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Return codesystem ID in upload terminology response

This commit is contained in:
James Agnew 2018-05-01 07:56:02 -04:00
parent 9be96c4130
commit 994f2992d1
6 changed files with 45 additions and 26 deletions
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10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseTerminologyUploaderProvider.java
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@ -27,10 +27,7 @@ import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.hl7.fhir.r4.model.Attachment;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.*;
import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletRequest;
@ -44,6 +41,8 @@ public abstract class BaseTerminologyUploaderProvider extends BaseJpaProvider {
public static final String UPLOAD_EXTERNAL_CODE_SYSTEM = "$upload-external-code-system";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseTerminologyUploaderProvider.class);
public static final String CONCEPT_COUNT = "conceptCount";
public static final String TARGET = "target";
@Autowired
private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
@ -125,7 +124,8 @@ public abstract class BaseTerminologyUploaderProvider extends BaseJpaProvider {
}
Parameters retVal = new Parameters();
retVal.addParameter().setName("conceptCount").setValue(new IntegerType(stats.getConceptCount()));
retVal.addParameter().setName(CONCEPT_COUNT).setValue(new IntegerType(stats.getConceptCount()));
retVal.addParameter().setName(TARGET).setValue(new Reference(stats.getTarget().getValue()));
return retVal;
} finally {
endRequest(theServletRequest);

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -850,7 +850,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
public IIdType storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
IIdType csId = createOrUpdateCodeSystem(theCodeSystemResource);
@ -865,6 +865,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
myDeferredConceptMaps.addAll(theConceptMaps);
myDeferredValueSets.addAll(theValueSets);
return csId;
}
@Override
@ -874,7 +876,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
}
private ArrayList<VersionIndependentConcept> toVersionIndependentConcepts(String theSystem, Set<TermConcept> codes) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>(codes.size());
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>(codes.size());
for (TermConcept next : codes) {
retVal.add(new VersionIndependentConcept(theSystem, next.getCode()));
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.term;
*/
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IIdType;
import java.io.InputStream;
import java.util.List;
@ -45,15 +46,21 @@ public interface IHapiTerminologyLoaderSvc {
class UploadStatistics {
private final int myConceptCount;
private final IIdType myTarget;
public UploadStatistics(int theConceptCount) {
public UploadStatistics(int theConceptCount, IIdType theTarget) {
myConceptCount = theConceptCount;
myTarget = theTarget;
}
public int getConceptCount() {
return myConceptCount;
}
public IIdType getTarget() {
return myTarget;
}
}
}

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
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@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.List;
@ -18,9 +19,9 @@ import java.util.Set;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -45,10 +46,14 @@ public interface IHapiTerminologySvc {
List<VersionIndependentConcept> findCodesAbove(String theSystem, String theCode);
List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode);
Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemResourceVersionPid, String theCode);
List<VersionIndependentConcept> findCodesBelow(String theSystem, String theCode);
List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode);
void saveDeferred();
/**
@ -59,12 +64,11 @@ public interface IHapiTerminologySvc {
void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, TermCodeSystemVersion theCodeSytemVersion);
/**
* @return Returns the ID of the created/updated code system
*/
IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<org.hl7.fhir.r4.model.ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
boolean supportsSystem(String theCodeSystem);
List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode);
List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode);
void storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<org.hl7.fhir.r4.model.ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
}
}

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
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@ -24,6 +24,7 @@ import org.apache.commons.io.input.BOMInputStream;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
@ -319,9 +320,9 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
int conceptCount = code2concept.size();
ourLog.info("Have {} total concepts, {} root concepts, {} ValueSets", conceptCount, rootConceptCount, valueSetCount);
storeCodeSystem(theRequestDetails, codeSystemVersion, loincCs, valueSets, conceptMaps);
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, loincCs, valueSets, conceptMaps);
return new UploadStatistics(conceptCount);
return new UploadStatistics(conceptCount, target);
}
private UploadStatistics processSnomedCtFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
@ -367,9 +368,9 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
cs.setUrl(SCT_URI);
cs.setName("SNOMED CT");
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null, null);
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null, null);
return new UploadStatistics(code2concept.size());
return new UploadStatistics(code2concept.size(), target);
}
@VisibleForTesting
@ -382,19 +383,22 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
myTermSvc = theTermSvc;
}
private void storeCodeSystem(RequestDetails theRequestDetails, final TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystem, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
private IIdType storeCodeSystem(RequestDetails theRequestDetails, final TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystem, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
Validate.isTrue(theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT);
List<ValueSet> valueSets = ObjectUtils.defaultIfNull(theValueSets, Collections.emptyList());
List<ConceptMap> conceptMaps = ObjectUtils.defaultIfNull(theConceptMaps, Collections.emptyList());
IIdType retVal;
myTermSvc.setProcessDeferred(false);
if (myTermSvcDstu3 != null) {
myTermSvcDstu3.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
retVal = myTermSvcDstu3.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
} else {
myTermSvcR4.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
retVal = myTermSvcR4.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
}
myTermSvc.setProcessDeferred(true);
return retVal;
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java
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@ -18,6 +18,7 @@ import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.Assert.*;
public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Test {
@ -90,6 +91,7 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
ourLog.info(resp);
assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
assertThat(((Reference) respParam.getParameter().get(1).getValue()).getReference(), matchesPattern("CodeSystem\\/[a-zA-Z0-9]+"));
/*
* Try uploading a second time