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Incremental progress on large ValueSet expansion with URL parameter.

This commit is contained in:
Diederik Muylwyk 2019-09-09 17:24:01 -04:00
parent c82c3a093f
commit 19676a01b7
4 changed files with 218 additions and 37 deletions
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6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
View File

@ -146,12 +146,12 @@ public class DaoConfig {
private boolean myEnableInMemorySubscriptionMatching = true;
private boolean myEnforceReferenceTargetTypes = true;
private ClientIdStrategyEnum myResourceClientIdStrategy = ClientIdStrategyEnum.ALPHANUMERIC;
private boolean myFilterParameterEnabled = false;
private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code false}!
*/
private boolean myPreExpandValueSetsExperimental = true; // FIXME: DM 2019-09-03 - Return to false before merging into master.
private boolean myFilterParameterEnabled = false;
private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
private boolean myPreExpandValueSetsExperimental = false;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code 0}!
*/

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
View File

@ -121,7 +121,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {//FIXME: DM COWABUNGA
ValueSet vs = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
if (vs == null) {
return Collections.emptyList();

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
View File

@ -156,7 +156,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
for (Long conceptId : conceptIds) {
myValueSetConceptDao.updateOrderById(conceptId, order++);
}
ourLog.info("Have remove gaps from concept order for {} concepts in ValueSet[{}]", conceptIds.size(), myTermValueSet.getUrl());
ourLog.info("Have removed gaps from concept order for {} concepts in ValueSet[{}]", conceptIds.size(), myTermValueSet.getUrl());
return true;
}

245
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
@ -24,10 +25,13 @@ import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
import org.hl7.fhir.r4.model.codesystems.HttpVerb;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
@ -40,18 +44,86 @@ import static org.junit.Assert.*;
public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4ValueSetTest.class);
private IIdType myExtensionalCsId;
private IIdType myExtensionalVsId;
private IIdType myLocalValueSetId;
private Long myExtensionalCsIdOnResourceTable;
private Long myExtensionalVsIdOnResourceTable;
private ValueSet myLocalVs;
@Before
@Transactional
public void before02() throws IOException {
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
myCodeSystemDao.create(cs, mySrd);
// @Before
// @Transactional
// public void before02() throws IOException {
// CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
// myCodeSystemDao.create(cs, mySrd);
//
// ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
// myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
// }
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
private void loadAndPersistCodeSystemAndValueSet(HttpVerb theVerb) throws IOException {
loadAndPersistCodeSystem(theVerb);
loadAndPersistValueSet(theVerb);
}
private void loadAndPersistCodeSystem(HttpVerb theVerb) throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem, theVerb);
}
private void persistCodeSystem(CodeSystem theCodeSystem, HttpVerb theVerb) {
switch (theVerb) {
case POST:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
break;
case PUT:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalCsId = myCodeSystemDao.update(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
break;
default:
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
}
myExtensionalCsIdOnResourceTable = myCodeSystemDao.readEntity(myExtensionalCsId, null).getId();
}
private void loadAndPersistValueSet(HttpVerb theVerb) throws IOException {
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
valueSet.setId("ValueSet/vs");
persistValueSet(valueSet, theVerb);
}
private void persistValueSet(ValueSet theValueSet, HttpVerb theVerb) {
switch (theVerb) {
case POST:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalVsId = myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
}
});
break;
case PUT:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalVsId = myValueSetDao.update(theValueSet, mySrd).getId().toUnqualifiedVersionless();
}
});
break;
default:
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
}
myExtensionalVsIdOnResourceTable = myValueSetDao.readEntity(myExtensionalVsId, null).getId();
}
private CodeSystem createExternalCs() {
@ -128,8 +200,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@Test
public void testExpandById() {
//@formatter:off
public void testExpandById() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
@ -137,7 +210,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.withNoParameters(Parameters.class)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
@ -158,9 +230,42 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@Test
public void testExpandByIdWithFilter() {
public void testExpandByIdWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withNoParameters(Parameters.class)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
assertThat(resp, containsString("<expansion>"));
assertThat(resp, containsString("<contains>"));
assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
assertThat(resp, containsString("<code value=\"8450-9\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
assertThat(resp, containsString("</contains>"));
assertThat(resp, containsString("<contains>"));
assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
assertThat(resp, containsString("<code value=\"11378-7\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
assertThat(resp, containsString("</contains>"));
assertThat(resp, containsString("</expansion>"));
}
@Test
public void testExpandByIdWithFilter() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
//@formatter:off
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
@ -168,7 +273,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.withParameter(Parameters.class, "filter", new StringType("first"))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
@ -178,12 +282,64 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@Test
public void testExpandByUrl() {
public void testExpandByIdWithFilterWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withParameter(Parameters.class, "filter", new StringType("first"))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
assertThat(resp, not(containsString("<display value=\"Systolic blood pressure--expiration\"/>")));
}
@Test
public void testExpandByUrl() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
// .withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2")) //FIXME: DM
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, stringContainsInOrder(
"<code value=\"11378-7\"/>",
"<display value=\"Systolic blood pressure at First encounter\"/>"));
}
@Test
public void testExpandByUrlWithPreExpansion() throws Exception {//FIXME: DM
myDaoConfig.setPreExpandValueSetsExperimental(true);
ourLog.info("DIEDERIK - before loading CD and VS");
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
ourLog.info("DIEDERIK - after loading CD and VS; before pre-expansion");
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ourLog.info("DIEDERIK - after pre-expansion");
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
// .withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2")) //FIXME: DM
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
@ -197,6 +353,8 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testExpandByValueSet() throws IOException {
loadAndPersistCodeSystem(HttpVerb.POST);
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
Parameters respParam = ourClient
@ -215,13 +373,36 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@Test
public void testExpandByValueSetWithPreExpansion() throws IOException {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystem(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "valueSet", toExpand)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, stringContainsInOrder(
"<code value=\"11378-7\"/>",
"<display value=\"Systolic blood pressure at First encounter\"/>"));
}
@Test
public void testExpandInlineVsAgainstBuiltInCs() {
createLocalVsPointingAtBuiltInCodeSystem();
assertNotNull(myLocalValueSetId);
//@formatter:off
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
@ -229,7 +410,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.withParameter(Parameters.class, "valueSet", myLocalVs)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
@ -243,7 +423,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
assertNotNull(myLocalVs);
myLocalVs.setId("");
//@formatter:off
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
@ -251,7 +430,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.withParameter(Parameters.class, "valueSet", myLocalVs)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
@ -263,7 +441,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@Test
public void testExpandInvalidParams() throws IOException {
public void testExpandInvalidParams() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
try {
ourClient
.operation()
@ -334,7 +514,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
createLocalVsPointingAtBuiltInCodeSystem();
assertNotNull(myLocalValueSetId);
//@formatter:off
Parameters respParam = ourClient
.operation()
.onInstance(myLocalValueSetId)
@ -342,7 +521,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.withNoParameters(Parameters.class)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
@ -355,7 +533,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
createExternalCsAndLocalVs();
assertNotNull(myLocalValueSetId);
//@formatter:off
Parameters respParam = ourClient
.operation()
.onInstance(myLocalValueSetId)
@ -363,7 +540,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.withNoParameters(Parameters.class)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
@ -401,7 +577,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
createExternalCsAndLocalVsWithUnknownCode();
assertNotNull(myLocalValueSetId);
//@formatter:off
try {
ourClient
.operation()
@ -412,7 +587,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
}
//@formatter:on
}
/**
@ -438,8 +612,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@Test
public void testValidateCodeOperationByCodeAndSystemInstance() {
//@formatter:off
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
@ -498,8 +673,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@Test
public void testValidateCodeOperationByCodeAndSystemType() {
//@formatter:off
public void testValidateCodeOperationByCodeAndSystemType() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
@ -585,6 +761,11 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@After
public void afterResetPreExpansionDefault() {
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();