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Merge branch 'loinc_loader_update' of github.com:jamesagnew/hapi-fhir into loinc_loader_update

This commit is contained in:
James Agnew 2018-04-06 09:13:08 -04:00
parent 832558b411 2c818d5b4a
commit f0f93d2330
44 changed files with 128 additions and 132 deletions
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1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java
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@ -51,6 +51,7 @@ import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.UrlUtil.UrlParts;
import com.google.common.collect.ArrayListMultimap;
import javolution.io.Struct;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.hl7.fhir.instance.model.api.*;

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -130,6 +130,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
}
}
private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincTop2000LabResultsSiHandler.java
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@ -29,8 +29,8 @@ import java.util.Map;
public class LoincTop2000LabResultsSiHandler extends BaseLoincTop2000LabResultsHandler {
public static final String TOP_2000_SI_VS_ID = "TOP-2000-LABRESULTS-SI";
public static final String TOP_2000_SI_VS_URI = "http://loinc.org/top-2000-lab-results-si";
public static final String TOP_2000_SI_VS_ID = "top-2000-lab-observations-si";
public static final String TOP_2000_SI_VS_URI = "http://loinc.org/vs/top-2000-lab-observations-si";
public static final String TOP_2000_SI_VS_NAME = "Top 2000 Lab Results SI";
public LoincTop2000LabResultsSiHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincTop2000LabResultsUsHandler.java
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@ -29,8 +29,8 @@ import java.util.Map;
public class LoincTop2000LabResultsUsHandler extends BaseLoincTop2000LabResultsHandler {
public static final String TOP_2000_US_VS_ID = "TOP-2000-LABRESULTS-US";
public static final String TOP_2000_US_VS_URI = "http://loinc.org/top-2000-lab-results-us";
public static final String TOP_2000_US_VS_ID = "top-2000-lab-observations-us";
public static final String TOP_2000_US_VS_URI = "http://loinc.org/vs/top-2000-lab-observations-us";
public static final String TOP_2000_US_VS_NAME = "Top 2000 Lab Results US";
public LoincTop2000LabResultsUsHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UniqueSearchParamTest.java
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@ -18,6 +18,7 @@ import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.test.context.TestPropertySource;
import java.util.Collections;
import java.util.List;
@ -27,6 +28,11 @@ import static org.hamcrest.Matchers.empty;
import static org.junit.Assert.*;
@SuppressWarnings({"unchecked", "deprecation"})
@TestPropertySource(properties = {
// Since scheduled tasks can cause searches, which messes up the
// value returned by SearchBuilder.getLastHandlerMechanismForUnitTest()
"scheduling_disabled=true"
})
public class FhirResourceDaoDstu3UniqueSearchParamTest extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3UniqueSearchParamTest.class);

78
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java
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@ -1,31 +1,19 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.io.IOException;
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.Coding;
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 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;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
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;
import java.io.IOException;
import static org.junit.Assert.*;
public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDstu3Test {
@ -58,31 +46,31 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals(("SYSTEM NAME"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
assertEquals(("SYSTEM NAME"), ((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("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());
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();
.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(("SYSTEM NAME"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
assertEquals(("SYSTEM NAME"), ((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("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());
assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue().booleanValue());
}
@ -100,11 +88,11 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals(("Unknown"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals("Accession ID", ((StringType)respParam.getParameter().get(1).getValue()).getValue());
assertEquals("Accession ID", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(2).getName());
assertEquals(false, ((BooleanType)respParam.getParameter().get(2).getValue()).getValue().booleanValue());
assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue().booleanValue());
}
@Test
@ -141,11 +129,11 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals(("Unknown"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals(("Systolic blood pressure--expiration"), ((StringType)respParam.getParameter().get(1).getValue()).getValue());
assertEquals(("Systolic blood pressure--expiration"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(2).getName());
assertEquals(false, ((BooleanType)respParam.getParameter().get(2).getValue()).getValue().booleanValue());
assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue().booleanValue());
}
@Test
@ -181,11 +169,11 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals(("Unknown"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
assertEquals(("Unknown"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals(("Systolic blood pressure--expiration"), ((StringType)respParam.getParameter().get(1).getValue()).getValue());
assertEquals(("Systolic blood pressure--expiration"), ((StringType) respParam.getParameter().get(1).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(2).getName());
assertEquals(false, ((BooleanType)respParam.getParameter().get(2).getValue()).getValue().booleanValue());
assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).getValue().booleanValue());
}
@Test
@ -259,11 +247,11 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
ourLog.info(resp);
assertEquals("name", respParam.getParameter().get(0).getName());
assertEquals("Unknown", ((StringType)respParam.getParameter().get(0).getValue()).getValue());
assertEquals("Unknown", ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("display", respParam.getParameter().get(1).getName());
assertEquals("Married", ((StringType)respParam.getParameter().get(1).getValue()).getValue());
assertEquals("Married", ((StringType) respParam.getParameter().get(1).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(2).getName());
assertEquals(false, ((BooleanType)respParam.getParameter().get(2).getValue()).booleanValue());
assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).booleanValue());
}
@AfterClass

2
pom.xml
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@ -998,7 +998,7 @@
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.20.0-GA</version>
<version>3.22.0-GA</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>