Merge branch 'master' of https://github.com/Phenomics/hpoweb.git

Conflicts: .classpath ivy.xml src/hpoweb/HpowebUI.java
drseb · Feb 26, 2018 · 499f828 · 499f828
2 parents c5177e9 + 5805a14
commit 499f828
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diff --git a/.classpath b/.classpath
@@ -15,7 +15,7 @@
  <attribute name="owner.project.facets" value="jst.web"/>
  </attributes>
  </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.launching.macosx.MacOSXType/Java SE 8 [1.8.0_161]">
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
  <attributes>
  <attribute name="owner.project.facets" value="java"/>
  </attributes>

diff --git a/ivy.xml b/ivy.xml
@@ -41,6 +41,5 @@
  <dependency org="com.github.vaadin4qbanos" name="jsclipboard" rev="1.0.2" />
  <dependency org="com.sebworks" name="vaadstrap" rev="0.1.2" /> 
  <dependency org="net.sourceforge.owlapi" name="owlapi-distribution" rev="4.1.3"/>
-
  </dependencies> 
 </ivy-module>
diff --git a/src/hpoweb/HpowebUI.java b/src/hpoweb/HpowebUI.java
@@ -20,6 +20,7 @@
 import com.vaadin.event.FieldEvents.FocusEvent;
 import com.vaadin.event.FieldEvents.FocusListener;
 import com.vaadin.jsclipboard.JSClipboard;
+import com.vaadin.server.ExternalResource;
 import com.vaadin.server.Page;
 import com.vaadin.server.VaadinRequest;
 import com.vaadin.server.VaadinServlet;
@@ -168,9 +169,9 @@ protected void init(VaadinRequest request) {
  * Bottom part
  */
  Label version = new Label("Ontology version: " + ontologyVersion);
- Label copyright = new Label("Copyright 2017 - Sebastian Köhler & The Human Phenotype Ontology Project");
- Link feedback = new Link("Question, Comments, Feedback: [email protected]",
- new com.vaadin.server.ExternalResource("http:https://drseb.github.io/"));
+ Label copyright = new Label("Copyright 2018 - Sebastian Köhler & The Phenomics Group Berlin");
+ Link feedback = new Link("Contact: [email protected]",
+ new ExternalResource("http:https://phenomics.github.io/"));
  addLabelRow(gridContainer, version);
  addLabelRow(gridContainer, copyright);
  addLabelRow(gridContainer, feedback);

diff --git a/src/hpoweb/uicontent/tabs/hpoclass/HpoClassTabFactory.java b/src/hpoweb/uicontent/tabs/hpoclass/HpoClassTabFactory.java
@@ -1,21 +1,9 @@
 package hpoweb.uicontent.tabs.hpoclass;
 
-import hpoweb.data.HpData;
-import hpoweb.data.dataprovider.IHpClassDataProvider;
-import hpoweb.uicontent.graph.GraphtestUI;
-import hpoweb.uicontent.table.DiseaseGeneTableEntry;
-import hpoweb.uicontent.table.GeneDiseaseTableEntry;
-import hpoweb.uicontent.table.TableLabel;
-import hpoweb.util.CONSTANTS;
-import hpoweb.util.TableUtils;
-
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 
-import org.apache.commons.lang3.RandomStringUtils;
-import org.semanticweb.owlapi.model.OWLClass;
-
 import com.google.common.base.Joiner;
 import com.sebworks.vaadstrap.Col;
 import com.sebworks.vaadstrap.ColMod;
@@ -28,7 +16,18 @@
 import com.vaadin.ui.VerticalLayout;
 import com.vaadin.ui.themes.ValoTheme;
 
+import org.apache.commons.lang3.RandomStringUtils;
+import org.semanticweb.owlapi.model.OWLClass;
+
 import de.charite.phenowl.hpowl.util.OboUtil;
+import hpoweb.data.HpData;
+import hpoweb.data.dataprovider.IHpClassDataProvider;
+import hpoweb.uicontent.graph.GraphtestUI;
+import hpoweb.uicontent.table.DiseaseGeneTableEntry;
+import hpoweb.uicontent.table.GeneDiseaseTableEntry;
+import hpoweb.uicontent.table.TableLabel;
+import hpoweb.util.CONSTANTS;
+import hpoweb.util.TableUtils;
 
 public class HpoClassTabFactory {
 
@@ -92,7 +91,12 @@ private VerticalLayout getAssociatedGenesTab(IHpClassDataProvider dataProvider)
  VerticalLayout tableVL = new VerticalLayout();
  tableVL.setSizeFull();
 
- Label lab1 = new Label("Associated genes");
+ List<GeneDiseaseTableEntry> tableContent = dataProvider.getGeneDiseaseTableContent();
+
+ int numberOfDiseases = tableContent.size();
+
+ Label lab1 = new Label(numberOfDiseases + " associated genes");
+
  lab1.addStyleName(ValoTheme.LABEL_LIGHT);
  lab1.addStyleName("tab-content-header");
  tableVL.addComponent(lab1);
@@ -103,17 +107,15 @@ private VerticalLayout getAssociatedGenesTab(IHpClassDataProvider dataProvider)
  table.setSizeFull();
  table.setHeight("275px");
 
- List<GeneDiseaseTableEntry> tableContent = dataProvider.getGeneDiseaseTableContent();
-
  int id = 0;
  for (GeneDiseaseTableEntry entry : tableContent) {
- TableLabel geneEntry = new TableLabel(entry.getGeneSymbol() + " (<a href='" + CONSTANTS.rootLocation + "?" + CONSTANTS.geneRequestId
- + "=" + entry.getGeneId() + "'>" + entry.getGeneId() + "</a>)", ContentMode.HTML);
+ TableLabel geneEntry = new TableLabel(entry.getGeneSymbol() + " (<a href='" + CONSTANTS.rootLocation + "?" + CONSTANTS.geneRequestId + "="
+ + entry.getGeneId() + "'>" + entry.getGeneId() + "</a>)", ContentMode.HTML);
 
  String diseasesString = tableUtils.getDiseasesAsHtmlString(entry.getAssociatedDiseases(), CONSTANTS.rootLocation);
 
  TableLabel diseases = new TableLabel(diseasesString, ContentMode.HTML);
- Integer itemId = new Integer(id++);
+ Integer itemId = Integer.valueOf(id++);
  table.addItem(new Object[] { geneEntry, diseases }, itemId);
  }
 
@@ -134,8 +136,12 @@ private VerticalLayout getAssociatedGenesTab(IHpClassDataProvider dataProvider)
  private VerticalLayout getAssociatedDiseasesTab(IHpClassDataProvider dataProvider) {
  VerticalLayout tableVL = new VerticalLayout();
  tableVL.setSizeFull();
+ List<DiseaseGeneTableEntry> tableContent = dataProvider.getDiseaseGeneTableContent();
+
+ int numberOfDiseases = tableContent.size();
+
+ Label lab1 = new Label(numberOfDiseases + " associated diseases");
 
- Label lab1 = new Label("Associated diseases");
  lab1.addStyleName(ValoTheme.LABEL_LIGHT);
  lab1.addStyleName("tab-content-header");
  tableVL.addComponent(lab1);
@@ -147,18 +153,16 @@ private VerticalLayout getAssociatedDiseasesTab(IHpClassDataProvider dataProvide
  table.setSizeFull();
  table.setHeight("275px");
 
- List<DiseaseGeneTableEntry> tableContent = dataProvider.getDiseaseGeneTableContent();
-
  int id = 0;
  for (DiseaseGeneTableEntry entry : tableContent) {
- TableLabel diseaseid = new TableLabel("<a href='" + CONSTANTS.rootLocation + "?" + CONSTANTS.diseaseRequestId + "="
- + entry.getDiseaseId() + "'>" + entry.getDiseaseId() + "</a>", ContentMode.HTML);
+ TableLabel diseaseid = new TableLabel("<a href='" + CONSTANTS.rootLocation + "?" + CONSTANTS.diseaseRequestId + "=" + entry.getDiseaseId()
+ + "'>" + entry.getDiseaseId() + "</a>", ContentMode.HTML);
  TableLabel diseasename = new TableLabel(entry.getDiseaseName(), ContentMode.HTML);
 
  String genesString = tableUtils.getGenesAsHtmlString(entry.getAssociatedGenes(), CONSTANTS.rootLocation);
 
  TableLabel genes = new TableLabel(genesString, ContentMode.HTML);
- Integer itemId = new Integer(id++);
+ Integer itemId = Integer.valueOf(id++);
  table.addItem(new Object[] { diseaseid, diseasename, genes }, itemId);
  }
 
@@ -186,9 +190,8 @@ private VerticalLayout getSynonymsVl(IHpClassDataProvider dataProvider) {
 
  Collection<String> synonyms = dataProvider.getSynonyms();
  if (synonyms.size() < 1) {
- Label suggestSyn = new Label(
- "Currently the HPO does not have any synonyms for this class. "
- + "Suggest a synonym at our <a href='https://github.com/obophenotype/human-phenotype-ontology/issues/' target='_new'>github tracker</a>",
+ Label suggestSyn = new Label("Currently the HPO does not have any synonyms for this class. "
+ + "Suggest a synonym at our <a href='https://github.com/obophenotype/human-phenotype-ontology/issues/' target='_new'>github tracker</a>",
  ContentMode.HTML);
  suggestSyn.addStyleName("tab-content-content");
  vl_syns.addComponent(suggestSyn);
@@ -223,8 +226,8 @@ private VerticalLayout getIdentifiersVl(IHpClassDataProvider dataProvider) {
  * Secondary ID
  */
  Label lab2 = new Label("Alternative IDs");
- lab2.setDescription("These are other identifiers which are referring to the same HPO class. "
- + "These are introduced when classes are merged.");
+ lab2.setDescription(
+ "These are other identifiers which are referring to the same HPO class. " + "These are introduced when classes are merged.");
  lab2.addStyleName(ValoTheme.LABEL_LIGHT);
  lab2.addStyleName("tab-content-header");
 
@@ -240,8 +243,9 @@ private VerticalLayout getIdentifiersVl(IHpClassDataProvider dataProvider) {
  * PURLs
  */
  Label lab3 = new Label("PURL");
- lab3.setDescription("This is a persistent URL. Please see <a href='https://en.wikipedia.org/wiki/Persistent_uniform_resource_locator' target='_new'>"
- + "this wikipedia article</a> for more information on PURLs.");
+ lab3.setDescription(
+ "This is a persistent URL. Please see <a href='https://en.wikipedia.org/wiki/Persistent_uniform_resource_locator' target='_new'>"
+ + "this wikipedia article</a> for more information on PURLs.");
  lab3.addStyleName(ValoTheme.LABEL_LIGHT);
  lab3.addStyleName("tab-content-header");
  Label iriLabel = new Label("<a href='" + dataProvider.getIRI() + "' target='_new'>" + dataProvider.getIRI() + "</a>", ContentMode.HTML);
@@ -282,7 +286,8 @@ private VerticalLayout getDefinitionsVl(IHpClassDataProvider dataProvider) {
  * Logical def
  */
  Label lab2 = new Label("Logical definition");
- lab2.setDescription("This is a computer readable logical definition of the HPO class. If you want to learn more about this please see <a href='http:https://nar.oxfordjournals.org/content/42/D1/D966.full' target='_new'>http:https://nar.oxfordjournals.org/content/42/D1/D966.full</a>.");
+ lab2.setDescription(
+ "This is a computer readable logical definition of the HPO class. If you want to learn more about this please see <a href='http:https://nar.oxfordjournals.org/content/42/D1/D966.full' target='_new'>http:https://nar.oxfordjournals.org/content/42/D1/D966.full</a>.");
  lab2.addStyleName(ValoTheme.LABEL_LIGHT);
  lab2.addStyleName("tab-content-header");
 
@@ -317,8 +322,8 @@ private VerticalLayout getSubSuperClassesVl(IHpClassDataProvider dataProvider) {
  Collection<String> superClassesHtmlString = convertToHtml(superClasses, CONSTANTS.rootLocation);
  Collection<String> subClassesHtmlString = convertToHtml(subClasses, CONSTANTS.rootLocation);
 
- addLabelsSupSub(superClassesHtmlString, "Superclasses", vlSubSuperClasses);
- addLabelsSupSub(subClassesHtmlString, "Subclasses", vlSubSuperClasses);
+ addLabelsSupSub(superClassesHtmlString, "Superclasses", vlSubSuperClasses, superClasses);
+ addLabelsSupSub(subClassesHtmlString, "Subclasses", vlSubSuperClasses, subClasses);
 
  vlSubSuperClasses.addStyleName("tab-content-vl");
  return vlSubSuperClasses;
@@ -328,7 +333,7 @@ private VerticalLayout getSuperClassesVl(IHpClassDataProvider dataProvider) {
  VerticalLayout vlSubSuperClasses = new VerticalLayout();
  Collection<OWLClass> superClasses = dataProvider.getSuperClasses();
  Collection<String> superClassesHtmlString = convertToHtml(superClasses, CONSTANTS.rootLocation);
- addLabelsSupSub(superClassesHtmlString, "Superclasses", vlSubSuperClasses);
+ addLabelsSupSub(superClassesHtmlString, "Superclasses", vlSubSuperClasses, superClasses);
  vlSubSuperClasses.addStyleName("tab-content-vl");
  return vlSubSuperClasses;
  }
@@ -337,12 +342,13 @@ private VerticalLayout getSubClassesVl(IHpClassDataProvider dataProvider) {
  VerticalLayout vlSubSuperClasses = new VerticalLayout();
  Collection<OWLClass> subClasses = dataProvider.getSubClasses();
  Collection<String> subClassesHtmlString = convertToHtml(subClasses, CONSTANTS.rootLocation);
- addLabelsSupSub(subClassesHtmlString, "Subclasses", vlSubSuperClasses);
+ addLabelsSupSub(subClassesHtmlString, "Subclasses", vlSubSuperClasses, subClasses);
  vlSubSuperClasses.addStyleName("tab-content-vl");
  return vlSubSuperClasses;
  }
 
- private void addLabelsSupSub(Collection<String> superClassesHtmlString, String string, VerticalLayout vlSubSuperClasses) {
+ private void addLabelsSupSub(Collection<String> superClassesHtmlString, String string, VerticalLayout vlSubSuperClasses,
+ Collection<OWLClass> classes) {
  /*
  * Super or sub classes
  */
@@ -356,6 +362,14 @@ private void addLabelsSupSub(Collection<String> superClassesHtmlString, String s
  vlSubSuperClasses.addComponent(labelSuperclasses);
  }
 
+ // for (OWLClass c : classes) {
+ // String id = OboUtil.IRI2ID(c.getIRI());
+ // String label = hpData.getExtOwlOntology().getLabel(c.getIRI());
+ // Button b = new Button(label);
+ // b.addClickListener(new UpdatePageClickListener(id, label));
+ // vlSubSuperClasses.addComponent(b);
+ // }
+
  }
 
  private Collection<String> convertToHtml(Collection<OWLClass> classes, String oldLocation) {

diff --git a/src/hpoweb/util/UpdatePageClickListener.java b/src/hpoweb/util/UpdatePageClickListener.java
@@ -0,0 +1,23 @@
+package hpoweb.util;
+
+import com.vaadin.ui.Button.ClickEvent;
+import com.vaadin.ui.Button.ClickListener;
+import com.vaadin.ui.Notification;
+
+public class UpdatePageClickListener implements ClickListener {
+
+ private String id;
+ private String label;
+
+ public UpdatePageClickListener(String id, String label) {
+ this.id = id;
+ this.label = label;
+
+ }
+
+ @Override
+ public void buttonClick(ClickEvent event) {
+ Notification.show(id + " " + label);
+ }
+
+}