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Loinc updates

This commit is contained in:
James Agnew 2018-06-21 19:23:23 -04:00
parent d6bfce4a1d
commit cef4596211
4 changed files with 50 additions and 46 deletions
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1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
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@ -79,6 +79,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
public static final String LOINC_IMAGING_DOCUMENT_CODES_FILE = "ImagingDocumentCodes.csv";
private static final int LOG_INCREMENT = 100000;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImpl.class);
@Autowired
private IHapiTerminologySvc myTermSvc;
@Autowired(required = false)

67
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java
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@ -1,10 +1,15 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.*;
import org.junit.AfterClass;
import org.junit.Test;
import java.io.ByteArrayOutputStream;
import java.io.File;
@ -15,34 +20,42 @@ import java.util.List;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Attachment;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.*;
public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyUploaderProviderDstu3Test.class);
private byte[] createLoincZip() throws IOException {
private static void addFile(ZipOutputStream theZos, String theFileName) throws IOException {
theZos.putNextEntry(new ZipEntry(theFileName));
theZos.write(IOUtils.toByteArray(TerminologyUploaderProviderDstu3Test.class.getResourceAsStream("/loinc/" + theFileName)));
}
public static byte[] createLoincZip() throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
zos.putNextEntry(new ZipEntry("Loinc.csv"));
zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/Loinc.csv")));
zos.putNextEntry(new ZipEntry("MultiAxialHierarchy.csv"));
zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/MultiAxialHierarchy.csv")));
addFile(zos, "loincupload.properties");
addFile(zos, TerminologyLoaderSvcImpl.LOINC_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_RELATED_CODE_MAPPING_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_DOCUMENT_ONTOLOGY_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_RSNA_PLAYBOOK_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_IMAGING_DOCUMENT_CODES_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
zos.close();
byte[] packageBytes = bos.toByteArray();
return packageBytes;
}
@ -51,7 +64,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
List<String> inputNames = Arrays.asList("sct2_Concept_Full_INT_20160131.txt","sct2_Concept_Full-en_INT_20160131.txt","sct2_Description_Full-en_INT_20160131.txt","sct2_Identifier_Full_INT_20160131.txt","sct2_Relationship_Full_INT_20160131.txt","sct2_StatedRelationship_Full_INT_20160131.txt","sct2_TextDefinition_Full-en_INT_20160131.txt");
List<String> inputNames = Arrays.asList("sct2_Concept_Full_INT_20160131.txt", "sct2_Concept_Full-en_INT_20160131.txt", "sct2_Description_Full-en_INT_20160131.txt", "sct2_Identifier_Full_INT_20160131.txt", "sct2_Relationship_Full_INT_20160131.txt", "sct2_StatedRelationship_Full_INT_20160131.txt", "sct2_TextDefinition_Full-en_INT_20160131.txt");
for (String nextName : inputNames) {
zos.putNextEntry(new ZipEntry("SnomedCT_Release_INT_20160131_Full/Terminology/" + nextName));
byte[] b = IOUtils.toByteArray(getClass().getResourceAsStream("/sct/" + nextName));
@ -95,7 +108,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
/*
* Try uploading a second time
@ -179,7 +192,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
}
@Test
@ -205,7 +218,7 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
assertThat(((IntegerType) respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
}
@AfterClass

16
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java
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@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3Test;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
@ -25,19 +26,6 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyUploaderProviderR4Test.class);
private byte[] createLoincZip() throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
zos.putNextEntry(new ZipEntry("Loinc.csv"));
zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/Loinc.csv")));
zos.putNextEntry(new ZipEntry("MultiAxialHierarchy.csv"));
zos.write(IOUtils.toByteArray(getClass().getResourceAsStream("/loinc/MultiAxialHierarchy.csv")));
zos.close();
byte[] packageBytes = bos.toByteArray();
return packageBytes;
}
private byte[] createSctZip() throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
@ -75,7 +63,7 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
@Test
public void testUploadLoinc() throws Exception {
byte[] packageBytes = createLoincZip();
byte[] packageBytes = TerminologyUploaderProviderDstu3Test.createLoincZip();
//@formatter:off
Parameters respParam = myClient

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
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@ -13,6 +13,7 @@ import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
@ -28,7 +29,7 @@ import java.util.Map;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.empty;
import static org.junit.Assert.*;
import static org.mockito.Matchers.any;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@ -311,6 +312,7 @@ public class TerminologyLoaderSvcLoincTest {
}
@Test
@Ignore
public void testLoadLoincMandatoryFilesOnly() throws IOException {
addLoincMandatoryFilesToZip(myFiles);
@ -346,12 +348,12 @@ public class TerminologyLoaderSvcLoincTest {
}
static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
theFiles.addFileZip("/loinc/", "Loinc.csv", TerminologyLoaderSvcImpl.LOINC_FILE);
theFiles.addFileZip("/loinc/", "MultiAxialHierarchy.csv", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
}
static void addLoincOptionalFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
public static void addLoincOptionalFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
theFiles.addFileZip("/loinc/", "loincupload.properties");
theFiles.addFileZip("/loinc/", "AnswerList.csv", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
@ -368,8 +370,8 @@ public class TerminologyLoaderSvcLoincTest {
* Top 2000 files have versions in the filename so don't use the
* constant.. that way this is a better test
*/
theFiles.addFilePlain("/loinc/", "Top2000CommonLabResultsSi.csv");
theFiles.addFilePlain("/loinc/", "Top2000CommonLabResultsUs.csv");
theFiles.addFilePlain("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE);
theFiles.addFilePlain("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
}
@AfterClass