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Work on custom search params

This commit is contained in:
James 2017-02-05 20:34:12 -05:00
parent d4dda1dace
commit 73924199a9
6 changed files with 200 additions and 97 deletions
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22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
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@ -27,6 +27,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.locks.ReentrantLock;
import javax.persistence.Query;
import javax.persistence.Tuple;
@ -64,15 +65,17 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirSystemDao.class);
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private IForcedIdDao myForcedIdDao;
private ReentrantLock myReindexLock = new ReentrantLock(false);
@Autowired
private ITermConceptDao myTermConceptDao;
@Autowired
private PlatformTransactionManager myTxManager;
@Transactional(propagation = Propagation.REQUIRED)
@Override
public void deleteAllTagsOnServer(RequestDetails theRequestDetails) {
@ -205,8 +208,14 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
@Transactional()
@Override
public int markAllResourcesForReindexing() {
ourLog.info("Marking all resources as needing reindexing");
int retVal = myEntityManager.createQuery("UPDATE " + ResourceTable.class.getSimpleName() + " t SET t.myIndexStatus = null").executeUpdate();
ourLog.info("Marking all concepts as needing reindexing");
retVal += myTermConceptDao.markAllForReindexing();
ourLog.info("Done marking reindexing");
return retVal;
}
@ -266,16 +275,21 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
}
});
}
@Override
@Transactional(propagation = Propagation.NOT_SUPPORTED)
public int performReindexingPass(final Integer theCount) {
if (!myReindexLock.tryLock()) {
return 0;
}
try {
return doPerformReindexingPass(theCount);
} catch (ReindexFailureException e) {
ourLog.warn("Reindexing failed for resource {}", e.getResourceId());
markResourceAsIndexingFailed(e.getResourceId());
return -1;
} finally {
myReindexLock.unlock();
}
}

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
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@ -41,6 +41,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
@ -187,6 +188,9 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
return retVal;
}
@Autowired
private ITermCodeSystemVersionDao myCsvDao;
@Override
protected ResourceTable updateEntity(IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime) {
@ -198,12 +202,22 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
String codeSystemUrl = cs.getUrl();
if (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == null) {
ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", retVal.getIdDt().getValue(), cs.getContentElement().getValueAsString());
TermCodeSystemVersion persCs = new TermCodeSystemVersion();
persCs.setResource(retVal);
persCs.setResourceVersionId(retVal.getVersion());
persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
Long codeSystemResourcePid = retVal.getId();
TermCodeSystemVersion persCs = myCsvDao.findByCodeSystemResourceAndVersion(codeSystemResourcePid, retVal.getVersion());
if (persCs != null) {
ourLog.info("Code system version already exists in database");
} else {
persCs = new TermCodeSystemVersion();
persCs.setResource(retVal);
persCs.setResourceVersionId(retVal.getVersion());
persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, persCs);
}
myTerminologySvc.storeNewCodeSystemVersion(retVal.getId(), codeSystemUrl, persCs);
}
}

174
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvc.java
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@ -45,6 +45,7 @@ import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Stopwatch;
import ca.uhn.fhir.context.FhirContext;
@ -66,6 +67,7 @@ import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.ValidateUtil;
public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
private static boolean ourForceSaveDeferredAlwaysForUnitTest;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiTerminologySvc.class);
private static final Object PLACEHOLDER_OBJECT = new Object();
@ -94,8 +96,11 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
private boolean myProcessDeferred = true;
private long myNextReindexPass;
private boolean myProcessDeferred = true;
@Autowired
private PlatformTransactionManager myTransactionMgr;
private boolean addToSet(Set<TermConcept> theSetToPopulate, TermConcept theConcept) {
boolean retVal = theSetToPopulate.add(theConcept);
@ -108,6 +113,25 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return retVal;
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
for (TermConceptParentChildLink nextLink : theParents) {
if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
TermConcept nextParent = nextLink.getParent();
retVal += ensureParentsSaved(nextParent.getParents());
if (nextParent.getId() == null) {
myConceptDao.saveAndFlush(nextParent);
retVal++;
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
}
}
}
return retVal;
}
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
TermConcept nextChild = nextChildLink.getChild();
@ -175,6 +199,15 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return retVal;
}
/**
* Subclasses may override
* @param theSystem The code system
* @param theCode The code
*/
protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
return Collections.emptyList();
}
@Transactional(propagation = Propagation.REQUIRED)
@Override
public Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
@ -206,7 +239,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ArrayList<VersionIndependentConcept> retVal = toVersionIndependentConcepts(theSystem, codes);
return retVal;
}
/**
* Subclasses may override
* @param theSystem The code system
@ -215,16 +247,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
protected List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
return Collections.emptyList();
}
/**
* Subclasses may override
* @param theSystem The code system
* @param theCode The code
*/
protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
return Collections.emptyList();
}
private TermCodeSystemVersion findCurrentCodeSystemVersionForSystem(String theCodeSystem) {
TermCodeSystem cs = getCodeSystem(theCodeSystem);
if (cs == null || cs.getCurrentVersion() == null) {
@ -233,11 +256,12 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
TermCodeSystemVersion csv = cs.getCurrentVersion();
return csv;
}
private TermCodeSystem getCodeSystem(String theSystem) {
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
return cs;
}
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
return;
@ -271,10 +295,47 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
}
private void saveConceptLink(TermConceptParentChildLink next) {
if (next.getId() == null) {
myConceptParentChildLinkDao.save(next);
private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
if (theNext.getCodeSystem() != null) {
return;
}
theNext.setCodeSystem(theCodeSystemVersion);
for (TermConceptParentChildLink next : theNext.getChildren()) {
populateVersion(next.getChild(), theCodeSystemVersion);
}
}
private void processReindexing() {
if (System.currentTimeMillis() < myNextReindexPass && !ourForceSaveDeferredAlwaysForUnitTest) {
return;
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
tt.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
Page<TermConcept> resources = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (resources.hasContent() == false) {
myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
return;
}
ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
int count = 0;
StopWatch stopwatch = new StopWatch();
for (TermConcept resourceTable : resources) {
saveConcept(resourceTable);
count++;
}
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
}
});
}
private int saveConcept(TermConcept theConcept) {
@ -289,33 +350,10 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ourLog.trace("Saved {} and got PID {}", theConcept.getCode(), theConcept.getId());
return retVal;
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
for (TermConceptParentChildLink nextLink : theParents) {
if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
TermConcept nextParent = nextLink.getParent();
retVal += ensureParentsSaved(nextParent.getParents());
if (nextParent.getId() == null) {
myConceptDao.saveAndFlush(nextParent);
retVal++;
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
}
}
}
return retVal;
}
private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
if (theNext.getCodeSystem() != null) {
return;
}
theNext.setCodeSystem(theCodeSystemVersion);
for (TermConceptParentChildLink next : theNext.getChildren()) {
populateVersion(next.getChild(), theCodeSystemVersion);
private void saveConceptLink(TermConceptParentChildLink next) {
if (next.getId() == null) {
myConceptParentChildLinkDao.save(next);
}
}
@ -368,43 +406,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ourLog.info("All deferred concepts and relationships have now been synchronized to the database");
}
}
@Autowired
private PlatformTransactionManager myTransactionMgr;
private void processReindexing() {
if (System.currentTimeMillis() < myNextReindexPass) {
return;
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
tt.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
Page<TermConcept> resources = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (resources.hasContent() == false) {
myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
return;
}
ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
int count = 0;
StopWatch stopwatch = new StopWatch();
for (TermConcept resourceTable : resources) {
saveConcept(resourceTable);
count++;
}
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
}
});
}
@Override
public void setProcessDeferred(boolean theProcessDeferred) {
myProcessDeferred = theProcessDeferred;
@ -470,7 +472,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts);
}
ourLog.info("Saving version");
ourLog.info("Saving version containing {} concepts", totalCodeCount);
TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.saveAndFlush(theCodeSystemVersion);
@ -503,13 +505,13 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ourLog.info("Note that some concept saving was deferred - still have {} concepts and {} relationships", myConceptsToSaveLater.size(), myConceptLinksToSaveLater.size());
}
}
@Override
public boolean supportsSystem(String theSystem) {
TermCodeSystem cs = getCodeSystem(theSystem);
return cs != null;
}
private ArrayList<VersionIndependentConcept> toVersionIndependentConcepts(String theSystem, Set<TermConcept> codes) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>(codes.size());
for (TermConcept next : codes) {
@ -547,4 +549,12 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return retVal;
}
/**
* This method is present only for unit tests, do not call from client code
*/
@VisibleForTesting
public static void setForceSaveDeferredAlwaysForUnitTest(boolean theForceSaveDeferredAlwaysForUnitTest) {
ourForceSaveDeferredAlwaysForUnitTest = theForceSaveDeferredAlwaysForUnitTest;
}
}

44
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java Normal file
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@ -0,0 +1,44 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.junit.Assert.assertNotEquals;
import java.nio.charset.StandardCharsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3CodeSystemTest.class);
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Test
public void testIndexContained() throws Exception {
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
String input = IOUtils.toString(getClass().getResource("/dstu3_codesystem_complete.json"), StandardCharsets.UTF_8);
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
myCodeSystemDao.create(cs, mySrd);
mySystemDao.markAllResourcesForReindexing();
int outcome = mySystemDao.performReindexingPass(100);
assertNotEquals(-1, outcome); // -1 means there was a failure
myTermSvc.saveDeferred();
}
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ContainedTest.java
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@ -1,8 +1,5 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.assertThat;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Reference;
@ -11,9 +8,6 @@ import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoDstu3ContainedTest extends BaseJpaDstu3Test {

27
hapi-fhir-jpaserver-base/src/test/resources/dstu3_codesystem_complete.json Normal file
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@ -0,0 +1,27 @@
{
"resourceType": "CodeSystem",
"id": "22472",
"meta": {
"versionId": "3",
"lastUpdated": "2017-01-27T10:53:39.457-05:00"
},
"url": "xvalue://dedalus.eu/mci/CodeSystem/AddressUse",
"name": "AddressUse",
"status": "active",
"publisher": "x1v1-mci",
"date": "2016-04-07",
"description": "AddressUse",
"caseSensitive": true,
"compositional": false,
"versionNeeded": false,
"content": "complete",
"concept": {
"code": "work",
"display": "Work",
"definition": "An office address. First choice for business related contacts during business hours.",
"designation": {
"language": "IT",
"value": "Lavoro"
}
}
}