add stub for HLA nomenclature terminology upload

2019-05-31 14:01:24 -06:00 · 2019-05-31 14:01:24 -06:00 · 1f5cbc36b3
parent 6d8465abe6
commit 1f5cbc36b3
4 changed files with 378 additions and 6 deletions
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseTerminologyUploaderProvider.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseTerminologyUploaderProvider.java
@ -115,12 +115,18 @@ public abstract class BaseTerminologyUploaderProvider extends BaseJpaProvider {
 			url = defaultString(url);

 			UploadStatistics stats;
-			if (IHapiTerminologyLoaderSvc.SCT_URI.equals(url)) {
-				stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
-			} else if (IHapiTerminologyLoaderSvc.LOINC_URI.equals(url)) {
-				stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
-			} else {
-				throw new InvalidRequestException("Unknown URL: " + url);
+			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);
 			}

 			Parameters retVal = new Parameters();
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java
@ -28,10 +28,13 @@ import java.util.List;

 public interface IHapiTerminologyLoaderSvc {

+	String IMGTHLA_URI = "http://www.ebi.ac.uk/ipd/imgt/hla";
 	String LOINC_URI = "http://loinc.org";
 	String SCT_URI = "http://snomed.info/sct";
 	String IEEE_11073_10101_URI = "urn:iso:std:iso:11073:10101";

+	UploadStatistics loadImgthla(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
+
 	UploadStatistics loadLoinc(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);

 	UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
@ -63,6 +63,8 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 	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";
+	public static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
+	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";
@ -187,6 +189,26 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {

 	}

+	@Override
+	public UploadStatistics loadImgthla(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
+		LoadedFileDescriptors descriptors = null;
+		try {
+			descriptors = new LoadedFileDescriptors(theFiles);
+			List<String> mandatoryFilenameFragments = Arrays.asList(
+				IMGTHLA_HLA_NOM_TXT,
+				IMGTHLA_HLA_XML
+			);
+			descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
+
+			ourLog.info("Beginning IMGTHLA processing");
+
+			return processImgthlaFiles(descriptors, theRequestDetails);
+		}
+		finally {
+			IOUtils.closeQuietly(descriptors);
+		}
+	}
+
 	@Override
 	public UploadStatistics loadLoinc(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
 		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
@ -235,6 +257,125 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		}
 	}

+	UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
+		final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
+		final Map<String, TermConcept> code2concept = new HashMap<>();
+		final List<ValueSet> valueSets = new ArrayList<>();
+		final List<ConceptMap> conceptMaps = new ArrayList<>();
+
+		CodeSystem imgthlaCs;
+		try {
+			String imgthlaCsString = IOUtils.toString(BaseHapiTerminologySvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/imgthla/imgthla.xml"), Charsets.UTF_8);
+			imgthlaCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, imgthlaCsString);
+		} catch (IOException e) {
+			throw new InternalErrorException("Failed to load imgthla.xml", e);
+		}
+
+		Map<String, CodeSystem.PropertyType> propertyNamesToTypes = new HashMap<>();
+		for (CodeSystem.PropertyComponent nextProperty : imgthlaCs.getProperty()) {
+			String nextPropertyCode = nextProperty.getCode();
+			CodeSystem.PropertyType nextPropertyType = nextProperty.getType();
+			if (isNotBlank(nextPropertyCode)) {
+				propertyNamesToTypes.put(nextPropertyCode, nextPropertyType);
+			}
+		}
+
+		boolean foundHlaNom = false;
+		boolean foundHlaXml = false;
+		for (FileDescriptor nextZipBytes : theDescriptors.getUncompressedFileDescriptors()) {
+			String nextFilename = nextZipBytes.getFilename();
+
+			if(!IMGTHLA_HLA_NOM_TXT.equals(nextFilename)
+				&& !IMGTHLA_HLA_XML.equals(nextFilename)) {
+				ourLog.info("Skipping unexpected file {}", nextFilename);
+				continue;
+			}
+
+			if(IMGTHLA_HLA_NOM_TXT.equals(nextFilename)) {
+				// process colon-delimited hla_nom.txt file
+				ourLog.info("Processing file {}", nextFilename);
+
+//				IRecordHandler handler = new HlaNomTxtHandler(codeSystemVersion, code2concept, propertyNamesToTypes);
+//				AntigenSource antigenSource = new WmdaAntigenSource(hlaNomFilename, relSerSerFilename, relDnaSerFilename);
+
+				Reader reader = null;
+				try {
+					reader = new InputStreamReader(nextZipBytes.getInputStream(), Charsets.UTF_8);
+
+					if (ourLog.isTraceEnabled()) {
+						String contents = IOUtils.toString(reader);
+						ourLog.info("File contents for: {}\n{}", nextFilename, contents);
+						reader = new StringReader(contents);
+					}
+
+					LineNumberReader lnr = new LineNumberReader(reader);
+					while(lnr.readLine() != null) {}
+					ourLog.warn("Lines read from {}:  {}", nextFilename, lnr.getLineNumber());
+
+				} catch (IOException e) {
+					throw new InternalErrorException(e);
+				}
+				finally {
+					IOUtils.closeQuietly(reader);
+				}
+
+				foundHlaNom = true;
+			}
+
+			if(IMGTHLA_HLA_XML.equals(nextFilename)) {
+				// process hla.xml file
+				ourLog.info("Processing file {}", nextFilename);
+
+//				IRecordHandler handler = new HlaXmlHandler(codeSystemVersion, code2concept, propertyNamesToTypes);
+//				AlleleSource alleleSource = new HlaXmlAlleleSource(hlaXmlFilename);
+
+				Reader reader = null;
+				try {
+					reader = new InputStreamReader(nextZipBytes.getInputStream(), Charsets.UTF_8);
+
+					if (ourLog.isTraceEnabled()) {
+						String contents = IOUtils.toString(reader);
+						ourLog.info("File contents for: {}\n{}", nextFilename, contents);
+						reader = new StringReader(contents);
+					}
+
+					LineNumberReader lnr = new LineNumberReader(reader);
+					while(lnr.readLine() != null) {}
+					ourLog.warn("Lines read from {}:  {}", nextFilename, lnr.getLineNumber());
+
+				} catch (IOException e) {
+					throw new InternalErrorException(e);
+				}
+				finally {
+					IOUtils.closeQuietly(reader);
+				}
+
+				foundHlaXml = true;
+			}
+
+		}
+
+		if (!foundHlaNom) {
+			throw new InvalidRequestException("Did not find file matching " + IMGTHLA_HLA_NOM_TXT);
+		}
+
+		if (!foundHlaXml) {
+			throw new InvalidRequestException("Did not find file matching " + IMGTHLA_HLA_XML);
+		}
+
+		int valueSetCount = valueSets.size();
+		int rootConceptCount = codeSystemVersion.getConcepts().size();
+		int conceptCount = code2concept.size();
+		ourLog.info("Have {} total concepts, {} root concepts, {} ValueSets", conceptCount, rootConceptCount, valueSetCount);
+
+		// remove this when fully implemented ...
+		throw new InternalErrorException("HLA nomenclature terminology upload not yet fully implemented.");
+
+//		IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, imgthlaCs, valueSets, conceptMaps);
+//
+//		return new UploadStatistics(conceptCount, target);
+	}
+
 	UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
 		final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
 		final Map<String, TermConcept> code2concept = new HashMap<>();
--- a/hapi-fhir-jpaserver-base/src/main/resources/ca/uhn/fhir/jpa/term/imgthla/imgthla.xml
+++ b/hapi-fhir-jpaserver-base/src/main/resources/ca/uhn/fhir/jpa/term/imgthla/imgthla.xml
@ -0,0 +1,222 @@
+<!--
+Links to additional information on HLA nomenclature:
+
+http://hla.alleles.org/nomenclature/
+http://www.ebi.ac.uk/ipd/imgt/hla
+
+New releases of the IPD-IMGT/HLA database are published periodically,
+typically once every 3 months.
+
+https://www.ebi.ac.uk/ipd/imgt/hla/docs/release.html
+
+In some cases, a new database release may delete or modify the definition
+of concepts introduced in a previous release.  For that reason, the HLA
+nomenclature is a versioned code system, using the IPD-IMGT/HLA release
+as its CodeSystem.version.
+
+Note that the following set of codes constitute the IMGTHLA code system:
+ - "allele" names, including ...
+   - allele-group names, e.g. HLA-A*01
+   - protein-level names, e.g. HLA-A*01:01
+   - exomic (coding-region level) names, e.g. HLA-A*01:01:01
+   - genomic (coding plus non-coding-region level) names, e.g. HLA-A*01:01:01:01
+ - P group names, e.g. HLA-A*01:01:01G
+ - G group names, e.g. HLA-A*01:01P
+ - serotype names, e.g. HLA-A1
+
+-->
+<!--
+Version History of this specification
+0.1 | published 2019-05-08
+-->
+<CodeSystem xmlns="http://hl7.org/fhir">
+  <id value="imgthla"/>
+
+  <!-- This url is unchanged for all versions of IMGTHLA. There
+    can only be one correct Code System resource for each value of the
+    version attribute (at least, only one per server) -->
+  <url value="http://www.ebi.ac.uk/ipd/imgt/hla"/>
+
+  <!-- the HL7 v3 OID assigned to IPD-IMGT/HLA nomenclature -->
+  <identifier>
+    <system value="urn:ietf:rfc:3986"/>
+    <value value="urn:oid:2.16.840.1.113883.6.341"/>
+  </identifier>
+
+  <!--
+  // if a version is specified:
+  <version value="2.59"/>
+  -->
+
+  <!-- if a specific version is specified, this information should be in the name (e.g. IMGTHLA_3360) and title -->
+  <name value="IMGTHLA"/>
+  <title value="HLA Nomenclature"/>
+  <status value="active"/>
+  <experimental value="true"/>
+
+  <publisher value="WHO Nomenclature Committee for Factors of the HLA System"/>
+  <contact>
+    <telecom>
+      <system value="url"/>
+      <value value="http://hla.alleles.org/nomenclature/committee.html"/>
+    </telecom>
+    <telecom>
+      <system value="url"/>
+      <value value="https://www.ebi.ac.uk/ipd/imgt/hla/"/>
+    </telecom>
+    <telecom>
+      <system value="url"/>
+      <value value="https://github.com/ANHIG/IMGTHLA"/>
+    </telecom>
+    <telecom>
+      <system value="other"/>
+      <value value="Professor Steven G. E. Marsh"/>
+    </telecom>
+    <telecom>
+      <system value="other"/>
+      <value value="hla [at] alleles [dot] org"/>
+    </telecom>
+  </contact>
+
+  <!--
+  <date value=[date for this version]"/>
+  -->
+  <description value="The IPD-IMGT/HLA Database provides a specialist database
+for sequences of the human major histocompatibility complex (MHC) and includes
+the official sequences named by the WHO Nomenclature Committee For Factors of
+the HLA System. The IPD-IMGT/HLA Database is part of the international
+ImMunoGeneTics project (IMGT).
+
+The IPD and IMGT/HLA database is described in the following publications.
+
+Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SGE:  
+The IPD and IMGT/HLA database: allele variant databases.  
+Nucleic Acids Research (2014) 43 Suppl 1:D423-31  
+&lt;https://doi.org/10.1093/nar/gku1161&gt;
+
+Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE:  
+IMGT/HLA - a sequence database for the human major histocompatibility complex  
+Tissue Antigens (2000), 55:280-287  
+&lt;https://doi.org/10.1034/j.1399-0039.2000.550314.x&gt;
+"/>
+  <copyright value="This content from the IPD-IMGT/HLA database is copyright © 2003 Anthony Nolan Research Institute and the WHO Nomenclature Committee for Factors of the HLA System, and available at no cost under a Creative Commons Attribution-NoDerivs License."/>
+  <caseSensitive  value="true"/>
+
+  <valueSet value="http://www.ebi.ac.uk/ipd/imgt/hla/vs"/>
+
+  <hierarchyMeaning value="grouped-by"/>
+  <compositional value="false"/> <!-- no compositional grammar defined by IPD-IMGT/HLA -->
+  <versionNeeded value="true"/>
+
+  <content value="complete"/>
+
+<!-- <count value="65000"/>... if working with a specific version, you could nominate a count of the total number of concepts -->
+
+  <!-- properties. There are 3 kinds of properties:
+    fhir: display, designation; these are not described here since they are inherent in the specification
+    infrastructural: defined by FHIR, but documented here for IMGTHLA
+    IMGTHLA properties: defined by the HLA nomenclature
+  -->
+  <!-- first, the infrastructural properties - inherited from FHIR, but documented here -->
+  <property>
+    <code value="inactive"/>
+    <uri value="http://hl7.org/fhir/concept-properties#inactive"/>
+    <description value="True if the concept is not considered active - e.g. not a valid concept any more. Property type is boolean, default value is false"/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="deprecated"/>
+    <uri value="http://hl7.org/fhir/concept-properties#deprecated"/>
+    <description value="The date at which a concept was deprecated. Concepts that are deprecated but not inactive can still be used, but their use is discouraged, and they should be expected to be made inactive in a future release. Property type is dateTime"/>
+    <type value="dateTime"/>
+  </property>
+  <property>
+    <code value="parent"/>
+    <uri value="http://hl7.org/fhir/concept-properties#parent"/>
+    <description value="The concept identified in this property is a parent of the concept on which it is a property. The property type will be 'code'. The meaning of 'parent' is defined by the hierarchyMeaning attribute"/>
+    <type value="code"/>
+  </property>
+  <!--
+    IMGTHLA concept properties.
+  -->
+  <property>
+    <code value="allele_id"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/allele_id"/>
+    <description value="IPD-IMGT/HLA database accession number."/>
+    <type value="string"/>
+  </property>
+  <property>
+    <code value="expression_suffix"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/expression_suffix"/>
+    <description value="Expression suffix (if any) assigned to the concept.  See http://hla.alleles.org/nomenclature/naming.html"/>
+    <type value="string"/>
+  </property>
+  <property>
+    <code value="hla_g_group"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/hla_g_group"/>
+    <description value="HLA G group containing this concept.  See http://hla.alleles.org/alleles/g_groups.html"/>
+    <type value="code"/>
+  </property>
+  <property>
+    <code value="hla_p_group"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/hla_p_group"/>
+    <description value="HLA P group containing this concept.  See http://hla.alleles.org/alleles/p_groups.html"/>
+    <type value="code"/>
+  </property>
+  <property>
+    <code value="is_allele_group_concept"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/is_allele_group_concept"/>
+    <description value="True if the concept is an allele group.  See http://hla.alleles.org/nomenclature/naming.html"/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="is_dna_concept"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/is_dna_concept"/>
+    <description value="True if the concept is DNA-level (as opposed to serology)."/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="is_exomic_concept"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/is_exomic_concept"/>
+    <description value="True if the concept represents a distinct (within this CodeSystem.version) nucleotide sequence across all coding regions of the full gene.  See http://hla.alleles.org/nomenclature/naming.html"/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="is_hla_g_group_concept"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/is_hla_g_group_concept"/>
+    <description value="True if the concept is a HLA G group.  See http://hla.alleles.org/alleles/g_groups.html"/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="is_hla_p_group_concept"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/is_hla_p_group_concept"/>
+    <description value="True if the concept is a HLA P group.  See http://hla.alleles.org/alleles/p_groups.html"/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="is_genomic_concept"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/is_genomic_concept"/>
+    <description value="True if the concept represents a distinct (within this CodeSystem.version) nucleotide sequence across all coding and non-coding regions of the full gene.  See http://hla.alleles.org/nomenclature/naming.html"/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="is_protein_concept"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/is_protein_concept"/>
+    <description value="True if the concept represents a distinct amino acid sequence across the full gene.  See http://hla.alleles.org/nomenclature/naming.html"/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="is_serology_concept"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/is_serology_concept"/>
+    <description value="True if the concept is serology-level (as opposed to DNA)."/>
+    <type value="boolean"/>
+  </property>
+  <property>
+    <code value="locus_name"/>
+    <uri value="http://www.ebi.ac.uk/ipd/imgt/hla/property/locus_name"/>
+    <description value="DNA or serology locus name, e.g. HLA-A, HLA-DR"/>
+    <type value="string"/>
+  </property>
+
+</CodeSystem>
+