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

Work on terminology service

This commit is contained in:
jamesagnew 2016-06-04 12:16:33 -04:00
parent 9fc6272951
commit f4b9c6423c
9 changed files with 532 additions and 382 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

66
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -39,6 +39,7 @@ import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
@ -53,6 +54,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@ -70,12 +72,15 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
return retVal;
}
private ValueSet doExpand(ValueSet source, String theFilter) {
private ValueSet doExpand(ValueSet theSource, String theFilter) {
validateIncludes("include", theSource.getCompose().getInclude());
validateIncludes("exclude", theSource.getCompose().getExclude());
HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
String filterLc = theFilter != null ? theFilter.toLowerCase() : null;
ValueSetExpansionOutcome outcome = workerContext.expand(source);
ValueSetExpansionOutcome outcome = workerContext.expand(theSource);
ValueSetExpansionComponent expansion = outcome.getValueset().getExpansion();
if (isNotBlank(theFilter)) {
for (Iterator<ValueSetExpansionContainsComponent> containsIter = expansion.getContains().iterator(); containsIter.hasNext();) {
@ -91,6 +96,14 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
return retVal;
}
private void validateIncludes(String name, List<ConceptSetComponent> listToValidate) {
for (ConceptSetComponent nextExclude : listToValidate) {
if (isBlank(nextExclude.getSystem()) && !ElementUtil.isEmpty(nextExclude.getConcept(), nextExclude.getFilter())) {
throw new InvalidRequestException("ValueSet contains " + name + " criteria with no system defined");
}
}
}
@Override
public ValueSet expandByIdentifier(String theUri, String theFilter) {
if (isBlank(theUri)) {
@ -120,55 +133,6 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
ValueSet retVal = doExpand(source, theFilter);
return retVal;
// ValueSet retVal = new ValueSet();
// retVal.setDate(new Date());
//
// /*
// * Add composed concepts
// */
//
// for (ConceptSetComponent nextInclude : source.getCompose().getInclude()) {
// if (nextInclude.getConcept().isEmpty()) {
//
// } else {
// for (ConceptReferenceComponent next : nextInclude.getConcept()) {
// if (isBlank(theFilter)) {
// addCompose(retVal, nextInclude.getSystem(), next.getCode(), next.getDisplay());
// } else {
// String filter = theFilter.toLowerCase();
// if (next.getDisplay().toLowerCase().contains(filter) || next.getCode().toLowerCase().contains(filter)) {
// addCompose(retVal, nextInclude.getSystem(), next.getCode(), next.getDisplay());
// }
// }
// }
// }
// }
//
// return retVal;
}
private void addCompose(String theFilter, ValueSet theValueSetToPopulate, ValueSet theSourceValueSet, ConceptDefinitionComponent theConcept, String theSystem) {
if (isBlank(theFilter)) {
addCompose(theValueSetToPopulate, theSystem, theConcept.getCode(), theConcept.getDisplay());
} else {
String filter = theFilter.toLowerCase();
if (theConcept.getDisplay().toLowerCase().contains(filter) || theConcept.getCode().toLowerCase().contains(filter)) {
addCompose(theValueSetToPopulate, theSystem, theConcept.getCode(), theConcept.getDisplay());
}
}
for (ConceptDefinitionComponent nextChild : theConcept.getConcept()) {
addCompose(theFilter, theValueSetToPopulate, theSourceValueSet, nextChild, theSystem);
}
}
private void addCompose(ValueSet retVal, String theSystem, String theCode, String theDisplay) {
if (isBlank(theCode)) {
return;
}
ValueSetExpansionContainsComponent contains = retVal.getExpansion().addContains();
contains.setSystem(theSystem);
contains.setCode(theCode);
contains.setDisplay(theDisplay);
}
@Override

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3.java
View File

@ -68,6 +68,8 @@ public class TerminologyUploaderProviderDstu3 extends BaseJpaProvider {
UploadStatistics stats;
if (IHapiTerminologyLoaderSvc.SCT_URL.equals(url)) {
stats = myTerminologyLoaderSvc.loadSnomedCt(data, theRequestDetails);
} else if (IHapiTerminologyLoaderSvc.LOINC_URL.equals(url)) {
stats = myTerminologyLoaderSvc.loadLoinc(data, theRequestDetails);
} else {
throw new InvalidRequestException("Unknown URL: " + url);
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java
View File

@ -4,21 +4,24 @@ import ca.uhn.fhir.rest.method.RequestDetails;
public interface IHapiTerminologyLoaderSvc {
String LOINC_URL = "http://loinc.org";
String SCT_URL = "http://snomed.info/sct";
UploadStatistics loadLoinc(byte[] theZipBytes, RequestDetails theRequestDetails);
UploadStatistics loadSnomedCt(byte[] theZipBytes, RequestDetails theRequestDetails);
public static class UploadStatistics {
private int myConceptCount;
private final int myConceptCount;
public UploadStatistics(int theConceptCount) {
myConceptCount = theConceptCount;
}
public int getConceptCount() {
return myConceptCount;
}
public UploadStatistics setConceptCount(int theConceptCount) {
myConceptCount = theConceptCount;
return this;
}
}
}

227
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvc.java
View File

@ -1,5 +1,7 @@
package ca.uhn.fhir.jpa.term;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
* HAPI FHIR JPA Server
@ -45,9 +47,11 @@ import java.util.zip.ZipInputStream;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.csv.QuoteMode;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.springframework.beans.factory.annotation.Autowired;
import com.google.common.annotations.VisibleForTesting;
@ -58,17 +62,26 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CoverageIgnore;
public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
public static final String LOINC_FILE = "loinc.csv";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvc.class);
static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full";
static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full";
static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
@Autowired
private IHapiTerminologySvc myTermSvc;
private void cleanUpTemporaryFiles(Map<String, File> filenameToFile) {
ourLog.info("Finished terminology file import, cleaning up temporary files");
for (File nextFile : filenameToFile.values()) {
nextFile.delete();
}
}
private void dropCircularRefs(TermConcept theConcept, LinkedHashSet<String> theChain, Map<String, TermConcept> theCode2concept) {
@ -101,56 +114,7 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
}
private TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
TermConcept concept = id2concept.get(id);
if (concept == null) {
concept = new TermConcept();
id2concept.put(id, concept);
concept.setCodeSystem(codeSystemVersion);
}
return concept;
}
private void iterateOverZipFile(Map<String, File> theFilenameToFile, String fileNamePart, IRecordHandler handler) {
for (Entry<String, File> nextEntry : theFilenameToFile.entrySet()) {
if (nextEntry.getKey().contains(fileNamePart)) {
ourLog.info("Processing file {}", nextEntry.getKey());
Reader reader = null;
CSVParser parsed = null;
try {
reader = new BufferedReader(new FileReader(nextEntry.getValue()));
parsed = new CSVParser(reader, CSVFormat.newFormat('\t').withFirstRecordAsHeader());
Iterator<CSVRecord> iter = parsed.iterator();
ourLog.debug("Header map: {}", parsed.getHeaderMap());
int count = 0;
int logIncrement = 100000;
int nextLoggedCount = logIncrement;
while (iter.hasNext()) {
CSVRecord nextRecord = iter.next();
handler.accept(nextRecord);
count++;
if (count >= nextLoggedCount) {
ourLog.info(" * Processed {} records in {}", count, fileNamePart);
nextLoggedCount += logIncrement;
}
}
} catch (IOException e) {
throw new InternalErrorException(e);
} finally {
IOUtils.closeQuietly(parsed);
IOUtils.closeQuietly(reader);
}
}
}
}
@Override
public UploadStatistics loadSnomedCt(byte[] theZipBytes, RequestDetails theRequestDetails) {
List<String> allFilenames = Arrays.asList(SCT_FILE_DESCRIPTION, SCT_FILE_RELATIONSHIP, SCT_FILE_CONCEPT);
private Map<String, File> extractFiles(byte[] theZipBytes, List<String> theExpectedFilenameFragments) {
Map<String, File> filenameToFile = new HashMap<String, File>();
ZipInputStream zis = new ZipInputStream(new BufferedInputStream(new ByteArrayInputStream(theZipBytes)));
try {
@ -158,7 +122,7 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
ZippedFileInputStream inputStream = new ZippedFileInputStream(zis);
boolean want = false;
for (String next : allFilenames) {
for (String next : theExpectedFilenameFragments) {
if (nextEntry.getName().contains(next)) {
want = true;
}
@ -188,18 +152,112 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
IOUtils.closeQuietly(zis);
}
if (filenameToFile.size() != theExpectedFilenameFragments.size()) {
throw new InvalidRequestException("Invalid input zip file, expected zip to contain the following name fragments: " + theExpectedFilenameFragments + " but found: " + filenameToFile.keySet());
}
return filenameToFile;
}
private TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
TermConcept concept = id2concept.get(id);
if (concept == null) {
concept = new TermConcept();
id2concept.put(id, concept);
concept.setCodeSystem(codeSystemVersion);
}
return concept;
}
private void iterateOverZipFile(Map<String, File> theFilenameToFile, String fileNamePart, IRecordHandler handler, char theDelimiter, QuoteMode theQuoteMode) {
boolean found = false;
for (Entry<String, File> nextEntry : theFilenameToFile.entrySet()) {
if (nextEntry.getKey().contains(fileNamePart)) {
ourLog.info("Processing file {}", nextEntry.getKey());
found = true;
Reader reader = null;
CSVParser parsed = null;
try {
reader = new BufferedReader(new FileReader(nextEntry.getValue()));
CSVFormat format = CSVFormat.newFormat(theDelimiter).withFirstRecordAsHeader();
if (theQuoteMode != null) {
format = format.withQuote('"').withQuoteMode(theQuoteMode);
}
parsed = new CSVParser(reader, format);
Iterator<CSVRecord> iter = parsed.iterator();
ourLog.debug("Header map: {}", parsed.getHeaderMap());
int count = 0;
int logIncrement = 100000;
int nextLoggedCount = logIncrement;
while (iter.hasNext()) {
CSVRecord nextRecord = iter.next();
handler.accept(nextRecord);
count++;
if (count >= nextLoggedCount) {
ourLog.info(" * Processed {} records in {}", count, fileNamePart);
nextLoggedCount += logIncrement;
}
}
} catch (IOException e) {
throw new InternalErrorException(e);
} finally {
IOUtils.closeQuietly(parsed);
IOUtils.closeQuietly(reader);
}
}
}
// This should always be true, but just in case we've introduced a bug...
Validate.isTrue(found);
}
@Override
public UploadStatistics loadLoinc(byte[] theZipBytes, RequestDetails theRequestDetails) {
List<String> expectedFilenameFragments = Arrays.asList(LOINC_FILE);
Map<String, File> filenameToFile = extractFiles(theZipBytes, expectedFilenameFragments);
ourLog.info("Beginning LOINC processing");
try {
return processLoincFiles(filenameToFile, theRequestDetails);
} finally {
cleanUpTemporaryFiles(filenameToFile);
}
}
@Override
public UploadStatistics loadSnomedCt(byte[] theZipBytes, RequestDetails theRequestDetails) {
List<String> expectedFilenameFragments = Arrays.asList(SCT_FILE_DESCRIPTION, SCT_FILE_RELATIONSHIP, SCT_FILE_CONCEPT);
Map<String, File> filenameToFile = extractFiles(theZipBytes, expectedFilenameFragments);
ourLog.info("Beginning SNOMED CT processing");
try {
return processSnomedCtFiles(filenameToFile, theRequestDetails);
} finally {
ourLog.info("Finished SNOMED CT file import, cleaning up temporary files");
for (File nextFile : filenameToFile.values()) {
nextFile.delete();
}
cleanUpTemporaryFiles(filenameToFile);
}
}
UploadStatistics processLoincFiles(Map<String, File> filenameToFile, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> code2concept = new HashMap<String, TermConcept>();
IRecordHandler handler = new LoincHandler(codeSystemVersion, code2concept);
iterateOverZipFile(filenameToFile, LOINC_FILE, handler, ',', QuoteMode.NON_NUMERIC);
ourLog.info("Have {} concepts", code2concept.size());
codeSystemVersion.getConcepts().addAll(code2concept.values());
myTermSvc.storeNewCodeSystemVersion(SCT_URL, codeSystemVersion, theRequestDetails);
return new UploadStatistics(code2concept.size());
}
UploadStatistics processSnomedCtFiles(Map<String, File> filenameToFile, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> id2concept = new HashMap<String, TermConcept>();
@ -207,18 +265,18 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
final Set<String> validConceptIds = new HashSet<String>();
IRecordHandler handler = new SctHandlerConcept(validConceptIds);
iterateOverZipFile(filenameToFile, SCT_FILE_CONCEPT, handler);
iterateOverZipFile(filenameToFile, SCT_FILE_CONCEPT, handler,'\t', null);
ourLog.info("Have {} valid concept IDs", validConceptIds.size());
handler = new SctHandlerDescription(validConceptIds, code2concept, id2concept, codeSystemVersion);
iterateOverZipFile(filenameToFile, SCT_FILE_DESCRIPTION, handler);
iterateOverZipFile(filenameToFile, SCT_FILE_DESCRIPTION, handler,'\t', null);
ourLog.info("Got {} concepts, cloning map", code2concept.size());
final HashMap<String, TermConcept> rootConcepts = new HashMap<String, TermConcept>(code2concept);
handler = new SctHandlerRelationship(codeSystemVersion, rootConcepts, code2concept);
iterateOverZipFile(filenameToFile, SCT_FILE_RELATIONSHIP, handler);
iterateOverZipFile(filenameToFile, SCT_FILE_RELATIONSHIP, handler,'\t', null);
ourLog.info("Done loading SNOMED CT files - {} root codes, {} total codes", rootConcepts.size(), code2concept.size());
@ -229,14 +287,15 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
codeSystemVersion.getConcepts().addAll(rootConcepts.values());
myTermSvc.storeNewCodeSystemVersion(SCT_URL, codeSystemVersion, theRequestDetails);
return new UploadStatistics().setConceptCount(code2concept.size());
return new UploadStatistics(code2concept.size());
}
@VisibleForTesting
void setTermSvcForUnitTests(IHapiTerminologySvc theTermSvc) {
myTermSvc = theTermSvc;
}
@CoverageIgnore
public static void main(String[] args) throws Exception {
TerminologyLoaderSvc svc = new TerminologyLoaderSvc();
@ -254,6 +313,33 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
void accept(CSVRecord theRecord);
}
public class LoincHandler implements IRecordHandler {
private final Map<String, TermConcept> myCode2Concept;
private final TermCodeSystemVersion myCodeSystemVersion;
public LoincHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept) {
myCodeSystemVersion = theCodeSystemVersion;
myCode2Concept = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
String code = theRecord.get("LOINC_NUM");
String longCommonName = theRecord.get("LONG_COMMON_NAME");
String shortName = theRecord.get("SHORTNAME");
String consumerName = theRecord.get("CONSUMER_NAME");
String display = firstNonBlank(longCommonName, shortName, consumerName);
TermConcept concept = new TermConcept(myCodeSystemVersion, code);
concept.setDisplay(display);
Validate.isTrue(!myCode2Concept.containsKey(code));
myCode2Concept.put(code, concept);
}
}
private final class SctHandlerConcept implements IRecordHandler {
private Set<String> myValidConceptIds;
@ -436,4 +522,15 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
}
}
public String firstNonBlank(String... theStrings) {
String retVal = "";
for (String nextString : theStrings) {
if (isNotBlank(nextString)) {
retVal = nextString;
break;
}
}
return retVal;
}
}

45
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -339,6 +339,51 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
assertEquals(URL_MY_CODE_SYSTEM, result.getExpansion().getContains().get(idx).getSystem());
}
@Test
public void testExpandWithExcludeInExternalValueSet() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
ConceptSetComponent exclude = vs.getCompose().addExclude();
exclude.setSystem(URL_MY_CODE_SYSTEM);
exclude.addConcept().setCode("childAA");
exclude.addConcept().setCode("childAAA");
ValueSet result = myValueSetDao.expand(vs, null);
String encoded = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result);
ourLog.info(encoded);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("ParentA", "ParentB", "childAB", "childAAB"));
}
@Test
public void testExpandWithInvalidExclude() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
/*
* No system set on exclude
*/
ConceptSetComponent exclude = vs.getCompose().addExclude();
exclude.addConcept().setCode("childAA");
exclude.addConcept().setCode("childAAA");
try {
myValueSetDao.expand(vs, null);
fail();
} catch (InvalidRequestException e) {
assertEquals("ValueSet contains exclude criteria with no system defined", e.getMessage());
}
}
@Test
public void testExpandWithSystemAndCodesAndFilterKeywordInLocalValueSet() {
createLocalCsAndVs();

36
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyProviderDstu3Test.java → hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java
View File

@ -27,9 +27,9 @@ import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
public class TerminologyProviderDstu3Test extends BaseResourceProviderDstu3Test {
public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyProviderDstu3Test.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyUploaderProviderDstu3Test.class);
@AfterClass
public static void afterClassClearContext() {
@ -58,6 +58,26 @@ public class TerminologyProviderDstu3Test extends BaseResourceProviderDstu3Test
assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
}
@Test
public void testUploadLoinc() throws Exception {
byte[] packageBytes = createLoincZip();
//@formatter:off
Parameters respParam = ourClient
.operation()
.onServer()
.named("upload-external-code-system")
.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.LOINC_URL))
.andParameter("package", new Attachment().setData(packageBytes))
.execute();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
}
@Test
public void testUploadSctLocalFile() throws Exception {
byte[] packageBytes = createSctZip();
@ -154,4 +174,16 @@ public class TerminologyProviderDstu3Test extends BaseResourceProviderDstu3Test
return packageBytes;
}
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.close();
byte[] packageBytes = bos.toByteArray();
return packageBytes;
}
}

40
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIntegrationTest.java
View File

@ -1,40 +0,0 @@
package ca.uhn.fhir.jpa.term;
import java.io.File;
import java.util.HashMap;
import java.util.Map;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.util.TestUtil;
public class TerminologyLoaderSvcIntegrationTest extends BaseJpaDstu3Test {
private TerminologyLoaderSvc myLoader;
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Before
public void beforeInitTest() {
myLoader = new TerminologyLoaderSvc();
myLoader.setTermSvcForUnitTests(myTermSvc);
}
@Test
@Ignore
public void testLoadAndStoreSnomedCt() {
Map<String, File> files = new HashMap<String, File>();
files.put(TerminologyLoaderSvc.SCT_FILE_CONCEPT, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Concept_Full_INT_20160131.txt"));
files.put(TerminologyLoaderSvc.SCT_FILE_DESCRIPTION, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Description_Full-en_INT_20160131.txt"));
files.put(TerminologyLoaderSvc.SCT_FILE_RELATIONSHIP, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Relationship_Full_INT_20160131.txt"));
myLoader.processSnomedCtFiles(files, mySrd);
}
}

57
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcTest.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.term;
import static org.junit.Assert.*;
import static org.mockito.Mockito.mock;
import java.io.ByteArrayOutputStream;
@ -15,6 +16,7 @@ import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
public class TerminologyLoaderSvcTest {
@ -34,18 +36,31 @@ public class TerminologyLoaderSvcTest {
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Test
public void testLoadLoinc() throws Exception {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
addEntry(zos,"/loinc/", "loinc.csv");
zos.close();
ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
RequestDetails details = mock(RequestDetails.class);
mySvc.loadLoinc(bos.toByteArray(), details);
}
@Test
public void testLoadSnomedCt() throws Exception {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
addEntry(zos, "sct2_Concept_Full_INT_20160131.txt");
addEntry(zos, "sct2_Concept_Full-en_INT_20160131.txt");
addEntry(zos, "sct2_Description_Full-en_INT_20160131.txt");
addEntry(zos, "sct2_Identifier_Full_INT_20160131.txt");
addEntry(zos, "sct2_Relationship_Full_INT_20160131.txt");
addEntry(zos, "sct2_StatedRelationship_Full_INT_20160131.txt");
addEntry(zos, "sct2_TextDefinition_Full-en_INT_20160131.txt");
addEntry(zos, "/sct/", "sct2_Concept_Full_INT_20160131.txt");
addEntry(zos, "/sct/", "sct2_Concept_Full-en_INT_20160131.txt");
addEntry(zos, "/sct/", "sct2_Description_Full-en_INT_20160131.txt");
addEntry(zos, "/sct/", "sct2_Identifier_Full_INT_20160131.txt");
addEntry(zos,"/sct/", "sct2_Relationship_Full_INT_20160131.txt");
addEntry(zos,"/sct/", "sct2_StatedRelationship_Full_INT_20160131.txt");
addEntry(zos, "/sct/", "sct2_TextDefinition_Full-en_INT_20160131.txt");
zos.close();
ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
@ -54,10 +69,28 @@ public class TerminologyLoaderSvcTest {
mySvc.loadSnomedCt(bos.toByteArray(), details);
}
private void addEntry(ZipOutputStream zos, String fileName) throws IOException {
ourLog.info("Adding {} to test zip", fileName);
zos.putNextEntry(new ZipEntry("SnomedCT_Release_INT_20160131_Full/Terminology/" + fileName));
byte[] byteArray = IOUtils.toByteArray(getClass().getResourceAsStream("/sct/" + fileName));
@Test
public void testLoadSnomedCtBadInput() throws Exception {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
addEntry(zos, "/sct/", "sct2_StatedRelationship_Full_INT_20160131.txt");
zos.close();
ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
RequestDetails details = mock(RequestDetails.class);
try {
mySvc.loadSnomedCt(bos.toByteArray(), details);
fail();
} catch (InvalidRequestException e) {
assertEquals("Invalid input zip file, expected zip to contain the following name fragments: [Terminology/sct2_Description_Full-en, Terminology/sct2_Relationship_Full, Terminology/sct2_Concept_Full_] but found: []", e.getMessage());
}
}
private void addEntry(ZipOutputStream zos, String theClasspathPrefix, String theFileName) throws IOException {
ourLog.info("Adding {} to test zip", theFileName);
zos.putNextEntry(new ZipEntry("SnomedCT_Release_INT_20160131_Full/Terminology/" + theFileName));
byte[] byteArray = IOUtils.toByteArray(getClass().getResourceAsStream(theClasspathPrefix + theFileName));
Validate.notNull(byteArray);
zos.write(byteArray);
zos.closeEntry();

428
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/terminologies/ValueSetExpanderSimple.java
View File

@ -36,20 +36,22 @@ POSSIBILITY OF SUCH DAMAGE.
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.dstu3.exceptions.TerminologyServiceException;
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.DateTimeType;
import org.hl7.fhir.dstu3.model.Factory;
import org.hl7.fhir.dstu3.model.PrimitiveType;
import org.hl7.fhir.dstu3.model.Type;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.dstu3.model.ValueSet;
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.ValueSet.ConceptReferenceComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
@ -59,221 +61,233 @@ import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionParameterComponent;
import org.hl7.fhir.dstu3.utils.IWorkerContext;
import org.hl7.fhir.dstu3.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
public class ValueSetExpanderSimple implements ValueSetExpander {
private IWorkerContext context;
private List<ValueSetExpansionContainsComponent> codes = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
private Map<String, ValueSetExpansionContainsComponent> map = new HashMap<String, ValueSet.ValueSetExpansionContainsComponent>();
private ValueSet focus;
private List<ValueSetExpansionContainsComponent> codes = new ArrayList<ValueSet.ValueSetExpansionContainsComponent>();
private IWorkerContext context;
private Set<String> excludeKeys = new HashSet<String>();
private ValueSetExpanderFactory factory;
public ValueSetExpanderSimple(IWorkerContext context, ValueSetExpanderFactory factory) {
super();
this.context = context;
this.factory = factory;
}
@Override
public ValueSetExpansionOutcome expand(ValueSet source) {
private ValueSet focus;
try {
focus = source.copy();
focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
focus.getExpansion().setTimestampElement(DateTimeType.now());
focus.getExpansion().setIdentifier(Factory.createUUID());
private Map<String, ValueSetExpansionContainsComponent> map = new HashMap<String, ValueSet.ValueSetExpansionContainsComponent>();
if (source.hasCompose())
handleCompose(source.getCompose(), focus.getExpansion().getParameter());
for (ValueSetExpansionContainsComponent c : codes) {
if (map.containsKey(key(c))) {
focus.getExpansion().getContains().add(c);
}
}
return new ValueSetExpansionOutcome(focus, null);
} catch (RuntimeException e) {
// TODO: we should put something more specific instead of just Exception below, since
// it swallows bugs.. what would be expected to be caught there?
throw e;
} catch (Exception e) {
// well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
// that might fail too, but it might not, later.
return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage());
}
}
private void handleCompose(ValueSetComposeComponent compose, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException, ETooCostly, FileNotFoundException, IOException {
for (UriType imp : compose.getImport())
importValueSet(imp.getValue(), params);
for (ConceptSetComponent inc : compose.getInclude())
includeCodes(inc, params);
for (ConceptSetComponent inc : compose.getExclude())
excludeCodes(inc, params);
}
private void importValueSet(String value, List<ValueSetExpansionParameterComponent> params) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException {
if (value == null)
throw new TerminologyServiceException("unable to find value set with no identity");
ValueSet vs = context.fetchResource(ValueSet.class, value);
if (vs == null)
throw new TerminologyServiceException("Unable to find imported value set "+value);
ValueSetExpansionOutcome vso = factory.getExpander().expand(vs);
if (vso.getService() != null)
throw new TerminologyServiceException("Unable to expand imported value set "+value);
if (vs.hasVersion())
if (!existsInParams(params, "version", new UriType(vs.getUrl()+"?version="+vs.getVersion())))
params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl()+"?version="+vs.getVersion())));
for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
if (!existsInParams(params, p.getName(), p.getValue()))
params.add(p);
}
for (ValueSetExpansionContainsComponent c : vso.getValueset().getExpansion().getContains()) {
addCode(c.getSystem(), c.getCode(), c.getDisplay());
}
}
private boolean existsInParams(List<ValueSetExpansionParameterComponent> params, String name, Type value) {
for (ValueSetExpansionParameterComponent p : params) {
if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false))
return true;
}
return false;
}
private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException, ETooCostly {
CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
addCodes(context.expandVS(inc), params);
return;
}
if (cs == null)
throw new TerminologyServiceException("unable to find code system "+inc.getSystem().toString());
if (cs.getContent() != CodeSystemContentMode.COMPLETE)
throw new TerminologyServiceException("Code system "+inc.getSystem().toString()+" is incomplete");
if (cs.hasVersion())
if (!existsInParams(params, "version", new UriType(cs.getUrl()+"?version="+cs.getVersion())))
params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl()+"?version="+cs.getVersion())));
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def);
}
}
for (ConceptReferenceComponent c : inc.getConcept()) {
addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay());
}
if (inc.getFilter().size() > 1)
throw new TerminologyServiceException("Multiple filters not handled yet"); // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
if (inc.getFilter().size() == 1) {
ConceptSetFilterComponent fc = inc.getFilter().get(0);
if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
// special: all non-abstract codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw new TerminologyServiceException("Code '"+fc.getValue()+"' not found in system '"+inc.getSystem()+"'");
addCodeAndDescendents(cs, inc.getSystem(), def);
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def != null) {
if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
if (def.getDisplay().contains(fc.getValue())) {
addCode(inc.getSystem(), def.getCode(), def.getDisplay());
}
}
}
} else
throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
}
}
private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) throws ETooCostly {
if (expand.getContains().size() > 500)
throw new ETooCostly("Too many codes to display (>"+Integer.toString(expand.getContains().size())+")");
for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
if (!existsInParams(params, p.getName(), p.getValue()))
params.add(p);
}
for (ValueSetExpansionContainsComponent c : expand.getContains()) {
addCode(c.getSystem(), c.getCode(), c.getDisplay());
}
}
private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def) {
if (!CodeSystemUtilities.isDeprecated(cs, def)) {
if (!CodeSystemUtilities.isAbstract(cs, def))
addCode(system, def.getCode(), def.getDisplay());
for (ConceptDefinitionComponent c : def.getConcept())
addCodeAndDescendents(cs, system, c);
}
}
private void excludeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException {
CodeSystem cs = context.fetchCodeSystem(inc.getSystem().toString());
if (cs == null)
throw new TerminologyServiceException("unable to find value set "+inc.getSystem().toString());
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
// for (ConceptDefinitionComponent def : cs.getDefine().getConcept()) {
//!!!! addCodeAndDescendents(inc.getSystem(), def);
// }
}
for (ConceptReferenceComponent c : inc.getConcept()) {
// we don't need to check whether the codes are valid here- they can't have gotten into this list if they aren't valid
map.remove(key(inc.getSystem(), c.getCode()));
}
if (inc.getFilter().size() > 0)
throw new NotImplementedException("not done yet");
}
private String getCodeDisplay(CodeSystem cs, String code) throws TerminologyServiceException {
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), code);
if (def == null)
throw new TerminologyServiceException("Unable to find code '"+code+"' in code system "+cs.getUrl());
return def.getDisplay();
}
private ConceptDefinitionComponent getConceptForCode(List<ConceptDefinitionComponent> clist, String code) {
for (ConceptDefinitionComponent c : clist) {
if (code.equals(c.getCode()))
return c;
ConceptDefinitionComponent v = getConceptForCode(c.getConcept(), code);
if (v != null)
return v;
}
return null;
}
private String key(ValueSetExpansionContainsComponent c) {
return key(c.getSystem(), c.getCode());
}
private String key(String uri, String code) {
return "{"+uri+"}"+code;
public ValueSetExpanderSimple(IWorkerContext context, ValueSetExpanderFactory factory) {
super();
this.context = context;
this.factory = factory;
}
private void addCode(String system, String code, String display) {
ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
n.setSystem(system);
n.setCode(code);
n.setDisplay(display);
String s = key(n);
if (!map.containsKey(s)) {
codes.add(n);
map.put(s, n);
}
}
n.setCode(code);
n.setDisplay(display);
String s = key(n);
if (!map.containsKey(s) && !excludeKeys.contains(s)) {
codes.add(n);
map.put(s, n);
}
}
private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def) {
if (!CodeSystemUtilities.isDeprecated(cs, def)) {
if (!CodeSystemUtilities.isAbstract(cs, def))
addCode(system, def.getCode(), def.getDisplay());
for (ConceptDefinitionComponent c : def.getConcept())
addCodeAndDescendents(cs, system, c);
}
}
private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) throws ETooCostly {
if (expand.getContains().size() > 500)
throw new ETooCostly("Too many codes to display (>" + Integer.toString(expand.getContains().size()) + ")");
for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
if (!existsInParams(params, p.getName(), p.getValue()))
params.add(p);
}
for (ValueSetExpansionContainsComponent c : expand.getContains()) {
addCode(c.getSystem(), c.getCode(), c.getDisplay());
}
}
private void excludeCode(String theSystem, String theCode) {
ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
n.setSystem(theSystem);
n.setCode(theCode);
String s = key(n);
excludeKeys.add(s);
}
private void excludeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException {
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
return;
}
CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
excludeCodes(context.expandVS(inc), params);
return;
}
for (ConceptReferenceComponent c : inc.getConcept()) {
excludeCode(inc.getSystem(), c.getCode());
}
if (inc.getFilter().size() > 0)
throw new NotImplementedException("not done yet");
}
private void excludeCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) {
for (ValueSetExpansionContainsComponent c : expand.getContains()) {
excludeCode(c.getSystem(), c.getCode());
}
}
private boolean existsInParams(List<ValueSetExpansionParameterComponent> params, String name, Type value) {
for (ValueSetExpansionParameterComponent p : params) {
if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false))
return true;
}
return false;
}
@Override
public ValueSetExpansionOutcome expand(ValueSet source) {
try {
focus = source.copy();
focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
focus.getExpansion().setTimestampElement(DateTimeType.now());
focus.getExpansion().setIdentifier(Factory.createUUID());
if (source.hasCompose())
handleCompose(source.getCompose(), focus.getExpansion().getParameter());
for (ValueSetExpansionContainsComponent c : codes) {
if (map.containsKey(key(c))) {
focus.getExpansion().getContains().add(c);
}
}
return new ValueSetExpansionOutcome(focus, null);
} catch (RuntimeException e) {
// TODO: we should put something more specific instead of just Exception below, since
// it swallows bugs.. what would be expected to be caught there?
throw e;
} catch (Exception e) {
// well, we couldn't expand, so we'll return an interface to a checker that can check membership of the set
// that might fail too, but it might not, later.
return new ValueSetExpansionOutcome(new ValueSetCheckerSimple(source, factory, context), e.getMessage());
}
}
private String getCodeDisplay(CodeSystem cs, String code) throws TerminologyServiceException {
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), code);
if (def == null)
throw new TerminologyServiceException("Unable to find code '" + code + "' in code system " + cs.getUrl());
return def.getDisplay();
}
private ConceptDefinitionComponent getConceptForCode(List<ConceptDefinitionComponent> clist, String code) {
for (ConceptDefinitionComponent c : clist) {
if (code.equals(c.getCode()))
return c;
ConceptDefinitionComponent v = getConceptForCode(c.getConcept(), code);
if (v != null)
return v;
}
return null;
}
private void handleCompose(ValueSetComposeComponent compose, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException, ETooCostly, FileNotFoundException, IOException {
// Exclude comes first because we build up a map of things to exclude
for (ConceptSetComponent inc : compose.getExclude())
excludeCodes(inc, params);
for (UriType imp : compose.getImport())
importValueSet(imp.getValue(), params);
for (ConceptSetComponent inc : compose.getInclude())
includeCodes(inc, params);
}
private void importValueSet(String value, List<ValueSetExpansionParameterComponent> params) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException {
if (value == null)
throw new TerminologyServiceException("unable to find value set with no identity");
ValueSet vs = context.fetchResource(ValueSet.class, value);
if (vs == null)
throw new TerminologyServiceException("Unable to find imported value set " + value);
ValueSetExpansionOutcome vso = factory.getExpander().expand(vs);
if (vso.getService() != null)
throw new TerminologyServiceException("Unable to expand imported value set " + value);
if (vs.hasVersion())
if (!existsInParams(params, "version", new UriType(vs.getUrl() + "?version=" + vs.getVersion())))
params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "?version=" + vs.getVersion())));
for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
if (!existsInParams(params, p.getName(), p.getValue()))
params.add(p);
}
for (ValueSetExpansionContainsComponent c : vso.getValueset().getExpansion().getContains()) {
addCode(c.getSystem(), c.getCode(), c.getDisplay());
}
}
private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params) throws TerminologyServiceException, ETooCostly {
CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
addCodes(context.expandVS(inc), params);
return;
}
if (cs == null)
throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
if (cs.getContent() != CodeSystemContentMode.COMPLETE)
throw new TerminologyServiceException("Code system " + inc.getSystem().toString() + " is incomplete");
if (cs.hasVersion())
if (!existsInParams(params, "version", new UriType(cs.getUrl() + "?version=" + cs.getVersion())))
params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "?version=" + cs.getVersion())));
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def);
}
}
for (ConceptReferenceComponent c : inc.getConcept()) {
addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay());
}
if (inc.getFilter().size() > 1)
throw new TerminologyServiceException("Multiple filters not handled yet"); // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
if (inc.getFilter().size() == 1) {
ConceptSetFilterComponent fc = inc.getFilter().get(0);
if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
// special: all non-abstract codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
addCodeAndDescendents(cs, inc.getSystem(), def);
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def != null) {
if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
if (def.getDisplay().contains(fc.getValue())) {
addCode(inc.getSystem(), def.getCode(), def.getDisplay());
}
}
}
} else
throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
}
}
private String key(String uri, String code) {
return "{" + uri + "}" + code;
}
private String key(ValueSetExpansionContainsComponent c) {
return key(c.getSystem(), c.getCode());
}
}