WIP supporting multiple type filters
This commit is contained in:
Tadgh
parent
27952ab5e4
commit
1a1a5ee661
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@ -24,6 +24,7 @@ import org.springframework.beans.factory.annotation.Value;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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@ -92,15 +93,24 @@ public abstract class BaseBulkItemReader implements ItemReader<List<ResourcePers
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.map(filter -> buildSearchParameterMapForTypeFilter(filter, theDef))
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.collect(Collectors.toList());
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return maps;
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} else {
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SearchParameterMap map = new SearchParameterMap();
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enhanceSearchParameterMapWithCommonParameters(map);
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return Collections.singletonList(map);
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}
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}
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private void enhanceSearchParameterMapWithCommonParameters(SearchParameterMap map) {
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map.setLoadSynchronous(true);
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if (getJobEntity().getSince() != null) {
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map.setLastUpdated(new DateRangeParam(getJobEntity().getSince(), null));
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}
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}
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public SearchParameterMap buildSearchParameterMapForTypeFilter(String theFilter, RuntimeResourceDefinition theDef) {
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SearchParameterMap searchParameterMap = myMatchUrlService.translateMatchUrl(theFilter, theDef);
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if (getJobEntity().getSince() != null) {
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searchParameterMap.setLastUpdated(new DateRangeParam(getJobEntity().getSince(), null));
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}
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searchParameterMap.setLoadSynchronous(true);
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enhanceSearchParameterMapWithCommonParameters(searchParameterMap);
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return searchParameterMap;
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}
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protected RuntimeResourceDefinition getResourceDefinition() {
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@ -30,8 +30,10 @@ import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import org.slf4j.Logger;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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/**
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* Basic Bulk Export implementation which simply reads all type filters and applies them, along with the _since param
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@ -40,19 +42,21 @@ import java.util.List;
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public class BulkItemReader extends BaseBulkItemReader {
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private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
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@Override
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Iterator<ResourcePersistentId> getResourcePidIterator() {
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ourLog.info("Bulk export assembling export of type {} for job {}", myResourceType, myJobUUID);
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Set<ResourcePersistentId> myReadPids = new HashSet<>();
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SearchParameterMap map = createSearchParameterMapsForResourceType();
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List<SearchParameterMap> map = createSearchParameterMapsForResourceType();
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ISearchBuilder sb = getSearchBuilderForLocalResourceType();
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IResultIterator myResultIterator = sb.createQuery(map, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
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List<ResourcePersistentId> myReadPids = new ArrayList<>();
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while (myResultIterator.hasNext()) {
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myReadPids.add(myResultIterator.next());
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for (SearchParameterMap spMap: map) {
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ourLog.debug("About to evaluate query {}", spMap.toNormalizedQueryString(myContext));
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IResultIterator myResultIterator = sb.createQuery(spMap, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
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while (myResultIterator.hasNext()) {
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myReadPids.add(myResultIterator.next());
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}
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}
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return myReadPids.iterator();
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}
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@ -27,6 +27,7 @@ import ca.uhn.fhir.jpa.dao.IResultIterator;
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import ca.uhn.fhir.jpa.dao.ISearchBuilder;
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import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
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import ca.uhn.fhir.jpa.dao.index.IdHelperService;
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import ca.uhn.fhir.jpa.entity.Search;
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import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.jpa.util.QueryChunker;
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@ -79,7 +80,7 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
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@Override
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Iterator<ResourcePersistentId> getResourcePidIterator() {
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List<ResourcePersistentId> myReadPids = new ArrayList<>();
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Set<ResourcePersistentId> myReadPids = new HashSet<>();
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//Short circuit out if we detect we are attempting to extract patients
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if (myResourceType.equalsIgnoreCase("Patient")) {
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@ -171,24 +172,26 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
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return expandedIds;
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}
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private void queryResourceTypeWithReferencesToPatients(List<ResourcePersistentId> myReadPids, List<String> idChunk) {
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private void queryResourceTypeWithReferencesToPatients(Set<ResourcePersistentId> myReadPids, List<String> idChunk) {
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//Build SP map
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//First, inject the _typeFilters and _since from the export job
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SearchParameterMap expandedSpMap = createSearchParameterMapsForResourceType();
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List<SearchParameterMap> expandedSpMaps = createSearchParameterMapsForResourceType();
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for (SearchParameterMap expandedSpMap: expandedSpMaps) {
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//Since we are in a bulk job, we have to ensure the user didn't jam in a patient search param, since we need to manually set that.
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validateSearchParameters(expandedSpMap);
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//Since we are in a bulk job, we have to ensure the user didn't jam in a patient search param, since we need to manually set that.
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validateSearchParameters(expandedSpMap);
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// Now, further filter the query with patient references defined by the chunk of IDs we have.
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filterSearchByResourceIds(idChunk, expandedSpMap);
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// Now, further filter the query with patient references defined by the chunk of IDs we have.
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filterSearchByResourceIds(idChunk, expandedSpMap);
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// Fetch and cache a search builder for this resource type
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ISearchBuilder searchBuilder = getSearchBuilderForLocalResourceType();
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// Fetch and cache a search builder for this resource type
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ISearchBuilder searchBuilder = getSearchBuilderForLocalResourceType();
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//Execute query and all found pids to our local iterator.
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IResultIterator resultIterator = searchBuilder.createQuery(expandedSpMap, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
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while (resultIterator.hasNext()) {
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myReadPids.add(resultIterator.next());
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//Execute query and all found pids to our local iterator.
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IResultIterator resultIterator = searchBuilder.createQuery(expandedSpMap, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
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while (resultIterator.hasNext()) {
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myReadPids.add(resultIterator.next());
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}
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}
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}
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@ -71,27 +71,28 @@ public class PatientBulkItemReader extends BaseBulkItemReader implements ItemRea
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List<ResourcePersistentId> myReadPids = new ArrayList<>();
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//use _typeFilter and _since and all those fancy bits and bobs to generate our basic SP map.
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SearchParameterMap map = createSearchParameterMapsForResourceType();
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List<SearchParameterMap> maps = createSearchParameterMapsForResourceType();
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String patientSearchParam = getPatientSearchParamForCurrentResourceType().getName();
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//Ensure users did not monkey with the patient compartment search parameter.
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validateSearchParameters(map);
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for (SearchParameterMap map: maps) {
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//Ensure users did not monkey with the patient compartment search parameter.
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validateSearchParameters(map);
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//Skip adding the parameter querying for patient= if we are in fact querying the patient resource type.
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if (!myResourceType.equalsIgnoreCase("Patient")) {
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//Now that we have our basic built Bulk Export SP map, we inject the condition that the resources returned
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//must have a patient= or subject= reference set.
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map.add(patientSearchParam, new ReferenceParam().setMissing(false));
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}
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//Skip adding the parameter querying for patient= if we are in fact querying the patient resource type.
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if (!myResourceType.equalsIgnoreCase("Patient")) {
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//Now that we have our basic built Bulk Export SP map, we inject the condition that the resources returned
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//must have a patient= or subject= reference set.
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map.add(patientSearchParam, new ReferenceParam().setMissing(false));
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ourLog.debug("About to execute query {}", map.toNormalizedQueryString(myContext));
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ISearchBuilder sb = getSearchBuilderForLocalResourceType();
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IResultIterator myResultIterator = sb.createQuery(map, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
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while (myResultIterator.hasNext()) {
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myReadPids.add(myResultIterator.next());
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}
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}
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ISearchBuilder sb = getSearchBuilderForLocalResourceType();
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IResultIterator myResultIterator = sb.createQuery(map, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
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while (myResultIterator.hasNext()) {
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myReadPids.add(myResultIterator.next());
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}
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return myReadPids.iterator();
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}
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@ -389,7 +389,6 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
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public void validateTypeFilters(Set<String> theTheFilters, Set<String> theResourceTypes) {
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if (theTheFilters != null) {
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Set<String> types = new HashSet<>();
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for (String next : theTheFilters) {
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if (!next.contains("?")) {
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throw new InvalidRequestException("Invalid " + JpaConstants.PARAM_EXPORT_TYPE_FILTER + " value \"" + next + "\". Must be in the form [ResourceType]?[params]");
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@ -398,9 +397,6 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
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if (!theResourceTypes.contains(resourceType)) {
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throw new InvalidRequestException("Invalid " + JpaConstants.PARAM_EXPORT_TYPE_FILTER + " value \"" + next + "\". Resource type does not appear in " + JpaConstants.PARAM_EXPORT_TYPE+ " list");
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}
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if (!types.add(resourceType)) {
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throw new InvalidRequestException("Invalid " + JpaConstants.PARAM_EXPORT_TYPE_FILTER + " value \"" + next + "\". Multiple filters found for type " + resourceType);
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}
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}
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}
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}
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@ -337,7 +337,6 @@ public class BulkDataExportProviderTest {
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@Test
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public void testInitiateWithGetAndMultipleTypeFilters() throws IOException {
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//TODO GGG FIX ME
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IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
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.setJobId(A_JOB_ID);
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when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo);
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@ -385,9 +384,8 @@ public class BulkDataExportProviderTest {
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Parameters input = new Parameters();
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input.addParameter(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, new StringType(Constants.CT_FHIR_NDJSON));
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input.addParameter(JpaConstants.PARAM_EXPORT_STYLE, new StringType("Patient, Practitioner"));
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input.addParameter(JpaConstants.PARAM_EXPORT_SINCE, now);
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input.addParameter(JpaConstants.PARAM_EXPORT_TYPE_FILTER, new StringType("Patient?identifier=foo"));
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input.addParameter(JpaConstants.PARAM_EXPORT_STYLE, new StringType("Patient"));
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input.addParameter(JpaConstants.PARAM_EXPORT_TYPE_FILTER, new StringType("Patient?gender=male,Patient?gender=female"));
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ourLog.info(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input));
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@ -406,9 +404,8 @@ public class BulkDataExportProviderTest {
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verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture());
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BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
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assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
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assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner"));
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assertThat(options.getSince(), notNullValue());
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assertThat(options.getFilters(), containsInAnyOrder("Patient?identifier=foo"));
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assertThat(options.getResourceTypes(), containsInAnyOrder("Patient"));
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assertThat(options.getFilters(), containsInAnyOrder("Patient?gender=male", "Patient?gender=female"));
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}
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@Test
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@ -447,5 +444,4 @@ public class BulkDataExportProviderTest {
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assertThat(options.getSince(), notNullValue());
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assertThat(options.getFilters(), containsInAnyOrder("Immunization?vaccine-code=foo"));
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}
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}
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@ -39,6 +39,7 @@ import org.hl7.fhir.r4.model.InstantType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Reference;
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import org.jetbrains.annotations.NotNull;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -613,10 +614,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
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// Iterate over the files
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Binary nextBinary = myBinaryDao.read(jobInfo.getFiles().get(0).getResourceId());
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assertEquals(Constants.CT_FHIR_NDJSON, nextBinary.getContentType());
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String nextContents = new String(nextBinary.getContent(), Constants.CHARSET_UTF8);
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ourLog.info("Next contents for type {}:\n{}", nextBinary.getResourceType(), nextContents);
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String nextContents = getBinaryContents(jobInfo, 0);
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
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assertThat(nextContents, is(containsString("IMM0")));
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@ -652,10 +650,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
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// Iterate over the files
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Binary nextBinary = myBinaryDao.read(jobInfo.getFiles().get(0).getResourceId());
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assertEquals(Constants.CT_FHIR_NDJSON, nextBinary.getContentType());
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String nextContents = new String(nextBinary.getContent(), Constants.CHARSET_UTF8);
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ourLog.info("Next contents for type {}:\n{}", nextBinary.getResourceType(), nextContents);
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String nextContents = getBinaryContents(jobInfo, 0);
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
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assertThat(nextContents, is(containsString("IMM0")));
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@ -695,16 +690,9 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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// Create a bulk job
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IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(bulkDataExportOptions);
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// GroupBulkExportJobParametersBuilder paramBuilder = new GroupBulkExportJobParametersBuilder();
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// paramBuilder.setGroupId(myPatientGroupId.getIdPart());
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// paramBuilder.setJobUUID(jobDetails.getJobId());
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// paramBuilder.setReadChunkSize(10L);
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//
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// JobExecution jobExecution = myBatchJobSubmitter.runJob(myGroupBulkJob, paramBuilder.toJobParameters());
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myBulkDataExportSvc.buildExportFiles();
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awaitAllBulkJobCompletions();
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// awaitJobCompletion(jobExecution);
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IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
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assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
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@ -712,10 +700,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("CareTeam")));
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// Iterate over the files
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Binary nextBinary = myBinaryDao.read(jobInfo.getFiles().get(0).getResourceId());
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assertEquals(Constants.CT_FHIR_NDJSON, nextBinary.getContentType());
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String nextContents = new String(nextBinary.getContent(), Constants.CHARSET_UTF8);
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ourLog.info("Next contents for type {}:\n{}", nextBinary.getResourceType(), nextContents);
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String nextContents = getBinaryContents(jobInfo, 0);
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("CareTeam")));
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assertThat(nextContents, is(containsString("CT0")));
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@ -731,12 +716,93 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
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JobParametersBuilder paramBuilder = new JobParametersBuilder().addString("jobUUID", "I'm not real!");
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try {
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myBatchJobSubmitter.runJob(myBulkJob, paramBuilder.toJobParameters());
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fail("Should have had invalid parameter execption!");
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fail("Should have had invalid parameter exception!");
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} catch (JobParametersInvalidException e) {
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// good
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}
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}
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@Test
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public void testSystemExportWithMultipleTypeFilters() {
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createResources();
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// Create a bulk job
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BulkDataExportOptions options = new BulkDataExportOptions();
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options.setResourceTypes(Sets.newHashSet("Immunization"));
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options.setExportStyle(BulkDataExportOptions.ExportStyle.SYSTEM);
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options.setFilters(Sets.newHashSet("Immunization?vaccine-code=Flu", "Immunization?patient=Patient/PAT1"));
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IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(options);
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myBulkDataExportSvc.buildExportFiles();
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awaitAllBulkJobCompletions();
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IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
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assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
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assertThat(jobInfo.getFiles().size(), equalTo(1));
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
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// Iterate over the files
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String nextContents = getBinaryContents(jobInfo, 0);
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
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//These are the COVID-19 entries
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assertThat(nextContents, is(containsString("IMM0")));
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assertThat(nextContents, is(containsString("IMM2")));
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assertThat(nextContents, is(containsString("IMM4")));
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assertThat(nextContents, is(containsString("IMM6")));
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assertThat(nextContents, is(containsString("IMM8")));
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//This is the entry for the one referencing patient/1
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assertThat(nextContents, is(containsString("IMM1")));
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}
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@Test
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public void testGroupExportWithMultipleTypeFilters() {
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createResources();
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// Create a bulk job
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BulkDataExportOptions options = new BulkDataExportOptions();
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options.setResourceTypes(Sets.newHashSet("Observation"));
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options.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
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options.setGroupId(myPatientGroupId);
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options.setExpandMdm(false);
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options.setFilters(Sets.newHashSet("Observation?identifier=VAL0,VAL2", "Observation?identifer=VAL4"));
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IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(options);
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myBulkDataExportSvc.buildExportFiles();
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awaitAllBulkJobCompletions();
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IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
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assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
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assertThat(jobInfo.getFiles().size(), equalTo(1));
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Observation")));
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String nextContents = getBinaryContents(jobInfo, 0);
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assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
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//These are the COVID-19 entries
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assertThat(nextContents, is(containsString("IMM0")));
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assertThat(nextContents, is(containsString("IMM2")));
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||||
assertThat(nextContents, is(containsString("IMM4")));
|
||||
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")));
|
||||
}
|
||||
|
||||
@NotNull
|
||||
public String getBinaryContents(IBulkDataExportSvc.JobInfo theJobInfo, int theIndex) {
|
||||
// Iterate over the files
|
||||
Binary nextBinary = myBinaryDao.read(theJobInfo.getFiles().get(theIndex).getResourceId());
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, nextBinary.getContentType());
|
||||
String nextContents = new String(nextBinary.getContent(), Constants.CHARSET_UTF8);
|
||||
ourLog.info("Next contents for type {}:\n{}", nextBinary.getResourceType(), nextContents);
|
||||
return nextContents;
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testMdmExpansionSuccessfullyExtractsPatients() throws JobParametersInvalidException {
|
||||
|
|
@ -761,10 +827,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
assertThat(jobInfo.getFiles().size(), equalTo(1));
|
||||
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Patient")));
|
||||
|
||||
Binary patientExportContent = myBinaryDao.read(jobInfo.getFiles().get(0).getResourceId());
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, patientExportContent.getContentType());
|
||||
String nextContents = new String(patientExportContent.getContent(), Constants.CHARSET_UTF8);
|
||||
ourLog.info("Next contents for type {}:\n{}", patientExportContent.getResourceType(), nextContents);
|
||||
String nextContents = getBinaryContents(jobInfo, 0);
|
||||
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Patient")));
|
||||
|
||||
//Output contains The entire group, plus the Mdm expansion, plus the golden resource
|
||||
|
|
@ -797,10 +860,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
|
||||
|
||||
// Check immunization Content
|
||||
Binary immunizationExportContent = myBinaryDao.read(jobInfo.getFiles().get(0).getResourceId());
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, immunizationExportContent.getContentType());
|
||||
String nextContents = new String(immunizationExportContent.getContent(), Constants.CHARSET_UTF8);
|
||||
ourLog.info("Next contents for type {}:\n{}", immunizationExportContent.getResourceType(), nextContents);
|
||||
String nextContents = getBinaryContents(jobInfo, 0);
|
||||
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
|
||||
assertThat(nextContents, is(containsString("IMM0")));
|
||||
assertThat(nextContents, is(containsString("IMM2")));
|
||||
|
|
@ -865,12 +925,8 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
|
||||
|
||||
// Check immunization Content
|
||||
Binary immunizationExportContent = myBinaryDao.read(jobInfo.getFiles().get(0).getResourceId());
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, immunizationExportContent.getContentType());
|
||||
String nextContents = new String(immunizationExportContent.getContent(), Constants.CHARSET_UTF8);
|
||||
ourLog.info("Next contents for type {}:\n{}", immunizationExportContent.getResourceType(), nextContents);
|
||||
String nextContents = getBinaryContents(jobInfo, 0);
|
||||
|
||||
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
|
||||
assertThat(nextContents, is(containsString("IMM1")));
|
||||
assertThat(nextContents, is(containsString("IMM3")));
|
||||
assertThat(nextContents, is(containsString("IMM5")));
|
||||
|
|
|
|||
Loading…
Reference in New Issue