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mherman22mherman22
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add fhir contact point map to initializer
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12 files changed

+453
-4
lines changed

12 files changed

+453
-4
lines changed

‎api-2.5/pom.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<parent>
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<groupId>org.openmrs.module</groupId>
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<artifactId>initializer</artifactId>
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<version>2.7.0-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>initializer-api-2.5</artifactId>
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<packaging>jar</packaging>
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<name>Initializer API 2.5</name>
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<description>API 2.5 project for Initializer</description>
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<properties>
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<openmrsPlatformVersion>${openmrsVersion2.5}</openmrsPlatformVersion>
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</properties>
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<dependencies>
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<dependency>
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<groupId>${project.parent.groupId}</groupId>
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<artifactId>${project.parent.artifactId}-api</artifactId>
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<version>${project.parent.version}</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>${project.parent.groupId}</groupId>
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<artifactId>${project.parent.artifactId}-api</artifactId>
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<version>${project.parent.version}</version>
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<scope>test</scope>
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<type>test-jar</type>
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</dependency>
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<dependency>
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<groupId>${project.parent.groupId}</groupId>
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<artifactId>${project.parent.artifactId}-api-2.4</artifactId>
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<version>${project.parent.version}</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>${project.parent.groupId}</groupId>
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<artifactId>${project.parent.artifactId}-api-2.3</artifactId>
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<version>${project.parent.version}</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>${project.parent.groupId}</groupId>
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<artifactId>${project.parent.artifactId}-api-2.3</artifactId>
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<version>${project.parent.version}</version>
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<scope>test</scope>
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<type>test-jar</type>
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</dependency>
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<dependency>
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<groupId>${project.parent.groupId}</groupId>
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<artifactId>${project.parent.artifactId}-api-2.2</artifactId>
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<version>${project.parent.version}</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>${project.parent.groupId}</groupId>
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<artifactId>${project.parent.artifactId}-api-2.2</artifactId>
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<version>${project.parent.version}</version>
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<scope>test</scope>
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<type>test-jar</type>
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</dependency>
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</dependencies>
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</project>

‎api-2.5/src/main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapCsvParser.java

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package org.openmrs.module.initializer.api.fhir.cpm;
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import org.openmrs.PersonAttributeType;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.api.LocationService;
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import org.openmrs.api.PersonService;
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import org.openmrs.api.ProviderService;
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import org.openmrs.attribute.BaseAttributeType;
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import org.openmrs.module.fhir2.api.FhirContactPointMapService;
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import org.openmrs.module.initializer.Domain;
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import org.openmrs.module.fhir2.model.FhirContactPointMap;
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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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@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.5.13 - 2.5.*, 2.6.2 - 2.6.*, 2.7.* - 9.*")
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public class FhirContactPointMapCsvParser extends CsvParser<FhirContactPointMap, BaseLineProcessor<FhirContactPointMap>> {
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public static final String ATTRIBUTE_TYPE_DOMAIN_HEADER = "Entity name";
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public static final String ATTRIBUTE_TYPE = "Attribute type";
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private static final String LOCATION = "location";
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private static final String PERSON = "person";
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private static final String PROVIDER = "provider";
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private final LocationService locationService;
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private final PersonService personService;
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private final ProviderService providerService;
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private final FhirContactPointMapService fhirContactPointMapService;
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@Autowired
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protected FhirContactPointMapCsvParser(FhirContactPointMapService fhirContactPointMapService,BaseLineProcessor<FhirContactPointMap> lineProcessor,
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LocationService locationService, PersonService personService, ProviderService providerService) {
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super(lineProcessor);
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this.fhirContactPointMapService = fhirContactPointMapService;
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this.locationService = locationService;
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this.personService = personService;
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this.providerService = providerService;
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}
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@Override
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public FhirContactPointMap bootstrap(CsvLine line) throws IllegalArgumentException {
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FhirContactPointMap contactPointMap = null;
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if (line.getUuid() != null) {
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contactPointMap = fhirContactPointMapService.getFhirContactPointMapByUuid(line.getUuid())
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.orElse(null);
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}
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if (contactPointMap != null) {
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return contactPointMap;
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}
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String attributeTypeDomain = line.get(ATTRIBUTE_TYPE_DOMAIN_HEADER, true);
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String attributeType = line.get(ATTRIBUTE_TYPE, true);
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if (attributeTypeDomain.equals(PERSON)) {
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PersonAttributeType personAttributeType = getPersonAttributeType(attributeType);
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if (personAttributeType == null) {
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throw new IllegalArgumentException("PersonAttributeType " + attributeType
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+ " does not exist. Please ensure your Initializer configuration contains this attribute type.");
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}
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contactPointMap = fhirContactPointMapService.getFhirContactPointMapForPersonAttributeType(personAttributeType)
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.orElse(null);
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} else {
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BaseAttributeType<?> baseAttributeType = getBaseAttributeType(attributeTypeDomain, attributeType);
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if (baseAttributeType == null) {
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throw new IllegalArgumentException(
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"Could not find attribute type " + attributeType + " for attribute domain " + attributeTypeDomain);
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}
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contactPointMap = fhirContactPointMapService.getFhirContactPointMapForAttributeType(baseAttributeType)
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.orElse(null);
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}
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if (contactPointMap != null) {
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return contactPointMap;
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}
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return new FhirContactPointMap();
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}
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@Override
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public FhirContactPointMap save(FhirContactPointMap instance) {
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return fhirContactPointMapService.saveFhirContactPointMap(instance);
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}
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@Override
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public Domain getDomain() {
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return Domain.FHIR_CONTACT_POINT_MAP;
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}
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protected PersonAttributeType getPersonAttributeType(String attributeType) {
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PersonAttributeType personAttributeType = personService.getPersonAttributeTypeByName(attributeType);
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if (personAttributeType != null) {
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return personAttributeType;
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}
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personAttributeType = personService.getPersonAttributeTypeByUuid(attributeType);
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return personAttributeType;
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}
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protected BaseAttributeType<?> getBaseAttributeType(String attributeDomain, String attributeType) {
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BaseAttributeType<?> baseAttributeType = null;
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switch (attributeDomain) {
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case LOCATION:
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baseAttributeType = locationService.getLocationAttributeTypeByName(attributeType);
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if (baseAttributeType != null) {
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return baseAttributeType;
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}
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return locationService.getLocationAttributeTypeByUuid(attributeType);
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break;
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case PROVIDER:
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baseAttributeType = providerService.getProviderAttributeTypeByName(attributeType);
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if (baseAttributeType != null) {
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return baseAttributeType;
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}
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return providerService.getProviderAttributeTypeByUuid(attributeType);
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break;
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}
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return baseAttributeType;
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}
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}

‎api-2.5/src/main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapLineProcessor.java

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package org.openmrs.module.initializer.api.fhir.cpm;
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import org.apache.commons.lang3.StringUtils;
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import org.hl7.fhir.r4.model.ContactPoint;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.module.fhir2.model.FhirContactPointMap;
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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 static org.openmrs.module.initializer.api.fhir.cpm.FhirContactPointMapCsvParser.ATTRIBUTE_TYPE_DOMAIN_HEADER;
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@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.5.13 - 2.5.*, 2.6.2 - 2.6.*, 2.7.* - 9.*")
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public class FhirContactPointMapLineProcessor extends BaseLineProcessor<FhirContactPointMap> {
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private static final String SYSTEM_HEADER = "system";
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private static final String USE_HEADER = "use";
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private static final String RANK_HEADER = "rank";
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@Override
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public FhirContactPointMap fill(FhirContactPointMap instance, CsvLine line) throws IllegalArgumentException {
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String uuid = line.getUuid();
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if (StringUtils.isNotBlank(uuid)) {
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instance.setUuid(line.getUuid());
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}
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line.get(ATTRIBUTE_TYPE_DOMAIN_HEADER, true);
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String system = line.get(SYSTEM_HEADER, false);
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String use = line.get(USE_HEADER, false);
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String rank = line.get(RANK_HEADER, false);
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if (system != null) {
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instance.setSystem(ContactPoint.ContactPointSystem.valueOf(system));
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}
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if (use != null) {
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instance.setUse(ContactPoint.ContactPointUse.valueOf(use));
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}
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if (rank != null) {
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int rankInt = Integer.parseInt(rank);
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if (rankInt < 1) {
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throw new IllegalArgumentException("Rank must be a positive integer, i.e., 1+");
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}
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instance.setRank(rankInt);
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}
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return instance;
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}
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}

‎api-2.5/src/main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapLoader.java

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package org.openmrs.module.initializer.api.fhir.cpm;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.module.fhir2.model.FhirContactPointMap;
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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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@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.5.13 - 2.5.*, 2.6.2 - 2.6.*, 2.7.* - 9.*")
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public class FhirContactPointMapLoader extends BaseCsvLoader<FhirContactPointMap, FhirContactPointMapCsvParser> {
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@Autowired
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public void setParser(FhirContactPointMapCsvParser parser) {
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this.parser = parser;
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}
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}

‎api-2.5/src/test/java/org/openmrs/module/initializer/DomainBaseModuleContextSensitive_2_5_Test.java

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/**
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* This Source Code Form is subject to the terms of the Mozilla Public License,
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* v. 2.0. If a copy of the MPL was not distributed with this file, You can
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* obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
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* the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
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*
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* Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
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* graphic logo is a trademark of OpenMRS Inc.
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*/
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package org.openmrs.module.initializer;
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public abstract class DomainBaseModuleContextSensitive_2_5_Test extends DomainBaseModuleContextSensitiveTest {
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@Override
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public void updateSearchIndex() {
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// to prevent Data Filter's 'Illegal Record Access'
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}
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}

‎api-2.5/src/test/resources/testAppDataDir/configuration/fhircontactpointmap/contactPointMap.csv

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Uuid,Void/Retire,Entity name,Attribute Type,System,Use,Rank,_order:1000
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fa48acc4-ef1f-46d6-b0af-150b00ddee9d,,person,717ec942-3c4a-11ea-b024-ffc81a23382e,phone,work,1,
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,,person,PAT_RENAME_NEW_NAME,phone,home,,
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bcf23315-a236-42aa-be95-b9e0931e22b0,,provider,Provider Speciality,email,home,2,
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800e48ba-666c-445c-b871-68e54eec6de8,,location,e7aacc6e-d151-4d9e-a808-6ed9ff761212,phone,temp,3,

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

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COHORT_ATTRIBUTE_TYPES,
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FHIR_CONCEPT_SOURCES,
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FHIR_PATIENT_IDENTIFIER_SYSTEMS,
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FHIR_CONTACT_POINT_MAP,
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AMPATH_FORMS,
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AMPATH_FORMS_TRANSLATIONS,
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HTML_FORMS;

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