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Merge remote-tracking branch 'refs/remotes/jamesagnew/master'

This commit is contained in:
Hugo Soares 2017-01-20 11:22:21 +00:00
parent c9e11f64aa d1542e98c5
commit 1dd0b01e81
13 changed files with 118 additions and 42 deletions
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19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
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@ -119,21 +119,12 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
system = theSystem.getValue();
}
// CodeValidationResult validateOutcome = myJpaValidationSupport.validateCode(getContext(), system, code, null);
//
// LookupCodeResult result = new LookupCodeResult();
// result.setSearchedForCode(code);
// result.setSearchedForSystem(system);
// result.setFound(false);
// if (validateOutcome.isOk()) {
// result.setFound(true);
// result.setCodeIsAbstract(validateOutcome.asConceptDefinition().getAbstract());
// result.setCodeDisplay(validateOutcome.asConceptDefinition().getDisplay());
// }
// return result;
ourLog.info("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(getContext(), system)) {
ourLog.info("Code system {} is supported", system);
CodeValidationResult result = myValidationSupport.validateCode(getContext(), system, code, null);
if (result != null) {
if (result.isOk()) {

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
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@ -74,7 +74,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
protected IFhirResourceDao<CarePlan> myCarePlanDao;
@Autowired
@Qualifier("myCodeSystemDaoDstu3")
protected IFhirResourceDao<CodeSystem> myCodeSystemDao;
protected IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
@Autowired
@Qualifier("myCompartmentDefinitionDaoDstu3")
protected IFhirResourceDao<CompartmentDefinition> myCompartmentDefinitionDao;

29
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
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@ -11,15 +11,11 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.dstu3.model.AllergyIntolerance;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
import org.hl7.fhir.dstu3.model.AuditEvent;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetComposeComponent;
@ -32,6 +28,7 @@ import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
@ -159,6 +156,28 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
}
@Test
public void testLookupSnomed() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl("http://snomed.info/sct");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", cs);
StringType code = new StringType("ParentA");
StringType system = new StringType("http://snomed.info/sct");
LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
assertEquals(true, outcome.isFound());
}
@Test
public void testCodeSystemWithDefinedCodes() {
//@formatter:off

46
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java
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@ -23,6 +23,7 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.TestUtil;
@ -48,10 +49,52 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
}
@Test
public void testLookupOnExternalCode() {
ResourceProviderDstu3ValueSetTest.createExternalCs(myCodeSystemDao, myResourceTableDao, myTermSvc, mySrd);
Parameters respParam = ourClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("ParentA"))
.andParameter("system", new UriType(FhirResourceDaoDstu3TerminologyTest.URL_MY_CODE_SYSTEM))
.execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals(("Unknown"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals("Parent A", ((StringType)respParam.getParameter().get(1).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(2).getName());
assertEquals(false, ((BooleanType)respParam.getParameter().get(2).getValue()).getValue().booleanValue());
// With HTTP GET
respParam = ourClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("ParentA"))
.andParameter("system", new UriType(FhirResourceDaoDstu3TerminologyTest.URL_MY_CODE_SYSTEM))
.useHttpGet()
.execute();
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals(("Unknown"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals("Parent A", ((StringType)respParam.getParameter().get(1).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(2).getName());
assertEquals(false, ((BooleanType)respParam.getParameter().get(2).getValue()).getValue().booleanValue());
}
@Test
public void testLookupOperationByCodeAndSystemBuiltInCode() {
//@formatter:off
Parameters respParam = ourClient
.operation()
.onType(CodeSystem.class)
@ -59,7 +102,6 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
.withParameter(Parameters.class, "code", new CodeType("ACSN"))
.andParameter("system", new UriType("http://hl7.org/fhir/v2/0203"))
.execute();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);

34
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
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@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.*;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.URL_MY_VALUE_SET;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
import static org.hamcrest.Matchers.not;
@ -18,30 +19,27 @@ import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3Test {
@ -87,12 +85,20 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
}
private CodeSystem createExternalCs() {
IFhirResourceDao<CodeSystem> codeSystemDao = myCodeSystemDao;
IResourceTableDao resourceTableDao = myResourceTableDao;
IHapiTerminologySvc termSvc = myTermSvc;
return createExternalCs(codeSystemDao, resourceTableDao, termSvc, mySrd);
}
public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, IHapiTerminologySvc theTermSvc, ServletRequestDetails theRequestDetails) {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
ResourceTable table = theResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
@ -116,7 +122,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
cs.getConcepts().add(parentB);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, cs);
theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, cs);
return codeSystem;
}

8
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/DbServerConfig.java Normal file
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@ -0,0 +1,8 @@
package ca.uhn.fhirtest.config;
import org.springframework.context.annotation.Configuration;
@Configuration
public class DbServerConfig {
}

1
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu2Config.java
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@ -68,7 +68,6 @@ public class TdlDstu2Config extends BaseJavaConfigDstu2 {
}
@Bean(name = "myPersistenceDataSourceDstu1", destroyMethod = "close")
@DependsOn("dbServer")
public DataSource dataSource() {
BasicDataSource retVal = new BasicDataSource();
// retVal.setDriver(new org.apache.derby.jdbc.ClientDriver());

1
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu3Config.java
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@ -65,7 +65,6 @@ public class TdlDstu3Config extends BaseJavaConfigDstu3 {
}
@Bean(name = "myPersistenceDataSourceDstu3", destroyMethod = "close")
@DependsOn("dbServer")
public DataSource dataSource() {
BasicDataSource retVal = new BasicDataSource();
// retVal.setDriver(new org.apache.derby.jdbc.ClientDriver());

1
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java
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@ -70,7 +70,6 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
}
@Bean(name = "myPersistenceDataSourceDstu1", destroyMethod = "close")
@DependsOn("dbServer")
public DataSource dataSource() {
BasicDataSource retVal = new BasicDataSource();
retVal.setDriver(new org.postgresql.Driver());

1
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java
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@ -74,7 +74,6 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
}
@Bean(name = "myPersistenceDataSourceDstu3", destroyMethod = "close")
@DependsOn("dbServer")
public DataSource dataSource() {
BasicDataSource retVal = new BasicDataSource();
retVal.setDriver(new org.postgresql.Driver());

3
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/validation/DefaultProfileValidationSupport.java
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@ -10,6 +10,7 @@ import org.apache.commons.io.Charsets;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
@ -142,7 +143,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
@Override
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
CodeSystem cs = fetchCodeSystem(theContext, theSystem);
return cs != null;
return cs != null && cs.getContent() != CodeSystemContentMode.NOTPRESENT;
}
private void loadCodeSystems(FhirContext theContext, Map<String, CodeSystem> theCodeSystems, Map<String, ValueSet> theValueSets, String theClasspath) {

11
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/validation/ValidationSupportChain.java
View File

@ -17,6 +17,8 @@ import ca.uhn.fhir.context.FhirContext;
public class ValidationSupportChain implements IValidationSupport {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidationSupportChain.class);
private List<IValidationSupport> myChain;
/**
@ -97,9 +99,16 @@ public class ValidationSupportChain implements IValidationSupport {
@Override
public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
ourLog.info("Validating code {} in chain with {} items", theCode, myChain.size());
for (IValidationSupport next : myChain) {
if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
return next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
CodeValidationResult result = next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
ourLog.info("Chain item {} returned outcome {}", next, result.isOk());
return result;
} else {
ourLog.info("Chain item {} does not support code system {}", next, theCodeSystem);
}
}
return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);

4
src/changes/changes.xml
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@ -213,6 +213,10 @@
Server AuthorizationInterceptor always rejects history operation
at the type level even if rules should allow it.
</action>
<action type="fix">
JPA server terminology service was not correctly validating or expanding codes
in SNOMED CT or LOINC code systems. Thanks to David Hay for reporting!
</action>
</release>
<release version="2.1" date="2016-11-11">
<action type="add">