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Fix up some mocks, fix empty search param maps being generated

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This commit is contained in:
Tadgh 2021-03-10 18:26:16 -05:00
parent 126fc212a7
commit c8ed81d338
3 changed files with 34 additions and 45 deletions
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18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BaseBulkItemReader.java
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@ -30,6 +30,7 @@ import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory; import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao; import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity; import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.util.JpaConstants; import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService; import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -107,17 +108,22 @@ public abstract class BaseBulkItemReader implements ItemReader<List<ResourcePers
RuntimeResourceDefinition theDef = getResourceDefinition(); RuntimeResourceDefinition theDef = getResourceDefinition();
Map<String, String[]> requestUrl = UrlUtil.parseQueryStrings(jobEntity.getRequest()); Map<String, String[]> requestUrl = UrlUtil.parseQueryStrings(jobEntity.getRequest());
String[] typeFilters = requestUrl.get(JpaConstants.PARAM_EXPORT_TYPE_FILTER); String[] typeFilters = requestUrl.get(JpaConstants.PARAM_EXPORT_TYPE_FILTER);
List<SearchParameterMap> spMaps = null;
if (typeFilters != null) { if (typeFilters != null) {
List<SearchParameterMap> maps = Arrays.stream(typeFilters) spMaps = Arrays.stream(typeFilters)
.filter(typeFilter -> typeFilter.startsWith(myResourceType + "?")) .filter(typeFilter -> typeFilter.startsWith(myResourceType + "?"))
.map(filter -> buildSearchParameterMapForTypeFilter(filter, theDef)) .map(filter -> buildSearchParameterMapForTypeFilter(filter, theDef))
.collect(Collectors.toList()); .collect(Collectors.toList());
return maps;
} else {
SearchParameterMap map = new SearchParameterMap();
enhanceSearchParameterMapWithCommonParameters(map);
return Collections.singletonList(map);
} }
//None of the _typeFilters applied to the current resource type, so just make a simple one.
if (spMaps == null || spMaps.isEmpty()) {
SearchParameterMap defaultMap = new SearchParameterMap();
enhanceSearchParameterMapWithCommonParameters(defaultMap);
spMaps = Collections.singletonList(defaultMap);
}
return spMaps;
} }
private void enhanceSearchParameterMapWithCommonParameters(SearchParameterMap map) { private void enhanceSearchParameterMapWithCommonParameters(SearchParameterMap map) {

28
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportProviderTest.java
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@ -116,7 +116,7 @@ public class BulkDataExportProviderTest {
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo() IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
.setJobId(A_JOB_ID); .setJobId(A_JOB_ID);
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo); when(myBulkDataExportSvc.submitJob(any(), any())).thenReturn(jobInfo);
InstantType now = InstantType.now(); InstantType now = InstantType.now();
@ -140,7 +140,7 @@ public class BulkDataExportProviderTest {
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue()); assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
} }
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture()); verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture(), any());
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue(); BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat()); assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner")); assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner"));
@ -153,7 +153,7 @@ public class BulkDataExportProviderTest {
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo() IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
.setJobId(A_JOB_ID); .setJobId(A_JOB_ID);
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo); when(myBulkDataExportSvc.submitJob(any(),any())).thenReturn(jobInfo);
InstantType now = InstantType.now(); InstantType now = InstantType.now();
@ -174,7 +174,7 @@ public class BulkDataExportProviderTest {
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue()); assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
} }
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture()); verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture(), any());
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue(); BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat()); assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner")); assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner"));
@ -303,7 +303,8 @@ public class BulkDataExportProviderTest {
public void testSuccessfulInitiateGroupBulkRequest_Post() throws IOException { public void testSuccessfulInitiateGroupBulkRequest_Post() throws IOException {
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo().setJobId(G_JOB_ID); IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo().setJobId(G_JOB_ID);
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo); when(myBulkDataExportSvc.submitJob(any(),any())).thenReturn(jobInfo);
when(myBulkDataExportSvc.getPatientCompartmentResources()).thenReturn(Sets.newHashSet("Observation", "DiagnosticReport"));
InstantType now = InstantType.now(); InstantType now = InstantType.now();
@ -329,7 +330,7 @@ public class BulkDataExportProviderTest {
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + G_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue()); assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + G_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
} }
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture()); verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture(), any());
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue(); BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat()); assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
assertThat(options.getResourceTypes(), containsInAnyOrder("Observation", "DiagnosticReport")); assertThat(options.getResourceTypes(), containsInAnyOrder("Observation", "DiagnosticReport"));
@ -343,7 +344,7 @@ public class BulkDataExportProviderTest {
public void testSuccessfulInitiateGroupBulkRequest_Get() throws IOException { public void testSuccessfulInitiateGroupBulkRequest_Get() throws IOException {
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo().setJobId(G_JOB_ID); IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo().setJobId(G_JOB_ID);
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo); when(myBulkDataExportSvc.submitJob(any(), any())).thenReturn(jobInfo);
when(myBulkDataExportSvc.getPatientCompartmentResources()).thenReturn(Sets.newHashSet("Patient", "Practitioner")); when(myBulkDataExportSvc.getPatientCompartmentResources()).thenReturn(Sets.newHashSet("Patient", "Practitioner"));
InstantType now = InstantType.now(); InstantType now = InstantType.now();
@ -366,7 +367,7 @@ public class BulkDataExportProviderTest {
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + G_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue()); assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + G_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
} }
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture()); verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture(), any());
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue(); BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat()); assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner")); assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner"));
@ -408,7 +409,7 @@ public class BulkDataExportProviderTest {
get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC); get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
myClient.execute(get); myClient.execute(get);
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture()); verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture(), anyBoolean());
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue(); BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
assertThat(options.getFilters(), containsInAnyOrder(immunizationTypeFilter1, immunizationTypeFilter2, observationFilter1)); assertThat(options.getFilters(), containsInAnyOrder(immunizationTypeFilter1, immunizationTypeFilter2, observationFilter1));
@ -436,7 +437,7 @@ public class BulkDataExportProviderTest {
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo() IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
.setJobId(A_JOB_ID); .setJobId(A_JOB_ID);
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo); when(myBulkDataExportSvc.submitJob(any(), any())).thenReturn(jobInfo);
InstantType now = InstantType.now(); InstantType now = InstantType.now();
@ -459,7 +460,7 @@ public class BulkDataExportProviderTest {
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue()); assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
} }
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture()); verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture(), myBooleanArgumentCaptor.capture());
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue(); BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat()); assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
assertThat(options.getResourceTypes(), containsInAnyOrder("Patient")); assertThat(options.getResourceTypes(), containsInAnyOrder("Patient"));
@ -470,7 +471,8 @@ public class BulkDataExportProviderTest {
public void testInitiatePatientExportRequest() throws IOException { public void testInitiatePatientExportRequest() throws IOException {
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo() IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
.setJobId(A_JOB_ID); .setJobId(A_JOB_ID);
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo); when(myBulkDataExportSvc.submitJob(any(), any())).thenReturn(jobInfo);
when(myBulkDataExportSvc.getPatientCompartmentResources()).thenReturn(Sets.newHashSet("Immunization", "Observation"));
InstantType now = InstantType.now(); InstantType now = InstantType.now();
@ -494,7 +496,7 @@ public class BulkDataExportProviderTest {
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue()); assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
} }
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture()); verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture(), myBooleanArgumentCaptor.capture());
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue(); BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat()); assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
assertThat(options.getResourceTypes(), containsInAnyOrder("Immunization", "Observation")); assertThat(options.getResourceTypes(), containsInAnyOrder("Immunization", "Observation"));

33
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
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@ -203,21 +203,6 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
} }
} }
@Test
public void testSubmit_MultipleTypeFiltersForSameType() {
try {
BulkDataExportOptions options = new BulkDataExportOptions();
options.setOutputFormat(Constants.CT_FHIR_NDJSON);
options.setResourceTypes(Sets.newHashSet("Patient"));
options.setFilters(Sets.newHashSet("Patient?name=a", "Patient?active=true"));
options.setExportStyle(BulkDataExportOptions.ExportStyle.SYSTEM);
myBulkDataExportSvc.submitJob(options);
fail();
} catch (InvalidRequestException e) {
assertEquals("Invalid _typeFilter value \"Patient?name=a\". Multiple filters found for type Patient", e.getMessage());
}
}
@Test @Test
public void testSubmit_TypeFilterForNonSelectedType() { public void testSubmit_TypeFilterForNonSelectedType() {
try { try {
@ -318,6 +303,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
options.setResourceTypes(Sets.newHashSet("Patient", "Observation")); options.setResourceTypes(Sets.newHashSet("Patient", "Observation"));
options.setFilters(Sets.newHashSet(TEST_FILTER)); options.setFilters(Sets.newHashSet(TEST_FILTER));
options.setExportStyle(BulkDataExportOptions.ExportStyle.SYSTEM); options.setExportStyle(BulkDataExportOptions.ExportStyle.SYSTEM);
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(options); IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(options);
assertNotNull(jobDetails.getJobId()); assertNotNull(jobDetails.getJobId());
@ -769,7 +755,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP); options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
options.setGroupId(myPatientGroupId); options.setGroupId(myPatientGroupId);
options.setExpandMdm(false); options.setExpandMdm(false);
options.setFilters(Sets.newHashSet("Observation?identifier=VAL0,VAL2", "Observation?identifer=VAL4")); options.setFilters(Sets.newHashSet("Observation?identifier=VAL0,VAL2", "Observation?identifier=VAL4"));
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(options); IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(options);
myBulkDataExportSvc.buildExportFiles(); myBulkDataExportSvc.buildExportFiles();
@ -782,16 +768,11 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Observation"))); assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Observation")));
String nextContents = getBinaryContents(jobInfo, 0); String nextContents = getBinaryContents(jobInfo, 0);
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization"))); //These are the Observation entries
//These are the COVID-19 entries assertThat(nextContents, is(containsString("OBS0")));
assertThat(nextContents, is(containsString("IMM0"))); assertThat(nextContents, is(containsString("OBS2")));
assertThat(nextContents, is(containsString("IMM2"))); assertThat(nextContents, is(containsString("OBS4")));
assertThat(nextContents, is(containsString("IMM4"))); assertEquals(3, nextContents.split("\n").length);
assertThat(nextContents, is(containsString("IMM6")));
assertThat(nextContents, is(containsString("IMM8")));
//This is the entry for the one referencing patient/1
assertThat(nextContents, is(containsString("IMM1")));
} }
public String getBinaryContents(IBulkDataExportSvc.JobInfo theJobInfo, int theIndex) { public String getBinaryContents(IBulkDataExportSvc.JobInfo theJobInfo, int theIndex) {