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Merge branch 'issue-2401-add-support-for-group-id-export' of github.com:jamesagnew/hapi-fhir into issue-2401-add-support-for-group-id-export

This commit is contained in:
Tadgh 2021-02-22 10:25:26 -05:00
parent d31b04ee65 61a7f9ed6a
commit d8ce476e99
5 changed files with 42 additions and 11 deletions
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14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/api/GroupBulkDataExportOptions.java
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@ -1,17 +1,25 @@
package ca.uhn.fhir.jpa.bulk.api;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.Date;
import java.util.Set;
public class GroupBulkDataExportOptions extends BulkDataExportOptions {
private final String myGroupId;
private final IIdType myGroupId;
private final boolean myMdm;
public GroupBulkDataExportOptions(String theOutputFormat, Set<String> theResourceTypes, Date theSince, Set<String> theFilters, String theGroupId) {
public GroupBulkDataExportOptions(String theOutputFormat, Set<String> theResourceTypes, Date theSince, Set<String> theFilters, IIdType theGroupId, boolean theMdm) {
super(theOutputFormat, theResourceTypes, theSince, theFilters);
myGroupId = theGroupId;
myMdm = theMdm;
}
public String getGroupId() {
public IIdType getGroupId() {
return myGroupId;
}
public boolean isMdm() {
return myMdm;
}
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/provider/BulkDataExportProvider.java
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@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.bulk.api.GroupBulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.model.BulkExportResponseJson;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.Constants;
@ -39,6 +40,7 @@ import ca.uhn.fhir.util.OperationOutcomeUtil;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.InstantType;
import org.springframework.beans.factory.annotation.Autowired;
@ -184,10 +186,12 @@ public class BulkDataExportProvider {
*/
@Operation(name = JpaConstants.OPERATION_EXPORT, manualResponse = true, idempotent = true, typeName = "Group")
public void groupExport(
@IdParam IIdType theIdParam,
@OperationParam(name = JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theOutputFormat,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theType,
@OperationParam(name = JpaConstants.PARAM_EXPORT_SINCE, min = 0, max = 1, typeName = "instant") IPrimitiveType<Date> theSince,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theTypeFilter,
@OperationParam(name = JpaConstants.PARAM_EXPORT_MDM, min = 0, max = 1, typeName = "boolean") IPrimitiveType<Boolean> theMdm,
ServletRequestDetails theRequestDetails
) {
@ -213,9 +217,7 @@ public class BulkDataExportProvider {
if (theTypeFilter != null) {
filters = ArrayUtil.commaSeparatedListToCleanSet(theTypeFilter.getValueAsString());
}
// FIXME set this
String groupId = "FIXME";
IBulkDataExportSvc.JobInfo outcome = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(outputFormat, resourceTypes, since, filters, groupId));
IBulkDataExportSvc.JobInfo outcome = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(outputFormat, resourceTypes, since, filters, theIdParam, theMdm.getValue()));
String serverBase = getServerBase(theRequestDetails);
String pollLocation = serverBase + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?" + JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + outcome.getJobId();

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/svc/BulkDataExportSvcImpl.java
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@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.GroupBulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
@ -76,7 +77,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
private static final Long READ_CHUNK_SIZE = 10L;
private static final Logger ourLog = LoggerFactory.getLogger(BulkDataExportSvcImpl.class);
private int myReuseBulkExportForMillis = (int) (60 * DateUtils.MILLIS_PER_MINUTE);
private final int myReuseBulkExportForMillis = (int) (60 * DateUtils.MILLIS_PER_MINUTE);
@Autowired
private IBulkExportJobDao myBulkExportJobDao;
@ -101,7 +102,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
@Qualifier("bulkExportJob")
private org.springframework.batch.core.Job myBulkExportJob;
private int myRetentionPeriod = (int) (2 * DateUtils.MILLIS_PER_HOUR);
private final int myRetentionPeriod = (int) (2 * DateUtils.MILLIS_PER_HOUR);
/**
* This method is called by the scheduler to run a pass of the
@ -239,6 +240,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
throw new InvalidRequestException("Invalid output format: " + theBulkDataExportOptions.getOutputFormat());
}
// FIXME GGG can we encode BulkDataExportOptions as a JSON string as opposed to this request string. Feels like it would be a more extensible encoding...
StringBuilder requestBuilder = new StringBuilder();
requestBuilder.append("/").append(JpaConstants.OPERATION_EXPORT);
requestBuilder.append("?").append(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT).append("=").append(escapeUrlParam(outputFormat));
@ -253,6 +255,11 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
if (theBulkDataExportOptions.getFilters() != null && theBulkDataExportOptions.getFilters().size() > 0) {
requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_TYPE_FILTER).append("=").append(String.join(",", escapeUrlParams(theBulkDataExportOptions.getFilters())));
}
if (theBulkDataExportOptions instanceof GroupBulkDataExportOptions) {
GroupBulkDataExportOptions groupOptions = (GroupBulkDataExportOptions) theBulkDataExportOptions;
requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_GROUP_ID).append("=").append(groupOptions.getGroupId().getValue());
requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_MDM).append("=").append(groupOptions.isMdm());
}
String request = requestBuilder.toString();
Date cutoff = DateUtils.addMilliseconds(new Date(), -myReuseBulkExportForMillis);

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportProviderTest.java
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@ -27,6 +27,7 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Parameters;
@ -50,6 +51,7 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.notNullValue;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.eq;
import static org.mockito.Mockito.times;
@ -61,7 +63,7 @@ public class BulkDataExportProviderTest {
private static final String A_JOB_ID = "0000000-AAAAAA";
private static final Logger ourLog = LoggerFactory.getLogger(BulkDataExportProviderTest.class);
private static final String GROUP_ID = "G2401";
private static final String GROUP_ID = "Group/G2401";
private static final String G_JOB_ID = "0000000-GGGGGG";
private Server myServer;
private final FhirContext myCtx = FhirContext.forCached(FhirVersionEnum.R4);
@ -306,10 +308,11 @@ public class BulkDataExportProviderTest {
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"));
input.addParameter(JpaConstants.PARAM_EXPORT_MDM, new BooleanType(true));
ourLog.info(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input));
HttpPost post = new HttpPost("http://localhost:" + myPort + "/Group/" + GROUP_ID + "/" + JpaConstants.OPERATION_EXPORT);
HttpPost post = new HttpPost("http://localhost:" + myPort + "/" + 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);
@ -326,6 +329,7 @@ public class BulkDataExportProviderTest {
assertThat(options.getResourceTypes(), containsInAnyOrder("Observation", "DiagnosticReport"));
assertThat(options.getSince(), notNullValue());
assertThat(options.getFilters(), containsInAnyOrder("Observation?code=OBSCODE", "DiagnosticReport?code=DRCODE"));
assertEquals(GROUP_ID, options.getGroupId());
assertEquals(GROUP_ID, options.getGroupId().getValue());
assertTrue(options.isMdm());
}
}

10
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java
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@ -183,6 +183,16 @@ public class JpaConstants {
*/
public static final String PARAM_EXPORT_TYPE_FILTER = "_typeFilter";
/**
* The [id] of the group when $export is called on /Group/[id]/$export
*/
public static final Object PARAM_EXPORT_GROUP_ID = "_groupId";
/**
* Whether mdm should be performed on group export items to expand the group items to linked items before performing the export
*/
public static final String PARAM_EXPORT_MDM = "_mdm";
/**
* Parameter for delete to indicate the deleted resources should also be expunged
*/