Merging master into working branch to resolve conflicts.
# Conflicts: # src/changes/changes.xml
This commit is contained in:
Diederik Muylwyk
commit
3e173bb07c
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|
@ -17,5 +17,3 @@ http://hapi.fhir.org/
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|||
This project is Open Source, licensed under the Apache Software License 2.0.
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||||
|
||||
Please see [this wiki page](https://github.com/jamesagnew/hapi-fhir/wiki/Getting-Help) for information on where to get help with HAPI FHIR. Please see [Smile CDR](https://smilecdr.com) for information on commercial support.
|
||||
|
||||
---
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||||
|
|
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|||
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@ -1,7 +1,4 @@
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|||
# Starter pipeline
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||||
# Start with a minimal pipeline that you can customize to build and deploy your code.
|
||||
# Add steps that build, run tests, deploy, and more:
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||||
# https://aka.ms/yaml
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||||
# HAPI FHIR Build Pipeline
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variables:
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MAVEN_CACHE_FOLDER: $(Pipeline.Workspace)/.m2/repository
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@ -13,7 +10,6 @@ trigger:
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pool:
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vmImage: 'ubuntu-latest'
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||||
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||||
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||||
jobs:
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- job: Build
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timeoutInMinutes: 360
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|
@ -23,37 +19,37 @@ jobs:
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key: maven
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path: $(MAVEN_CACHE_FOLDER)
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displayName: Cache Maven local repo
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|
||||
- task: Maven@3
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inputs:
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#mavenPomFile: 'pom.xml'
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goals: 'clean install' # Optional
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options: '-P ALLMODULES,JACOCO'
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||||
#publishJUnitResults: true
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||||
#testResultsFiles: '**/surefire-reports/TEST-*.xml' # Required when publishJUnitResults == True
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||||
#testRunTitle: # Optional
|
||||
#codeCoverageToolOption: 'None' # Optional. Options: none, cobertura, jaCoCo. Enabling code coverage inserts the `clean` goal into the Maven goals list when Maven runs.
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||||
#codeCoverageClassFilter: # Optional. Comma-separated list of filters to include or exclude classes from collecting code coverage. For example: +:com.*,+:org.*,-:my.app*.*
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||||
#codeCoverageClassFilesDirectories: # Optional
|
||||
#codeCoverageSourceDirectories: # Optional
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||||
#codeCoverageFailIfEmpty: false # Optional
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||||
#javaHomeOption: 'JDKVersion' # Options: jDKVersion, path
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#jdkVersionOption: 'default' # Optional. Options: default, 1.11, 1.10, 1.9, 1.8, 1.7, 1.6
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#jdkDirectory: # Required when javaHomeOption == Path
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||||
#jdkArchitectureOption: 'x64' # Optional. Options: x86, x64
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||||
#mavenVersionOption: 'Default' # Options: default, path
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||||
#mavenDirectory: # Required when mavenVersionOption == Path
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||||
#mavenSetM2Home: false # Required when mavenVersionOption == Path
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||||
mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS' # Optional
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#mavenAuthenticateFeed: false
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||||
#effectivePomSkip: false
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||||
#sonarQubeRunAnalysis: false
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||||
#sqMavenPluginVersionChoice: 'latest' # Required when sonarQubeRunAnalysis == True# Options: latest, pom
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||||
#checkStyleRunAnalysis: false # Optional
|
||||
#pmdRunAnalysis: false # Optional
|
||||
#findBugsRunAnalysis: false # Optional
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||||
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goals: 'clean install'
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# These are Maven CLI options (and show up in the build logs) - "-nsu"=Don't update snapshots. We can remove this when Maven OSS is more healthy
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options: '-P ALLMODULES,JACOCO -nsu'
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# These are JVM options (and don't show up in the build logs)
|
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mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto'
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||||
- script: bash <(curl https://codecov.io/bash) -t $(CODECOV_TOKEN)
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displayName: 'codecov'
|
||||
|
||||
|
||||
# Potential Additional Maven3 Options:
|
||||
#publishJUnitResults: true
|
||||
#testResultsFiles: '**/surefire-reports/TEST-*.xml' # Required when publishJUnitResults == True
|
||||
#testRunTitle: # Optional
|
||||
#codeCoverageToolOption: 'None' # Optional. Options: none, cobertura, jaCoCo. Enabling code coverage inserts the `clean` goal into the Maven goals list when Maven runs.
|
||||
#codeCoverageClassFilter: # Optional. Comma-separated list of filters to include or exclude classes from collecting code coverage. For example: +:com.*,+:org.*,-:my.app*.*
|
||||
#codeCoverageClassFilesDirectories: # Optional
|
||||
#codeCoverageSourceDirectories: # Optional
|
||||
#codeCoverageFailIfEmpty: false # Optional
|
||||
#javaHomeOption: 'JDKVersion' # Options: jDKVersion, path
|
||||
#jdkVersionOption: 'default' # Optional. Options: default, 1.11, 1.10, 1.9, 1.8, 1.7, 1.6
|
||||
#jdkDirectory: # Required when javaHomeOption == Path
|
||||
#jdkArchitectureOption: 'x64' # Optional. Options: x86, x64
|
||||
#mavenVersionOption: 'Default' # Options: default, path
|
||||
#mavenDirectory: # Required when mavenVersionOption == Path
|
||||
#mavenSetM2Home: false # Required when mavenVersionOption == Path
|
||||
#mavenAuthenticateFeed: false
|
||||
#effectivePomSkip: false
|
||||
#sonarQubeRunAnalysis: false
|
||||
#sqMavenPluginVersionChoice: 'latest' # Required when sonarQubeRunAnalysis == True# Options: latest, pom
|
||||
#checkStyleRunAnalysis: false # Optional
|
||||
#pmdRunAnalysis: false # Optional
|
||||
#findBugsRunAnalysis: false # Optional
|
||||
|
|
|
|||
|
|
@ -52,15 +52,6 @@ public class GsonStructure implements JsonLikeStructure {
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|||
super();
|
||||
}
|
||||
|
||||
public GsonStructure (JsonObject json) {
|
||||
super();
|
||||
setNativeObject(json);
|
||||
}
|
||||
public GsonStructure (JsonArray json) {
|
||||
super();
|
||||
setNativeArray(json);
|
||||
}
|
||||
|
||||
public void setNativeObject (JsonObject json) {
|
||||
this.rootType = ROOT_TYPE.OBJECT;
|
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this.nativeRoot = json;
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||||
|
|
@ -111,8 +102,7 @@ public class GsonStructure implements JsonLikeStructure {
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|||
if (nextInt == '{') {
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JsonObject root = gson.fromJson(pbr, JsonObject.class);
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||||
setNativeObject(root);
|
||||
} else
|
||||
if (nextInt == '[') {
|
||||
} else if (nextInt == '[') {
|
||||
JsonArray root = gson.fromJson(pbr, JsonArray.class);
|
||||
setNativeArray(root);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -108,9 +108,13 @@ public class OperationOutcomeUtil {
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|||
if (theOutcome == null) {
|
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return false;
|
||||
}
|
||||
return getIssueCount(theCtx, theOutcome) > 0;
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}
|
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|
||||
public static int getIssueCount(FhirContext theCtx, IBaseOperationOutcome theOutcome) {
|
||||
RuntimeResourceDefinition ooDef = theCtx.getResourceDefinition(theOutcome);
|
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BaseRuntimeChildDefinition issueChild = ooDef.getChildByName("issue");
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return issueChild.getAccessor().getValues(theOutcome).size() > 0;
|
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return issueChild.getAccessor().getValues(theOutcome).size();
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}
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public static IBaseOperationOutcome newInstance(FhirContext theCtx) {
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|
@ -152,5 +156,4 @@ public class OperationOutcomeUtil {
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locationChild.getMutator().addValue(theIssue, locationElem);
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}
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||||
}
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||||
|
||||
}
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||||
|
|
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|||
|
|
@ -53,21 +53,6 @@ public class Search implements ICachedSearchDetails, Serializable {
|
|||
private static final int FAILURE_MESSAGE_LENGTH = 500;
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||||
private static final long serialVersionUID = 1L;
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(Search.class);
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return new ToStringBuilder(this)
|
||||
.append("myLastUpdatedHigh", myLastUpdatedHigh)
|
||||
.append("myLastUpdatedLow", myLastUpdatedLow)
|
||||
.append("myNumFound", myNumFound)
|
||||
.append("myNumBlocked", myNumBlocked)
|
||||
.append("myStatus", myStatus)
|
||||
.append("myTotalCount", myTotalCount)
|
||||
.append("myUuid", myUuid)
|
||||
.append("myVersion", myVersion)
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||||
.toString();
|
||||
}
|
||||
|
||||
@Temporal(TemporalType.TIMESTAMP)
|
||||
@Column(name = "CREATED", nullable = false, updatable = false)
|
||||
private Date myCreated;
|
||||
|
|
@ -139,6 +124,20 @@ public class Search implements ICachedSearchDetails, Serializable {
|
|||
super();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return new ToStringBuilder(this)
|
||||
.append("myLastUpdatedHigh", myLastUpdatedHigh)
|
||||
.append("myLastUpdatedLow", myLastUpdatedLow)
|
||||
.append("myNumFound", myNumFound)
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||||
.append("myNumBlocked", myNumBlocked)
|
||||
.append("myStatus", myStatus)
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||||
.append("myTotalCount", myTotalCount)
|
||||
.append("myUuid", myUuid)
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||||
.append("myVersion", myVersion)
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||||
.toString();
|
||||
}
|
||||
|
||||
public int getNumBlocked() {
|
||||
return myNumBlocked != null ? myNumBlocked : 0;
|
||||
}
|
||||
|
|
@ -351,8 +350,8 @@ public class Search implements ICachedSearchDetails, Serializable {
|
|||
return myVersion;
|
||||
}
|
||||
|
||||
public SearchParameterMap getSearchParameterMap() {
|
||||
return SerializationUtils.deserialize(mySearchParameterMap);
|
||||
public Optional<SearchParameterMap> getSearchParameterMap() {
|
||||
return Optional.ofNullable(mySearchParameterMap).map(t -> SerializationUtils.deserialize(mySearchParameterMap));
|
||||
}
|
||||
|
||||
public void setSearchParameterMap(SearchParameterMap theSearchParameterMap) {
|
||||
|
|
|
|||
|
|
@ -173,4 +173,11 @@ public class TermCodeSystemVersion implements Serializable {
|
|||
"Version ID exceeds maximum length (" + MAX_VERSION_LENGTH + "): " + length(theCodeSystemDisplayName));
|
||||
myCodeSystemDisplayName = theCodeSystemDisplayName;
|
||||
}
|
||||
|
||||
public TermConcept addConcept() {
|
||||
TermConcept concept = new TermConcept();
|
||||
concept.setCodeSystemVersion(this);
|
||||
getConcepts().add(concept);
|
||||
return concept;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -28,6 +28,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
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|||
|
||||
import javax.annotation.Nullable;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
public interface ISearchCoordinatorSvc {
|
||||
|
||||
|
|
@ -37,4 +38,10 @@ public interface ISearchCoordinatorSvc {
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|||
|
||||
IBundleProvider registerSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, CacheControlDirective theCacheControlDirective, @Nullable RequestDetails theRequestDetails);
|
||||
|
||||
/**
|
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* Fetch the total number of search results for the given currently executing search, if one is currently executing and
|
||||
* the total is known. Will return empty otherwise
|
||||
*/
|
||||
Optional<Integer> getSearchTotal(String theUuid);
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -191,12 +191,12 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
|
|||
if (mySearchEntity == null) {
|
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ensureDependenciesInjected();
|
||||
|
||||
Optional<Search> search = mySearchCacheSvc.fetchByUuid(myUuid);
|
||||
if (!search.isPresent()) {
|
||||
Optional<Search> searchOpt = mySearchCacheSvc.fetchByUuid(myUuid);
|
||||
if (!searchOpt.isPresent()) {
|
||||
return false;
|
||||
}
|
||||
|
||||
setSearchEntity(search.get());
|
||||
setSearchEntity(searchOpt.get());
|
||||
|
||||
ourLog.trace("Retrieved search with version {} and total {}", mySearchEntity.getVersion(), mySearchEntity.getTotalCount());
|
||||
|
||||
|
|
@ -292,10 +292,16 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
|
|||
SearchCoordinatorSvcImpl.verifySearchHasntFailedOrThrowInternalErrorException(mySearchEntity);
|
||||
|
||||
Integer size = mySearchEntity.getTotalCount();
|
||||
if (size == null) {
|
||||
return null;
|
||||
if (size != null) {
|
||||
return Math.max(0, size);
|
||||
}
|
||||
return Math.max(0, size);
|
||||
|
||||
if (mySearchEntity.getSearchType() == SearchTypeEnum.HISTORY) {
|
||||
return null;
|
||||
} else {
|
||||
return mySearchCoordinatorSvc.getSearchTotal(myUuid).orElse(null);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
// Note: Leave as protected, HSPC depends on this
|
||||
|
|
|
|||
|
|
@ -62,6 +62,8 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
|
|||
public List<IBaseResource> getResources(int theFromIndex, int theToIndex) {
|
||||
SearchCoordinatorSvcImpl.verifySearchHasntFailedOrThrowInternalErrorException(mySearch);
|
||||
|
||||
mySearchTask.awaitInitialSync();
|
||||
|
||||
ourLog.trace("Fetching search resource PIDs from task: {}", mySearchTask.getClass());
|
||||
final List<Long> pids = mySearchTask.getResourcePids(theFromIndex, theToIndex);
|
||||
ourLog.trace("Done fetching search resource PIDs");
|
||||
|
|
|
|||
|
|
@ -92,7 +92,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
public static final int DEFAULT_SYNC_SIZE = 250;
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchCoordinatorSvcImpl.class);
|
||||
private final ConcurrentHashMap<String, BaseTask> myIdToSearchTask = new ConcurrentHashMap<>();
|
||||
private final ConcurrentHashMap<String, SearchTask> myIdToSearchTask = new ConcurrentHashMap<>();
|
||||
@Autowired
|
||||
private FhirContext myContext;
|
||||
@Autowired
|
||||
|
|
@ -151,7 +151,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
|
||||
@Override
|
||||
public void cancelAllActiveSearches() {
|
||||
for (BaseTask next : myIdToSearchTask.values()) {
|
||||
for (SearchTask next : myIdToSearchTask.values()) {
|
||||
next.requestImmediateAbort();
|
||||
try {
|
||||
next.getCompletionLatch().await(30, TimeUnit.SECONDS);
|
||||
|
|
@ -171,17 +171,35 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
|
||||
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
|
||||
|
||||
// If we're actively searching right now, don't try to do anything until at least one batch has been
|
||||
// persisted in the DB
|
||||
SearchTask searchTask = myIdToSearchTask.get(theUuid);
|
||||
if (searchTask != null) {
|
||||
searchTask.awaitInitialSync();
|
||||
}
|
||||
|
||||
ourLog.trace("About to start looking for resources {}-{}", theFrom, theTo);
|
||||
|
||||
Search search;
|
||||
StopWatch sw = new StopWatch();
|
||||
while (true) {
|
||||
|
||||
if (myNeverUseLocalSearchForUnitTests == false) {
|
||||
BaseTask task = myIdToSearchTask.get(theUuid);
|
||||
if (task != null) {
|
||||
if (searchTask != null) {
|
||||
ourLog.trace("Local search found");
|
||||
List<Long> resourcePids = task.getResourcePids(theFrom, theTo);
|
||||
List<Long> resourcePids = searchTask.getResourcePids(theFrom, theTo);
|
||||
if (resourcePids != null) {
|
||||
return resourcePids;
|
||||
ourLog.trace("Local search returned {} pids, wanted {}-{} - Search: {}", resourcePids.size(), theFrom, theTo, searchTask.getSearch());
|
||||
|
||||
/*
|
||||
* Generally, if a search task is open, the fastest possible thing is to just return its results. This
|
||||
* will work most of the time, but can fail if the task hit a search threshold and the client is requesting
|
||||
* results beyond that threashold. In that case, we'll keep going below, since that will trigger another
|
||||
* task.
|
||||
*/
|
||||
if ((searchTask.getSearch().getNumFound() - searchTask.getSearch().getNumBlocked()) >= theTo || resourcePids.size() == (theTo - theFrom)) {
|
||||
return resourcePids;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -189,18 +207,18 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
search = mySearchCacheSvc
|
||||
.fetchByUuid(theUuid)
|
||||
.orElseThrow(() -> {
|
||||
ourLog.debug("Client requested unknown paging ID[{}]", theUuid);
|
||||
ourLog.trace("Client requested unknown paging ID[{}]", theUuid);
|
||||
String msg = myContext.getLocalizer().getMessage(PageMethodBinding.class, "unknownSearchId", theUuid);
|
||||
return new ResourceGoneException(msg);
|
||||
});
|
||||
|
||||
verifySearchHasntFailedOrThrowInternalErrorException(search);
|
||||
if (search.getStatus() == SearchStatusEnum.FINISHED) {
|
||||
ourLog.debug("Search entity marked as finished with {} results", search.getNumFound());
|
||||
ourLog.trace("Search entity marked as finished with {} results", search.getNumFound());
|
||||
break;
|
||||
}
|
||||
if (search.getNumFound() >= theTo) {
|
||||
ourLog.debug("Search entity has {} results so far", search.getNumFound());
|
||||
ourLog.trace("Search entity has {} results so far", search.getNumFound());
|
||||
break;
|
||||
}
|
||||
|
||||
|
|
@ -212,11 +230,12 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
// If the search was saved in "pass complete mode" it's probably time to
|
||||
// start a new pass
|
||||
if (search.getStatus() == SearchStatusEnum.PASSCMPLET) {
|
||||
ourLog.trace("Going to try to start next search");
|
||||
Optional<Search> newSearch = mySearchCacheSvc.tryToMarkSearchAsInProgress(search);
|
||||
if (newSearch.isPresent()) {
|
||||
search = newSearch.get();
|
||||
String resourceType = search.getResourceType();
|
||||
SearchParameterMap params = search.getSearchParameterMap();
|
||||
SearchParameterMap params = search.getSearchParameterMap().orElseThrow(() -> new IllegalStateException("No map in PASSCOMPLET search"));
|
||||
IFhirResourceDao<?> resourceDao = myDaoRegistry.getResourceDao(resourceType);
|
||||
SearchContinuationTask task = new SearchContinuationTask(search, resourceDao, params, resourceType, theRequestDetails);
|
||||
myIdToSearchTask.put(search.getUuid(), task);
|
||||
|
|
@ -231,10 +250,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
}
|
||||
}
|
||||
|
||||
ourLog.trace("Finished looping");
|
||||
|
||||
List<Long> pids = mySearchResultCacheSvc.fetchResultPids(search, theFrom, theTo);
|
||||
|
||||
|
||||
ourLog.trace("Fetched {} results", pids.size());
|
||||
|
||||
return pids;
|
||||
}
|
||||
|
|
@ -290,6 +310,38 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
|
||||
}
|
||||
|
||||
@Override
|
||||
public Optional<Integer> getSearchTotal(String theUuid) {
|
||||
SearchTask task = myIdToSearchTask.get(theUuid);
|
||||
if (task != null) {
|
||||
return Optional.ofNullable(task.awaitInitialSync());
|
||||
}
|
||||
|
||||
/*
|
||||
* In case there is no running search, if the total is listed as accurate we know one is coming
|
||||
* so let's wait a bit for it to show up
|
||||
*/
|
||||
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
|
||||
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
|
||||
Optional<Search> search = mySearchCacheSvc.fetchByUuid(theUuid);
|
||||
if (search.isPresent()) {
|
||||
Optional<SearchParameterMap> searchParameterMap = search.get().getSearchParameterMap();
|
||||
if (searchParameterMap.isPresent() && searchParameterMap.get().getSearchTotalMode() == SearchTotalModeEnum.ACCURATE) {
|
||||
for (int i = 0; i < 10; i++) {
|
||||
if (search.isPresent()) {
|
||||
verifySearchHasntFailedOrThrowInternalErrorException(search.get());
|
||||
if (search.get().getTotalCount() != null) {
|
||||
return Optional.of(search.get().getTotalCount());
|
||||
}
|
||||
}
|
||||
search = mySearchCacheSvc.fetchByUuid(theUuid);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return Optional.empty();
|
||||
}
|
||||
|
||||
@NotNull
|
||||
private IBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, String theQueryString) {
|
||||
StopWatch w = new StopWatch();
|
||||
|
|
@ -516,7 +568,20 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
myInterceptorBroadcaster = theInterceptorBroadcaster;
|
||||
}
|
||||
|
||||
public abstract class BaseTask implements Callable<Void> {
|
||||
/**
|
||||
* A search task is a Callable task that runs in
|
||||
* a thread pool to handle an individual search. One instance
|
||||
* is created for any requested search and runs from the
|
||||
* beginning to the end of the search.
|
||||
* <p>
|
||||
* Understand:
|
||||
* This class executes in its own thread separate from the
|
||||
* web server client thread that made the request. We do that
|
||||
* so that we can return to the client as soon as possible,
|
||||
* but keep the search going in the background (and have
|
||||
* the next page of results ready to go when the client asks).
|
||||
*/
|
||||
public class SearchTask implements Callable<Void> {
|
||||
private final SearchParameterMap myParams;
|
||||
private final IDao myCallingDao;
|
||||
private final String myResourceType;
|
||||
|
|
@ -538,7 +603,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
/**
|
||||
* Constructor
|
||||
*/
|
||||
protected BaseTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequest) {
|
||||
protected SearchTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequest) {
|
||||
mySearch = theSearch;
|
||||
myCallingDao = theCallingDao;
|
||||
myParams = theParams;
|
||||
|
|
@ -549,6 +614,29 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
myRequest = theRequest;
|
||||
}
|
||||
|
||||
/**
|
||||
* This method is called by the server HTTP thread, and
|
||||
* will block until at least one page of results have been
|
||||
* fetched from the DB, and will never block after that.
|
||||
*/
|
||||
Integer awaitInitialSync() {
|
||||
ourLog.trace("Awaiting initial sync");
|
||||
do {
|
||||
try {
|
||||
if (getInitialCollectionLatch().await(250, TimeUnit.MILLISECONDS)) {
|
||||
break;
|
||||
}
|
||||
} catch (InterruptedException e) {
|
||||
// Shouldn't happen
|
||||
Thread.currentThread().interrupt();
|
||||
throw new InternalErrorException(e);
|
||||
}
|
||||
} while (getSearch().getStatus() == SearchStatusEnum.LOADING);
|
||||
ourLog.trace("Initial sync completed");
|
||||
|
||||
return getSearch().getTotalCount();
|
||||
}
|
||||
|
||||
protected Search getSearch() {
|
||||
return mySearch;
|
||||
}
|
||||
|
|
@ -1010,7 +1098,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
}
|
||||
|
||||
|
||||
public class SearchContinuationTask extends BaseTask {
|
||||
public class SearchContinuationTask extends SearchTask {
|
||||
|
||||
public SearchContinuationTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequest) {
|
||||
super(theSearch, theCallingDao, theParams, theResourceType, theRequest);
|
||||
|
|
@ -1041,51 +1129,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
|
|||
|
||||
}
|
||||
|
||||
/**
|
||||
* A search task is a Callable task that runs in
|
||||
* a thread pool to handle an individual search. One instance
|
||||
* is created for any requested search and runs from the
|
||||
* beginning to the end of the search.
|
||||
* <p>
|
||||
* Understand:
|
||||
* This class executes in its own thread separate from the
|
||||
* web server client thread that made the request. We do that
|
||||
* so that we can return to the client as soon as possible,
|
||||
* but keep the search going in the background (and have
|
||||
* the next page of results ready to go when the client asks).
|
||||
*/
|
||||
class SearchTask extends BaseTask {
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*/
|
||||
SearchTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails) {
|
||||
super(theSearch, theCallingDao, theParams, theResourceType, theRequestDetails);
|
||||
}
|
||||
|
||||
/**
|
||||
* This method is called by the server HTTP thread, and
|
||||
* will block until at least one page of results have been
|
||||
* fetched from the DB, and will never block after that.
|
||||
*/
|
||||
Integer awaitInitialSync() {
|
||||
ourLog.trace("Awaiting initial sync");
|
||||
do {
|
||||
try {
|
||||
if (getInitialCollectionLatch().await(250, TimeUnit.MILLISECONDS)) {
|
||||
break;
|
||||
}
|
||||
} catch (InterruptedException e) {
|
||||
// Shouldn't happen
|
||||
throw new InternalErrorException(e);
|
||||
}
|
||||
} while (getSearch().getStatus() == SearchStatusEnum.LOADING);
|
||||
ourLog.trace("Initial sync completed");
|
||||
|
||||
return getSearch().getTotalCount();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public static void populateSearchEntity(SearchParameterMap theParams, String theResourceType, String theSearchUuid, String theQueryString, Search theSearch) {
|
||||
theSearch.setDeleted(false);
|
||||
|
|
|
|||
|
|
@ -58,9 +58,6 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
|
|||
|
||||
ourLog.debug("fetchResultPids for range {}-{} returned {} pids", theFrom, theTo, retVal.size());
|
||||
|
||||
// FIXME: should we remove the blocked number from this message?
|
||||
Validate.isTrue((theSearch.getNumFound() - theSearch.getNumBlocked()) < theTo || retVal.size() == (theTo - theFrom), "Failed to find results in cache, requested %d - %d and got %d with total found=%d and blocked %s", theFrom, theTo, retVal.size(), theSearch.getNumFound(), theSearch.getNumBlocked());
|
||||
|
||||
return new ArrayList<>(retVal);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -270,7 +270,7 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
|
|||
public IValidationSupport.CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
|
||||
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
|
||||
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
|
||||
return txTemplate.execute(t-> {
|
||||
return txTemplate.execute(t -> {
|
||||
Optional<TermConcept> codeOpt = findCode(theCodeSystem, theCode);
|
||||
if (codeOpt.isPresent()) {
|
||||
TermConcept code = codeOpt.get();
|
||||
|
|
|
|||
|
|
@ -367,6 +367,11 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
|
|||
myInterceptorRegistry.registerInterceptor(myPerformanceTracingLoggingInterceptor);
|
||||
}
|
||||
|
||||
@Before
|
||||
public void beforeUnregisterAllSubscriptions() {
|
||||
mySubscriptionRegistry.unregisterAllSubscriptions();
|
||||
}
|
||||
|
||||
@Before
|
||||
public void beforeFlushFT() {
|
||||
runInTransaction(() -> {
|
||||
|
|
|
|||
|
|
@ -120,20 +120,24 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
myPatientDao.update(p);
|
||||
|
||||
myDaoConfig.setSearchPreFetchThresholds(Arrays.asList(20, 50, 190));
|
||||
SearchParameterMap params;
|
||||
IBundleProvider results;
|
||||
String uuid;
|
||||
List<String> ids;
|
||||
|
||||
// Search with count only
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params = new SearchParameterMap();
|
||||
params.add(Patient.SP_NAME, new StringParam("FAM"));
|
||||
params.setSummaryMode((SummaryEnum.COUNT));
|
||||
IBundleProvider results = myPatientDao.search(params);
|
||||
String uuid = results.getUuid();
|
||||
results = myPatientDao.search(params);
|
||||
uuid = results.getUuid();
|
||||
ourLog.info("** Search returned UUID: {}", uuid);
|
||||
assertEquals(201, results.size().intValue());
|
||||
List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
|
||||
ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
|
||||
assertThat(ids, empty());
|
||||
assertEquals(201, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size().intValue());
|
||||
|
||||
// Seach with total explicitly requested
|
||||
// Search with total explicitly requested
|
||||
params = new SearchParameterMap();
|
||||
params.add(Patient.SP_NAME, new StringParam("FAM"));
|
||||
params.setSearchTotalMode(SearchTotalModeEnum.ACCURATE);
|
||||
|
|
@ -213,7 +217,6 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
assertEquals("Patient/PT00000", ids.get(0));
|
||||
assertEquals("Patient/PT00009", ids.get(9));
|
||||
|
||||
await().until(() -> myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size() != null);
|
||||
results = myDatabaseBackedPagingProvider.retrieveResultList(null, uuid);
|
||||
Integer resultsSize = results.size();
|
||||
assertEquals(200, resultsSize.intValue());
|
||||
|
|
@ -354,6 +357,15 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
* 20 should be prefetched since that's the initial page size
|
||||
*/
|
||||
|
||||
await().until(()->{
|
||||
return runInTransaction(()->{
|
||||
return mySearchEntityDao
|
||||
.findByUuidAndFetchIncludes(uuid)
|
||||
.orElseThrow(() -> new InternalErrorException(""))
|
||||
.getStatus() == SearchStatusEnum.PASSCMPLET;
|
||||
});
|
||||
});
|
||||
|
||||
runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
assertEquals(20, search.getNumFound());
|
||||
|
|
@ -636,6 +648,10 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
assertEquals("Patient/PT00000", ids.get(0));
|
||||
assertEquals(1, ids.size());
|
||||
|
||||
await().until(()-> runInTransaction(()-> mySearchEntityDao
|
||||
.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""))
|
||||
.getStatus() == SearchStatusEnum.FINISHED));
|
||||
|
||||
runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
assertEquals(SearchStatusEnum.FINISHED, search.getStatus());
|
||||
|
|
@ -778,6 +794,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
search.getResources(0, 20);
|
||||
ourLog.info("** Done retrieving resources");
|
||||
|
||||
await().until(()->myCaptureQueriesListener.countSelectQueries() == 4);
|
||||
|
||||
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
|
||||
assertEquals(4, myCaptureQueriesListener.countSelectQueries());
|
||||
|
|
|
|||
|
|
@ -1,6 +1,8 @@
|
|||
package ca.uhn.fhir.jpa.dao.r4;
|
||||
|
||||
import ca.uhn.fhir.jpa.dao.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
|
||||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import ca.uhn.fhir.rest.api.MethodOutcome;
|
||||
import ca.uhn.fhir.rest.api.ValidationModeEnum;
|
||||
|
|
@ -8,10 +10,12 @@ import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
|
|||
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||
import ca.uhn.fhir.util.OperationOutcomeUtil;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.validation.IValidatorModule;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
|
||||
|
|
@ -28,16 +32,18 @@ import org.springframework.test.util.AopTestUtils;
|
|||
|
||||
import java.io.IOException;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.util.Collections;
|
||||
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.hamcrest.Matchers.not;
|
||||
import static org.junit.Assert.assertThat;
|
||||
import static org.junit.Assert.fail;
|
||||
import static org.junit.Assert.*;
|
||||
|
||||
public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ValidateTest.class);
|
||||
@Autowired
|
||||
private IValidatorModule myValidatorModule;
|
||||
@Autowired
|
||||
private IHapiTerminologySvc myTerminologySvc;
|
||||
|
||||
@Test
|
||||
public void testValidateStructureDefinition() throws Exception {
|
||||
|
|
@ -106,6 +112,43 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
|
|||
assertThat(ooString, containsString("Element '/f:Observation.device': minimum required = 1, but only found 0"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateUsingExternallyDefinedCode() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl("http://foo");
|
||||
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType csId = myCodeSystemDao.create(codeSystem).getId();
|
||||
|
||||
TermCodeSystemVersion csv = new TermCodeSystemVersion();
|
||||
csv.addConcept().setCode("bar").setDisplay("Bar Code");
|
||||
myTerminologySvc.storeNewCodeSystemVersion(codeSystem, csv, mySrd, Collections.emptyList(), Collections.emptyList());
|
||||
|
||||
// Validate a resource containing this codesystem in a field with an extendable binding
|
||||
Patient patient = new Patient();
|
||||
patient.getText().setStatus(Narrative.NarrativeStatus.GENERATED).setDivAsString("<div>hello</div>");
|
||||
patient
|
||||
.addIdentifier()
|
||||
.setSystem("http://example.com")
|
||||
.setValue("12345")
|
||||
.getType()
|
||||
.addCoding()
|
||||
.setSystem("http://foo")
|
||||
.setCode("bar");
|
||||
MethodOutcome outcome = myPatientDao.validate(patient, null, encode(patient), EncodingEnum.JSON, ValidationModeEnum.CREATE, null, mySrd);
|
||||
IBaseOperationOutcome oo = outcome.getOperationOutcome();
|
||||
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
|
||||
|
||||
// It would be ok for this to produce 0 issues, or just an information message too
|
||||
assertEquals(1, OperationOutcomeUtil.getIssueCount(myFhirCtx, oo));
|
||||
assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code) (codes = http://foo#bar)", OperationOutcomeUtil.getFirstIssueDetails(myFhirCtx, oo));
|
||||
|
||||
}
|
||||
|
||||
private String encode(Patient thePatient) {
|
||||
return myFhirCtx.newJsonParser().encodeResourceToString(thePatient);
|
||||
}
|
||||
|
||||
|
||||
private OperationOutcome doTestValidateResourceContainingProfileDeclaration(String methodName, EncodingEnum enc) throws IOException {
|
||||
Bundle vss = loadResourceFromClasspath(Bundle.class, "/org/hl7/fhir/r4/model/valueset/valuesets.xml");
|
||||
myValueSetDao.update((ValueSet) findResourceByIdInBundle(vss, "observation-status"), mySrd);
|
||||
|
|
|
|||
|
|
@ -293,6 +293,7 @@ public class SearchCoordinatorSvcImplTest {
|
|||
myExpectedNumberOfSearchBuildersCreated = 4;
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testAsyncSearchSmallResultSetSameCoordinator() {
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
|
|
|
|||
|
|
@ -98,11 +98,9 @@ public class ValidationSupportChain implements IValidationSupport {
|
|||
@Override
|
||||
public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
|
||||
for (IValidationSupport next : myChain) {
|
||||
if (next.isCodeSystemSupported(theCtx, theSystem)) {
|
||||
CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
|
||||
if (retVal != null) {
|
||||
return retVal;
|
||||
}
|
||||
CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
|
||||
if (retVal != null) {
|
||||
return retVal;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
|
|
|
|||
|
|
@ -77,11 +77,9 @@ public class ValidationSupportChain implements IValidationSupport {
|
|||
@Override
|
||||
public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
|
||||
for (IValidationSupport next : myChain) {
|
||||
if (next.isCodeSystemSupported(theCtx, theSystem)) {
|
||||
CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
|
||||
if (retVal != null) {
|
||||
return retVal;
|
||||
}
|
||||
CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
|
||||
if (retVal != null) {
|
||||
return retVal;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
|
|
|
|||
|
|
@ -75,11 +75,9 @@ public class ValidationSupportChain implements IValidationSupport {
|
|||
@Override
|
||||
public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
|
||||
for (IValidationSupport next : myChain) {
|
||||
if (next.isCodeSystemSupported(theCtx, theSystem)) {
|
||||
CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
|
||||
if (retVal != null) {
|
||||
return retVal;
|
||||
}
|
||||
CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
|
||||
if (retVal != null) {
|
||||
return retVal;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
|
|
|
|||
|
|
@ -248,6 +248,10 @@
|
|||
<![CDATA[<code>=</code>]]> or <![CDATA[<code>in</code>]]> operators. At present, the
|
||||
<![CDATA[<code>ancestor</code>]]> filter can only be used with the <![CDATA[<code>=</code>]]> operator.
|
||||
</action>
|
||||
<action type="fix">
|
||||
The JPA server failed to find codes defined in not-present codesystems in some cases, and reported
|
||||
that the CodeSystem did not exist. This has been corrected.
|
||||
</action>
|
||||
</release>
|
||||
<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
|
||||
<action type="fix">
|
||||
|
|
|
|||
Loading…
Reference in New Issue