001/*-
002 * #%L
003 * HAPI FHIR JPA Server
004 * %%
005 * Copyright (C) 2014 - 2024 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 org.apache.commons.csv.CSVRecord;
025import org.hl7.fhir.r4.model.ConceptMap;
026import org.hl7.fhir.r4.model.ValueSet;
027
028import java.util.List;
029import java.util.Map;
030import java.util.Properties;
031
032import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
033import static org.apache.commons.lang3.StringUtils.trim;
034
035public class LoincGroupFileHandler extends BaseLoincHandler implements IZipContentsHandlerCsv {
036
037        public static final String VS_URI_PREFIX = "http://loinc.org/vs/";
038
039        public LoincGroupFileHandler(
040                        Map<String, TermConcept> theCode2concept,
041                        List<ValueSet> theValueSets,
042                        List<ConceptMap> theConceptMaps,
043                        Properties theUploadProperties,
044                        String theCopyrightStatement) {
045                super(theCode2concept, theValueSets, theConceptMaps, theUploadProperties, theCopyrightStatement);
046        }
047
048        @Override
049        public void accept(CSVRecord theRecord) {
050                // "ParentGroupId","GroupId","Group","Archetype","Status","VersionFirstReleased"
051                String parentGroupId = trim(theRecord.get("ParentGroupId"));
052                String groupId = trim(theRecord.get("GroupId"));
053                String groupName = trim(theRecord.get("Group"));
054
055                String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
056                String parentGroupValueSetId;
057                String groupValueSetId;
058                if (codeSystemVersionId != null) {
059                        parentGroupValueSetId = parentGroupId + "-" + codeSystemVersionId;
060                        groupValueSetId = groupId + "-" + codeSystemVersionId;
061                } else {
062                        parentGroupValueSetId = parentGroupId;
063                        groupValueSetId = groupId;
064                }
065
066                ValueSet parentValueSet = getValueSet(parentGroupValueSetId, VS_URI_PREFIX + parentGroupId, null, null);
067                parentValueSet.getCompose().getIncludeFirstRep().addValueSet(VS_URI_PREFIX + groupId);
068
069                // Create group to set its name (terms are added in a different
070                // handler)
071                getValueSet(groupValueSetId, VS_URI_PREFIX + groupId, groupName, null);
072        }
073}