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Merge pull request #1448 from jamesagnew/1447-loinc-filenames-should-be-configurable 

Resolve "LOINC filenames should be configurable."
This commit is contained in:
Diederik Muylwyk 2019-08-27 13:47:40 -04:00 committed by GitHub
parent 70d0a8aa8f 94c7fc49fd
commit 6b0084fc3b
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 374 additions and 142 deletions
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189
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
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@ -34,6 +34,7 @@ import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap; import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Enumerations; import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ValueSet; import org.hl7.fhir.r4.model.ValueSet;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import java.io.*; import java.io.*;
@ -42,6 +43,7 @@ import java.util.Map.Entry;
import java.util.zip.ZipEntry; import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream; import java.util.zip.ZipInputStream;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank;
/* /*
@ -68,26 +70,10 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_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_DESCRIPTION = "Terminology/sct2_Description_Full-en";
public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full"; public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
public static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt"; public static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
public static final String IMGTHLA_HLA_XML = "hla.xml"; public static final String IMGTHLA_HLA_XML = "hla.xml";
public static final String LOINC_ANSWERLIST_FILE = "AnswerList.csv";
public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink.csv";
public static final String LOINC_DOCUMENT_ONTOLOGY_FILE = "DocumentOntology.csv";
public static final String LOINC_UPLOAD_PROPERTIES_FILE = "loincupload.properties";
public static final String LOINC_FILE = "LoincTable/Loinc.csv";
public static final String LOINC_HIERARCHY_FILE = "MultiAxialHierarchy.csv";
public static final String LOINC_PART_FILE = "Part.csv";
public static final String LOINC_PART_LINK_FILE = "LoincPartLink.csv";
public static final String LOINC_PART_RELATED_CODE_MAPPING_FILE = "PartRelatedCodeMapping.csv";
public static final String LOINC_RSNA_PLAYBOOK_FILE = "LoincRsnaRadiologyPlaybook.csv";
public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE = "Top2000CommonLabResultsUs.csv";
public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE = "Top2000CommonLabResultsSi.csv";
public static final String LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE = "LoincUniversalLabOrdersValueSet.csv";
public static final String LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV = "LoincIeeeMedicalDeviceCodeMappingTable.csv";
public static final String LOINC_IMAGING_DOCUMENT_CODES_FILE = "ImagingDocumentCodes.csv";
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_CONCEPTS_FILE = "concepts.csv";
public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.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_JSON = "codesystem.json";
@ -220,35 +206,61 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
@Override @Override
public UploadStatistics loadLoinc(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { public UploadStatistics loadLoinc(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) { try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
List<String> loincUploadPropertiesFragment = Arrays.asList(
LOINC_UPLOAD_PROPERTIES_FILE.getCode()
);
descriptors.verifyMandatoryFilesExist(loincUploadPropertiesFragment);
Properties uploadProperties = getProperties(descriptors, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
List<String> mandatoryFilenameFragments = Arrays.asList( List<String> mandatoryFilenameFragments = Arrays.asList(
LOINC_FILE, uploadProperties.getProperty(LOINC_ANSWERLIST_FILE.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode()),
LOINC_HIERARCHY_FILE, uploadProperties.getProperty(LOINC_ANSWERLIST_LINK_FILE.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode()),
LOINC_UPLOAD_PROPERTIES_FILE, uploadProperties.getProperty(LOINC_DOCUMENT_ONTOLOGY_FILE.getCode(), LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode()),
LOINC_ANSWERLIST_FILE, uploadProperties.getProperty(LOINC_FILE.getCode(), LOINC_FILE_DEFAULT.getCode()),
LOINC_ANSWERLIST_LINK_FILE, uploadProperties.getProperty(LOINC_HIERARCHY_FILE.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode()),
LOINC_PART_FILE, uploadProperties.getProperty(LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE.getCode(), LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode()),
LOINC_PART_LINK_FILE, uploadProperties.getProperty(LOINC_IMAGING_DOCUMENT_CODES_FILE.getCode(), LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode()),
LOINC_PART_RELATED_CODE_MAPPING_FILE, uploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()),
LOINC_DOCUMENT_ONTOLOGY_FILE, uploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()),
LOINC_RSNA_PLAYBOOK_FILE, uploadProperties.getProperty(LOINC_PART_RELATED_CODE_MAPPING_FILE.getCode(), LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode()),
LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE, uploadProperties.getProperty(LOINC_RSNA_PLAYBOOK_FILE.getCode(), LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode()),
LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE, uploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode()),
LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE, uploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode()),
LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV, uploadProperties.getProperty(LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE.getCode(), LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode())
LOINC_IMAGING_DOCUMENT_CODES_FILE
); );
descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments); descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
List<String> optionalFilenameFragments = Arrays.asList( List<String> optionalFilenameFragments = Arrays.asList(
uploadProperties.getProperty(LOINC_GROUP_FILE.getCode(), LOINC_GROUP_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_GROUP_TERMS_FILE.getCode(), LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_PARENT_GROUP_FILE.getCode(), LOINC_PARENT_GROUP_FILE_DEFAULT.getCode())
); );
descriptors.verifyOptionalFilesExist(optionalFilenameFragments); descriptors.verifyOptionalFilesExist(optionalFilenameFragments);
ourLog.info("Beginning LOINC processing"); ourLog.info("Beginning LOINC processing");
return processLoincFiles(descriptors, theRequestDetails); return processLoincFiles(descriptors, theRequestDetails, uploadProperties);
} }
} }
@NotNull
private Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
Properties retVal = new Properties();
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
if (next.getFilename().endsWith(thePropertiesFile)) {
try {
try (InputStream inputStream = next.getInputStream()) {
retVal.load(inputStream);
}
} catch (IOException e) {
throw new InternalErrorException("Failed to read " + thePropertiesFile, e);
}
}
}
return retVal;
}
@Override @Override
public UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { public UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) { try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
@ -445,7 +457,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
// return new UploadStatistics(conceptCount, target); // return new UploadStatistics(conceptCount, target);
} }
UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) { UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails, Properties theUploadProperties) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion(); final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> code2concept = new HashMap<>(); final Map<String, TermConcept> code2concept = new HashMap<>();
final List<ValueSet> valueSets = new ArrayList<>(); final List<ValueSet> valueSets = new ArrayList<>();
@ -470,90 +482,77 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
IRecordHandler handler; IRecordHandler handler;
Properties uploadProperties = new Properties(); // Part
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
if (next.getFilename().endsWith("loincupload.properties")) {
try {
try (InputStream inputStream = next.getInputStream()) {
uploadProperties.load(inputStream);
}
} catch (IOException e) {
throw new InternalErrorException("Failed to read loincupload.properties", e);
}
}
}
// Part file
handler = new LoincPartHandler(codeSystemVersion, code2concept); handler = new LoincPartHandler(codeSystemVersion, code2concept);
iterateOverZipFile(theDescriptors, LOINC_PART_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
Map<PartTypeAndPartName, String> partTypeAndPartNameToPartNumber = ((LoincPartHandler) handler).getPartTypeAndPartNameToPartNumber(); Map<PartTypeAndPartName, String> partTypeAndPartNameToPartNumber = ((LoincPartHandler) handler).getPartTypeAndPartNameToPartNumber();
// Loinc Codes // LOINC codes
handler = new LoincHandler(codeSystemVersion, code2concept, propertyNamesToTypes, partTypeAndPartNameToPartNumber); handler = new LoincHandler(codeSystemVersion, code2concept, propertyNamesToTypes, partTypeAndPartNameToPartNumber);
iterateOverZipFile(theDescriptors, LOINC_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_FILE.getCode(), LOINC_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Loinc Hierarchy // LOINC hierarchy
handler = new LoincHierarchyHandler(codeSystemVersion, code2concept); handler = new LoincHierarchyHandler(codeSystemVersion, code2concept);
iterateOverZipFile(theDescriptors, LOINC_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_HIERARCHY_FILE.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Answer lists (ValueSets of potential answers/values for loinc "questions") // Answer lists (ValueSets of potential answers/values for LOINC "questions")
handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_ANSWERLIST_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_ANSWERLIST_FILE.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Answer list links (connects loinc observation codes to answerlist codes) // Answer list links (connects LOINC observation codes to answer list codes)
handler = new LoincAnswerListLinkHandler(code2concept, valueSets); handler = new LoincAnswerListLinkHandler(code2concept, valueSets);
iterateOverZipFile(theDescriptors, LOINC_ANSWERLIST_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_ANSWERLIST_LINK_FILE.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// RSNA Playbook file // RSNA playbook
// Note that this should come before the "Part Related Code Mapping" // Note that this should come before the "Part Related Code Mapping"
// file because there are some duplicate mappings between these // file because there are some duplicate mappings between these
// two files, and the RSNA Playbook file has more metadata // two files, and the RSNA Playbook file has more metadata
handler = new LoincRsnaPlaybookHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincRsnaPlaybookHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_RSNA_PLAYBOOK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_RSNA_PLAYBOOK_FILE.getCode(), LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Part link file // Part link
handler = new LoincPartLinkHandler(codeSystemVersion, code2concept); handler = new LoincPartLinkHandler(codeSystemVersion, code2concept);
iterateOverZipFile(theDescriptors, LOINC_PART_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Part related code mapping // Part related code mapping
handler = new LoincPartRelatedCodeMappingHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincPartRelatedCodeMappingHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_PART_RELATED_CODE_MAPPING_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_RELATED_CODE_MAPPING_FILE.getCode(), LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Document Ontology File // Document ontology
handler = new LoincDocumentOntologyHandler(code2concept, propertyNamesToTypes, valueSets, conceptMaps, uploadProperties); handler = new LoincDocumentOntologyHandler(code2concept, propertyNamesToTypes, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_DOCUMENT_ONTOLOGY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_DOCUMENT_ONTOLOGY_FILE.getCode(), LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Top 2000 Codes - US // Top 2000 codes - US
handler = new LoincTop2000LabResultsUsHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincTop2000LabResultsUsHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Top 2000 Codes - SI // Top 2000 codes - SI
handler = new LoincTop2000LabResultsSiHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincTop2000LabResultsSiHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Universal Lab Order ValueSet // Universal lab order ValueSet
handler = new LoincUniversalOrderSetHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincUniversalOrderSetHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE.getCode(), LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// IEEE Medical Device Codes // IEEE medical device codes
handler = new LoincIeeeMedicalDeviceCodeHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincIeeeMedicalDeviceCodeHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE.getCode(), LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Imaging Document Codes // Imaging document codes
handler = new LoincImagingDocumentCodeHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincImagingDocumentCodeHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_IMAGING_DOCUMENT_CODES_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_IMAGING_DOCUMENT_CODES_FILE.getCode(), LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Group File // Group
handler = new LoincGroupFileHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincGroupFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_GROUP_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_GROUP_FILE.getCode(), LOINC_GROUP_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Group Terms File // Group terms
handler = new LoincGroupTermsFileHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincGroupTermsFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_GROUP_TERMS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_GROUP_TERMS_FILE.getCode(), LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Parent Group File // Parent group
handler = new LoincParentGroupFileHandler(code2concept, valueSets, conceptMaps, uploadProperties); handler = new LoincParentGroupFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, LOINC_PARENT_GROUP_FILE, handler, ',', QuoteMode.NON_NUMERIC, false); iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PARENT_GROUP_FILE.getCode(), LOINC_PARENT_GROUP_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
IOUtils.closeQuietly(theDescriptors); IOUtils.closeQuietly(theDescriptors);
@ -580,7 +579,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
ValueSet retVal = new ValueSet(); ValueSet retVal = new ValueSet();
retVal.setId("loinc-all"); retVal.setId("loinc-all");
retVal.setUrl("http://loinc.org/fhir/ValueSet/loinc-all"); retVal.setUrl("http://loinc.org/vs");
retVal.setVersion("1.0.0"); retVal.setVersion("1.0.0");
retVal.setName("All LOINC codes"); retVal.setName("All LOINC codes");
retVal.setStatus(Enumerations.PublicationStatus.ACTIVE); retVal.setStatus(Enumerations.PublicationStatus.ACTIVE);
@ -752,7 +751,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
private void verifyOptionalFilesExist(List<String> theExpectedFilenameFragments) { private void verifyOptionalFilesExist(List<String> theExpectedFilenameFragments) {
List<String> notFound = notFound(theExpectedFilenameFragments); List<String> notFound = notFound(theExpectedFilenameFragments);
if (!notFound.isEmpty()) { if (!notFound.isEmpty()) {
ourLog.warn("Could not find the following optional file: " + notFound); ourLog.warn("Could not find the following optional files: " + notFound);
} }
} }

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
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@ -34,6 +34,7 @@ import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Properties; import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.*; import static org.apache.commons.lang3.StringUtils.*;
public abstract class BaseLoincHandler implements IRecordHandler { public abstract class BaseLoincHandler implements IRecordHandler {
@ -114,7 +115,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
conceptMap.setId(theMapping.getConceptMapId()); conceptMap.setId(theMapping.getConceptMapId());
conceptMap.setUrl(theMapping.getConceptMapUri()); conceptMap.setUrl(theMapping.getConceptMapUri());
conceptMap.setName(theMapping.getConceptMapName()); conceptMap.setName(theMapping.getConceptMapName());
conceptMap.setVersion(myUploadProperties.getProperty("conceptmap.version")); conceptMap.setVersion(myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()));
conceptMap.setPublisher(REGENSTRIEF_INSTITUTE_INC); conceptMap.setPublisher(REGENSTRIEF_INSTITUTE_INC);
conceptMap.addContact() conceptMap.addContact()
.setName(REGENSTRIEF_INSTITUTE_INC) .setName(REGENSTRIEF_INSTITUTE_INC)

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
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@ -31,7 +31,9 @@ import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Properties; import java.util.Properties;
import static org.apache.commons.lang3.StringUtils.*; import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincAnswerListHandler extends BaseLoincHandler { public class LoincAnswerListHandler extends BaseLoincHandler {
@ -72,7 +74,7 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
} }
// Answer list ValueSet // Answer list ValueSet
ValueSet vs = getValueSet(answerListId, "http://loinc.org/vs/" + answerListId, answerListName, "answerlist.version"); ValueSet vs = getValueSet(answerListId, "http://loinc.org/vs/" + answerListId, answerListName, LOINC_ANSWERLIST_VERSION.getCode());
if (vs.getIdentifier().isEmpty()) { if (vs.getIdentifier().isEmpty()) {
vs.addIdentifier() vs.addIdentifier()
.setSystem("urn:ietf:rfc:3986") .setSystem("urn:ietf:rfc:3986")

142
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java Normal file
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@ -0,0 +1,142 @@
package ca.uhn.fhir.jpa.term.loinc;
/*
* #%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 java.util.Collections;
import java.util.HashMap;
import java.util.Map;
/**
* This enum is used to facilitate configurable filenames when uploading LOINC.
*/
public enum LoincUploadPropertiesEnum {
/**
* Sorting agnostic.
*/
LOINC_UPLOAD_PROPERTIES_FILE("loincupload.properties"),
/*
* MANDATORY
*/
// Answer lists (ValueSets of potential answers/values for LOINC "questions")
LOINC_ANSWERLIST_FILE("loinc.answerlist.file"),
LOINC_ANSWERLIST_FILE_DEFAULT("AnswerList.csv"),
// Answer list links (connects LOINC observation codes to answer list codes)
LOINC_ANSWERLIST_LINK_FILE("loinc.answerlist.link.file"),
LOINC_ANSWERLIST_LINK_FILE_DEFAULT("LoincAnswerListLink.csv"),
// Document ontology
LOINC_DOCUMENT_ONTOLOGY_FILE("loinc.document.ontology.file"),
LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT("DocumentOntology.csv"),
// LOINC codes
LOINC_FILE("loinc.file"),
LOINC_FILE_DEFAULT("LoincTable/Loinc.csv"),
// LOINC hierarchy
LOINC_HIERARCHY_FILE("loinc.hierarchy.file"),
LOINC_HIERARCHY_FILE_DEFAULT("MultiAxialHierarchy.csv"),
// IEEE medical device codes
LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE("loinc.ieee.medical.device.code.mapping.table.file"),
LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT("LoincIeeeMedicalDeviceCodeMappingTable.csv"),
// Imaging document codes
LOINC_IMAGING_DOCUMENT_CODES_FILE("loinc.imaging.document.codes.file"),
LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT("ImagingDocumentCodes.csv"),
// Part
LOINC_PART_FILE("loinc.part.file"),
LOINC_PART_FILE_DEFAULT("Part.csv"),
// Part link
LOINC_PART_LINK_FILE("loinc.part.link.file"),
LOINC_PART_LINK_FILE_DEFAULT("LoincPartLink.csv"),
// Part related code mapping
LOINC_PART_RELATED_CODE_MAPPING_FILE("loinc.part.related.code.mapping.file"),
LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT("PartRelatedCodeMapping.csv"),
// RSNA playbook
LOINC_RSNA_PLAYBOOK_FILE("loinc.rsna.playbook.file"),
LOINC_RSNA_PLAYBOOK_FILE_DEFAULT("LoincRsnaRadiologyPlaybook.csv"),
// Top 2000 codes - SI
LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE("loinc.top2000.common.lab.results.si.file"),
LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT("Top2000CommonLabResultsSi.csv"),
// Top 2000 codes - US
LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE("loinc.top2000.common.lab.results.us.file"),
LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT("Top2000CommonLabResultsUs.csv"),
// Universal lab order ValueSet
LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE("loinc.universal.lab.order.valueset.file"),
LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT("LoincUniversalLabOrdersValueSet.csv"),
/*
* OPTIONAL
*/
// This is the version identifier for the answer list file
LOINC_ANSWERLIST_VERSION("loinc.answerlist.version"),
// This is the version identifier for uploaded ConceptMap resources
LOINC_CONCEPTMAP_VERSION("loinc.conceptmap.version"),
// Group
LOINC_GROUP_FILE("loinc.group.file"),
LOINC_GROUP_FILE_DEFAULT("Group.csv"),
// Group terms
LOINC_GROUP_TERMS_FILE("loinc.group.terms.file"),
LOINC_GROUP_TERMS_FILE_DEFAULT("GroupLoincTerms.csv"),
// Parent group
LOINC_PARENT_GROUP_FILE("loinc.parent.group.file"),
LOINC_PARENT_GROUP_FILE_DEFAULT("ParentGroup.csv");
private static Map<String, LoincUploadPropertiesEnum> ourValues;
private String myCode;
LoincUploadPropertiesEnum(String theCode) {
myCode = theCode;
}
public String getCode() {
return myCode;
}
public static LoincUploadPropertiesEnum fromCode(String theCode) {
if (ourValues == null) {
HashMap<String, LoincUploadPropertiesEnum> values = new HashMap<String, LoincUploadPropertiesEnum>();
for (LoincUploadPropertiesEnum next : values()) {
values.put(next.getCode(), next);
}
ourValues = Collections.unmodifiableMap(values);
}
return ourValues.get(theCode);
}
/**
* Convert from Enum ordinal to Enum type.
*
* Usage:
*
* <code>LoincUploadPropertiesEnum loincUploadPropertiesEnum = LoincUploadPropertiesEnum.values[ordinal];</code>
*/
public static final LoincUploadPropertiesEnum values[] = values();
}

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java
View File

@ -1,8 +1,6 @@
package ca.uhn.fhir.jpa.provider.dstu3; package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc; import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil; import ca.uhn.fhir.util.TestUtil;
@ -20,6 +18,7 @@ import java.util.List;
import java.util.zip.ZipEntry; import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream; import java.util.zip.ZipOutputStream;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.hamcrest.CoreMatchers.containsString; import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.greaterThan; import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.*; import static org.junit.Assert.*;
@ -37,24 +36,24 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
ByteArrayOutputStream bos = new ByteArrayOutputStream(); ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos); ZipOutputStream zos = new ZipOutputStream(bos);
addFile(zos, "loincupload.properties"); addFile(zos, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_FILE); addFile(zos, LOINC_PART_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_FILE); addFile(zos, LOINC_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE); addFile(zos, LOINC_HIERARCHY_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE); addFile(zos, LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE); addFile(zos, LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_GROUP_FILE); addFile(zos, LOINC_GROUP_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_GROUP_TERMS_FILE); addFile(zos, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PARENT_GROUP_FILE); addFile(zos, LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE); addFile(zos, LOINC_PART_LINK_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_RELATED_CODE_MAPPING_FILE); addFile(zos, LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_DOCUMENT_ONTOLOGY_FILE); addFile(zos, LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_RSNA_PLAYBOOK_FILE); addFile(zos, LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE); addFile(zos, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV); addFile(zos, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_IMAGING_DOCUMENT_CODES_FILE); addFile(zos, LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE); addFile(zos, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
addFile(zos, TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE); addFile(zos, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
zos.close(); zos.close();

43
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
View File

@ -24,6 +24,7 @@ import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.hamcrest.Matchers.*; import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*; import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.any;
@ -258,7 +259,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
// All LOINC codes // All LOINC codes
assertTrue(valueSets.containsKey("loinc-all")); assertTrue(valueSets.containsKey("loinc-all"));
vs = valueSets.get("loinc-all"); vs = valueSets.get("loinc-all");
assertEquals("http://loinc.org/fhir/ValueSet/loinc-all", vs.getUrl()); assertEquals("http://loinc.org/vs", vs.getUrl());
assertEquals("1.0.0", vs.getVersion()); assertEquals("1.0.0", vs.getVersion());
assertEquals("All LOINC codes", vs.getName()); assertEquals("All LOINC codes", vs.getName());
assertEquals(Enumerations.PublicationStatus.ACTIVE, vs.getStatus()); assertEquals(Enumerations.PublicationStatus.ACTIVE, vs.getStatus());
@ -341,8 +342,8 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
@Test @Test
public void testLoadLoincMissingMandatoryFiles() throws IOException { public void testLoadLoincMissingMandatoryFiles() throws IOException {
myFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE); myFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
myFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE); myFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
// Actually do the load // Actually do the load
try { try {
@ -356,24 +357,24 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
} }
public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException { public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE); theFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE); theFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_TERMS_FILE); theFiles.addFileZip("/loinc/", LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PARENT_GROUP_FILE); theFiles.addFileZip("/loinc/", LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_FILE, TerminologyLoaderSvcImpl.LOINC_FILE); theFiles.addFileZip("/loinc/", LOINC_FILE_DEFAULT.getCode(), LOINC_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE); theFiles.addFileZip("/loinc/", LOINC_HIERARCHY_FILE_DEFAULT.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE); theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_FILE_DEFAULT.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE); theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_FILE, TerminologyLoaderSvcImpl.LOINC_PART_FILE); theFiles.addFileZip("/loinc/", LOINC_PART_FILE_DEFAULT.getCode(), LOINC_PART_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE); theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_DEFAULT.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_RELATED_CODE_MAPPING_FILE); theFiles.addFileZip("/loinc/", LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_DOCUMENT_ONTOLOGY_FILE); theFiles.addFileZip("/loinc/", LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_RSNA_PLAYBOOK_FILE); theFiles.addFileZip("/loinc/", LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE); theFiles.addFileZip("/loinc/", LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV); theFiles.addFileZip("/loinc/", LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_IMAGING_DOCUMENT_CODES_FILE); theFiles.addFileZip("/loinc/", LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE); theFiles.addFileZip("/loinc/", LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE); theFiles.addFileZip("/loinc/", LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
} }
@Test @Test

94
hapi-fhir-jpaserver-base/src/test/resources/loinc/loincupload.properties
View File

@ -1,7 +1,95 @@
#################
### MANDATORY ###
#################
# This is the version identifier for the AnswerList file # Answer lists (ValueSets of potential answers/values for LOINC "questions")
answerlist.version=Beta.1 ## Default value if key not provided: AnswerList.csv
## File must be present
loinc.answerlist.file=AnswerList.csv
# Answer list links (connects LOINC observation codes to answer list codes)
## Default value if key not provided: LoincAnswerListLink.csv
## File must be present
loinc.answerlist.link.file=LoincAnswerListLink.csv
# Document ontology
## Default value if key not provided: DocumentOntology.csv
## File must be present
loinc.document.ontology.file=DocumentOntology.csv
# LOINC codes
## Default value if key not provided: LoincTable/Loinc.csv
## File must be present
loinc.file=LoincTable/Loinc.csv
# LOINC hierarchy
## Default value if key not provided: MultiAxialHierarchy.csv
## File must be present
loinc.hierarchy.file=MultiAxialHierarchy.csv
# IEEE medical device codes
## Default value if key not provided: LoincIeeeMedicalDeviceCodeMappingTable.csv
## File must be present
loinc.ieee.medical.device.code.mapping.table.file=LoincIeeeMedicalDeviceCodeMappingTable.csv
# Imaging document codes
## Default value if key not provided: ImagingDocumentCodes.csv
## File must be present
loinc.imaging.document.codes.file=ImagingDocumentCodes.csv
# Part
## Default value if key not provided: Part.csv
## File must be present
loinc.part.file=Part.csv
# Part link
## Default value if key not provided: LoincPartLink.csv
## File must be present
loinc.part.link.file=LoincPartLink.csv
# Part related code mapping
## Default value if key not provided: PartRelatedCodeMapping.csv
## File must be present
loinc.part.related.code.mapping.file=PartRelatedCodeMapping.csv
# RSNA playbook
## Default value if key not provided: LoincRsnaRadiologyPlaybook.csv
## File must be present
loinc.rsna.playbook.file=LoincRsnaRadiologyPlaybook.csv
# Top 2000 codes - SI
## Default value if key not provided: Top2000CommonLabResultsSi.csv
## File must be present
loinc.top2000.common.lab.results.si.file=Top2000CommonLabResultsSi.csv
# Top 2000 codes - US
## Default value if key not provided: Top2000CommonLabResultsUs.csv
## File must be present
loinc.top2000.common.lab.results.us.file=Top2000CommonLabResultsUs.csv
# Universal lab order ValueSet
## Default value if key not provided: LoincUniversalLabOrdersValueSet.csv
## File must be present
loinc.universal.lab.order.valueset.file=LoincUniversalLabOrdersValueSet.csv
################
### OPTIONAL ###
################
# This is the version identifier for the answer list file
## Key may be omitted
loinc.answerlist.version=Beta.1
# This is the version identifier for uploaded ConceptMap resources # This is the version identifier for uploaded ConceptMap resources
conceptmap.version=Beta.1 ## Key may be omitted
loinc.conceptmap.version=Beta.1
# Group
## Default value if key not provided: Group.csv
## File may be omitted
loinc.group.file=Group.csv
# Group terms
## Default value if key not provided: GroupLoincTerms.csv
## File may be omitted
loinc.group.terms.file=GroupLoincTerms.csv
# Parent group
## Default value if key not provided: ParentGroup.csv
## File may be omitted
loinc.parent.group.file=ParentGroup.csv