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WIP working out bug in typefilters

This commit is contained in:
Tadgh 2021-03-05 10:35:52 -05:00
parent 9547048848
commit 5b75ff2425
4 changed files with 85 additions and 4 deletions
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1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BaseBulkItemReader.java
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@ -87,6 +87,7 @@ public abstract class BaseBulkItemReader implements ItemReader<List<ResourcePers
Map<String, String[]> requestUrl = UrlUtil.parseQueryStrings(jobEntity.getRequest());
String[] typeFilters = requestUrl.get(JpaConstants.PARAM_EXPORT_TYPE_FILTER);
if (typeFilters != null) {
//TODO GGG START HERE
Optional<String> filter = Arrays.stream(typeFilters).filter(t -> t.startsWith(myResourceType + "?")).findFirst();
if (filter.isPresent()) {
String matchUrl = filter.get();

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/provider/BulkDataExportProvider.java
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@ -48,6 +48,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
public class BulkDataExportProvider {
@ -75,7 +77,7 @@ public class BulkDataExportProvider {
@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 = OperationParam.MAX_UNLIMITED, typeName = "string") IPrimitiveType<String> theTypeFilter,
@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theTypeFilter,
ServletRequestDetails theRequestDetails
) {
@ -97,9 +99,11 @@ public class BulkDataExportProvider {
since = theSince.getValue();
}
Set<String> filters = null;
Set<String> filters = new HashSet<>();
if (theTypeFilter != null) {
// theTypeFilter.stream().forEach(filter -> filters.addAll(ArrayUtil.commaSeparatedListToCleanSet(filter.getValueAsString())));
filters = ArrayUtil.commaSeparatedListToCleanSet(theTypeFilter.getValueAsString());
// theTypeFilter.stream().forEach(filter -> filters.addAll(ArrayUtil.commaSeparatedListToCleanSet(filter.getValueAsString())));
}
IBulkDataExportSvc.JobInfo outcome = myBulkDataExportSvc.submitJob(new BulkDataExportOptions(outputFormat, resourceTypes, since, filters, true));

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/svc/BulkDataExportSvcImpl.java
View File

@ -312,7 +312,8 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_SINCE).append("=").append(new InstantType(since).setTimeZoneZulu(true).getValueAsString());
}
if (theBulkDataExportOptions.getFilters() != null && theBulkDataExportOptions.getFilters().size() > 0) {
requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_TYPE_FILTER).append("=").append(String.join(",", escapeUrlParams(theBulkDataExportOptions.getFilters())));
theBulkDataExportOptions.getFilters().stream()
.forEach(filter -> requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_TYPE_FILTER).append("=").append(escapeUrlParam(filter)));
}
if (theBulkDataExportOptions instanceof GroupBulkDataExportOptions) {
GroupBulkDataExportOptions groupOptions = (GroupBulkDataExportOptions) theBulkDataExportOptions;

77
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportProviderTest.java
View File

@ -267,7 +267,6 @@ public class BulkDataExportProviderTest {
assertEquals("Patient", responseJson.getOutput().get(2).getType());
assertEquals("http://localhost:" + myPort + "/Binary/333", responseJson.getOutput().get(2).getUrl());
}
}
@Test
@ -339,4 +338,80 @@ public class BulkDataExportProviderTest {
assertEquals(GROUP_ID, options.getGroupId().getValue());
assertThat(options.isMdm(), is(equalTo(true)));
}
@Test
public void testInitiateWithGetAndMultipleTypeFilters() throws IOException {
//TODO GGG FIX ME
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
.setJobId(A_JOB_ID);
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo);
InstantType now = InstantType.now();
String url = "http://localhost:" + myPort + "/" + JpaConstants.OPERATION_EXPORT
+ "?" + JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT + "=" + UrlUtil.escapeUrlParam(Constants.CT_FHIR_NDJSON)
+ "&" + JpaConstants.PARAM_EXPORT_TYPE + "=" + UrlUtil.escapeUrlParam("Patient, Practitioner")
+ "&" + JpaConstants.PARAM_EXPORT_SINCE + "=" + UrlUtil.escapeUrlParam(now.getValueAsString())
// + "&" + JpaConstants.PARAM_EXPORT_TYPE_FILTER + "=" + UrlUtil.escapeUrlParam("Patient?identifier=foo")
// + "&" + JpaConstants.PARAM_EXPORT_TYPE_FILTER + "=" + UrlUtil.escapeUrlParam("Practitioner?identifier=bar")
// + "&" + JpaConstants.PARAM_EXPORT_TYPE_FILTER + "=" + UrlUtil.escapeUrlParam("Patient?name=zoop");
+ "&" + JpaConstants.PARAM_EXPORT_TYPE_FILTER + "=" + // "MedicationRequest%3Fstatus%3Dactive,MedicationRequest%3Fstatus%3Dcompleted%26date%3Dgt2018-07-01T00%3A00%3A00Z";
"Immunization?patient.identifier%3DSC378274-MRN%7C009999997%2CSC378274-MRN%7C009999998%2CSC378274-MRN%7C009999999%26date%3D2020-01-02";
HttpGet get = new HttpGet(url);
get.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
ourLog.info("Request: {}", url);
try (CloseableHttpResponse response = myClient.execute(get)) {
ourLog.info("Response: {}", response.toString());
assertEquals(202, response.getStatusLine().getStatusCode());
assertEquals("Accepted", response.getStatusLine().getReasonPhrase());
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_JOB_ID, response.getFirstHeader(Constants.HEADER_CONTENT_LOCATION).getValue());
}
verify(myBulkDataExportSvc, times(1)).submitJob(myBulkDataExportOptionsCaptor.capture());
BulkDataExportOptions options = myBulkDataExportOptionsCaptor.getValue();
assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
assertThat(options.getResourceTypes(), containsInAnyOrder("Patient", "Practitioner"));
assertThat(options.getSince(), notNullValue());
assertThat(options.getFilters(), containsInAnyOrder("Patient?identifier=foo", "Practitioner?identifier=bar", "Patient?name=zoop"));
}
@Test
public void testInitiateWithPostAndMultipleTypeFilters() throws IOException {
IBulkDataExportSvc.JobInfo jobInfo = new IBulkDataExportSvc.JobInfo()
.setJobId(A_JOB_ID);
when(myBulkDataExportSvc.submitJob(any())).thenReturn(jobInfo);
InstantType now = InstantType.now();
Parameters input = new Parameters();
input.addParameter(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, new StringType(Constants.CT_FHIR_NDJSON));
input.addParameter(JpaConstants.PARAM_EXPORT_TYPE, new StringType("Patient, Practitioner"));
input.addParameter(JpaConstants.PARAM_EXPORT_SINCE, now);
input.addParameter(JpaConstants.PARAM_EXPORT_TYPE_FILTER, new StringType("Patient?identifier=foo"));
ourLog.info(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input));
HttpPost post = new HttpPost("http://localhost:" + myPort + "/" + JpaConstants.OPERATION_EXPORT);
post.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
post.setEntity(new ResourceEntity(myCtx, input));
ourLog.info("Request: {}", post);
try (CloseableHttpResponse response = myClient.execute(post)) {
ourLog.info("Response: {}", response.toString());
assertEquals(202, response.getStatusLine().getStatusCode());
assertEquals("Accepted", response.getStatusLine().getReasonPhrase());
assertEquals("http://localhost:" + myPort + "/$export-poll-status?_jobId=" + A_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("Patient", "Practitioner"));
assertThat(options.getSince(), notNullValue());
assertThat(options.getFilters(), containsInAnyOrder("Patient?identifier=foo"));
}
}