001/*-
002 * #%L
003 * HAPI FHIR JPA Server
004 * %%
005 * Copyright (C) 2014 - 2025 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.TermConcept;
023import ca.uhn.fhir.jpa.term.IZipContentsHandlerCsv;
024import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
025import org.apache.commons.csv.CSVRecord;
026
027import java.util.Map;
028
029import static org.apache.commons.lang3.StringUtils.isBlank;
030import static org.apache.commons.lang3.StringUtils.trim;
031import static org.apache.commons.lang3.StringUtils.trimToEmpty;
032
033public class LoincLinguisticVariantHandler implements IZipContentsHandlerCsv {
034
035        private final Map<String, TermConcept> myCode2Concept;
036        private final String myLanguageCode;
037
038        public LoincLinguisticVariantHandler(Map<String, TermConcept> theCode2Concept, String theLanguageCode) {
039                myCode2Concept = theCode2Concept;
040                myLanguageCode = theLanguageCode;
041        }
042
043        @Override
044        public void accept(CSVRecord theRecord) {
045
046                String loincNumber = trim(theRecord.get("LOINC_NUM"));
047                if (isBlank(loincNumber)) {
048                        return;
049                }
050
051                TermConcept concept = myCode2Concept.get(loincNumber);
052                if (concept == null) {
053                        return;
054                }
055
056                // The following should be created as designations for each term:
057                // COMPONENT:PROPERTY:TIME_ASPCT:SYSTEM:SCALE_TYP:METHOD_TYP (as colon-separated concatenation - FormalName)
058                // SHORTNAME
059                // LONG_COMMON_NAME
060                // LinguisticVariantDisplayName
061
062                // -- add formalName designation
063                StringBuilder fullySpecifiedName = new StringBuilder();
064                fullySpecifiedName.append(trimToEmpty(theRecord.get("COMPONENT") + ":"));
065                fullySpecifiedName.append(trimToEmpty(theRecord.get("PROPERTY") + ":"));
066                fullySpecifiedName.append(trimToEmpty(theRecord.get("TIME_ASPCT") + ":"));
067                fullySpecifiedName.append(trimToEmpty(theRecord.get("SYSTEM") + ":"));
068                fullySpecifiedName.append(trimToEmpty(theRecord.get("SCALE_TYP") + ":"));
069                fullySpecifiedName.append(trimToEmpty(theRecord.get("METHOD_TYP")));
070
071                String fullySpecifiedNameStr = fullySpecifiedName.toString();
072
073                // skip if COMPONENT, PROPERTY, TIME_ASPCT, SYSTEM, SCALE_TYP and METHOD_TYP are all empty
074                if (!fullySpecifiedNameStr.equals(":::::")) {
075                        concept.addDesignation()
076                                        .setLanguage(myLanguageCode)
077                                        .setUseSystem(ITermLoaderSvc.LOINC_URI)
078                                        .setUseCode("FullySpecifiedName")
079                                        .setUseDisplay("FullySpecifiedName")
080                                        .setValue(fullySpecifiedNameStr);
081                }
082
083                // -- other designations
084                addDesignation(theRecord, concept, "SHORTNAME");
085                addDesignation(theRecord, concept, "LONG_COMMON_NAME");
086                addDesignation(theRecord, concept, "LinguisticVariantDisplayName");
087        }
088
089        private void addDesignation(CSVRecord theRecord, TermConcept concept, String fieldName) {
090
091                String field = trim(theRecord.get(fieldName));
092                if (isBlank(field)) {
093                        return;
094                }
095
096                concept.addDesignation()
097                                .setLanguage(myLanguageCode)
098                                .setUseSystem(ITermLoaderSvc.LOINC_URI)
099                                .setUseCode(fieldName)
100                                .setUseDisplay(fieldName)
101                                .setValue(field);
102        }
103}