-
Notifications
You must be signed in to change notification settings - Fork 49
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Updated JpaTerminologyProvider to support expansion with version and …
…code system bindings (#645) * Removed exception thrown in JpaTerminologyProvider when expanding with version and codesystem bindings ... added tests to validate support * Added canonical versioning to urls and test for multiple valueset versions
- Loading branch information
Showing
10 changed files
with
12,115 additions
and
30 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
142 changes: 142 additions & 0 deletions
142
plugin/cql/src/test/java/org/opencds/cqf/ruler/cql/JpaTerminologyProviderIT.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,142 @@ | ||
| package org.opencds.cqf.ruler.cql; | ||
|
|
||
| import ca.uhn.fhir.jpa.api.config.DaoConfig; | ||
| import ca.uhn.fhir.jpa.partition.SystemRequestDetails; | ||
| import org.apache.commons.collections4.IterableUtils; | ||
| import org.junit.jupiter.api.BeforeAll; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.opencds.cqf.cql.engine.terminology.ValueSetInfo; | ||
| import org.opencds.cqf.ruler.test.RestIntegrationTest; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.boot.test.context.SpringBootTest; | ||
|
|
||
| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertNotNull; | ||
|
|
||
| @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, | ||
| classes = { JpaTerminologyProviderIT.class }, | ||
| properties = { "hapi.fhir.fhir_version=r4" }) | ||
| class JpaTerminologyProviderIT extends RestIntegrationTest { | ||
|
|
||
| @Autowired | ||
| DaoConfig daoConfig; | ||
| @Autowired | ||
| private JpaTerminologyProviderFactory jpaTerminologyProviderFactory; | ||
| private JpaTerminologyProvider terminologyProvider; | ||
|
|
||
| @BeforeAll | ||
| void setup() { | ||
| SystemRequestDetails requestDetails = new SystemRequestDetails(); | ||
| requestDetails.setFhirContext(getFhirContext()); | ||
| requestDetails.setFhirServerBase(getServerBase()); | ||
| terminologyProvider = jpaTerminologyProviderFactory.create(requestDetails); | ||
| } | ||
|
|
||
| @Test | ||
| void testExpandFhirCodeSystem() { | ||
| Iterable<org.opencds.cqf.cql.engine.runtime.Code> expandResult = getExpansion( | ||
| "valueset-filter-comparator.json", | ||
| "http://hl7.org/fhir/us/cqfmeasures/ValueSet/value-filter-comparator", | ||
| "3.0.0"); | ||
| assertNotNull(expandResult); | ||
| assertEquals(7, IterableUtils.size(expandResult)); | ||
| } | ||
|
|
||
| /* | ||
| Possible issue with the following codes having the same code, but different display values: | ||
| /[HPF] | ||
| /[LPF] | ||
| [beth'U] | ||
| [pptr] | ||
| [todd'U] | ||
| [iU] | ||
| {Ehrlich'U}/100.g | ||
| The ValueSet composition includes 1364 codes, but the expansion returns 1357 codes | ||
| - display values are not present in the expansion | ||
| */ | ||
| @Test | ||
| void testExpandUnitsOfMeasureCodeSystemMoreThan1000() { | ||
| daoConfig.setMaximumExpansionSize(Integer.MAX_VALUE); | ||
| Iterable<org.opencds.cqf.cql.engine.runtime.Code> expandResult = getExpansion( | ||
| "valueset-ucum-common.json", "http://hl7.org/fhir/ValueSet/ucum-common", "1.0.0"); | ||
| assertEquals(1357, IterableUtils.size(expandResult)); | ||
| } | ||
|
|
||
| @Test | ||
| void testPreExpandedRxNormCodeSystemMoreThan1000() { | ||
| daoConfig.setMaximumExpansionSize(Integer.MAX_VALUE); | ||
| Iterable<org.opencds.cqf.cql.engine.runtime.Code> expandResult = getExpansion( | ||
| "valueset-opioid-analgesics-with-ambulatory-misuse-potential.json", | ||
| "http://fhir.org/guides/cdc/opioid-cds/ValueSet/opioid-analgesics-with-ambulatory-misuse-potential", | ||
| "0.1.1"); | ||
| assertNotNull(expandResult); | ||
| assertEquals(1180, IterableUtils.size(expandResult)); | ||
| } | ||
|
|
||
| @Test | ||
| void testPreExpandedSnomedCodeSystem() { | ||
| Iterable<org.opencds.cqf.cql.engine.runtime.Code> expandResult = getExpansion( | ||
| "valueset-hospice-procedure.json", | ||
| "http://fhir.org/guides/cdc/opioid-cds/ValueSet/hospice-procedure", | ||
| "1.0.0"); | ||
| assertNotNull(expandResult); | ||
| assertEquals(6, IterableUtils.size(expandResult)); | ||
| } | ||
|
|
||
| @Test | ||
| void testExpandIgDefinedCodeSystem() { | ||
| Iterable<org.opencds.cqf.cql.engine.runtime.Code> expandResult = getExpansion( | ||
| "valueset-opioidcds-indicator.json", | ||
| "http://fhir.org/guides/cdc/opioid-cds/ValueSet/opioidcds-indicator", | ||
| "0.1.1"); | ||
| assertNotNull(expandResult); | ||
| assertEquals(3, IterableUtils.size(expandResult)); | ||
| } | ||
|
|
||
| @Test | ||
| void testExpandFilterWithoutExpansion() { | ||
| Iterable<org.opencds.cqf.cql.engine.runtime.Code> expandResult = getExpansion( | ||
| "valueset-hospice-finding.json", | ||
| "http://fhir.org/guides/cdc/opioid-cds/ValueSet/hospice-finding", | ||
| "0.1.1"); | ||
| assertNotNull(expandResult); | ||
| assertEquals(0, IterableUtils.size(expandResult)); | ||
| } | ||
|
|
||
| @Test | ||
| void testMultipleVersions() { | ||
| Iterable<org.opencds.cqf.cql.engine.runtime.Code> expandResult = getExpansion( | ||
| "valueset-event-status-4.3.0.json", | ||
| "http://example.org/fhir/ValueSet/event-status", | ||
| "4.3.0"); | ||
| assertNotNull(expandResult); | ||
| assertEquals(8, IterableUtils.size(expandResult)); | ||
| expandResult = getExpansion( | ||
| "valueset-event-status-3.0.2.json", | ||
| "http://example.org/fhir/ValueSet/event-status", | ||
| "3.0.2"); | ||
| assertNotNull(expandResult); | ||
| assertEquals(7, IterableUtils.size(expandResult)); | ||
| /* | ||
| The last ValueSet added to the cache will be used when no version is supplied. | ||
| In theory, this is the desired behavior as the "latest" ValueSet is picked for expansion by default. | ||
| However, as in this case, the 4.3.0 version of the ValueSet was added to the cache before the 3.0.2 version. | ||
| Therefore, the latest version of the ValueSet was not picked for expansion. | ||
| This is not exactly ideal behavior and the FHIR spec states: | ||
| "Note that if a References to a canonical URL does not have a version, and the server finds | ||
| multiple versions for the value set, the system using the reference should pick the latest | ||
| version of the target resource and use that." (http://www.hl7.org/fhir/references.html#canonical) | ||
| Based on that, this is not a bug in the HAPI code. It is not the preferred approach though. | ||
| */ | ||
| ValueSetInfo vsInfo = new ValueSetInfo().withId("http://example.org/fhir/ValueSet/event-status"); | ||
| expandResult = terminologyProvider.expand(vsInfo); | ||
| assertEquals(7, IterableUtils.size(expandResult)); | ||
| } | ||
|
|
||
| private Iterable<org.opencds.cqf.cql.engine.runtime.Code> getExpansion( | ||
| String vsFileName, String url, String version) { | ||
| loadResource(vsFileName); | ||
| ValueSetInfo vsInfo = new ValueSetInfo().withId(url).withVersion(version); | ||
| return terminologyProvider.expand(vsInfo); | ||
| } | ||
| } |
68 changes: 68 additions & 0 deletions
68
plugin/cql/src/test/resources/valueset-event-status-3.0.2.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| { | ||
| "resourceType" : "ValueSet", | ||
| "id" : "event-status-3.0.2", | ||
| "meta" : { | ||
| "profile" : ["http://hl7.org/fhir/StructureDefinition/shareablevalueset"] | ||
| }, | ||
| "url" : "http://example.org/fhir/ValueSet/event-status", | ||
| "version" : "3.0.2", | ||
| "name" : "EventStatus", | ||
| "title" : "EventStatus", | ||
| "status" : "draft", | ||
| "experimental" : false, | ||
| "date" : "2021-03-11T17:06:20+11:00", | ||
| "publisher" : "HL7 (FHIR Project)", | ||
| "contact" : [ | ||
| { | ||
| "telecom" : [ | ||
| { | ||
| "system" : "url", | ||
| "value" : "http://hl7.org/fhir" | ||
| }, | ||
| { | ||
| "system" : "email", | ||
| "value" : "fhir@lists.hl7.org" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "description" : "Codes identifying the lifecycle stage of an event.", | ||
| "immutable" : true, | ||
| "compose" : { | ||
| "include" : [ | ||
| { | ||
| "system": "http://example.org/fhir/event-status", | ||
| "concept": [ | ||
| { | ||
| "code" : "preparation", | ||
| "display" : "Preparation" | ||
| }, | ||
| { | ||
| "code" : "in-progress", | ||
| "display" : "In Progress" | ||
| }, | ||
| { | ||
| "code" : "on-hold", | ||
| "display" : "On Hold" | ||
| }, | ||
| { | ||
| "code" : "stopped", | ||
| "display" : "Stopped" | ||
| }, | ||
| { | ||
| "code" : "completed", | ||
| "display" : "Completed" | ||
| }, | ||
| { | ||
| "code" : "entered-in-error", | ||
| "display" : "Entered in Error" | ||
| }, | ||
| { | ||
| "code" : "unknown", | ||
| "display" : "Unknown" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| } |
78 changes: 78 additions & 0 deletions
78
plugin/cql/src/test/resources/valueset-event-status-4.3.0.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| { | ||
| "resourceType" : "ValueSet", | ||
| "id" : "event-status-4.3.0", | ||
| "meta" : { | ||
| "profile" : ["http://hl7.org/fhir/StructureDefinition/shareablevalueset"] | ||
| }, | ||
| "url" : "http://example.org/fhir/ValueSet/event-status", | ||
| "identifier" : [ | ||
| { | ||
| "system" : "urn:ietf:rfc:3986", | ||
| "value" : "urn:oid:2.16.840.1.113883.4.642.3.109" | ||
| } | ||
| ], | ||
| "version" : "4.3.0", | ||
| "name" : "EventStatus", | ||
| "title" : "EventStatus", | ||
| "status" : "draft", | ||
| "experimental" : true, | ||
| "date" : "2022-05-28T12:47:40+10:00", | ||
| "publisher" : "HL7 (FHIR Project)", | ||
| "contact" : [ | ||
| { | ||
| "telecom" : [ | ||
| { | ||
| "system" : "url", | ||
| "value" : "http://hl7.org/fhir" | ||
| }, | ||
| { | ||
| "system" : "email", | ||
| "value" : "fhir@lists.hl7.org" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "description" : "Codes identifying the lifecycle stage of an event.", | ||
| "immutable" : true, | ||
| "compose" : { | ||
| "include" : [ | ||
| { | ||
| "system": "http://example.org/fhir/event-status", | ||
| "concept": [ | ||
| { | ||
| "code" : "preparation", | ||
| "display" : "Preparation" | ||
| }, | ||
| { | ||
| "code" : "in-progress", | ||
| "display" : "In Progress" | ||
| }, | ||
| { | ||
| "code" : "not-done", | ||
| "display" : "Not Done" | ||
| }, | ||
| { | ||
| "code" : "on-hold", | ||
| "display" : "On Hold" | ||
| }, | ||
| { | ||
| "code" : "stopped", | ||
| "display" : "Stopped" | ||
| }, | ||
| { | ||
| "code" : "completed", | ||
| "display" : "Completed" | ||
| }, | ||
| { | ||
| "code" : "entered-in-error", | ||
| "display" : "Entered in Error" | ||
| }, | ||
| { | ||
| "code" : "unknown", | ||
| "display" : "Unknown" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| } |
Oops, something went wrong.