honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Term service enhancements

This commit is contained in:
James Agnew 2016-06-30 17:45:41 -04:00
parent 38d30eef49
commit 7ef48413c4
21 changed files with 503 additions and 85 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeElementCompositeDefinition.java
View File

@ -45,12 +45,10 @@ import org.hl7.fhir.instance.model.api.IBaseEnumeration;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IBaseXhtml;
import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.instance.model.api.INarrative;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IBoundCodeableConcept;
import ca.uhn.fhir.model.api.IDatatype;
import ca.uhn.fhir.model.api.IElement;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/BaseDateTimeDt.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.model.primitive;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.Calendar;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/AtParameter.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.rest.annotation.At;
import ca.uhn.fhir.rest.server.Constants;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseJavaPrimitiveBinder.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.Collections;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/CalendarBinder.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Calendar;
import ca.uhn.fhir.model.primitive.InstantDt;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/DateBinder.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Date;
import ca.uhn.fhir.model.primitive.InstantDt;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/FhirPrimitiveBinder.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.defaultString;
import org.hl7.fhir.instance.model.api.IPrimitiveType;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/SinceParameter.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.rest.annotation.Since;
import ca.uhn.fhir.rest.server.Constants;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/StringBinder.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.method;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
final class StringBinder extends BaseJavaPrimitiveBinder<String> {
StringBinder() {
}

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/VerboseLoggingInterceptor.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.interceptor;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Enumeration;
import javax.servlet.http.HttpServletRequest;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/BaseRule.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.interceptor.auth;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationInterceptor.Verdict;
abstract class BaseRule implements IAuthRule {

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderOperation.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.interceptor.auth;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public interface IAuthRuleBuilderOperation {
/**

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderOperationNamed.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.interceptor.auth;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/OperationRule.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.interceptor.auth;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.HashSet;
import java.util.List;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/PortUtil.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.util;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.net.ServerSocket;
/**

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProviderDstu2Plus.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.provider;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/DeferConceptIndexingInterceptor.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.search;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.hibernate.search.indexes.interceptor.EntityIndexingInterceptor;
import org.hibernate.search.indexes.interceptor.IndexingOverride;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -64,6 +64,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CoverageIgnore;
@ -278,6 +279,8 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
return retVal;
} catch (BaseServerResponseException e) {
throw e;
} catch (Exception e) {
throw new InternalErrorException(e);
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/Counter.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.util;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public class Counter {
private long myCount;

241
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -56,7 +56,6 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
}
@Before
public void before() {
myDaoConfig.setMaximumExpansionSize(5000);
@ -133,7 +132,6 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
createLocalVs(codeSystem);
}
private void createLocalVs(CodeSystem codeSystem) {
ValueSet valueSet = new ValueSet();
valueSet.setUrl(URL_MY_VALUE_SET);
@ -141,17 +139,16 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
myValueSetDao.create(valueSet, mySrd);
}
@Test
public void testCodeSystemCreateDuplicateFails() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
try {
myCodeSystemDao.create(codeSystem, mySrd);
fail();
@ -175,14 +172,14 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
.addConcept(new ConceptDefinitionComponent().setCode("BA").setDisplay("Code AA"))
.addConcept(new ConceptDefinitionComponent().setCode("BB").setDisplay("Code AB"));
//@formatter:on
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
Set<TermConcept> codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "A");
assertThat(toCodes(codes), containsInAnyOrder("A", "AA", "AB"));
}
@Test
public void testExpandWithExcludeInExternalValueSet() {
createExternalCsAndLocalVs();
@ -195,10 +192,10 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
exclude.setSystem(URL_MY_CODE_SYSTEM);
exclude.addConcept().setCode("childAA");
exclude.addConcept().setCode("childAAA");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("ParentA", "ParentB", "childAB", "childAAB", "ParentC", "childBA", "childCA"));
}
@ -207,19 +204,18 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
IParser parser = myFhirCtx.newXmlParser().setPrettyPrint(true);
String encoded = parser.encodeResourceToString(theResult);
ourLog.info(encoded);
FhirValidator validator = myFhirCtx.newValidator();
validator.setValidateAgainstStandardSchema(true);
validator.setValidateAgainstStandardSchematron(true);
ValidationResult result = validator.validateWithResult(theResult);
if (!result.isSuccessful()) {
ourLog.info(parser.encodeResourceToString(result.toOperationOutcome()));
fail(parser.encodeResourceToString(result.toOperationOutcome()));
}
}
@Test
public void testExpandWithInvalidExclude() {
createExternalCsAndLocalVs();
@ -257,7 +253,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
} catch (InvalidRequestException e) {
assertEquals("Unable to find code 'ZZZZ' in code system http://example.com/my_code_system", e.getMessage());
}
}
@Test
@ -277,10 +273,8 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
}
@Test
public void testExpandWithSystemAndCodesAndFilterInExternalValueSet() {
public void testExpandWithSystemAndCodesInExternalValueSet() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
@ -290,20 +284,36 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
include.addConcept().setCode("childAA");
include.addConcept().setCode("childAAA");
include.addFilter().setProperty("display").setOp(FilterOperator.EQUAL).setValue("Parent B");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("ParentA", "childAA", "childAAA", "ParentB"));
assertThat(codes, containsInAnyOrder("ParentA", "childAA", "childAAA"));
int idx = codes.indexOf("childAA");
assertEquals("childAA", result.getExpansion().getContains().get(idx).getCode());
assertEquals("Child AA", result.getExpansion().getContains().get(idx).getDisplay());
assertEquals(URL_MY_CODE_SYSTEM, result.getExpansion().getContains().get(idx).getSystem());
}
@Test
public void testExpandWithSystemAndFilterInExternalValueSet() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setProperty("display").setOp(FilterOperator.EQUAL).setValue("Parent B");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("ParentB"));
}
@Test
public void testExpandWithDisplayInExternalValueSetFuzzyMatching() {
createExternalCsAndLocalVs();
@ -344,23 +354,23 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
// include.addConcept().setCode("A");
// include.addConcept().setCode("AA");
// include.addConcept().setCode("AAA");
// include.addConcept().setCode("AB");
// include.addConcept().setCode("A");
// include.addConcept().setCode("AA");
// include.addConcept().setCode("AAA");
// include.addConcept().setCode("AB");
include.addFilter().setProperty("display").setOp(FilterOperator.EQUAL).setValue("AAA");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("AAA"));
assertEquals("AAA", result.getExpansion().getContains().get(0).getCode());
assertEquals("Code AAA", result.getExpansion().getContains().get(0).getDisplay());
assertEquals(URL_MY_CODE_SYSTEM, result.getExpansion().getContains().get(0).getSystem());
//
//
}
@Test
@ -374,40 +384,40 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
include.addConcept().setCode("AA");
include.addConcept().setCode("AAA");
include.addConcept().setCode("AB");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("A", "AA", "AAA", "AB"));
int idx = codes.indexOf("AAA");
assertEquals("AAA", result.getExpansion().getContains().get(idx).getCode());
assertEquals("Code AAA", result.getExpansion().getContains().get(idx).getDisplay());
assertEquals(URL_MY_CODE_SYSTEM, result.getExpansion().getContains().get(idx).getSystem());
// ValueSet expansion = myValueSetDao.expandByIdentifier(URL_MY_VALUE_SET, "cervical");
// ValueSet expansion = myValueSetDao.expandByIdentifier(URL_MY_VALUE_SET, "cervical");
//
// ValueSet expansion = myValueSetDao.expandByIdentifier(URL_MY_VALUE_SET, "cervical");
// ValueSet expansion = myValueSetDao.expandByIdentifier(URL_MY_VALUE_SET, "cervical");
//
}
@Test
public void testIndexingIsDeferredForLargeCodeSystems() {
myDaoConfig.setDeferIndexingForCodesystemsOfSize(1);
myTermSvc.setProcessDeferred(false);
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
assertEquals(0, result.getExpansion().getContains().size());
myTermSvc.setProcessDeferred(true);
myTermSvc.saveDeferred();
myTermSvc.saveDeferred();
@ -416,14 +426,14 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
myTermSvc.saveDeferred();
myTermSvc.saveDeferred();
myTermSvc.saveDeferred();
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
assertEquals(4, result.getExpansion().getContains().size());
String encoded = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result);
@ -431,14 +441,14 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
/**
* Can't currently abort costly
* Can't currently abort costly
*/
@Test
@Ignore
public void testRefuseCostlyExpansionFhirCodesystem() {
createLocalCsAndVs();
myDaoConfig.setMaximumExpansionSize(1);
SearchParameterMap params = new SearchParameterMap();
params.add(AuditEvent.SP_TYPE, new TokenParam(null, "http://hl7.org/fhir/ValueSet/audit-event-type").setModifier(TokenParamModifier.IN));
try {
@ -453,7 +463,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
public void testRefuseCostlyExpansionLocalCodesystem() {
createLocalCsAndVs();
myDaoConfig.setMaximumExpansionSize(1);
SearchParameterMap params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "AAA").setModifier(TokenParamModifier.ABOVE));
try {
@ -467,7 +477,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
@Test
public void testSearchCodeAboveLocalCodesystem() {
createLocalCsAndVs();
Observation obsAA = new Observation();
obsAA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("AA");
IIdType idAA = myObservationDao.create(obsAA, mySrd).getId().toUnqualifiedVersionless();
@ -483,18 +493,18 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
SearchParameterMap params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "AAA").setModifier(TokenParamModifier.ABOVE));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(idAA.getValue()));
params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "A").setModifier(TokenParamModifier.ABOVE));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
}
@Test
public void testSearchCodeBelowAndAboveUnknownCodeSystem() {
SearchParameterMap params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "childAA").setModifier(TokenParamModifier.BELOW));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
@ -503,14 +513,13 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
}
}
@Test
public void testSearchCodeBelowLocalCodesystem() {
createLocalCsAndVs();
Observation obsAA = new Observation();
obsAA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("AA");
IIdType idAA = myObservationDao.create(obsAA, mySrd).getId().toUnqualifiedVersionless();
@ -526,32 +535,106 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
SearchParameterMap params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "A").setModifier(TokenParamModifier.BELOW));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(idAA.getValue()));
params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "AAA").setModifier(TokenParamModifier.BELOW));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
}
@Test
public void testSearchCodeInBuiltInValueSet() {
AllergyIntolerance ai1 = new AllergyIntolerance();
ai1.setStatus(AllergyIntoleranceStatus.ACTIVE);
String id1 = myAllergyIntoleranceDao.create(ai1, mySrd).getId().toUnqualifiedVersionless().getValue();
AllergyIntolerance ai2 = new AllergyIntolerance();
ai2.setStatus(AllergyIntoleranceStatus.CONFIRMED);
String id2 = myAllergyIntoleranceDao.create(ai2, mySrd).getId().toUnqualifiedVersionless().getValue();
AllergyIntolerance ai3 = new AllergyIntolerance();
ai3.setStatus(AllergyIntoleranceStatus.INACTIVE);
String id3 = myAllergyIntoleranceDao.create(ai3, mySrd).getId().toUnqualifiedVersionless().getValue();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, "http://hl7.org/fhir/ValueSet/allergy-intolerance-status").setModifier(TokenParamModifier.IN));
assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1, id2, id3));
// No codes in this one
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, "http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality").setModifier(TokenParamModifier.IN));
assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), empty());
// Invalid VS
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, "http://hl7.org/fhir/ValueSet/FOO").setModifier(TokenParamModifier.IN));
try {
myAllergyIntoleranceDao.search(params);
} catch (InvalidRequestException e) {
assertEquals("Unable to find imported value set http://hl7.org/fhir/ValueSet/FOO", e.getMessage());
}
}
/**
* Todo: not yet implemented
*/
@Test
@Ignore
public void testSearchCodeNotInBuiltInValueSet() {
AllergyIntolerance ai1 = new AllergyIntolerance();
ai1.setStatus(AllergyIntoleranceStatus.ACTIVE);
String id1 = myAllergyIntoleranceDao.create(ai1, mySrd).getId().toUnqualifiedVersionless().getValue();
AllergyIntolerance ai2 = new AllergyIntolerance();
ai2.setStatus(AllergyIntoleranceStatus.CONFIRMED);
String id2 = myAllergyIntoleranceDao.create(ai2, mySrd).getId().toUnqualifiedVersionless().getValue();
AllergyIntolerance ai3 = new AllergyIntolerance();
ai3.setStatus(AllergyIntoleranceStatus.INACTIVE);
String id3 = myAllergyIntoleranceDao.create(ai3, mySrd).getId().toUnqualifiedVersionless().getValue();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, "http://hl7.org/fhir/ValueSet/allergy-intolerance-status").setModifier(TokenParamModifier.NOT_IN));
assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), empty());
// No codes in this one
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, "http://hl7.org/fhir/ValueSet/allergy-intolerance-criticality").setModifier(TokenParamModifier.NOT_IN));
assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1, id2, id3));
// Invalid VS
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, "http://hl7.org/fhir/ValueSet/FOO").setModifier(TokenParamModifier.NOT_IN));
try {
myAllergyIntoleranceDao.search(params);
} catch (InvalidRequestException e) {
assertEquals("Unable to find imported value set http://hl7.org/fhir/ValueSet/FOO", e.getMessage());
}
}
@Test
public void testSearchCodeBelowBuiltInCodesystem() {
AllergyIntolerance ai1 = new AllergyIntolerance();
ai1.setStatus(AllergyIntoleranceStatus.ACTIVE);
String id1 = myAllergyIntoleranceDao.create(ai1, mySrd).getId().toUnqualifiedVersionless().getValue();
AllergyIntolerance ai2 = new AllergyIntolerance();
ai2.setStatus(AllergyIntoleranceStatus.CONFIRMED);
String id2 = myAllergyIntoleranceDao.create(ai2, mySrd).getId().toUnqualifiedVersionless().getValue();
AllergyIntolerance ai3 = new AllergyIntolerance();
ai3.setStatus(AllergyIntoleranceStatus.INACTIVE);
String id3 = myAllergyIntoleranceDao.create(ai3, mySrd).getId().toUnqualifiedVersionless().getValue();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status", AllergyIntoleranceStatus.ACTIVE.toCode()));
assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1));
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam("http://hl7.org/fhir/allergy-intolerance-status", AllergyIntoleranceStatus.ACTIVE.toCode()).setModifier(TokenParamModifier.BELOW));
assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1, id2));
@ -586,20 +669,20 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
AllergyIntolerance ai1 = new AllergyIntolerance();
ai1.setStatus(AllergyIntoleranceStatus.ACTIVE);
String id1 = myAllergyIntoleranceDao.create(ai1, mySrd).getId().toUnqualifiedVersionless().getValue();
AllergyIntolerance ai2 = new AllergyIntolerance();
ai2.setStatus(AllergyIntoleranceStatus.CONFIRMED);
String id2 = myAllergyIntoleranceDao.create(ai2, mySrd).getId().toUnqualifiedVersionless().getValue();
AllergyIntolerance ai3 = new AllergyIntolerance();
ai3.setStatus(AllergyIntoleranceStatus.INACTIVE);
String id3 = myAllergyIntoleranceDao.create(ai3, mySrd).getId().toUnqualifiedVersionless().getValue();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, AllergyIntoleranceStatus.ACTIVE.toCode()));
assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1));
params = new SearchParameterMap();
params.add(AllergyIntolerance.SP_STATUS, new TokenParam(null, AllergyIntoleranceStatus.ACTIVE.toCode()).setModifier(TokenParamModifier.BELOW));
assertThat(toUnqualifiedVersionlessIdValues(myAllergyIntoleranceDao.search(params)), containsInAnyOrder(id1, id2));
@ -618,14 +701,13 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
@Test
@Ignore
public void testSearchCodeInEmptyValueSet() {
ValueSet valueSet = new ValueSet();
valueSet.setUrl(URL_MY_VALUE_SET);
myValueSetDao.create(valueSet, mySrd);
Observation obsAA = new Observation();
obsAA.setStatus(ObservationStatus.FINAL);
obsAA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("AA");
@ -642,11 +724,11 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
myObservationDao.create(obsCA, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
params.add(Observation.SP_STATUS, new TokenParam(null, "final"));
@ -656,7 +738,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
@Test
public void testSearchCodeInExternalCodesystem() {
createExternalCsAndLocalVs();
Observation obsPA = new Observation();
obsPA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("ParentA");
IIdType idPA = myObservationDao.create(obsPA, mySrd).getId().toUnqualifiedVersionless();
@ -673,7 +755,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
obsCA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("CA");
IIdType idCA = myObservationDao.create(obsCA, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap params = new SearchParameterMap();
SearchParameterMap params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "childAA").setModifier(TokenParamModifier.BELOW));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(idAAA.getValue(), idAAB.getValue()));
@ -684,17 +766,17 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(idPA.getValue(), idAAA.getValue(), idAAB.getValue()));
}
@Test
public void testSearchCodeInFhirCodesystem() {
createLocalCsAndVs();
AuditEvent aeIn1 = new AuditEvent();
aeIn1.getType().setSystem("http://nema.org/dicom/dicm").setCode("110102");
IIdType idIn1 = myAuditEventDao.create(aeIn1, mySrd).getId().toUnqualifiedVersionless();
AuditEvent aeIn2 = new AuditEvent();
aeIn2.getType().setSystem("http://hl7.org/fhir/audit-event-type").setCode("rest");
IIdType idIn2 = myAuditEventDao.create(aeIn2, mySrd).getId().toUnqualifiedVersionless();
@ -705,17 +787,17 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
SearchParameterMap params = new SearchParameterMap();
params.add(AuditEvent.SP_TYPE, new TokenParam(null, "http://hl7.org/fhir/ValueSet/audit-event-type").setModifier(TokenParamModifier.IN));
assertThat(toUnqualifiedVersionlessIdValues(myAuditEventDao.search(params)), containsInAnyOrder(idIn1.getValue(), idIn2.getValue()));
assertThat(toUnqualifiedVersionlessIdValues(myAuditEventDao.search(params)), containsInAnyOrder(idIn1.getValue(), idIn2.getValue()));
params = new SearchParameterMap();
params.add(AuditEvent.SP_TYPE, new TokenParam(null, "http://hl7.org/fhir/ValueSet/v3-PurposeOfUse").setModifier(TokenParamModifier.IN));
assertThat(toUnqualifiedVersionlessIdValues(myAuditEventDao.search(params)), empty());
assertThat(toUnqualifiedVersionlessIdValues(myAuditEventDao.search(params)), empty());
}
@Test
public void testSearchCodeInLocalCodesystem() {
createLocalCsAndVs();
Observation obsAA = new Observation();
obsAA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("AA");
IIdType idAA = myObservationDao.create(obsAA, mySrd).getId().toUnqualifiedVersionless();
@ -731,9 +813,8 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
SearchParameterMap params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(idAA.getValue(), idBA.getValue()));
}
}
private ArrayList<String> toCodesContains(List<ValueSetExpansionContainsComponent> theContains) {
ArrayList<String> retVal = new ArrayList<String>();
@ -743,13 +824,9 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
return retVal;
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

2
hapi-fhir-structures-dstu/src/main/java/ca/uhn/fhir/rest/server/audit/IResourceAuditor.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.rest.server.audit;
/*
* #%L
* HAPI FHIR - Core Library
* HAPI FHIR Structures - DSTU1 (FHIR v0.80)
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%