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

Add support for uploading custom terminology using the 

$upload-external-code-system operation
This commit is contained in:
James Agnew 2019-07-30 17:28:29 -04:00
parent b030d1af31
commit 04ce9cfc1a
20 changed files with 563 additions and 193 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java
View File

@ -165,6 +165,13 @@ public class ParametersUtil {
}
@SuppressWarnings("unchecked")
public static void addParameterToParametersCode(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("code").newInstance();
value.setValue(theValue);
addParameterToParameters(theCtx, theParameters, theName, value);
}
@SuppressWarnings("unchecked")
public static void addParameterToParametersInteger(FhirContext theCtx, IBaseParameters theParameters, String theName, int theValue) {
IPrimitiveType<Integer> count = (IPrimitiveType<Integer>) theCtx.getElementDefinition("integer").newInstance();
@ -184,6 +191,13 @@ public class ParametersUtil {
IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("string").newInstance();
value.setValue(theValue);
addParameterToParameters(theCtx, theParameters, theName, value);
}
@SuppressWarnings("unchecked")
public static void addParameterToParametersUri(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("uri").newInstance();
value.setValue(theValue);
addParameterToParameters(theCtx, theParameters, theName, value);
}

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java
View File

@ -63,15 +63,21 @@ public class ValidateUtil {
}
}
public static void isNotNullOrThrowUnprocessableEntity(Object theObject, String theMessage, Object... theValues) {
if (theObject == null) {
throw new UnprocessableEntityException(String.format(theMessage, theValues));
}
}
public static void isNotTooLongOrThrowIllegalArgument(String theString, int theMaxLength, String theMessage) {
if (length(theString) > theMaxLength) {
throw new IllegalArgumentException(theMessage);
}
}
public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage) {
public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage, Object... theValues) {
if (theSuccess == false) {
throw new InvalidRequestException(theMessage);
throw new InvalidRequestException(String.format(theMessage, theValues));
}
}

15
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/ValidateUtilTest.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.util;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.junit.Test;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -69,4 +70,18 @@ public class ValidateUtilTest {
}
}
@Test
public void testIsNotNull() {
ValidateUtil.isNotNullOrThrowUnprocessableEntity("aa", "");
try {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(null, "The message %s", "123");
fail();
} catch (UnprocessableEntityException e) {
assertEquals("The message 123", e.getMessage());
}
}
}

26
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
@ -56,6 +57,7 @@ public class UploadTerminologyCommand extends BaseCommand {
addBaseUrlOption(options);
addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
addOptionalOption(options, null, "custom", false, "Indicates that this upload uses the HAPI FHIR custom external terminology format");
addBasicAuthOption(options);
addVerboseLoggingOption(options);
@ -78,23 +80,13 @@ public class UploadTerminologyCommand extends BaseCommand {
}
IGenericClient client = super.newClient(theCommandLine);
IBaseParameters inputParameters;
if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
org.hl7.fhir.dstu3.model.Parameters p = new org.hl7.fhir.dstu3.model.Parameters();
p.addParameter().setName("url").setValue(new org.hl7.fhir.dstu3.model.UriType(termUrl));
for (String next : datafile) {
p.addParameter().setName("localfile").setValue(new org.hl7.fhir.dstu3.model.StringType(next));
}
inputParameters = p;
} else if (ctx.getVersion().getVersion() == FhirVersionEnum.R4) {
org.hl7.fhir.r4.model.Parameters p = new org.hl7.fhir.r4.model.Parameters();
p.addParameter().setName("url").setValue(new org.hl7.fhir.r4.model.UriType(termUrl));
for (String next : datafile) {
p.addParameter().setName("localfile").setValue(new org.hl7.fhir.r4.model.StringType(next));
}
inputParameters = p;
} else {
throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
IBaseParameters inputParameters = ParametersUtil.newInstance(myFhirCtx);
ParametersUtil.addParameterToParametersUri(myFhirCtx, inputParameters, "url", termUrl);
for (String next : datafile) {
ParametersUtil.addParameterToParametersString(myFhirCtx, inputParameters, "localfile", next);
}
if (theCommandLine.hasOption("custom")) {
ParametersUtil.addParameterToParametersCode(myFhirCtx, inputParameters, "contentMode", "custom");
}
if (theCommandLine.hasOption(VERBOSE_LOGGING_PARAM)) {

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -50,15 +50,12 @@ import static org.apache.commons.lang3.StringUtils.length;
@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
})
public class TermConcept implements Serializable {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
private static final long serialVersionUID = 1L;
public static final int MAX_CODE_LENGTH = 500;
public static final int MAX_DESC_LENGTH = 400;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
private static final long serialVersionUID = 1L;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
private Collection<TermConceptParentChildLink> myChildren;
private List<TermConceptParentChildLink> myChildren;
@Column(name = "CODEVAL", nullable = false, length = MAX_CODE_LENGTH)
@Fields({@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),})
@ -178,7 +175,7 @@ public class TermConcept implements Serializable {
return b.isEquals();
}
public Collection<TermConceptParentChildLink> getChildren() {
public List<TermConceptParentChildLink> getChildren() {
if (myChildren == null) {
myChildren = new ArrayList<>();
}

36
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
View File

@ -160,6 +160,7 @@ public abstract class TerminologyUploaderProvider extends BaseJpaProvider {
public IBaseParameters uploadExternalCodeSystem(
HttpServletRequest theServletRequest,
@OperationParam(name = "url", min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
@OperationParam(name = "contentMode", min = 0, typeName = "code") IPrimitiveType<String> theContentMode,
@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theLocalFile,
@OperationParam(name = "package", min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> thePackage,
RequestDetails theRequestDetails
@ -210,7 +211,7 @@ public abstract class TerminologyUploaderProvider extends BaseJpaProvider {
final String url = AttachmentUtil.getOrCreateUrl(myCtx, nextPackage).getValueAsString();
if (isBlank(url)) {
throw new UnprocessableEntityException("Package is missing mandatory url element");
throw new UnprocessableEntityException("Package is missing mandatory codeSystemUrl element");
}
localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
@ -228,22 +229,27 @@ public abstract class TerminologyUploaderProvider extends BaseJpaProvider {
}
}
String url = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
url = defaultString(url);
String codeSystemUrl = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
codeSystemUrl = defaultString(codeSystemUrl);
String contentMode = theContentMode != null ? theContentMode.getValue() : null;
UploadStatistics stats;
switch (url) {
case IHapiTerminologyLoaderSvc.SCT_URI:
stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
break;
case IHapiTerminologyLoaderSvc.LOINC_URI:
stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
break;
case IHapiTerminologyLoaderSvc.IMGTHLA_URI:
stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
break;
default:
throw new InvalidRequestException("Unknown URL: " + url);
if ("custom".equals(contentMode)) {
stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
} else {
switch (codeSystemUrl) {
case IHapiTerminologyLoaderSvc.SCT_URI:
stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
break;
case IHapiTerminologyLoaderSvc.LOINC_URI:
stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
break;
case IHapiTerminologyLoaderSvc.IMGTHLA_URI:
stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
break;
default:
throw new InvalidRequestException("Unknown URL: " + codeSystemUrl);
}
}
IBaseParameters retVal = ParametersUtil.newInstance(myCtx);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java
View File

@ -39,6 +39,8 @@ public interface IHapiTerminologyLoaderSvc {
UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
interface FileDescriptor {
String getFilename();

169
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
View File

@ -4,15 +4,19 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.custom.ConceptHandler;
import ca.uhn.fhir.jpa.term.custom.HierarchyHandler;
import ca.uhn.fhir.jpa.term.loinc.*;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerRelationship;
import ca.uhn.fhir.jpa.util.Counter;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import org.apache.commons.csv.CSVFormat;
@ -83,15 +87,19 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
public static final String LOINC_GROUP_FILE = "Group.csv";
public static final String LOINC_GROUP_TERMS_FILE = "GroupLoincTerms.csv";
public static final String LOINC_PARENT_GROUP_FILE = "ParentGroup.csv";
public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
public static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
public static final String CUSTOM_CODESYSTEM_XML = "codesystem.xml";
private static final int LOG_INCREMENT = 1000;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImpl.class);
@Autowired
private IHapiTerminologySvc myTermSvc;
@Autowired(required = false)
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
@Autowired(required = false)
private IHapiTerminologySvcR4 myTermSvcR4;
// FYI: Hardcoded to R4 because that's what the term svc uses internally
private final FhirContext myCtx = FhirContext.forR4();
private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {
@ -165,7 +173,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
int nextLoggedCount = 0;
while (iter.hasNext()) {
CSVRecord nextRecord = iter.next();
if (nextRecord.isConsistent()==false) {
if (nextRecord.isConsistent() == false) {
continue;
}
theHandler.accept(nextRecord);
@ -203,8 +211,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
ourLog.info("Beginning IMGTHLA processing");
return processImgthlaFiles(descriptors, theRequestDetails);
}
finally {
} finally {
IOUtils.closeQuietly(descriptors);
}
}
@ -229,15 +236,15 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV,
LOINC_IMAGING_DOCUMENT_CODES_FILE
);
descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
List<String> optionalFilenameFragments = Arrays.asList(
);
descriptors.verifyOptionalFilesExist(optionalFilenameFragments);
descriptors.verifyOptionalFilesExist(optionalFilenameFragments);
ourLog.info("Beginning LOINC processing");
ourLog.info("Beginning LOINC processing");
return processLoincFiles(descriptors, theRequestDetails);
return processLoincFiles(descriptors, theRequestDetails);
}
}
@ -257,6 +264,67 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
}
@Override
public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
final Map<String, TermConcept> code2concept = new HashMap<>();
IRecordHandler handler;
Optional<String> codeSystemContent = loadFile(descriptors, CUSTOM_CODESYSTEM_JSON, CUSTOM_CODESYSTEM_XML);
CodeSystem codeSystem;
if (codeSystemContent.isPresent()) {
codeSystem = EncodingEnum
.detectEncoding(codeSystemContent.get())
.newParser(myCtx)
.parseResource(CodeSystem.class, codeSystemContent.get());
ValidateUtil.isTrueOrThrowInvalidRequest(theSystem.equalsIgnoreCase(codeSystem.getUrl()), "CodeSystem.url does not match the supplied system: %s", theSystem);
ValidateUtil.isTrueOrThrowInvalidRequest(CodeSystem.CodeSystemContentMode.NOTPRESENT.equals(codeSystem.getContent()), "CodeSystem.content does not match the expected value: %s", CodeSystem.CodeSystemContentMode.NOTPRESENT.toCode());
} else {
codeSystem = new CodeSystem();
codeSystem.setUrl(theSystem);
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
}
TermCodeSystemVersion csv = new TermCodeSystemVersion();
// Concept File
handler = new ConceptHandler(code2concept, csv);
iterateOverZipFile(descriptors, CUSTOM_CONCEPTS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Hierarchy
if (descriptors.hasFile(CUSTOM_HIERARCHY_FILE)) {
handler = new HierarchyHandler(code2concept);
iterateOverZipFile(descriptors, CUSTOM_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
}
// Add root concepts to CodeSystemVersion
for (TermConcept nextConcept : code2concept.values()) {
if (nextConcept.getParents().isEmpty()) {
csv.getConcepts().add(nextConcept);
}
}
IIdType target = storeCodeSystem(theRequestDetails, csv, codeSystem, null, null);
return new UploadStatistics(code2concept.size(), target);
}
}
private Optional<String> loadFile(LoadedFileDescriptors theDescriptors, String... theFilenames) {
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
for (String nextFilename : theFilenames) {
if (next.getFilename().endsWith(nextFilename)) {
try {
String contents = IOUtils.toString(next.getInputStream(), Charsets.UTF_8);
return Optional.of(contents);
} catch (IOException e) {
throw new InternalErrorException(e);
}
}
}
}
return Optional.empty();
}
UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> code2concept = new HashMap<>();
@ -285,13 +353,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
for (FileDescriptor nextZipBytes : theDescriptors.getUncompressedFileDescriptors()) {
String nextFilename = nextZipBytes.getFilename();
if(!IMGTHLA_HLA_NOM_TXT.equals(nextFilename) && !nextFilename.endsWith("/" + IMGTHLA_HLA_NOM_TXT)
if (!IMGTHLA_HLA_NOM_TXT.equals(nextFilename) && !nextFilename.endsWith("/" + IMGTHLA_HLA_NOM_TXT)
&& !IMGTHLA_HLA_XML.equals(nextFilename) && !nextFilename.endsWith("/" + IMGTHLA_HLA_XML)) {
ourLog.info("Skipping unexpected file {}", nextFilename);
continue;
}
if(IMGTHLA_HLA_NOM_TXT.equals(nextFilename) || nextFilename.endsWith("/" + IMGTHLA_HLA_NOM_TXT)) {
if (IMGTHLA_HLA_NOM_TXT.equals(nextFilename) || nextFilename.endsWith("/" + IMGTHLA_HLA_NOM_TXT)) {
// process colon-delimited hla_nom.txt file
ourLog.info("Processing file {}", nextFilename);
@ -309,20 +377,20 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
LineNumberReader lnr = new LineNumberReader(reader);
while(lnr.readLine() != null) {}
while (lnr.readLine() != null) {
}
ourLog.warn("Lines read from {}: {}", nextFilename, lnr.getLineNumber());
} catch (IOException e) {
throw new InternalErrorException(e);
}
finally {
} finally {
IOUtils.closeQuietly(reader);
}
foundHlaNom = true;
}
if(IMGTHLA_HLA_XML.equals(nextFilename) || nextFilename.endsWith("/" + IMGTHLA_HLA_XML)) {
if (IMGTHLA_HLA_XML.equals(nextFilename) || nextFilename.endsWith("/" + IMGTHLA_HLA_XML)) {
// process hla.xml file
ourLog.info("Processing file {}", nextFilename);
@ -340,13 +408,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
LineNumberReader lnr = new LineNumberReader(reader);
while(lnr.readLine() != null) {}
while (lnr.readLine() != null) {
}
ourLog.warn("Lines read from {}: {}", nextFilename, lnr.getLineNumber());
} catch (IOException e) {
throw new InternalErrorException(e);
}
finally {
} finally {
IOUtils.closeQuietly(reader);
}
@ -553,11 +621,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
return new UploadStatistics(code2concept.size(), target);
}
@VisibleForTesting
void setTermSvcDstu3ForUnitTest(IHapiTerminologySvcDstu3 theTermSvcDstu3) {
myTermSvcDstu3 = theTermSvcDstu3;
}
@VisibleForTesting
void setTermSvcForUnitTests(IHapiTerminologySvc theTermSvc) {
myTermSvc = theTermSvc;
@ -571,38 +634,12 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
IIdType retVal;
myTermSvc.setProcessDeferred(false);
if (myTermSvcDstu3 != null) {
retVal = myTermSvcDstu3.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
} else {
retVal = myTermSvcR4.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
}
retVal = myTermSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
myTermSvc.setProcessDeferred(true);
return retVal;
}
public static String firstNonBlank(String... theStrings) {
String retVal = "";
for (String nextString : theStrings) {
if (isNotBlank(nextString)) {
retVal = nextString;
break;
}
}
return retVal;
}
public static 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.setCodeSystemVersion(codeSystemVersion);
}
return concept;
}
static class LoadedFileDescriptors implements Closeable {
private List<File> myTemporaryFiles = new ArrayList<>();
@ -651,6 +688,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
}
boolean hasFile(String theFilename) {
return myUncompressedFileDescriptors
.stream()
.map(t -> t.getFilename().replaceAll(".*[\\\\/]", "")) // Strip the path from the filename
.anyMatch(t -> t.equals(theFilename));
}
@Override
public void close() {
for (File next : myTemporaryFiles) {
@ -694,4 +738,25 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
public static String firstNonBlank(String... theStrings) {
String retVal = "";
for (String nextString : theStrings) {
if (isNotBlank(nextString)) {
retVal = nextString;
break;
}
}
return retVal;
}
public static 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.setCodeSystemVersion(codeSystemVersion);
}
return concept;
}
}

63
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/ConceptHandler.java Normal file
View File

@ -0,0 +1,63 @@
package ca.uhn.fhir.jpa.term.custom;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 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.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.lang3.Validate;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class ConceptHandler implements IRecordHandler {
private static final Logger ourLog = LoggerFactory.getLogger(ConceptHandler.class);
private final Map<String, TermConcept> myCode2Concept;
private final TermCodeSystemVersion myCodeSystemVersion;
public ConceptHandler(Map<String, TermConcept> theCode2concept, TermCodeSystemVersion theCodeSystemVersion) {
myCode2Concept = theCode2concept;
myCodeSystemVersion = theCodeSystemVersion;
}
@Override
public void accept(CSVRecord theRecord) {
String code = trim(theRecord.get("CODE"));
if (isNotBlank(code)) {
String display = trim(theRecord.get("DISPLAY"));
Validate.isTrue(!myCode2Concept.containsKey(code), "The code %s has appeared more than once", code);
TermConcept concept = TerminologyLoaderSvcImpl.getOrCreateConcept(myCodeSystemVersion, myCode2Concept, code);
concept.setCode(code);
concept.setDisplay(display);
myCode2Concept.put(code, concept);
}
}
}

58
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/HierarchyHandler.java Normal file
View File

@ -0,0 +1,58 @@
package ca.uhn.fhir.jpa.term.custom;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 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.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.csv.CSVRecord;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class HierarchyHandler implements IRecordHandler {
private final Map<String, TermConcept> myCode2Concept;
public HierarchyHandler(Map<String, TermConcept> theCode2concept) {
myCode2Concept = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
String parent = trim(theRecord.get("PARENT"));
String child = trim(theRecord.get("CHILD"));
if (isNotBlank(parent) && isNotBlank(child)) {
TermConcept parentConcept = myCode2Concept.get(parent);
ValidateUtil.isNotNullOrThrowUnprocessableEntity(parentConcept, "Parent code %s not found", parent);
TermConcept childConcept = myCode2Concept.get(child);
ValidateUtil.isNotNullOrThrowUnprocessableEntity(childConcept, "Child code %s not found", child);
parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
}
}
}

58
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/BaseLoaderTest.java Normal file
View File

@ -0,0 +1,58 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@RunWith(MockitoJUnitRunner.class)
abstract class BaseLoaderTest {
@Mock
protected RequestDetails mySrd;
@Captor
protected ArgumentCaptor<List<ConceptMap>> myConceptMapCaptor;
@Captor
protected ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
@Captor
protected ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
@Captor
protected ArgumentCaptor<CodeSystem> mySystemCaptor;
Map<String, ConceptMap> extractConceptMaps() {
Map<String, ConceptMap> conceptMaps = new HashMap<>();
for (ConceptMap next : myConceptMapCaptor.getAllValues().get(0)) {
conceptMaps.put(next.getId(), next);
}
return conceptMaps;
}
Map<String, TermConcept> extractConcepts() {
Map<String, TermConcept> concepts = new HashMap<>();
for (TermConcept next : myCsvCaptor.getValue().getConcepts()) {
concepts.put(next.getCode(), next);
}
return concepts;
}
Map<String, ValueSet> extractValueSets() {
Map<String, ValueSet> valueSets = new HashMap<>();
for (ValueSet next : myValueSetsCaptor.getValue()) {
valueSets.put(next.getId(), next);
}
return valueSets;
}
}

115
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcCustomTest.java Normal file
View File

@ -0,0 +1,115 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.util.Map;
import static org.junit.Assert.assertEquals;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcCustomTest extends BaseLoaderTest {
private TerminologyLoaderSvcImpl mySvc;
@Mock
private IHapiTerminologySvc myTermSvc;
private ZipCollectionBuilder myFiles;
@Before
public void before() {
mySvc = new TerminologyLoaderSvcImpl();
mySvc.setTermSvcForUnitTests(myTermSvc);
myFiles = new ZipCollectionBuilder();
}
@Test
public void testLoadComplete() throws Exception {
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CODESYSTEM_JSON);
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_HIERARCHY_FILE);
// Actually do the load
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
// Verify codesystem
assertEquals("http://example.com/labCodes", mySystemCaptor.getValue().getUrl());
assertEquals(CodeSystem.CodeSystemContentMode.NOTPRESENT, mySystemCaptor.getValue().getContent());
assertEquals("Example Lab Codes", mySystemCaptor.getValue().getName());
// Root code
TermConcept code;
assertEquals(2, concepts.size());
code = concepts.get("CHEM");
assertEquals("CHEM", code.getCode());
assertEquals("Chemistry", code.getDisplay());
assertEquals(2, code.getChildren().size());
assertEquals("HB", code.getChildren().get(0).getChild().getCode());
assertEquals("Hemoglobin", code.getChildren().get(0).getChild().getDisplay());
assertEquals("NEUT", code.getChildren().get(1).getChild().getCode());
assertEquals("Neutrophils", code.getChildren().get(1).getChild().getDisplay());
}
@Test
public void testLoadWithNoCodeSystem() throws Exception {
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
// Actually do the load
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
// Verify codesystem
assertEquals("http://example.com/labCodes", mySystemCaptor.getValue().getUrl());
assertEquals(CodeSystem.CodeSystemContentMode.NOTPRESENT, mySystemCaptor.getValue().getContent());
}
/**
* No hierarchy file supplied
*/
@Test
public void testLoadCodesOnly() throws Exception {
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
// Actually do the load
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
TermConcept code;
// Root code
assertEquals(5, concepts.size());
code = concepts.get("CHEM");
assertEquals("CHEM", code.getCode());
assertEquals("Chemistry", code.getDisplay());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImgthlaTest.java
View File

@ -1,6 +1,5 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
@ -8,9 +7,7 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.io.IOException;
@ -18,19 +15,12 @@ import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcImgthlaTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImgthlaTest.class);
public class TerminologyLoaderSvcImgthlaTest extends BaseLoaderTest {
private TerminologyLoaderSvcImpl mySvc;
@Mock
private IHapiTerminologySvc myTermSvc;
@Mock
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
@Mock
private RequestDetails details;
private ZipCollectionBuilder myFiles;
@ -38,7 +28,6 @@ public class TerminologyLoaderSvcImgthlaTest {
public void before() {
mySvc = new TerminologyLoaderSvcImpl();
mySvc.setTermSvcForUnitTests(myTermSvc);
mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
myFiles = new ZipCollectionBuilder();
}
@ -49,7 +38,7 @@ public class TerminologyLoaderSvcImgthlaTest {
// Actually do the load
try {
mySvc.loadImgthla(myFiles.getFiles(), details);
mySvc.loadImgthla(myFiles.getFiles(), mySrd);
fail("Expected \"not yet fully implemented\" InternalErrorException");
} catch(InternalErrorException e) {
// for now, expect "not yet fully implemented" exception
@ -65,7 +54,7 @@ public class TerminologyLoaderSvcImgthlaTest {
addImgthlaMandatoryFilesToZip(myFiles);
// Actually do the load
mySvc.loadImgthla(myFiles.getFiles(), details);
mySvc.loadImgthla(myFiles.getFiles(), mySrd);
// TODO: verify the code system was loaded correctly (similarly to TerminologyLoaderSvcLoincTest.testLoadLoincMandatoryFilesOnly)
}
@ -76,7 +65,7 @@ public class TerminologyLoaderSvcImgthlaTest {
// Actually do the load
try {
mySvc.loadImgthla(myFiles.getFiles(), details);
mySvc.loadImgthla(myFiles.getFiles(), mySrd);
fail("Expected UnprocessableEntityException");
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input:"));

60
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
View File

@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.loinc.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -15,46 +14,28 @@ 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;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcLoincTest {
public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcLoincTest.class);
private TerminologyLoaderSvcImpl mySvc;
@Mock
private IHapiTerminologySvc myTermSvc;
@Mock
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
@Captor
private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
@Captor
private ArgumentCaptor<CodeSystem> mySystemCaptor;
@Mock
private RequestDetails details;
@Captor
private ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
@Captor
private ArgumentCaptor<List<ConceptMap>> myConceptMapCaptor;
private ZipCollectionBuilder myFiles;
@ -62,43 +43,18 @@ public class TerminologyLoaderSvcLoincTest {
public void before() {
mySvc = new TerminologyLoaderSvcImpl();
mySvc.setTermSvcForUnitTests(myTermSvc);
mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
myFiles = new ZipCollectionBuilder();
}
private Map<String, ConceptMap> extractConceptMaps() {
Map<String, ConceptMap> conceptMaps = new HashMap<>();
for (ConceptMap next : myConceptMapCaptor.getAllValues().get(0)) {
conceptMaps.put(next.getId(), next);
}
return conceptMaps;
}
private Map<String, TermConcept> extractConcepts() {
Map<String, TermConcept> concepts = new HashMap<>();
for (TermConcept next : myCsvCaptor.getValue().getConcepts()) {
concepts.put(next.getCode(), next);
}
return concepts;
}
private Map<String, ValueSet> extractValueSets() {
Map<String, ValueSet> valueSets = new HashMap<>();
for (ValueSet next : myValueSetsCaptor.getValue()) {
valueSets.put(next.getId(), next);
}
return valueSets;
}
@Test
public void testLoadLoinc() throws Exception {
addLoincMandatoryFilesToZip(myFiles);
// Actually do the load
mySvc.loadLoinc(myFiles.getFiles(), details);
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
Map<String, ValueSet> valueSets = extractValueSets();
Map<String, ConceptMap> conceptMaps = extractConceptMaps();
@ -347,9 +303,9 @@ public class TerminologyLoaderSvcLoincTest {
addLoincMandatoryFilesToZip(myFiles);
// Actually do the load
mySvc.loadLoinc(myFiles.getFiles(), details);
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
Map<String, ValueSet> valueSets = extractValueSets();
Map<String, ConceptMap> conceptMaps = extractConceptMaps();
@ -371,7 +327,7 @@ public class TerminologyLoaderSvcLoincTest {
// Actually do the load
try {
mySvc.loadLoinc(myFiles.getFiles(), details);
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input:"));

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcSnomedCtTest.java
View File

@ -4,39 +4,36 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.rest.api.server.RequestDetails;
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.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
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;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.runners.MockitoJUnitRunner;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.InputStream;
import java.util.*;
import java.util.ArrayList;
import java.util.TreeSet;
import java.util.zip.ZipOutputStream;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyListOf;
import static org.mockito.Mockito.mock;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.*;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcSnomedCtTest {
public class TerminologyLoaderSvcSnomedCtTest extends BaseLoaderTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcSnomedCtTest.class);
private TerminologyLoaderSvcImpl mySvc;
@ -44,15 +41,12 @@ public class TerminologyLoaderSvcSnomedCtTest {
private IHapiTerminologySvc myTermSvc;
@Captor
private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
@Mock
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
private ZipCollectionBuilder myFiles;
@Before
public void before() {
mySvc = new TerminologyLoaderSvcImpl();
mySvc.setTermSvcForUnitTests(myTermSvc);
mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
myFiles = new ZipCollectionBuilder();
}
@ -84,17 +78,16 @@ public class TerminologyLoaderSvcSnomedCtTest {
myFiles.addFileZip("/sct/", "sct2_StatedRelationship_Full_INT_20160131.txt");
myFiles.addFileZip("/sct/", "sct2_TextDefinition_Full-en_INT_20160131.txt");
RequestDetails details = mock(RequestDetails.class);
mySvc.loadSnomedCt(myFiles.getFiles(), details);
mySvc.loadSnomedCt(myFiles.getFiles(), mySrd);
verify(myTermSvcDstu3).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyListOf(ValueSet.class), anyListOf(ConceptMap.class));
verify(myTermSvc).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyList(), anyListOf(ConceptMap.class));
TermCodeSystemVersion csv = myCsvCaptor.getValue();
TreeSet<String> allCodes = toCodes(csv, true);
ourLog.info(allCodes.toString());
assertThat(allCodes, containsInRelativeOrder("116680003"));
assertThat(allCodes, not(containsInRelativeOrder("207527008")));
assertThat(allCodes, hasItem("116680003"));
assertThat(allCodes, not(hasItem("207527008")));
allCodes = toCodes(csv, false);
ourLog.info(allCodes.toString());
@ -110,8 +103,7 @@ public class TerminologyLoaderSvcSnomedCtTest {
public void testLoadSnomedCtAgainstRealFile() throws Exception {
byte[] bytes = IOUtils.toByteArray(new FileInputStream("/Users/james/Downloads/SnomedCT_Release_INT_20160131_Full.zip"));
RequestDetails details = mock(RequestDetails.class);
mySvc.loadSnomedCt(list(bytes), details);
mySvc.loadSnomedCt(list(bytes), mySrd);
}
@Test
@ -123,9 +115,8 @@ public class TerminologyLoaderSvcSnomedCtTest {
ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
RequestDetails details = mock(RequestDetails.class);
try {
mySvc.loadSnomedCt(list(bos.toByteArray()), details);
mySvc.loadSnomedCt(list(bos.toByteArray()), mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input: "));

10
hapi-fhir-jpaserver-base/src/test/resources/custom_term/codesystem.json Normal file
View File

@ -0,0 +1,10 @@
{
"resourceType": "CodeSystem",
"url": "http://example.com/labCodes",
"name": "Example Lab Codes",
"description": "A set of lab codes",
"status": "active",
"publisher": "Example Organization Corporation Worldwide",
"date": "2019-07-30",
"content": "not-present"
}

8
hapi-fhir-jpaserver-base/src/test/resources/custom_term/concepts.csv Normal file
View File

@ -0,0 +1,8 @@
CODE,DISPLAY
CHEM,Chemistry
HB,Hemoglobin
NEUT,Neutrophils
MICRO,Microbiology
C&S,Culture and Sensitivity
1 CODE DISPLAY
2 CHEM Chemistry
3 HB Hemoglobin
4 NEUT Neutrophils
5 MICRO Microbiology
6 C&S Culture and Sensitivity

6
hapi-fhir-jpaserver-base/src/test/resources/custom_term/hierarchy.csv Normal file
View File

@ -0,0 +1,6 @@
PARENT,CHILD
CHEM,HB
CHEM,NEUT
MICRO,C&S
1 PARENT CHILD
2 CHEM HB
3 CHEM NEUT
4 MICRO C&S

32
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/CachingValidationSupport.java
View File

@ -3,15 +3,17 @@ package org.hl7.fhir.r4.hapi.validation;
import ca.uhn.fhir.context.FhirContext;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import org.checkerframework.checker.nullness.qual.Nullable;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.terminologies.ValueSetExpander;
import java.util.List;
import java.util.concurrent.TimeUnit;
import java.util.function.Function;
@SuppressWarnings("unchecked")
public class CachingValidationSupport implements IValidationSupport {
@ -21,7 +23,11 @@ public class CachingValidationSupport implements IValidationSupport {
public CachingValidationSupport(IValidationSupport theWrap) {
myWrap = theWrap;
myCache = Caffeine.newBuilder().expireAfterWrite(60, TimeUnit.SECONDS).build();
myCache = Caffeine
.newBuilder()
.expireAfterWrite(60, TimeUnit.SECONDS)
.maximumSize(5000)
.build();
}
@Override
@ -31,14 +37,14 @@ public class CachingValidationSupport implements IValidationSupport {
@Override
public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
return (List<IBaseResource>) myCache.get("fetchAllConformanceResources",
t -> myWrap.fetchAllConformanceResources(theContext));
String key = "fetchAllConformanceResources";
return loadFromCache(key, t -> myWrap.fetchAllConformanceResources(theContext));
}
@Override
public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
return (List<StructureDefinition>) myCache.get("fetchAllStructureDefinitions",
t -> myWrap.fetchAllStructureDefinitions(theContext));
String key = "fetchAllStructureDefinitions";
return loadFromCache(key, t -> myWrap.fetchAllStructureDefinitions(theContext));
}
@Override
@ -63,7 +69,8 @@ public class CachingValidationSupport implements IValidationSupport {
@Override
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return myWrap.isCodeSystemSupported(theContext, theSystem);
String key = "isCodeSystemSupported " + theSystem;
return loadFromCache(key, t -> myWrap.isCodeSystemSupported(theContext, theSystem));
}
@Override
@ -73,11 +80,18 @@ public class CachingValidationSupport implements IValidationSupport {
@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
return myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay);
String key = "validateCode " + theCodeSystem + " " + theCode;
return loadFromCache(key, t -> myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay));
}
@Override
public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
return myWrap.lookupCode(theContext, theSystem, theCode);
String key = "lookupCode " + theSystem + " " + theCode;
return loadFromCache(key, t -> myWrap.lookupCode(theContext, theSystem, theCode));
}
@Nullable
private <T> T loadFromCache(String theKey, Function<String, T> theLoader) {
return (T) myCache.get(theKey, theLoader);
}
}

5
src/changes/changes.xml
View File

@ -354,6 +354,11 @@
type for an operation declared on a plain provider without needing to use
a specific version of the FHIR structures.
</action>
<action type="add">
The $upload-external-code-system operation and the corresponding HAPI FHIR CLI command
can now be used to upload custom vocabulary that has been converted into a standard file format
defined by HAPI FHIR. This is useful for uploading large organizational code systems.
</action>
</release>
<release version="3.8.0" date="2019-05-30" description="Hippo">
<action type="fix">