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current state of $document

This commit is contained in:
patrick-werner 2018-06-05 18:32:59 +02:00
parent 38b7b00f52
commit 49bdff1862
9 changed files with 71 additions and 135 deletions
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3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoCompositionDstu2.java
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@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.model.dstu2.resource.Composition;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
@ -38,7 +37,7 @@ public class FhirResourceDaoCompositionDstu2 extends FhirResourceDaoDstu2<Compos
private ISearchParamRegistry mySearchParamRegistry;
@Override
public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
public org.hl7.fhir.instance.model.Bundle getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
throw new NotImplementedOperationException("$document in DSTU2 is not implemented ");
}
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoComposition.java
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@ -1,10 +1,10 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import org.hl7.fhir.instance.model.Bundle;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -33,6 +33,6 @@ import javax.servlet.http.HttpServletRequest;
public interface IFhirResourceDaoComposition<T extends IBaseResource> extends IFhirResourceDao<T> {
IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails);
IBaseBundle getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails);
}

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCompositionDstu3.java
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@ -21,28 +21,26 @@ package ca.uhn.fhir.jpa.dao.dstu3;
*/
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoComposition;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.dao.SearchParameterMap.EverythingModeEnum;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringParam;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Composition;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletRequest;
import java.util.Collections;
import java.util.Date;
import java.util.List;
public class FhirResourceDaoCompositionDstu3 extends FhirResourceDaoDstu3<Composition> implements IFhirResourceDaoComposition<Composition> {
@ -50,7 +48,7 @@ public class FhirResourceDaoCompositionDstu3 extends FhirResourceDaoDstu3<Compos
private ISearchParamRegistry mySearchParamRegistry;
@Override
public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
public Bundle getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
SearchParameterMap paramMap = new SearchParameterMap();
if (theCount != null) {
paramMap.setCount(theCount.getValue());
@ -65,7 +63,13 @@ public class FhirResourceDaoCompositionDstu3 extends FhirResourceDaoDstu3<Compos
paramMap.add("_id", new StringParam(theId.getIdPart()));
}
IBundleProvider retVal = search(paramMap);
return retVal;
List<IBaseResource> resourceList = retVal.getResources(0, retVal.size());
Bundle bundle = new Bundle().setType(Bundle.BundleType.DOCUMENT);
for (IBaseResource resource : resourceList)
bundle.addEntry(new Bundle.BundleEntryComponent().setResource((Resource) resource));
return bundle;
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCompositionR4.java
View File

@ -23,7 +23,6 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoComposition;
import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import org.hl7.fhir.instance.model.api.IIdType;
@ -39,7 +38,7 @@ public class FhirResourceDaoCompositionR4 extends FhirResourceDaoR4<Composition>
private ISearchParamRegistry mySearchParamRegistry;
@Override
public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
public org.hl7.fhir.instance.model.Bundle getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {
return null;
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderCompositionDstu2.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.provider;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoComposition;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Composition;
import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import ca.uhn.fhir.rest.annotation.IdParam;
@ -14,6 +15,7 @@ import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@ -44,7 +46,7 @@ public class BaseJpaResourceProviderCompositionDstu2 extends JpaResourceProvider
*/
//@formatter:off
@Operation(name = "document", idempotent = true, bundleType=BundleTypeEnum.SEARCHSET)
public IBundleProvider getDocumentForComposition(
public IBaseBundle getDocumentForComposition(
javax.servlet.http.HttpServletRequest theServletRequest) {
//@formatter:on

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCompositionDstu3.java
View File

@ -14,6 +14,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseBundle;
/*
* #%L
@ -42,8 +43,8 @@ public class BaseJpaResourceProviderCompositionDstu3 extends JpaResourceProvider
* @param theRequestDetails
*/
//@formatter:off
@Operation(name = "document", idempotent = true, bundleType=BundleTypeEnum.SEARCHSET)
public IBundleProvider getDocumentForComposition(
@Operation(name = "document", idempotent = true, bundleType=BundleTypeEnum.DOCUMENT)
public IBaseBundle getDocumentForComposition(
javax.servlet.http.HttpServletRequest theServletRequest,

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCompositionR4.java
View File

@ -13,6 +13,7 @@ import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.UnsignedIntType;
@ -46,7 +47,7 @@ public class BaseJpaResourceProviderCompositionR4 extends JpaResourceProviderR4<
*/
//@formatter:off
@Operation(name = "document", idempotent = true, bundleType=BundleTypeEnum.SEARCHSET)
public IBundleProvider getDocumentForComposition(
public IBaseBundle getDocumentForComposition(
javax.servlet.http.HttpServletRequest theServletRequest,

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDocumentDstu3Test.java
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@ -26,13 +26,4 @@ public class FhirResourceDaoDocumentDstu3Test extends BaseJpaDstu3Test {
Bundle inputBundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
DaoMethodOutcome responseBundle = myBundleDao.create(inputBundle, mySrd);
}
@Test
public void testGetDocument() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/sample-document.xml"), StandardCharsets.UTF_8);
Bundle inputBundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
DaoMethodOutcome responseBundle = myBundleDao.create(inputBundle, mySrd);
}
}

133
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/CompositionDocumentDstu3Test.java
View File

@ -13,10 +13,7 @@ import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.*;
import java.io.IOException;
import java.util.ArrayList;
@ -31,11 +28,10 @@ public class CompositionDocumentDstu3Test extends BaseResourceProviderDstu3Test
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CompositionDocumentDstu3Test.class);
private String orgId;
private String patId;
private String encId1;
private String encId2;
private ArrayList<String> myObsIds;
private String myWrongPatId;
private String myWrongEnc1;
private String encId;
private String listId;
private String compId;
@Before
public void beforeDisableResultReuse() {
@ -66,73 +62,50 @@ public class CompositionDocumentDstu3Test extends BaseResourceProviderDstu3Test
patient.getManagingOrganization().setReference(orgId);
patId = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless().getValue();
Patient patient2 = new Patient();
patient2.getManagingOrganization().setReference(orgId);
myWrongPatId = ourClient.create().resource(patient2).execute().getId().toUnqualifiedVersionless().getValue();
Encounter enc = new Encounter();
enc.setStatus(EncounterStatus.ARRIVED);
enc.getSubject().setReference(patId);
enc.getServiceProvider().setReference(orgId);
encId = ourClient.create().resource(enc).execute().getId().toUnqualifiedVersionless().getValue();
Encounter enc1 = new Encounter();
enc1.setStatus(EncounterStatus.CANCELLED);
enc1.getSubject().setReference(patId);
enc1.getServiceProvider().setReference(orgId);
encId1 = ourClient.create().resource(enc1).execute().getId().toUnqualifiedVersionless().getValue();
Encounter enc2 = new Encounter();
enc2.setStatus(EncounterStatus.ARRIVED);
enc2.getSubject().setReference(patId);
enc2.getServiceProvider().setReference(orgId);
encId2 = ourClient.create().resource(enc2).execute().getId().toUnqualifiedVersionless().getValue();
Encounter wrongEnc1 = new Encounter();
wrongEnc1.setStatus(EncounterStatus.ARRIVED);
wrongEnc1.getSubject().setReference(myWrongPatId);
wrongEnc1.getServiceProvider().setReference(orgId);
myWrongEnc1 = ourClient.create().resource(wrongEnc1).execute().getId().toUnqualifiedVersionless().getValue();
ListResource listResource = new ListResource();
ArrayList<Observation> myObs = new ArrayList<>();
myObsIds = new ArrayList<String>();
for (int i = 0; i < 20; i++) {
for (int i = 0; i < 5; i++) {
Observation obs = new Observation();
obs.getSubject().setReference(patId);
obs.setStatus(ObservationStatus.FINAL);
String obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless().getValue();
listResource.addEntry(new ListResource.ListEntryComponent().setItem(new Reference(obs)));
myObs.add(obs);
myObsIds.add(obsId);
}
}
listId = ourClient.create().resource(listResource).execute().getId().toUnqualifiedVersionless().getValue();
/**
* See #674
*/
@Test
public void testEverythingReturnsCorrectResources() throws Exception {
Composition composition = new Composition();
composition.setSubject(new Reference(patient));
composition.addSection().addEntry(new Reference(patient));
composition.addSection().addEntry(new Reference(org));
composition.addSection().addEntry(new Reference(enc));
composition.addSection().addEntry(new Reference(listResource));
composition.addSection().addEntry(new Reference(listResource));
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
assertNull(bundle.getLink("next"));
Set<String> actual = new TreeSet<String>();
for (BundleEntryComponent nextEntry : bundle.getEntry()) {
actual.add(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
for (Observation obs : myObs) {
composition.addSection().addEntry(new Reference(obs));
}
ourLog.info("Found IDs: {}", actual);
assertThat(actual, hasItem(patId));
assertThat(actual, hasItem(encId1));
assertThat(actual, hasItem(encId2));
assertThat(actual, hasItem(orgId));
assertThat(actual, hasItems(myObsIds.toArray(new String[0])));
assertThat(actual, not(hasItem(myWrongPatId)));
assertThat(actual, not(hasItem(myWrongEnc1)));
compId = ourClient.create().resource(composition).execute().getId().toUnqualifiedVersionless().getValue();
}
/**
* See #674
*/
@Test
public void testEverythingReturnsCorrectResourcesSmallPage() throws Exception {
public void testDocumentBundleReturnedCorrect() throws Exception {
myDaoConfig.setEverythingIncludesFetchPageSize(1);
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
String theUrl = ourServerBase + "/" + compId + "/$document?_format=json&_count=100";
System.out.println(theUrl);
Bundle bundle = fetchBundle(theUrl, EncodingEnum.JSON);
assertNull(bundle.getLink("next"));
@ -144,57 +117,23 @@ public class CompositionDocumentDstu3Test extends BaseResourceProviderDstu3Test
ourLog.info("Found IDs: {}", actual);
assertThat(actual, hasItem(patId));
assertThat(actual, hasItem(encId1));
assertThat(actual, hasItem(encId2));
assertThat(actual, hasItem(encId));
assertThat(actual, hasItem(encId));
assertThat(actual, hasItem(orgId));
assertThat(actual, hasItems(myObsIds.toArray(new String[0])));
assertThat(actual, not(hasItem(myWrongPatId)));
assertThat(actual, not(hasItem(myWrongEnc1)));
}
/**
* See #674
*/
@Test
public void testEverythingPagesWithCorrectEncodingJson() throws Exception {
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=json&_count=1", EncodingEnum.JSON);
assertNotNull(bundle.getLink("next").getUrl());
assertThat(bundle.getLink("next").getUrl(), containsString("_format=json"));
bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.JSON);
assertNotNull(bundle.getLink("next").getUrl());
assertThat(bundle.getLink("next").getUrl(), containsString("_format=json"));
bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.JSON);
}
/**
* See #674
*/
@Test
public void testEverythingPagesWithCorrectEncodingXml() throws Exception {
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=xml&_count=1", EncodingEnum.XML);
assertNotNull(bundle.getLink("next").getUrl());
ourLog.info("Next link: {}", bundle.getLink("next").getUrl());
assertThat(bundle.getLink("next").getUrl(), containsString("_format=xml"));
bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.XML);
assertNotNull(bundle.getLink("next").getUrl());
ourLog.info("Next link: {}", bundle.getLink("next").getUrl());
assertThat(bundle.getLink("next").getUrl(), containsString("_format=xml"));
bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.XML);
}
private Bundle fetchBundle(String theUrl, EncodingEnum theEncoding) throws IOException, ClientProtocolException {
Bundle bundle;
HttpGet get = new HttpGet(theUrl);
CloseableHttpResponse resp = ourHttpClient.execute(get);
try {
String test = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
System.out.println(test);
assertEquals(theEncoding.getResourceContentTypeNonLegacy(), resp.getFirstHeader(ca.uhn.fhir.rest.api.Constants.HEADER_CONTENT_TYPE).getValue().replaceAll(";.*", ""));
bundle = theEncoding.newParser(myFhirCtx).parseResource(Bundle.class, IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8));
bundle = theEncoding.newParser(myFhirCtx).parseResource(Bundle.class, test);
} finally {
IOUtils.closeQuietly(resp);
}