
001/*- 002 * #%L 003 * HAPI FHIR JPA Server 004 * %% 005 * Copyright (C) 2014 - 2023 Smile CDR, Inc. 006 * %% 007 * Licensed under the Apache License, Version 2.0 (the "License"); 008 * you may not use this file except in compliance with the License. 009 * You may obtain a copy of the License at 010 * 011 * http://www.apache.org/licenses/LICENSE-2.0 012 * 013 * Unless required by applicable law or agreed to in writing, software 014 * distributed under the License is distributed on an "AS IS" BASIS, 015 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 016 * See the License for the specific language governing permissions and 017 * limitations under the License. 018 * #L% 019 */ 020package ca.uhn.fhir.jpa.term.loinc; 021 022import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion; 023import ca.uhn.fhir.jpa.entity.TermConcept; 024import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc; 025import org.apache.commons.csv.CSVRecord; 026import org.hl7.fhir.r4.model.ConceptMap; 027import org.hl7.fhir.r4.model.ValueSet; 028 029import java.util.List; 030import java.util.Map; 031import java.util.Properties; 032 033import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*; 034import static org.apache.commons.lang3.StringUtils.isNotBlank; 035import static org.apache.commons.lang3.StringUtils.trim; 036 037public class LoincAnswerListHandler extends BaseLoincHandler { 038 039 private final Map<String, TermConcept> myCode2Concept; 040 private final TermCodeSystemVersion myCodeSystemVersion; 041 042 public LoincAnswerListHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept, 043 List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties, String theCopyrightStatement) { 044 super(theCode2concept, theValueSets, theConceptMaps, theUploadProperties, theCopyrightStatement); 045 myCodeSystemVersion = theCodeSystemVersion; 046 myCode2Concept = theCode2concept; 047 } 048 049 @Override 050 public void accept(CSVRecord theRecord) { 051 052 // this is the code for the list (will repeat) 053 String answerListId = trim(theRecord.get("AnswerListId")); 054 String answerListName = trim(theRecord.get("AnswerListName")); 055 String answerListOid = trim(theRecord.get("AnswerListOID")); 056 String externallyDefined = trim(theRecord.get("ExtDefinedYN")); 057 String extenrallyDefinedCs = trim(theRecord.get("ExtDefinedAnswerListCodeSystem")); 058 String externallyDefinedLink = trim(theRecord.get("ExtDefinedAnswerListLink")); 059 // this is the code for the actual answer (will not repeat) 060 String answerString = trim(theRecord.get("AnswerStringId")); 061 String sequenceNumber = trim(theRecord.get("SequenceNumber")); 062 String displayText = trim(theRecord.get("DisplayText")); 063 String extCodeId = trim(theRecord.get("ExtCodeId")); 064 String extCodeDisplayName = trim(theRecord.get("ExtCodeDisplayName")); 065 String extCodeSystem = trim(theRecord.get("ExtCodeSystem")); 066 String extCodeSystemVersion = trim(theRecord.get("ExtCodeSystemVersion")); 067 068 069 // Answer list code 070 if (!myCode2Concept.containsKey(answerListId)) { 071 TermConcept concept = new TermConcept(myCodeSystemVersion, answerListId); 072 concept.setDisplay(answerListName); 073 myCode2Concept.put(answerListId, concept); 074 } 075 076 // Answer list ValueSet 077 String valueSetId; 078 String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode()); 079 if (codeSystemVersionId != null) { 080 valueSetId = answerListId + "-" + codeSystemVersionId; 081 } else { 082 valueSetId = answerListId; 083 } 084 ValueSet vs = getValueSet(valueSetId, "http://loinc.org/vs/" + answerListId, answerListName, LOINC_ANSWERLIST_VERSION.getCode()); 085 if (vs.getIdentifier().isEmpty()) { 086 vs.addIdentifier() 087 .setSystem("urn:ietf:rfc:3986") 088 .setValue("urn:oid:" + answerListOid); 089 } 090 091 if (isNotBlank(answerString)) { 092 093 // Answer code 094 if (!myCode2Concept.containsKey(answerString)) { 095 TermConcept concept = new TermConcept(myCodeSystemVersion, answerString); 096 concept.setDisplay(displayText); 097 if (isNotBlank(sequenceNumber) && sequenceNumber.matches("^[0-9]$")) { 098 concept.setSequence(Integer.parseInt(sequenceNumber)); 099 } 100 myCode2Concept.put(answerString, concept); 101 } 102 103 vs 104 .getCompose() 105 .getIncludeFirstRep() 106 .setSystem(ITermLoaderSvc.LOINC_URI) 107 .setVersion(codeSystemVersionId) 108 .addConcept() 109 .setCode(answerString) 110 .setDisplay(displayText); 111 112 } 113 114 } 115 116}