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SQL-on-FHIR processResource #4678
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@@ -0,0 +1,243 @@ | |||
import { Resource, ViewDefinition, ViewDefinitionSelect } from '@medplum/fhirtypes'; |
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I got these types working on a branch locally too. Curious how you approached it (it's not committed in the PR). I loaded up the structure definitions manually into @medplum/generator from the IG's package.
This is actually something that's generally very useful and under-explored in TypeScript FHIR support - typings for profiles.
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Yes, sorry for confusion, the types were added in separate PR: #4674
For lack of a better place, we stuffed them in packages/definitions/dist/fhir/r4/profiles-medplum.json
for now.
This is pretty promising...
This probably makes sense - this is basically the point of this shared test suite. Take the tests, implement a function that generates a report on the test cases that can be committed back to the project to show community implementation progress. @Diferti could help chase down test coverage here - he handled some corner cases for the reference implementation (lowBoundary and highBoundary support) |
… into cody-sql-on-fhir-process
Current errors: [
"basic.json: where returns non-boolean for some cases: Error: WHERE clause must evaluate to a boolean",
"collection.json: collection = false relative to forEach parent: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoMatchObject\u001b[2m(\u001b[22m\u001b[32mexpected\u001b[39m\u001b[2m)\u001b[22m\n\n\u001b[32m- Expected - 6\u001b[39m\n\u001b[31m+ Received + 2\u001b[39m\n\n\u001b[33m@@ -1,10 +1,8 @@\u001b[39m\n\u001b[2m Array [\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"first_name\": Array [\u001b[39m\n\u001b[32m- \"g1.1\",\u001b[39m\n\u001b[32m- ],\u001b[39m\n\u001b[31m+ \"first_name\": \"g1.1\",\u001b[39m\n\u001b[2m \"id\": \"pt1\",\u001b[22m\n\u001b[2m \"last_name\": \"f1.1\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[2m \"first_name\": Array [\u001b[22m\n\u001b[33m@@ -13,13 +11,11 @@\u001b[39m\n\u001b[2m ],\u001b[22m\n\u001b[2m \"id\": \"pt1\",\u001b[22m\n\u001b[2m \"last_name\": \"f1.2\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"first_name\": Array [\u001b[39m\n\u001b[32m- \"g2.1\",\u001b[39m\n\u001b[32m- ],\u001b[39m\n\u001b[31m+ \"first_name\": \"g2.1\",\u001b[39m\n\u001b[2m \"id\": \"pt2\",\u001b[22m\n\u001b[2m \"last_name\": \"f2.1\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[2m \"first_name\": Array [\u001b[22m",
"collection.json: collection = false relative to forEachOrNull parent: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoMatchObject\u001b[2m(\u001b[22m\u001b[32mexpected\u001b[39m\u001b[2m)\u001b[22m\n\n\u001b[32m- Expected - 6\u001b[39m\n\u001b[31m+ Received + 2\u001b[39m\n\n\u001b[33m@@ -1,10 +1,8 @@\u001b[39m\n\u001b[2m Array [\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"first_name\": Array [\u001b[39m\n\u001b[32m- \"g1.1\",\u001b[39m\n\u001b[32m- ],\u001b[39m\n\u001b[31m+ \"first_name\": \"g1.1\",\u001b[39m\n\u001b[2m \"id\": \"pt1\",\u001b[22m\n\u001b[2m \"last_name\": \"f1.1\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[2m \"first_name\": Array [\u001b[22m\n\u001b[33m@@ -13,13 +11,11 @@\u001b[39m\n\u001b[2m ],\u001b[22m\n\u001b[2m \"id\": \"pt1\",\u001b[22m\n\u001b[2m \"last_name\": \"f1.2\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"first_name\": Array [\u001b[39m\n\u001b[32m- \"g2.1\",\u001b[39m\n\u001b[32m- ],\u001b[39m\n\u001b[31m+ \"first_name\": \"g2.1\",\u001b[39m\n\u001b[2m \"id\": \"pt2\",\u001b[22m\n\u001b[2m \"last_name\": \"f2.1\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[2m \"first_name\": Array [\u001b[22m",
"constant.json: constant in path: Error: FhirPathError on \"name.where(use = %name_use).family\": Error: Undefined variable %name_use",
"constant.json: constant in forEach: Error: FhirPathError on \"name.where(use = %name_use)\": Error: Undefined variable %name_use",
"constant.json: constant in where element: Error: FhirPathError on \"name.where(use = %name_use).exists()\": Error: Undefined variable %name_use",
"constant.json: constant in unionAll: Error: FhirPathError on \"name.where(use = %use1)\": Error: Undefined variable %use1",
"constant.json: integer constant: Error: FhirPathError on \"name[%name_index].family\": Error: Undefined variable %name_index",
"constant.json: boolean constant: Error: FhirPathError on \"deceased.ofType(boolean).exists() and deceased.ofType(boolean) = %is_deceased\": Error: Undefined variable %is_deceased",
"constant_types.json: base64Binary: Error: FhirPathError on \"udiCarrier.first().carrierAIDC = %aidc\": Error: Undefined variable %aidc",
"constant_types.json: code: Error: FhirPathError on \"gender = %gender\": Error: Undefined variable %gender",
"constant_types.json: date: Error: FhirPathError on \"birthDate = %bd\": Error: Undefined variable %bd",
"constant_types.json: dateTime: Error: FhirPathError on \"identified.ofType(DateTime) = %id_time\": Error: Undefined variable %id_time",
"constant_types.json: decimal: Error: FhirPathError on \"value.ofType(Quantity).value < %v\": Error: Undefined variable %v",
"constant_types.json: id: Error: FhirPathError on \"output.first().value.ofType(id) = %id\": Error: Undefined variable %id",
"constant_types.json: instant: Error: FhirPathError on \"effective.ofType(Instant) = %eff\": Error: Undefined variable %eff",
"constant_types.json: oid: Error: FhirPathError on \"output.first().value.ofType(oid) = %oid\": Error: Undefined variable %oid",
"constant_types.json: positiveInt: Error: FhirPathError on \"item.first().itemSequence = %seq\": Error: Undefined variable %seq",
"constant_types.json: time: Error: FhirPathError on \"value.ofType(Time) = %t\": Error: Undefined variable %t",
"constant_types.json: unsignedInt: Error: FhirPathError on \"numberOfSeries = %series\": Error: Undefined variable %series",
"constant_types.json: uri: Error: FhirPathError on \"url = %uri\": Error: Undefined variable %uri",
"constant_types.json: url: Error: FhirPathError on \"output.first().value.ofType(url) = %url\": Error: Undefined variable %url",
"constant_types.json: uuid: Error: FhirPathError on \"output.first().value.ofType(uuid) = %uuid\": Error: Undefined variable %uuid",
"fhirpath.json: collection: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoMatchObject\u001b[2m(\u001b[22m\u001b[32mexpected\u001b[39m\u001b[2m)\u001b[22m\n\n\u001b[32m- Expected - 1\u001b[39m\n\u001b[31m+ Received + 1\u001b[39m\n\n\u001b[33m@@ -10,8 +10,8 @@\u001b[39m\n\u001b[2m \"f2.1\",\u001b[22m\n\u001b[2m \"f2.2\",\u001b[22m\n\u001b[2m ],\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"v\": Array [],\u001b[39m\n\u001b[31m+ \"v\": null,\u001b[39m\n\u001b[2m },\u001b[22m\n\u001b[2m ]\u001b[22m",
"fhirpath.json: string join: Error: FhirPathError on \"name.given.join(', ' )\": Error: Unrecognized function: join",
"fhirpath.json: string join: default separator: Error: FhirPathError on \"name.given.join()\": Error: Unrecognized function: join",
"fhirpath_numbers.json: add observation: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoMatchObject\u001b[2m(\u001b[22m\u001b[32mexpected\u001b[39m\u001b[2m)\u001b[22m\n\n\u001b[32m- Expected - 9\u001b[39m\n\u001b[31m+ Received + 9\u001b[39m\n\n\u001b[2m Array [\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"add\": 5,\u001b[39m\n\u001b[32m- \"div\": 1.5,\u001b[39m\n\u001b[32m- \"eq\": false,\u001b[39m\n\u001b[32m- \"ge\": true,\u001b[39m\n\u001b[32m- \"gt\": true,\u001b[39m\n\u001b[31m+ \"add\": null,\u001b[39m\n\u001b[31m+ \"div\": null,\u001b[39m\n\u001b[31m+ \"eq\": null,\u001b[39m\n\u001b[31m+ \"ge\": null,\u001b[39m\n\u001b[31m+ \"gt\": null,\u001b[39m\n\u001b[2m \"id\": \"o1\",\u001b[22m\n\u001b[32m- \"le\": false,\u001b[39m\n\u001b[32m- \"lt\": false,\u001b[39m\n\u001b[32m- \"mul\": 6,\u001b[39m\n\u001b[32m- \"sub\": 1,\u001b[39m\n\u001b[31m+ \"le\": null,\u001b[39m\n\u001b[31m+ \"lt\": null,\u001b[39m\n\u001b[31m+ \"mul\": null,\u001b[39m\n\u001b[31m+ \"sub\": null,\u001b[39m\n\u001b[2m },\u001b[22m\n\u001b[2m ]\u001b[22m",
"fn_boundary.json: decimal lowBoundary: Error: FhirPathError on \"value.ofType(Quantity).value.lowBoundary()\": Error: Unrecognized function: lowBoundary",
"fn_boundary.json: decimal highBoundary: Error: FhirPathError on \"value.ofType(Quantity).value.highBoundary()\": Error: Unrecognized function: highBoundary",
"fn_boundary.json: datetime lowBoundary: Error: FhirPathError on \"value.ofType(dateTime).lowBoundary()\": Error: Unrecognized function: lowBoundary",
"fn_boundary.json: datetime highBoundary: Error: FhirPathError on \"value.ofType(dateTime).highBoundary()\": Error: Unrecognized function: highBoundary",
"fn_boundary.json: date lowBoundary: Error: FhirPathError on \"birthDate.lowBoundary()\": Error: Unrecognized function: lowBoundary",
"fn_boundary.json: date highBoundary: Error: FhirPathError on \"birthDate.highBoundary()\": Error: Unrecognized function: highBoundary",
"fn_boundary.json: time lowBoundary: Error: FhirPathError on \"value.ofType(time).lowBoundary()\": Error: Unrecognized function: lowBoundary",
"fn_boundary.json: time highBoundary: Error: FhirPathError on \"value.ofType(time).highBoundary()\": Error: Unrecognized function: highBoundary",
"fn_extension.json: simple extension: Error: FhirPathError on \"extension('http:https://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex').value.ofType(code).first()\": Error: Unrecognized function: extension",
"fn_extension.json: nested extension: Error: FhirPathError on \"extension('http:https://hl7.org/fhir/us/core/StructureDefinition/us-core-race').extension('ombCategory').value.ofType(Coding).code.first()\": Error: Unrecognized function: extension",
"fn_join.json: join with comma: Error: FhirPathError on \"name.given.join(',')\": Error: Unrecognized function: join",
"fn_join.json: join with empty value: Error: FhirPathError on \"name.given.join('')\": Error: Unrecognized function: join",
"fn_join.json: join with no value - default to no separator: Error: FhirPathError on \"name.given.join()\": Error: Unrecognized function: join",
"fn_reference_keys.json: getReferenceKey result matches getResourceKey without type specifier: Error: FhirPathError on \"getResourceKey() = link.other.getReferenceKey()\": Error: Unrecognized function: getResourceKey",
"fn_reference_keys.json: getReferenceKey result matches getResourceKey with right type specifier: Error: FhirPathError on \"getResourceKey() = link.other.getReferenceKey(Patient)\": Error: Unrecognized function: getResourceKey",
"fn_reference_keys.json: getReferenceKey result matches getResourceKey with wrong type specifier: Error: FhirPathError on \"link.other.getReferenceKey(Observation)\": Error: Unrecognized function: getReferenceKey",
"foreach.json: forEach: two on the same level: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoMatchObject\u001b[2m(\u001b[22m\u001b[32mexpected\u001b[39m\u001b[2m)\u001b[22m\n\n\u001b[32m- Expected - 4\u001b[39m\n\u001b[31m+ Received + 4\u001b[39m\n\n\u001b[33m@@ -2,16 +2,16 @@\u001b[39m\n\u001b[2m Object {\u001b[22m\n\u001b[2m \"cont_family\": \"FC1.1\",\u001b[22m\n\u001b[2m \"pat_family\": \"F1.1\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"cont_family\": \"FC1.2\",\u001b[39m\n\u001b[32m- \"pat_family\": \"F1.1\",\u001b[39m\n\u001b[32m- },\u001b[39m\n\u001b[32m- Object {\u001b[39m\n\u001b[2m \"cont_family\": \"FC1.1\",\u001b[22m\n\u001b[2m \"pat_family\": \"F1.2\",\u001b[22m\n\u001b[31m+ },\u001b[39m\n\u001b[31m+ Object {\u001b[39m\n\u001b[31m+ \"cont_family\": \"FC1.2\",\u001b[39m\n\u001b[31m+ \"pat_family\": \"F1.1\",\u001b[39m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[2m \"cont_family\": \"FC1.2\",\u001b[22m\n\u001b[2m \"pat_family\": \"F1.2\",\u001b[22m\n\u001b[2m },\u001b[22m",
"foreach.json: forEachOrNull & unionAll on the same level: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoMatchObject\u001b[2m(\u001b[22m\u001b[32mexpected\u001b[39m\u001b[2m)\u001b[22m\n\n\u001b[32m- Expected - 2\u001b[39m\n\u001b[31m+ Received + 0\u001b[39m\n\n\u001b[33m@@ -19,12 +19,10 @@\u001b[39m\n\u001b[2m \"id\": \"pt1\",\u001b[22m\n\u001b[2m \"name\": \"N2\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[2m \"id\": \"pt2\",\u001b[22m\n\u001b[32m- \"name\": null,\u001b[39m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[2m \"id\": \"pt3\",\u001b[22m\n\u001b[32m- \"name\": null,\u001b[39m\n\u001b[2m },\u001b[22m\n\u001b[2m ]\u001b[22m",
"foreach.json: forEachOrNull & unionAll & column & select on the same level: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoMatchObject\u001b[2m(\u001b[22m\u001b[32mexpected\u001b[39m\u001b[2m)\u001b[22m\n\n\u001b[32m- Expected - 4\u001b[39m\n\u001b[31m+ Received + 0\u001b[39m\n\n\u001b[33m@@ -28,17 +28,13 @@\u001b[39m\n\u001b[2m \"id\": \"pt1\",\u001b[22m\n\u001b[2m \"name\": \"N2\",\u001b[22m\n\u001b[2m \"tel_system\": \"email\",\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"gender\": null,\u001b[39m\n\u001b[2m \"id\": \"pt2\",\u001b[22m\n\u001b[32m- \"name\": null,\u001b[39m\n\u001b[2m \"tel_system\": null,\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m Object {\u001b[22m\n\u001b[32m- \"gender\": null,\u001b[39m\n\u001b[2m \"id\": \"pt3\",\u001b[22m\n\u001b[32m- \"name\": null,\u001b[39m\n\u001b[2m \"tel_system\": null,\u001b[22m\n\u001b[2m },\u001b[22m\n\u001b[2m ]\u001b[22m",
"logic.json: filtering with 'or': Error: WHERE clause must evaluate to a boolean",
"union.json: column mismatch: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoThrow\u001b[2m()\u001b[22m\n\nReceived function did not throw",
"union.json: column order mismatch: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoThrow\u001b[2m()\u001b[22m\n\nReceived function did not throw",
"validate.json: wrong fhirpath: Error: \u001b[2mexpect(\u001b[22m\u001b[31mreceived\u001b[39m\u001b[2m).\u001b[22mtoThrow\u001b[2m()\u001b[22m\n\nReceived function did not throw"
] |
Quality Gate passedIssues Measures |
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LGTM. Just one comment that may be a noop.
// Process UnionAlls: | ||
// Initialize urows as an empty list of rows | ||
// For each selection structure u of S.unionAll | ||
if (s.unionAll) { |
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Should this be wrapped in the if (s.unionAll)
check? Reading the pseudocode, it seems like you're still supposed to append an empty list if S.unionAll
is missing. It may not matter given the cartesianProduct step below, but wanted to call it out.
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Great question, and astute observation.
My first stab did exactly that; however, it doesn't work.
The reason is that it ends with a call to parts.push(urows);
If urows
is empty, you then have an empty array in parts
. When calculating the cartesian product, an empty array is like multiplying by zero, it wipes out everything.
It could be handled by doing if (urows.length > 0) { parts.push(urows); }
, or updating the cartesian product logic, but this felt cleaner 🤷
## What's Changed fix(ci): fix `\n` missing due to reversal, use `git log --reverse` (#4649) Allow chained search in _filter (#4647) Polish eligibility demo (#4637) cleanup(core): remove stray `console.log` (#4653) Update sidebar.ts (#4652) Feat: Configure refresh token expiry (#4525) Dependency upgrades 2024-06-10 (#4650) cleanup(chart-demo): rm ignored `example-bots.json` (#4656) Adding instructions to the example app READMEs on how to build bots (#4660) Update useSearch.ts (#4663) Export QuestionnaireFormContext and QuestionnairePageSequence from QuestionnaireForm (#4664) Add `expo-polyfills` to README packages list (#4666) revert(react): remove export of `QuestionnairePageSequence` (#4669) Fix wrong pipe character in README (#4671) Document Terminology Service operation endpoints (#4665) Dependency upgrades 2024-06-17 (#4673) Gracefully handle no major dep upgrades (#4675) SQL on FHIR ViewDefinition types (#4674) fix(build) Update deprecated import assertion into import attribute (#4682) Fixes #4398 - add mapByIdentifier util function (#4635) Fixes #4600 - Add Auto Confirmation Parameter for Headless Deployment (#4625) fix(react-hooks): make `loading` track `MedplumClient#isLoading()` (#4677) Implements FHIRPath string join (stu) (#4683) SQL-on-FHIR processResource (#4678) feat(useSubscription): add `subscriptionProps` as optional param (#4180) Resolve conditional references (#4633) feat(subscriptions): add `unbind-from-token` message for WebSocket subscriptions (#4672) Document remaining Terminology Service operations (#4680) feat(agent): add `keepAlive` setting to `Agent` (#4657) Update README.md (#4687) Fix all copyright dates (#4689) Fixes subject input on PlanDefinitionApplyForm (#4699) Deprecate non-strict mode (#4651) Validate certain references with systemRepo (#4700) docs(useSubscription): clean up examples, add JSDoc comment (#4692) cleanup(repo): `handleMaybeCacheOnly` -> `handleStorage` (#4696) Minor fixes to Eligibility Demo (#4703) **Full Changelog**: v3.1.8...v3.1.9
## What's Changed fix(ci): fix `\n` missing due to reversal, use `git log --reverse` (#4649) Allow chained search in _filter (#4647) Polish eligibility demo (#4637) cleanup(core): remove stray `console.log` (#4653) Update sidebar.ts (#4652) Feat: Configure refresh token expiry (#4525) Dependency upgrades 2024-06-10 (#4650) cleanup(chart-demo): rm ignored `example-bots.json` (#4656) Adding instructions to the example app READMEs on how to build bots (#4660) Update useSearch.ts (#4663) Export QuestionnaireFormContext and QuestionnairePageSequence from QuestionnaireForm (#4664) Add `expo-polyfills` to README packages list (#4666) revert(react): remove export of `QuestionnairePageSequence` (#4669) Fix wrong pipe character in README (#4671) Document Terminology Service operation endpoints (#4665) Dependency upgrades 2024-06-17 (#4673) Gracefully handle no major dep upgrades (#4675) SQL on FHIR ViewDefinition types (#4674) fix(build) Update deprecated import assertion into import attribute (#4682) Fixes #4398 - add mapByIdentifier util function (#4635) Fixes #4600 - Add Auto Confirmation Parameter for Headless Deployment (#4625) fix(react-hooks): make `loading` track `MedplumClient#isLoading()` (#4677) Implements FHIRPath string join (stu) (#4683) SQL-on-FHIR processResource (#4678) feat(useSubscription): add `subscriptionProps` as optional param (#4180) Resolve conditional references (#4633) feat(subscriptions): add `unbind-from-token` message for WebSocket subscriptions (#4672) Document remaining Terminology Service operations (#4680) feat(agent): add `keepAlive` setting to `Agent` (#4657) Update README.md (#4687) Fix all copyright dates (#4689) Fixes subject input on PlanDefinitionApplyForm (#4699) Deprecate non-strict mode (#4651) Validate certain references with systemRepo (#4700) docs(useSubscription): clean up examples, add JSDoc comment (#4692) cleanup(repo): `handleMaybeCacheOnly` -> `handleStorage` (#4696) Minor fixes to Eligibility Demo (#4703) **Full Changelog**: v3.1.8...v3.1.9
I got nerd sniped by @jdjkelly's discussion: #4661
This PR implements the main skeleton of the SQL-on-FHIR
processResource
andprocess
algorithms.See: https://build.fhir.org/ig/FHIR/sql-on-fhir-v2/implementer_guidance.html#process-a-resource-entry-point
With this, we're at 57% pass rate
Examples of open issues:
join()
)Questions:
@medplum/core
, or should it be a separate package (i.e.,@medplum/sql-on-fhir
)?