeneListTour.d.ts.map b/dist/tours/AddColumnToGeneListTour.d.ts.map index 626fd2bc..8d4694bc 100644 --- a/dist/tours/AddColumnToGeneListTour.d.ts.map +++ b/dist/tours/AddColumnToGeneListTour.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"AddColumnToGeneListTour.d.ts","sourceRoot":"","sources":["../../src/tours/AddColumnToGeneListTour.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,uBAAuB;IAClC,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CAqQ7B"} \ No newline at end of file +{"version":3,"file":"AddColumnToGeneListTour.d.ts","sourceRoot":"","sources":["../../src/tours/AddColumnToGeneListTour.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAG5C,qBAAa,uBAAuB;IAClC,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CAiQ7B"} \ No newline at end of file diff --git a/dist/tours/AddColumnToGeneListTour.js b/dist/tours/AddColumnToGeneListTour.js index 2b93b3ed..9ed04561 100644 --- a/dist/tours/AddColumnToGeneListTour.js +++ b/dist/tours/AddColumnToGeneListTour.js @@ -1,4 +1,5 @@ import { TourUtils } from 'tdp_core'; +import { openAddColumPanel } from './utils'; export class AddColumnToGeneListTour { static createTour() { return [ @@ -61,7 +62,7 @@ export class AddColumnToGeneListTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `Additional columns can be added using the plus sign.`, placement: 'centered', - postAction: TourUtils.clickSelector, + postAction: openAddColumPanel, }, { selector: '.lu-search ul', @@ -123,9 +124,7 @@ export class AddColumnToGeneListTour { selector: '.lu-search .lu-search-group .lu-search-item', placement: 'centered', html: `Now, we want to add two columns containing the copy number information of two specific cell lines. To do so, we open the 'Cell Line Score (Single)' dialog`, - preAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - }, + preAction: openAddColumPanel, postAction: () => { TourUtils.click('.lu-search .lu-search-group .lu-search-item'); TourUtils.toggleClass('.lu-adder.once', 'once', false); @@ -165,9 +164,7 @@ export class AddColumnToGeneListTour { placement: 'centered', html: `Finally, we want to add an aggregated column containing the mean/average copy number values of all breast cancer cell lines. To do so, we open the 'Cell Line Score (Aggregated)' dialog`, - preAction: () => { - TourUtils.click('.lu-side-panel-wrapper .lu-adder > button'); - }, + preAction: openAddColumPanel, postAction: () => { TourUtils.click('.lu-search .lu-search-group .lu-search-item:nth-child(2)'); TourUtils.toggleClass('.lu-adder.once', 'once', false); diff --git a/dist/tours/AddColumnToGeneListTour.js.map b/dist/tours/AddColumnToGeneListTour.js.map index 5652a909..f25c4790 100644 --- a/dist/tours/AddColumnToGeneListTour.js.map +++ b/dist/tours/AddColumnToGeneListTour.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/tours/WelcomeTour.d.ts.map b/dist/tours/WelcomeTour.d.ts.map index b1882c68..ccfba649 100644 --- a/dist/tours/WelcomeTour.d.ts.map +++ b/dist/tours/WelcomeTour.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"WelcomeTour.d.ts","sourceRoot":"","sources":["../../src/tours/WelcomeTour.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAE5C,qBAAa,WAAW;IACtB,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CA+K7B"} \ No newline at end of file +{"version":3,"file":"WelcomeTour.d.ts","sourceRoot":"","sources":["../../src/tours/WelcomeTour.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAa,MAAM,UAAU,CAAC;AAG5C,qBAAa,WAAW;IACtB,MAAM,CAAC,UAAU,IAAI,KAAK,EAAE;CA+K7B"} \ No newline at end of file diff --git a/dist/tours/WelcomeTour.js b/dist/tours/WelcomeTour.js index 9a0e18a5..eb8e4e7d 100644 --- a/dist/tours/WelcomeTour.js +++ b/dist/tours/WelcomeTour.js @@ -1,4 +1,5 @@ import { TourUtils } from 'tdp_core'; +import { openAddColumPanel } from './utils'; export class WelcomeTour { static createTour() { return [ @@ -57,7 +58,7 @@ export class WelcomeTour { selector: '.lu-side-panel-wrapper .lu-adder > button', html: `Additional columns can be added using the plus sign.`, placement: 'centered', - postAction: TourUtils.clickSelector, + postAction: openAddColumPanel, }, { selector: '.lu-search .lu-search-item', diff --git a/dist/tours/WelcomeTour.js.map b/dist/tours/WelcomeTour.js.map index 0957a44f..f1433c3e 100644 --- a/dist/tours/WelcomeTour.js.map +++ b/dist/tours/WelcomeTour.js.map @@ -1 +1 @@ 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\ No newline at end of file From 963e5c2ae1475fef78d521936da94af76ccb17b1 Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Tue, 11 Apr 2023 12:32:19 +0200 Subject: [PATCH 38/38] fix: add hi-res tour preview images --- src/assets/previews/tourAddColumn.png | Bin 7770 -> 12883 bytes src/assets/previews/tourBreastCancerCL.png | Bin 11358 -> 58086 bytes src/assets/previews/tourDrugDiscovery.png | Bin 22449 -> 31760 bytes src/assets/previews/tourOrdinoWelcome.png | Bin 5809 -> 15411 bytes src/assets/previews/tourStartMenu.png | Bin 8664 -> 13652 bytes src/assets/previews/tourTP53Predictor.png | Bin 10594 -> 57643 bytes src/phovea.ts | 4 ++-- 7 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/assets/previews/tourAddColumn.png b/src/assets/previews/tourAddColumn.png index 5a67cc5f8d9fb24f215175ab4203170ca13cf9ec..f6bf7c6c1ae844624e22375aff592adc2805cb69 100644 GIT binary patch literal 12883 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zJyvQi<#fVmqIl)(>G-My+(KbLLi(+ZjSZDDi`ZR$X6EluLdlM4l2J+LQ$W|TbFvpA zMj-s=Kb}U{ABSqWCdAYT6eaIYS9hWi3AYWM_6udkwH603id(PvoDWkV$rYJ{((ekU zCLCl7Du42k60XuwQT%nX2F_Sr(ZEasc2}ft<K#;n;r}>bQcj+C1(hpK<vxa?;<l1g zMNGOJfM3Lax=OKKU#2FvQe&hwUO$pt0!%(S8Km+9ct^k7>({UG<c+gAC99=nA%pwB z?(Y5CA5`9>_qy{IWyLlA&lmUpzi#>c*M|qMFw=2&TKxs?XT$wRgqX1On_NNd&;JX{ C@dUU4 diff --git a/src/phovea.ts b/src/phovea.ts index 636d0211..ebf57363 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -1092,7 +1092,7 @@ export default function (registry) { }, { factory: 'createTour', - name: 'Prediction of TP53 Mutation Status', + name: 'Prediction of TP53 Mutation Status (Part 1)', description: 'This case study summarizes another analysis session, this time involving the prediction of the mutation status for TP53.', preview() { return import('./assets/previews/tourTP53Predictor.png'); @@ -1111,7 +1111,7 @@ export default function (registry) { }, { factory: 'createTour', - name: 'Prediction of TP53 Mutation Status: Continued', + name: 'Prediction of TP53 Mutation Status (Part 2)', description: 'This case study serves as a continuation of the initial tour "Prediction of TP53 Mutation Status".', preview() { return import('./assets/previews/tourTP53Predictor.png');