begin with failing test
This commit is contained in:
Ken Stevens
parent
3eda19c65a
commit
70b2b83d1a
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@ -0,0 +1,34 @@
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package ca.uhn.fhir.jpa.bulk.api;
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import java.util.Date;
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import java.util.Set;
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public class BulkDataExportOptions {
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private final String myOutputFormat;
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private final Set<String> myResourceTypes;
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private final Date mySince;
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private final Set<String> myFilters;
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public BulkDataExportOptions(String theOutputFormat, Set<String> theResourceTypes, Date theSince, Set<String> theFilters) {
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myOutputFormat = theOutputFormat;
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myResourceTypes = theResourceTypes;
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mySince = theSince;
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myFilters = theFilters;
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}
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public String getOutputFormat() {
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return myOutputFormat;
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}
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public Set<String> getResourceTypes() {
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return myResourceTypes;
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}
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public Date getSince() {
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return mySince;
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}
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public Set<String> getFilters() {
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return myFilters;
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}
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}
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@ -27,7 +27,6 @@ import javax.transaction.Transactional;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.List;
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import java.util.Set;
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public interface IBulkDataExportSvc {
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void buildExportFiles();
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@ -35,7 +34,7 @@ public interface IBulkDataExportSvc {
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@Transactional(value = Transactional.TxType.NEVER)
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void purgeExpiredFiles();
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JobInfo submitJob(String theOutputFormat, Set<String> theResourceTypes, Date theSince, Set<String> theFilters);
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JobInfo submitJob(BulkDataExportOptions theBulkDataExportOptions);
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JobInfo getJobInfoOrThrowResourceNotFound(String theJobId);
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@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.bulk.job;
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* #L%
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*/
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import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
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import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
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import ca.uhn.fhir.rest.api.Constants;
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import org.apache.commons.lang3.StringUtils;
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@ -60,12 +61,12 @@ public class CreateBulkExportEntityTasklet implements Tasklet {
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}
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Set<String> resourceTypeSet = Arrays.stream(resourceTypes.split(",")).collect(Collectors.toSet());
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String outputFormat = (String)jobParameters.get("outputFormat");
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String outputFormat = (String) jobParameters.get("outputFormat");
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if (StringUtils.isBlank(outputFormat)) {
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outputFormat = Constants.CT_FHIR_NDJSON;
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}
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IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.submitJob(outputFormat, resourceTypeSet, since, filterSet);
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IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(outputFormat, resourceTypeSet, since, filterSet));
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addUUIDToJobContext(theChunkContext, jobInfo.getJobId());
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return RepeatStatus.FINISHED;
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@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.bulk.provider;
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*/
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
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import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
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import ca.uhn.fhir.jpa.bulk.model.BulkExportResponseJson;
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import ca.uhn.fhir.jpa.model.util.JpaConstants;
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@ -98,7 +99,7 @@ public class BulkDataExportProvider {
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filters = ArrayUtil.commaSeparatedListToCleanSet(theTypeFilter.getValueAsString());
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}
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IBulkDataExportSvc.JobInfo outcome = myBulkDataExportSvc.submitJob(outputFormat, resourceTypes, since, filters);
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IBulkDataExportSvc.JobInfo outcome = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(outputFormat, resourceTypes, since, filters));
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String serverBase = getServerBase(theRequestDetails);
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String pollLocation = serverBase + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?" + JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + outcome.getJobId();
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@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
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import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
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import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
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import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
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import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
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import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
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@ -229,28 +230,28 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
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@Transactional
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@Override
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public JobInfo submitJob(String theOutputFormat, Set<String> theResourceTypes, Date theSince, Set<String> theFilters) {
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public JobInfo submitJob(BulkDataExportOptions theBulkDataExportOptions) {
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String outputFormat = Constants.CT_FHIR_NDJSON;
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if (isNotBlank(theOutputFormat)) {
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outputFormat = theOutputFormat;
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if (isNotBlank(theBulkDataExportOptions.getOutputFormat())) {
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outputFormat = theBulkDataExportOptions.getOutputFormat();
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}
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if (!Constants.CTS_NDJSON.contains(outputFormat)) {
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throw new InvalidRequestException("Invalid output format: " + theOutputFormat);
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throw new InvalidRequestException("Invalid output format: " + theBulkDataExportOptions.getOutputFormat());
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}
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StringBuilder requestBuilder = new StringBuilder();
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requestBuilder.append("/").append(JpaConstants.OPERATION_EXPORT);
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requestBuilder.append("?").append(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT).append("=").append(escapeUrlParam(outputFormat));
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Set<String> resourceTypes = theResourceTypes;
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Set<String> resourceTypes = theBulkDataExportOptions.getResourceTypes();
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if (resourceTypes != null) {
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requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_TYPE).append("=").append(String.join(",", escapeUrlParams(resourceTypes)));
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}
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Date since = theSince;
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Date since = theBulkDataExportOptions.getSince();
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if (since != null) {
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requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_SINCE).append("=").append(new InstantType(since).setTimeZoneZulu(true).getValueAsString());
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}
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if (theFilters != null && theFilters.size() > 0) {
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requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_TYPE_FILTER).append("=").append(String.join(",", escapeUrlParams(theFilters)));
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if (theBulkDataExportOptions.getFilters() != null && theBulkDataExportOptions.getFilters().size() > 0) {
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requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_TYPE_FILTER).append("=").append(String.join(",", escapeUrlParams(theBulkDataExportOptions.getFilters())));
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}
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String request = requestBuilder.toString();
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@ -291,7 +292,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
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// Validate types
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validateTypes(resourceTypes);
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validateTypeFilters(theFilters, resourceTypes);
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validateTypeFilters(theBulkDataExportOptions.getFilters(), resourceTypes);
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updateExpiry(job);
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myBulkExportJobDao.save(job);
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@ -8,7 +8,24 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
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import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
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import ca.uhn.fhir.jpa.term.loinc.*;
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import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListLinkHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincDocumentOntologyHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincGroupFileHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincGroupTermsFileHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincHierarchyHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincIeeeMedicalDeviceCodeHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincImagingDocumentCodeHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincParentGroupFileHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincPartHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincPartLinkHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincPartRelatedCodeMappingHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincRsnaPlaybookHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincTop2000LabResultsSiHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincTop2000LabResultsUsHandler;
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import ca.uhn.fhir.jpa.term.loinc.LoincUniversalOrderSetHandler;
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import ca.uhn.fhir.jpa.term.loinc.PartTypeAndPartName;
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import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
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import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
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import ca.uhn.fhir.jpa.term.snomedct.SctHandlerRelationship;
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@ -38,12 +55,66 @@ import org.springframework.beans.factory.annotation.Autowired;
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import javax.annotation.Nonnull;
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import javax.validation.constraints.NotNull;
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import java.io.*;
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import java.util.*;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.LineNumberReader;
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import java.io.Reader;
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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.Date;
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import java.util.HashMap;
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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.Map;
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import java.util.Map.Entry;
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import java.util.Optional;
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import java.util.Properties;
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import java.util.Set;
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import java.util.stream.Collectors;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_DOCUMENT_ONTOLOGY_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_TERMS_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_TERMS_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_HIERARCHY_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_HIERARCHY_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IMAGING_DOCUMENT_CODES_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PARENT_GROUP_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PARENT_GROUP_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_PRIMARY;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_PRIMARY_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_SUPPLEMENTARY;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_RELATED_CODE_MAPPING_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_RSNA_PLAYBOOK_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_RSNA_PLAYBOOK_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT;
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import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UPLOAD_PROPERTIES_FILE;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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/*
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@ -592,7 +663,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
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Counter circularCounter = new Counter();
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for (TermConcept next : rootConcepts.values()) {
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long count = circularCounter.getThenAdd();
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long count = circularCounter.getnAdd();
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float pct = ((float) count / rootConcepts.size()) * 100.0f;
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ourLog.info(" * Scanning for circular refs - have scanned {} / {} codes ({}%)", count, rootConcepts.size(), pct);
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dropCircularRefs(next, new ArrayList<>(), code2concept);
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@ -23,9 +23,9 @@ package ca.uhn.fhir.jpa.util;
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public class Counter {
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private long myCount;
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public long getThenAdd() {
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public long getnAdd() {
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return myCount++;
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}
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}
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.bulk;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
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import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
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import ca.uhn.fhir.jpa.bulk.model.BulkExportResponseJson;
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import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
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@ -41,8 +42,6 @@ import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.util.Date;
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import java.util.Set;
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import java.util.concurrent.TimeUnit;
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import static org.hamcrest.MatcherAssert.assertThat;
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@ -61,6 +60,8 @@ public class BulkDataExportProviderTest {
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private static final String A_JOB_ID = "0000000-AAAAAA";
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private static final Logger ourLog = LoggerFactory.getLogger(BulkDataExportProviderTest.class);
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private static final String GROUP_ID = "G2401";
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private static final String G_JOB_ID = "0000000-GGGGGG";
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private Server myServer;
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private FhirContext myCtx = FhirContext.forCached(FhirVersionEnum.R4);
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private int myPort;
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@ -68,13 +69,7 @@ public class BulkDataExportProviderTest {
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private IBulkDataExportSvc myBulkDataExportSvc;
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private CloseableHttpClient myClient;
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@Captor
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private ArgumentCaptor<String> myOutputFormatCaptor;
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@Captor
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private ArgumentCaptor<Set<String>> myResourceTypesCaptor;
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@Captor
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private ArgumentCaptor<Date> mySinceCaptor;
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@Captor
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private ArgumentCaptor<Set<String>> myFiltersCaptor;
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private ArgumentCaptor<BulkDataExportOptions> myBulkDataExportOptionsCaptor;
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@AfterEach
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public void after() throws Exception {
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@ -111,7 +106,7 @@ public class BulkDataExportProviderTest {
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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(), any(), any(), any())).thenReturn(jobInfo);
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when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo);
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InstantType now = InstantType.now();
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@ -135,12 +130,12 @@ public class BulkDataExportProviderTest {
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assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
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}
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verify(myBulkDataExportSvc, times(1)).submitJob(myOutputFormatCaptor.capture(), myResourceTypesCaptor.capture(), mySinceCaptor.capture(), myFiltersCaptor.capture());
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assertEquals(Constants.CT_FHIR_NDJSON, myOutputFormatCaptor.getValue());
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assertThat(myResourceTypesCaptor.getValue(), containsInAnyOrder("Patient", "Practitioner"));
|
||||
assertThat(mySinceCaptor.getValue(), notNullValue());
|
||||
assertThat(myFiltersCaptor.getValue(), containsInAnyOrder("Patient?identifier=foo"));
|
||||
|
||||
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture());
|
||||
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
|
||||
assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner"));
|
||||
assertThat(options.getSince(), notNullValue());
|
||||
assertThat(options.getFilters(), containsInAnyOrder("Patient?identifier=foo"));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -148,7 +143,7 @@ public class BulkDataExportProviderTest {
|
|||
|
||||
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
|
||||
.setJobId(A_JOB_ID);
|
||||
when(myBulkDataExportSvc.submitJob(any(), any(), any(), any())).thenReturn(jobInfo);
|
||||
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo);
|
||||
|
||||
InstantType now = InstantType.now();
|
||||
|
||||
|
|
@ -169,12 +164,12 @@ public class BulkDataExportProviderTest {
|
|||
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
|
||||
}
|
||||
|
||||
verify(myBulkDataExportSvc, times(1)).submitJob(myOutputFormatCaptor.capture(), myResourceTypesCaptor.capture(), mySinceCaptor.capture(), myFiltersCaptor.capture());
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, myOutputFormatCaptor.getValue());
|
||||
assertThat(myResourceTypesCaptor.getValue(), containsInAnyOrder("Patient", "Practitioner"));
|
||||
assertThat(mySinceCaptor.getValue(), notNullValue());
|
||||
assertThat(myFiltersCaptor.getValue(), containsInAnyOrder("Patient?identifier=foo"));
|
||||
|
||||
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture());
|
||||
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
|
||||
assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner"));
|
||||
assertThat(options.getSince(), notNullValue());
|
||||
assertThat(options.getFilters(), containsInAnyOrder("Patient?identifier=foo"));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -286,5 +281,48 @@ public class BulkDataExportProviderTest {
|
|||
|
||||
}
|
||||
|
||||
/**
|
||||
* Group export tests
|
||||
* See https://build.fhir.org/ig/HL7/us-bulk-data/
|
||||
* <p>
|
||||
* GET [fhir base]/Group/[id]/$export
|
||||
* <p>
|
||||
* FHIR Operation to obtain data on all patients listed in a single FHIR Group Resource.
|
||||
*/
|
||||
|
||||
@Test
|
||||
public void testSuccessfulInitiateGroupBulkRequest_Post() throws IOException {
|
||||
|
||||
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo().setJobId(G_JOB_ID);
|
||||
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo);
|
||||
|
||||
InstantType now = InstantType.now();
|
||||
|
||||
Parameters input = new Parameters();
|
||||
input.addParameter(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, new StringType(Constants.CT_FHIR_NDJSON));
|
||||
input.addParameter(JpaConstants.PARAM_EXPORT_TYPE, new StringType("Observation, DiagnosticReport"));
|
||||
input.addParameter(JpaConstants.PARAM_EXPORT_SINCE, now);
|
||||
input.addParameter(JpaConstants.PARAM_EXPORT_TYPE_FILTER, new StringType("Observation?code=OBSCODE,DiagnosticReport?code=DRCODE"));
|
||||
|
||||
ourLog.info(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input));
|
||||
|
||||
HttpPost post = new HttpPost("http://localhost:" + myPort + "/Group/" + GROUP_ID + "/" + JpaConstants.OPERATION_EXPORT);
|
||||
post.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
|
||||
post.setEntity(new ResourceEntity(myCtx, input));
|
||||
ourLog.info("Request: {}", post);
|
||||
try (CloseableHttpResponse response = myClient.execute(post)) {
|
||||
ourLog.info("Response: {}", response.toString());
|
||||
|
||||
assertEquals(202, response.getStatusLine().getStatusCode());
|
||||
assertEquals("Accepted", response.getStatusLine().getReasonPhrase());
|
||||
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + G_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
|
||||
}
|
||||
|
||||
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture());
|
||||
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
|
||||
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
|
||||
assertThat(options.getResourceTypes(), containsInAnyOrder("Observation", "DiagnosticReport"));
|
||||
assertThat(options.getSince(), notNullValue());
|
||||
assertThat(options.getFilters(), containsInAnyOrder("Observation?code=OBSCODE", "DiagnosticReport?code=DRCODE"));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.bulk;
|
|||
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
|
||||
import ca.uhn.fhir.interceptor.api.Pointcut;
|
||||
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
|
||||
import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
|
||||
import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
|
||||
import ca.uhn.fhir.jpa.bulk.job.BulkExportJobParametersBuilder;
|
||||
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
|
||||
|
|
@ -134,7 +135,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
@Test
|
||||
public void testSubmit_InvalidOutputFormat() {
|
||||
try {
|
||||
myBulkDataExportSvc.submitJob(Constants.CT_FHIR_JSON_NEW, Sets.newHashSet("Patient", "Observation"), null, null);
|
||||
myBulkDataExportSvc.submitJob(new BulkDataExportOptions(Constants.CT_FHIR_JSON_NEW, Sets.newHashSet("Patient", "Observation"), null, null));
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Invalid output format: application/fhir+json", e.getMessage());
|
||||
|
|
@ -144,7 +145,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
@Test
|
||||
public void testSubmit_OnlyBinarySelected() {
|
||||
try {
|
||||
myBulkDataExportSvc.submitJob(Constants.CT_FHIR_JSON_NEW, Sets.newHashSet("Binary"), null, null);
|
||||
myBulkDataExportSvc.submitJob(new BulkDataExportOptions(Constants.CT_FHIR_JSON_NEW, Sets.newHashSet("Binary"), null, null));
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Invalid output format: application/fhir+json", e.getMessage());
|
||||
|
|
@ -154,7 +155,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
@Test
|
||||
public void testSubmit_InvalidResourceTypes() {
|
||||
try {
|
||||
myBulkDataExportSvc.submitJob(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient", "FOO"), null, null);
|
||||
myBulkDataExportSvc.submitJob(new BulkDataExportOptions(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient", "FOO"), null, null));
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Unknown or unsupported resource type: FOO", e.getMessage());
|
||||
|
|
@ -164,7 +165,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
@Test
|
||||
public void testSubmit_MultipleTypeFiltersForSameType() {
|
||||
try {
|
||||
myBulkDataExportSvc.submitJob(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient"), null, Sets.newHashSet("Patient?name=a", "Patient?active=true"));
|
||||
myBulkDataExportSvc.submitJob(new BulkDataExportOptions(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient"), null, Sets.newHashSet("Patient?name=a", "Patient?active=true")));
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Invalid _typeFilter value \"Patient?name=a\". Multiple filters found for type Patient", e.getMessage());
|
||||
|
|
@ -174,7 +175,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
@Test
|
||||
public void testSubmit_TypeFilterForNonSelectedType() {
|
||||
try {
|
||||
myBulkDataExportSvc.submitJob(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient"), null, Sets.newHashSet("Observation?code=123"));
|
||||
myBulkDataExportSvc.submitJob(new BulkDataExportOptions(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient"), null, Sets.newHashSet("Observation?code=123")));
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Invalid _typeFilter value \"Observation?code=123\". Resource type does not appear in _type list", e.getMessage());
|
||||
|
|
@ -184,7 +185,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
@Test
|
||||
public void testSubmit_TypeFilterInvalid() {
|
||||
try {
|
||||
myBulkDataExportSvc.submitJob(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient"), null, Sets.newHashSet("Hello"));
|
||||
myBulkDataExportSvc.submitJob(new BulkDataExportOptions(Constants.CT_FHIR_NDJSON, Sets.newHashSet("Patient"), null, Sets.newHashSet("Hello")));
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Invalid _typeFilter value \"Hello\". Must be in the form [ResourceType]?[params]", e.getMessage());
|
||||
|
|
@ -195,11 +196,11 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
public void testSubmit_ReusesExisting() {
|
||||
|
||||
// Submit
|
||||
IBulkDataExportSvc.JobInfo jobDetails1 = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), null, null);
|
||||
IBulkDataExportSvc.JobInfo jobDetails1 = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(null, Sets.newHashSet("Patient", "Observation"), null, null));
|
||||
assertNotNull(jobDetails1.getJobId());
|
||||
|
||||
// Submit again
|
||||
IBulkDataExportSvc.JobInfo jobDetails2 = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), null, null);
|
||||
IBulkDataExportSvc.JobInfo jobDetails2 = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(null, Sets.newHashSet("Patient", "Observation"), null, null));
|
||||
assertNotNull(jobDetails2.getJobId());
|
||||
|
||||
assertEquals(jobDetails1.getJobId(), jobDetails2.getJobId());
|
||||
|
|
@ -220,7 +221,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
createResources();
|
||||
|
||||
// Create a bulk job
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient"), null, null);
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(null, Sets.newHashSet("Patient"), null, null));
|
||||
assertNotNull(jobDetails.getJobId());
|
||||
|
||||
// Check the status
|
||||
|
|
@ -250,7 +251,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
createResources();
|
||||
|
||||
// Create a bulk job
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), null, Sets.newHashSet(TEST_FILTER));
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(null, Sets.newHashSet("Patient", "Observation"), null, Sets.newHashSet(TEST_FILTER)));
|
||||
assertNotNull(jobDetails.getJobId());
|
||||
|
||||
// Check the status
|
||||
|
|
@ -303,7 +304,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
myBinaryDao.create(b);
|
||||
|
||||
// Create a bulk job
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(null, null, null, null);
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(null, null, null, null));
|
||||
assertNotNull(jobDetails.getJobId());
|
||||
|
||||
// Check the status
|
||||
|
|
@ -350,7 +351,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
// Create a bulk job
|
||||
HashSet<String> types = Sets.newHashSet("Patient");
|
||||
Set<String> typeFilters = Sets.newHashSet("Patient?_has:Observation:patient:identifier=SYS|VAL3");
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(null, types, null, typeFilters);
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(null, types, null, typeFilters));
|
||||
assertNotNull(jobDetails.getJobId());
|
||||
|
||||
// Check the status
|
||||
|
|
@ -402,7 +403,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
}
|
||||
|
||||
// Create a bulk job
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), cutoff.getValue(), null);
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(null, Sets.newHashSet("Patient", "Observation"), cutoff.getValue(), null));
|
||||
assertNotNull(jobDetails.getJobId());
|
||||
|
||||
// Check the status
|
||||
|
|
@ -480,7 +481,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
|
|||
createResources();
|
||||
|
||||
// Create a bulk job
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(null, Sets.newHashSet("Patient", "Observation"), null, null);
|
||||
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(null, Sets.newHashSet("Patient", "Observation"), null, null));
|
||||
|
||||
//Add the UUID to the job
|
||||
BulkExportJobParametersBuilder paramBuilder = new BulkExportJobParametersBuilder()
|
||||
|
|
|
|||
Loading…
Reference in New Issue