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Add domain for FHIR ObservationCategoryMaps
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‎README.md‎

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@@ -29,6 +29,7 @@ configuration/
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├── drugs/
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├── encountertypes/
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├── fhirconceptsources/
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├── fhirobservationcategorymaps/
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├── fhirpatientidentifiersystems/
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├── globalproperties/
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├── htmlforms/
@@ -114,6 +115,7 @@ This is the list of currently supported domains in their loading order:
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1. [Metadata Term Mappings (CSV files)](readme/mdm.md#domain-metadatatermmappings)
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1. [FHIR Concept Sources (CSV files)](readme/fhir.md#domain-fhirconceptsources)
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1. [FHIR Patient Identifier Systems (CSV Files)](readme/fhir.md#domain-fhirpatientidentifiersystems)
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1. [FHIR Observation Category Maps (CSV Files)](readme/fhir.md#domain-fhirobservationcategorymaps)
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1. [AMPATH Forms (JSON files)](readme/ampathforms.md)
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1. [HTML Forms (XML files)](readme/htmlforms.md)
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@@ -136,6 +138,7 @@ mvn clean package
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* Metadata Sharing 1.2.2 (*compatible*)
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* Metadata Mapping 1.3.4 (*compatible*)
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* Open Concept Lab 1.2.9 (*compatible*)
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* FHIR2 1.2.0 (*compatible*)
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### How to test out your OpenMRS configs?
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See the [Initializer Validator README page](readme/validator.md).
@@ -162,6 +165,7 @@ https://github.com/mekomsolutions/openmrs-module-initializer/issues
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#### Version 2.4.0
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* 'concepts' domain to support a new expandable `MAPPINGS` header, thereby discouraging the older `Same as mappings`.
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* Concept references expanded to allow use of concept names in locales other than the default system locale
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* Support for FHIR2 module and domains related to the metadata needed for FHIR
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#### Version 2.3.0
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* Added configuration options for logging.

‎api/src/main/java/org/openmrs/module/initializer/Domain.java‎

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@@ -42,6 +42,7 @@ public enum Domain {
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METADATA_SET_MEMBERS,
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METADATA_TERM_MAPPINGS,
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FHIR_CONCEPT_SOURCES,
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FHIR_OBSERVATION_CATEGORY_MAPS,
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FHIR_PATIENT_IDENTIFIER_SYSTEMS,
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AMPATH_FORMS,
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HTML_FORMS;

‎api/src/main/java/org/openmrs/module/initializer/api/CsvParser.java‎

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@@ -220,7 +220,7 @@ private T initialize(String[] line) throws APIException {
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final CsvLine csvLine = new CsvLine(headerLine, line);
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//
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// 1. Boostrapping
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// 1. Bootstrapping
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//
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T instance = bootstrap(csvLine);
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‎api/src/main/java/org/openmrs/module/initializer/api/fhir/ocm/FhirObservationCategoryMapCsvParser.java‎

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package org.openmrs.module.initializer.api.fhir.ocm;
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import org.hibernate.SessionFactory;
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import org.openmrs.ConceptClass;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.module.fhir2.model.FhirObservationCategoryMap;
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import org.openmrs.module.initializer.Domain;
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import org.openmrs.module.initializer.api.BaseLineProcessor;
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import org.openmrs.module.initializer.api.CsvLine;
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import org.openmrs.module.initializer.api.CsvParser;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.stereotype.Component;
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import static org.openmrs.module.initializer.Domain.FHIR_OBSERVATION_CATEGORY_MAPS;
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@Component
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@OpenmrsProfile(modules = { "fhir2:1.*" })
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public class FhirObservationCategoryMapCsvParser extends CsvParser<FhirObservationCategoryMap, BaseLineProcessor<FhirObservationCategoryMap>> {
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public static final String FHIR_OBS_CATEGORY_HEADER = "Fhir observation category";
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public static final String CONCEPT_CLASS_HEADER = "Concept class";
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private final SessionFactory sessionFactory;
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@Autowired
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protected FhirObservationCategoryMapCsvParser(@Qualifier("sessionFactory") SessionFactory sessionFactory,
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BaseLineProcessor<FhirObservationCategoryMap> lineProcessor) {
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super(lineProcessor);
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this.sessionFactory = sessionFactory;
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}
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@Override
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public Domain getDomain() {
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return FHIR_OBSERVATION_CATEGORY_MAPS;
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}
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@Override
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public FhirObservationCategoryMap bootstrap(CsvLine line) throws IllegalArgumentException {
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FhirObservationCategoryMap result = null;
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String fhirObsCategory = line.get(FHIR_OBS_CATEGORY_HEADER);
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String conceptClass = line.get(CONCEPT_CLASS_HEADER);
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if (fhirObsCategory != null && !fhirObsCategory.isEmpty() && conceptClass != null && !conceptClass.isEmpty()) {
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result = (FhirObservationCategoryMap) sessionFactory.getCurrentSession()
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.createQuery("from " + FhirObservationCategoryMap.class.getSimpleName()
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+ " where observationCategory = :fhirObsCategory and conceptClass = (" + "select cc from "
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+ ConceptClass.class.getSimpleName() + " cc where cc.name = :conceptClassName" + ")")
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.setParameter("fhirObsCategory", fhirObsCategory).setParameter("conceptClassName", conceptClass)
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.uniqueResult();
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}
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if (result == null && line.getUuid() != null && !line.getUuid().isEmpty()) {
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result = (FhirObservationCategoryMap) sessionFactory.getCurrentSession()
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.createQuery("from " + FhirObservationCategoryMap.class.getSimpleName() + " where uuid = :uuid")
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.setParameter("uuid", line.getUuid()).uniqueResult();
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}
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if (result == null) {
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result = new FhirObservationCategoryMap();
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result.setUuid(line.getUuid());
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}
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return result;
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}
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@Override
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public FhirObservationCategoryMap save(FhirObservationCategoryMap instance) {
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sessionFactory.getCurrentSession().saveOrUpdate(instance);
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return instance;
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}
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}

‎api/src/main/java/org/openmrs/module/initializer/api/fhir/ocm/FhirObservationCategoryMapLineProcessor.java‎

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package org.openmrs.module.initializer.api.fhir.ocm;
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import org.apache.commons.lang3.StringUtils;
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import org.openmrs.ConceptClass;
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import org.openmrs.ConceptSource;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.api.ConceptService;
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import org.openmrs.module.fhir2.model.FhirConceptSource;
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import org.openmrs.module.fhir2.model.FhirObservationCategoryMap;
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import org.openmrs.module.initializer.api.BaseLineProcessor;
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import org.openmrs.module.initializer.api.CsvLine;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Component;
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import static org.openmrs.module.initializer.api.fhir.cs.FhirConceptSourceCsvParser.CONCEPT_SOURCE_NAME_HEADER;
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import static org.openmrs.module.initializer.api.fhir.ocm.FhirObservationCategoryMapCsvParser.CONCEPT_CLASS_HEADER;
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import static org.openmrs.module.initializer.api.fhir.ocm.FhirObservationCategoryMapCsvParser.FHIR_OBS_CATEGORY_HEADER;
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@Component
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@OpenmrsProfile(modules = { "fhir2:1.*" })
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public class FhirObservationCategoryMapLineProcessor extends BaseLineProcessor<FhirObservationCategoryMap> {
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private final ConceptService conceptService;
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@Autowired
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public FhirObservationCategoryMapLineProcessor(ConceptService conceptService) {
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this.conceptService = conceptService;
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}
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@Override
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public FhirObservationCategoryMap fill(FhirObservationCategoryMap instance, CsvLine line)
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throws IllegalArgumentException {
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if (StringUtils.isBlank(instance.getUuid()) && StringUtils.isBlank(line.getUuid())) {
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throw new IllegalArgumentException("No UUID was found for FHIR observation category map");
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}
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String fhirObsCategory = line.get(FHIR_OBS_CATEGORY_HEADER, true);
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if (StringUtils.isBlank(fhirObsCategory) && !instance.getRetired()) {
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throw new IllegalArgumentException("'" + FHIR_OBS_CATEGORY_HEADER
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+ "' was not found for FHIR observation category map " + instance.getUuid());
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}
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String conceptClass = line.get(CONCEPT_CLASS_HEADER, true);
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if (StringUtils.isBlank(conceptClass) && !instance.getRetired()) {
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throw new IllegalArgumentException(
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"'" + CONCEPT_CLASS_HEADER + "' was not found for FHIR observation category map " + instance.getUuid());
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}
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ConceptClass cc = conceptService.getConceptClassByName(conceptClass);
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if (cc == null && !instance.getRetired()) {
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throw new IllegalArgumentException("Concept class " + conceptClass
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+ " was not found while creating FHIR observation category map " + instance.getUuid());
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}
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if (StringUtils.isNotBlank(line.getUuid())) {
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instance.setUuid(line.getUuid());
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}
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instance.setObservationCategory(fhirObsCategory);
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instance.setConceptClass(cc);
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return instance;
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}
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}

‎api/src/main/java/org/openmrs/module/initializer/api/fhir/ocm/FhirObservationCategoryMapLoader.java‎

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package org.openmrs.module.initializer.api.fhir.ocm;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.module.fhir2.model.FhirConceptSource;
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import org.openmrs.module.fhir2.model.FhirObservationCategoryMap;
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import org.openmrs.module.initializer.api.loaders.BaseCsvLoader;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Component;
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@Component
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@OpenmrsProfile(modules = { "fhir2:1.*" })
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public class FhirObservationCategoryMapLoader extends BaseCsvLoader<FhirObservationCategoryMap, FhirObservationCategoryMapCsvParser> {
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@Autowired
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public void setParser(FhirObservationCategoryMapCsvParser parser) {
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this.parser = parser;
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}
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}

‎api/src/test/java/org/openmrs/module/initializer/api/FhirObservationCategoryMapIntegrationTest.java‎

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package org.openmrs.module.initializer.api;
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import java.util.List;
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import org.hibernate.Query;
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import org.hibernate.Session;
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import org.hibernate.SessionFactory;
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import org.junit.Before;
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import org.junit.Test;
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import org.openmrs.ConceptClass;
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import org.openmrs.api.ConceptService;
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import org.openmrs.api.context.Context;
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import org.openmrs.module.fhir2.model.FhirObservationCategoryMap;
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import org.openmrs.module.initializer.DomainBaseModuleContextSensitiveTest;
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import org.openmrs.module.initializer.api.fhir.ocm.FhirObservationCategoryMapLoader;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.allOf;
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import static org.hamcrest.Matchers.equalTo;
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import static org.hamcrest.Matchers.hasItem;
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import static org.hamcrest.Matchers.hasProperty;
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import static org.hamcrest.Matchers.hasSize;
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public class FhirObservationCategoryMapIntegrationTest extends DomainBaseModuleContextSensitiveTest {
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@Autowired
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@Qualifier("sessionFactory")
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private SessionFactory sessionFactory;
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@Autowired
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private ConceptService conceptService;
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@Autowired
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private FhirObservationCategoryMapLoader loader;
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@Before
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public void setup() {
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{
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ConceptClass conceptClass = conceptService.getConceptClassByName("Test");
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if (conceptClass == null) {
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conceptClass = new ConceptClass();
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conceptClass.setName("Test");
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conceptClass.setUuid(ConceptClass.TEST_UUID);
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sessionFactory.getCurrentSession().saveOrUpdate(conceptClass);
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}
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}
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{
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ConceptClass conceptClass = conceptService.getConceptClassByName("Finding");
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if (conceptClass == null) {
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conceptClass = new ConceptClass();
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conceptClass.setName("Finding");
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conceptClass.setUuid(ConceptClass.FINDING_UUID);
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sessionFactory.getCurrentSession().saveOrUpdate(conceptClass);
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}
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}
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{
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FhirObservationCategoryMap observationCategoryMap = new FhirObservationCategoryMap();
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observationCategoryMap.setObservationCategory("laboratory");
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observationCategoryMap.setConceptClass(conceptService.getConceptClassByName("Test"));
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observationCategoryMap.setUuid("2309836d-bf13-4fea-b2d4-87bb997425c7");
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sessionFactory.getCurrentSession().saveOrUpdate(observationCategoryMap);
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}
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Context.flushSession();
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}
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@Test
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public void loader_shouldLoadFhirObservationCategoryMapsAccordingToCsvFiles() {
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// Replay
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loader.load();
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// Verify
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Session session = sessionFactory.getCurrentSession();
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Query getObsCategoryByCategoryQuery = session.createQuery("from " + FhirObservationCategoryMap.class.getSimpleName()
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+ " where observationCategory = :observationCategory");
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{
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List<FhirObservationCategoryMap> observationCategories = getObsCategoryByCategoryQuery
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.setParameter("observationCategory", "laboratory").list();
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assertThat(observationCategories, hasSize(2));
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assertThat(observationCategories,
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hasItem(allOf(hasProperty("uuid", equalTo("e518de2a-be31-4202-9772-cc65c3ef7227")),
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hasProperty("conceptClass", hasProperty("name", equalTo("Test"))))));
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assertThat(observationCategories,
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hasItem(allOf(hasProperty("uuid", equalTo("2374215a-8808-4eee-b5a5-9190423862a0")),
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hasProperty("conceptClass", hasProperty("name", equalTo("LabSet"))))));
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}
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{
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List<FhirObservationCategoryMap> observationCategories = getObsCategoryByCategoryQuery
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.setParameter("observationCategory", "exam").list();
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assertThat(observationCategories, hasSize(1));
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assertThat(observationCategories.get(0), hasProperty("uuid", equalTo("5f8e2dd2-ce1f-42d3-bb34-55acb3f58c5d")));
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assertThat(observationCategories.get(0).getConceptClass(), hasProperty("name", equalTo("Finding")));
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}
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}
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}

‎api/src/test/java/org/openmrs/module/initializer/api/UtilsTest.java‎

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Assert.assertEquals("EncounterType", Utils.unProxy("EncounterType_$$_javassist_26"));
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Assert.assertEquals("EncounterType", Utils.unProxy("EncounterType"));
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}
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@Test
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public void fetchConcept_shouldFetchConceptByUuid() {
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ConceptService cs = mock(ConceptService.class);
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when(cs.getConceptByName("concept:lookup")).thenReturn(nameConcept);
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Assert.assertEquals(uuidConcept, Utils.fetchConcept("concept:lookup", cs));
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}
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@Test
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public void fetchConcept_shouldFetchConceptByMapping() {
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ConceptService cs = mock(ConceptService.class);
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when(cs.getConceptByName("concept:lookup")).thenReturn(nameConcept);
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Assert.assertEquals(mappingConcept, Utils.fetchConcept("concept:lookup", cs));
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}
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@Test
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public void fetchConcept_shouldFetchConceptByName() {
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ConceptService cs = mock(ConceptService.class);

‎api/src/test/resources/testAppDataDir/configuration/fhirobservationcategorymaps/observationcategorymaps.csv‎

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Uuid,Void/Retire,Fhir observation category,Concept class,_order:1000
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e518de2a-be31-4202-9772-cc65c3ef7227,,laboratory,Test,
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5f8e2dd2-ce1f-42d3-bb34-55acb3f58c5d,,exam,Finding,
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2374215a-8808-4eee-b5a5-9190423862a0,,laboratory,LabSet,

‎readme/fhir.md‎

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Headers that start with an underscore such as `_order:1000` are metadata headers. The values in the columns under those headers are never read by the CSV parser.
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## Domain 'fhirobservationcategorymaps'
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The **fhirobservationcategorymaps** subfolder contains CSV import files for defining mappings between [FHIR Observation category
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values](https://www.hl7.org/fhir/valueset-observation-category.html) and OpenMRS ConceptClasses. When configured, this ensures
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that the `Observation.category` field on a FHIR Observation will have the value specified by the mapping and the ConceptClass.
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`ConceptClass`es referenced in this domain must exist before a category map can be created. However, arbitrary strings can
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be used for the category name. However, it is recommended to use strings in the
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[FHIR ValueSet for Observation category](https://www.hl7.org/fhir/valueset-observation-category.html) wherever possible to
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ensure maximum compatibility.
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Please note that the ability to map OpenMRS ConceptClasses to FHIR Observation categories should be regarded as an experimental
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feature and may be subject to change in the future.
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This is a possible example of its contents:
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```bash
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fhirobservationcategorymaps/
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├──categorymaps.csv
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└── ...
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```
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The format of this CSV should be as follows:
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| <sub>Uuid</sub> |<sub>Void/Retire</sub> | <sub>Fhir observation category</sub> | <sub>Concept class</sub> | <sub>_order:1000</sub> |
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| - | - | - | - | - |
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| <sub>e518de2a-be31-4202-9772-cc65c3ef7227</sub> | | <sub>laboratory</sub> | <sub>Test</sub> | |
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Headers that start with an underscore such as `_order:1000` are metadata headers. The values in the columns under those headers are never read by the CSV parser.
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