Merge branch 'master' into tinder-for-non-java
This commit is contained in:
Bill Denton
commit
698c21c6c1
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@ -2209,10 +2209,14 @@ public class SearchBuilder {
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for (ResourceLink resourceLink : results) {
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if (theReverseMode) {
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Long pid = resourceLink.getSourceResourcePid();
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pidsToInclude.add(pid);
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if (pid != null) {
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pidsToInclude.add(pid);
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}
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} else {
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Long pid = resourceLink.getTargetResourcePid();
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pidsToInclude.add(pid);
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if (pid != null) {
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pidsToInclude.add(pid);
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}
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}
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}
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}
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@ -22,91 +22,40 @@ import static org.mockito.Mockito.reset;
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import static org.mockito.Mockito.verify;
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import static org.mockito.Mockito.verifyNoMoreInteractions;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.nio.charset.StandardCharsets;
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import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.RandomStringUtils;
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import org.hamcrest.Matchers;
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import org.hamcrest.core.StringContains;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Test;
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import org.mockito.ArgumentCaptor;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.FhirResourceDaoDstu2;
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import ca.uhn.fhir.jpa.dao.SearchParameterMap;
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import ca.uhn.fhir.jpa.dao.*;
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import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3Test;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
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import ca.uhn.fhir.jpa.entity.TagTypeEnum;
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import ca.uhn.fhir.model.api.IQueryParameterType;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.api.Include;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.model.api.Tag;
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import ca.uhn.fhir.model.api.TagList;
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import ca.uhn.fhir.model.api.*;
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import ca.uhn.fhir.model.base.composite.BaseCodingDt;
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import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
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import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
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import ca.uhn.fhir.model.dstu2.composite.CodingDt;
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import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
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import ca.uhn.fhir.model.dstu2.composite.MetaDt;
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import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
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import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
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import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
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import ca.uhn.fhir.model.dstu2.resource.BaseResource;
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import ca.uhn.fhir.model.dstu2.composite.*;
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import ca.uhn.fhir.model.dstu2.resource.*;
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import ca.uhn.fhir.model.dstu2.resource.Bundle;
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import ca.uhn.fhir.model.dstu2.resource.ConceptMap;
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import ca.uhn.fhir.model.dstu2.resource.Device;
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import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
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import ca.uhn.fhir.model.dstu2.resource.Encounter;
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import ca.uhn.fhir.model.dstu2.resource.Observation;
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import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
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import ca.uhn.fhir.model.dstu2.resource.Organization;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.model.dstu2.resource.Questionnaire;
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import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
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import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
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import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
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import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
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import ca.uhn.fhir.model.dstu2.valueset.IssueTypeEnum;
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import ca.uhn.fhir.model.dstu2.valueset.QuantityComparatorEnum;
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import ca.uhn.fhir.model.primitive.CodeDt;
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import ca.uhn.fhir.model.primitive.DateDt;
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import ca.uhn.fhir.model.primitive.DateTimeDt;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.model.primitive.InstantDt;
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import ca.uhn.fhir.model.primitive.StringDt;
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import ca.uhn.fhir.model.primitive.UriDt;
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import ca.uhn.fhir.model.dstu2.valueset.*;
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import ca.uhn.fhir.model.primitive.*;
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import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
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import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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import ca.uhn.fhir.rest.api.SortOrderEnum;
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import ca.uhn.fhir.rest.api.SortSpec;
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import ca.uhn.fhir.rest.param.DateParam;
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import ca.uhn.fhir.rest.param.DateRangeParam;
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import ca.uhn.fhir.rest.param.QuantityParam;
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import ca.uhn.fhir.rest.param.ReferenceParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenOrListParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.api.*;
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import ca.uhn.fhir.rest.param.*;
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import ca.uhn.fhir.rest.server.Constants;
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import ca.uhn.fhir.rest.server.EncodingEnum;
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import ca.uhn.fhir.rest.server.IBundleProvider;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.rest.server.exceptions.*;
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import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
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import ca.uhn.fhir.util.TestUtil;
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@ -130,6 +79,31 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
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}
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}
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@After
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public final void after() {
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myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
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}
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@Test
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public void testValidateAgainstDstu2Profile() throws Exception {
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myDaoConfig.setAllowExternalReferences(true);
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String stream = IOUtils.toString(getClass().getResourceAsStream("/binu_testpatient_structuredefinition_dstu2.xml"), StandardCharsets.UTF_8);
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StructureDefinition sd = myFhirCtx.newXmlParser().parseResource(StructureDefinition.class, stream);
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myStructureDefinitionDao.create(sd, mySrd);
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String rawResource = IOUtils.toString(getClass().getResourceAsStream("/binu_testpatient_resource.json"), StandardCharsets.UTF_8);
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try {
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myValueSetDao.validate(null, null, rawResource, EncodingEnum.JSON, ValidationModeEnum.UPDATE, null, mySrd);
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fail();
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} catch (PreconditionFailedException e) {
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ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
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}
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}
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@Test
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public void testCreateBundleAllowsDocumentAndCollection() {
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String methodName = "testCreateBundleAllowsDocumentAndCollection";
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@ -29,13 +29,7 @@ import java.net.Socket;
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import java.net.SocketTimeoutException;
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import java.net.URLEncoder;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.TreeSet;
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import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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@ -43,79 +37,31 @@ import org.apache.commons.lang3.Validate;
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import org.apache.http.NameValuePair;
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import org.apache.http.client.ClientProtocolException;
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import org.apache.http.client.entity.UrlEncodedFormEntity;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpDelete;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.client.methods.HttpPatch;
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import org.apache.http.client.methods.HttpPost;
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import org.apache.http.client.methods.HttpPut;
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import org.apache.http.client.methods.*;
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import org.apache.http.entity.ContentType;
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import org.apache.http.entity.StringEntity;
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import org.apache.http.message.BasicNameValuePair;
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import org.hl7.fhir.dstu3.model.AuditEvent;
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import org.hl7.fhir.dstu3.model.BaseResource;
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import org.hl7.fhir.dstu3.model.Basic;
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import org.hl7.fhir.dstu3.model.Bundle;
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import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.dstu3.model.Bundle.BundleLinkComponent;
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import org.hl7.fhir.dstu3.model.Bundle.BundleType;
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import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
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import org.hl7.fhir.dstu3.model.Bundle.SearchEntryMode;
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import org.hl7.fhir.dstu3.model.CodeSystem;
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import org.hl7.fhir.dstu3.model.CodeType;
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import org.hl7.fhir.dstu3.model.Coding;
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import org.hl7.fhir.dstu3.model.Condition;
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import org.hl7.fhir.dstu3.model.DateTimeType;
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import org.hl7.fhir.dstu3.model.DateType;
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import org.hl7.fhir.dstu3.model.Device;
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import org.hl7.fhir.dstu3.model.DiagnosticRequest;
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import org.hl7.fhir.dstu3.model.DocumentManifest;
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import org.hl7.fhir.dstu3.model.DocumentReference;
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import org.hl7.fhir.dstu3.model.Encounter;
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import org.hl7.fhir.dstu3.model.*;
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import org.hl7.fhir.dstu3.model.Bundle.*;
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import org.hl7.fhir.dstu3.model.Encounter.EncounterLocationComponent;
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import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
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import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
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import org.hl7.fhir.dstu3.model.Extension;
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import org.hl7.fhir.dstu3.model.IdType;
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import org.hl7.fhir.dstu3.model.ImagingStudy;
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import org.hl7.fhir.dstu3.model.InstantType;
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import org.hl7.fhir.dstu3.model.IntegerType;
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import org.hl7.fhir.dstu3.model.Location;
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import org.hl7.fhir.dstu3.model.Medication;
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import org.hl7.fhir.dstu3.model.MedicationAdministration;
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import org.hl7.fhir.dstu3.model.MedicationRequest;
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import org.hl7.fhir.dstu3.model.Meta;
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import org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus;
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import org.hl7.fhir.dstu3.model.Observation;
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import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
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import org.hl7.fhir.dstu3.model.OperationOutcome;
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import org.hl7.fhir.dstu3.model.Organization;
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import org.hl7.fhir.dstu3.model.Parameters;
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import org.hl7.fhir.dstu3.model.Patient;
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import org.hl7.fhir.dstu3.model.Period;
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import org.hl7.fhir.dstu3.model.Practitioner;
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import org.hl7.fhir.dstu3.model.Quantity;
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import org.hl7.fhir.dstu3.model.Questionnaire;
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import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
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import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
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import org.hl7.fhir.dstu3.model.Reference;
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import org.hl7.fhir.dstu3.model.StringType;
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import org.hl7.fhir.dstu3.model.StructureDefinition;
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import org.hl7.fhir.dstu3.model.Subscription;
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import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
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import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
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import org.hl7.fhir.dstu3.model.TemporalPrecisionEnum;
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import org.hl7.fhir.dstu3.model.UnsignedIntType;
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import org.hl7.fhir.dstu3.model.ValueSet;
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import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Ignore;
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import org.junit.Test;
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import com.google.common.collect.Lists;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.model.primitive.InstantDt;
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import ca.uhn.fhir.model.primitive.UriDt;
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import ca.uhn.fhir.parser.IParser;
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@ -124,11 +70,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.SummaryEnum;
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import ca.uhn.fhir.rest.client.IGenericClient;
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import ca.uhn.fhir.rest.gclient.StringClientParam;
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import ca.uhn.fhir.rest.param.DateRangeParam;
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import ca.uhn.fhir.rest.param.ParamPrefixEnum;
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import ca.uhn.fhir.rest.param.StringAndListParam;
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import ca.uhn.fhir.rest.param.StringOrListParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.*;
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import ca.uhn.fhir.rest.server.Constants;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
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|
@ -148,6 +90,29 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
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myDaoConfig.setAllowMultipleDelete(true);
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}
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@Override
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@After
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public void after() throws Exception {
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super.after();
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myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
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myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
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}
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@Test
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public void testIncludeWithExternalReferences() {
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myDaoConfig.setAllowExternalReferences(true);
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Patient p = new Patient();
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p.getManagingOrganization().setReference("http://example.com/Organization/123");
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ourClient.create().resource(p).execute();
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Bundle b = ourClient.search().forResource("Patient").include(Patient.INCLUDE_ORGANIZATION).returnBundle(Bundle.class).execute();
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assertEquals(1, b.getEntry().size());
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}
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private void checkParamMissing(String paramName) throws IOException, ClientProtocolException {
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HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
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CloseableHttpResponse resp = ourHttpClient.execute(get);
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|
|
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@ -0,0 +1,40 @@
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{
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"resourceType": "Patient",
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"id": "67.20068.14731",
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"meta": {
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"versionId": "1",
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"lastUpdated": "2016-11-30T02:18:24.929-05:00",
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"profile": [
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"http://example.org/fhir/StructureDefinition/DutchPatient"
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]
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},
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"text": {
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"status": "generated",
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"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> GHASIYA <b>AL WAHEIBI </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>14731</td></tr><tr><td>Address</td><td></td></tr><tr><td>Date of birth</td><td><span>01 January 1981</span></td></tr></tbody></table></div>"
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},
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"identifier": [{
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"value": "14731",
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"period": {
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"start": "2005-03-15"
|
||||
}
|
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}],
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"active": false,
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"name": [{
|
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"family": [
|
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"AL WAHEIBI"
|
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],
|
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"given": [
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"GHASIYA"
|
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]
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}],
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"gender": "female",
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"birthDate": "1981-01-01",
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"deceasedBoolean": true,
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"address": {
|
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"use": "home"
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},
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"placeOfBirth": {
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"url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
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"valueString": "Narakal"
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}
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||||
}
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File diff suppressed because it is too large
Load Diff
|
|
@ -61,6 +61,11 @@
|
|||
CapabilityStatement resource. Thanks to Michael Lawley
|
||||
for the pull request!
|
||||
</action>
|
||||
<action type="fix">
|
||||
Fix a crash in JPA server when searching using an _include if _include targets are
|
||||
external references (and therefore can't be loaded
|
||||
by the server). Thanks to Hannes Ulrich for reporting!
|
||||
</action>
|
||||
</release>
|
||||
<release version="2.1" date="2016-11-11">
|
||||
<action type="add">
|
||||
|
|
|
|||
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Reference in New Issue