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O3-5658: Add support for Procedure Types domain in the Initializer module (#323)
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‎README.md‎

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@@ -129,6 +129,7 @@ This is the list of currently supported domains in their loading order:
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1. [Privileges (CSV files)](readme/priv.md)
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1. [Encounter Types (CSV files)](readme/et.md)
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1. [Encounter Roles (CSV files)](readme/encounterroles.md)
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1. [Procedure Types (CSV files)](readme/proceduretypes.md)
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1. [Roles (CSV files)](readme/roles.md)
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1. [Global Properties (XML files)](readme/globalproperties.md)
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1. [Attribute Types (CSV files)](readme/atttypes.md)
@@ -232,6 +233,7 @@ See the [documentation on Initializer's logging properties](readme/rtprops.md#lo
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* Fix to ensure concept lookups correctly handle concepts with % characters
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* Fix for performance to only process displays preloaders if they are present within csvs
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* Add support for row-level checksums in CSV domains to enable only re-loading those rows that have changed
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* Added support for 'proceduretypes' domain (requires emrapi 3.4+ on OpenMRS Core 2.8+)
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#### Version 2.11.0
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* Added support for patient flags (flags, flagpriorities, flagtags) domains

‎api-2.3/src/test/java/org/openmrs/module/initializer/api/loaders/LoadersOrderTest.java‎

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@@ -77,6 +77,7 @@ protected boolean matchesSafely(List<Loader> loaders, Description mismatchDescri
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exclude.add(Domain.FLAGS.getName());
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exclude.add(Domain.FLAG_PRIORITIES.getName());
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exclude.add(Domain.FLAG_TAGS.getName());
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exclude.add(Domain.PROCEDURE_TYPES.getName());
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boolean result = true;
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Set<String> loaderDomains = loaders.stream().map(Loader::getDomainName).collect(Collectors.toSet());

‎api-2.8/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>2.12.0-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>initializer-api-2.8</artifactId>
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<packaging>jar</packaging>
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<name>Initializer API 2.8</name>
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<description>API 2.8 project for Initializer</description>
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<properties>
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<openmrsPlatformVersion>${openmrsVersion2.8}</openmrsPlatformVersion>
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<emrapiVersion>3.4.0</emrapiVersion>
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</properties>
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<repositories>
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<repository>
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<id>openmrs-repo-snapshots</id>
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<name>OpenMRS Nexus Snapshots</name>
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<url>https://mavenrepo.openmrs.org/snapshots</url>
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<releases>
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<enabled>false</enabled>
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</releases>
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<snapshots>
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<enabled>true</enabled>
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</snapshots>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>org.openmrs.test</groupId>
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<artifactId>openmrs-test</artifactId>
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<type>pom</type>
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<version>${openmrsPlatformVersion}</version>
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<scope>test</scope>
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<exclusions>
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<exclusion>
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<groupId>org.powermock</groupId>
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<artifactId>powermock-api-mockito2</artifactId>
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</exclusion>
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</exclusions>
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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>${project.parent.version}</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>${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-2.2</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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<dependency>
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<groupId>org.openmrs.module</groupId>
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<artifactId>emrapi-api</artifactId>
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<version>${emrapiVersion}</version>
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<scope>provided</scope>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<!-- Inherited from parent pom; not used by api-2.8 and each breaks the Spring test context on Core 2.8. -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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<configuration>
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<classpathDependencyExcludes>
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<classpathDependencyExclude>org.openmrs.module:providermanagement-api</classpathDependencyExclude>
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<classpathDependencyExclude>org.openmrs.module:htmlformentry-api</classpathDependencyExclude>
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<classpathDependencyExclude>org.openmrs.module:fhir2-api</classpathDependencyExclude>
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<classpathDependencyExclude>org.openmrs.module:fhir2-api-2.1</classpathDependencyExclude>
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<classpathDependencyExclude>org.openmrs.module:fhir2-api-2.2</classpathDependencyExclude>
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<classpathDependencyExclude>org.openmrs.module:tasks-api</classpathDependencyExclude>
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<classpathDependencyExclude>org.openmrs.module:reporting-api</classpathDependencyExclude>
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<classpathDependencyExclude>org.openmrs.module:reporting-api-2.0</classpathDependencyExclude>
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</classpathDependencyExcludes>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>

‎api-2.8/src/main/java/org/openmrs/module/initializer/api/procedure/ProcedureTypeLineProcessor.java‎

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package org.openmrs.module.initializer.api.procedure;
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import org.apache.commons.lang3.StringUtils;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.module.emrapi.procedure.ProcedureType;
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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.stereotype.Component;
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@OpenmrsProfile(modules = { "emrapi:3.4.* - 9.*" })
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@Component
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public class ProcedureTypeLineProcessor extends BaseLineProcessor<ProcedureType> {
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@Override
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public ProcedureType fill(ProcedureType instance, CsvLine line) throws IllegalArgumentException {
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String name = line.getName(true);
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if (StringUtils.isBlank(name)) {
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throw new IllegalArgumentException("'Name' is required for procedure types.");
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}
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instance.setName(name);
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instance.setDescription(line.get(HEADER_DESC));
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return instance;
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}
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}

‎api-2.8/src/main/java/org/openmrs/module/initializer/api/procedure/ProcedureTypesCsvParser.java‎

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package org.openmrs.module.initializer.api.procedure;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.commons.lang3.StringUtils;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.module.emrapi.procedure.ProcedureService;
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import org.openmrs.module.emrapi.procedure.ProcedureType;
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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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@OpenmrsProfile(modules = { "emrapi:3.4.* - 9.*" })
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@Component
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public class ProcedureTypesCsvParser extends CsvParser<ProcedureType, BaseLineProcessor<ProcedureType>> {
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private final ProcedureService procedureService;
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@Autowired
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public ProcedureTypesCsvParser(@Qualifier("procedureService") ProcedureService procedureService,
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ProcedureTypeLineProcessor lineProcessor) {
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super(lineProcessor);
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this.procedureService = procedureService;
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}
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@Override
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public Domain getDomain() {
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return Domain.PROCEDURE_TYPES;
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}
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@Override
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public ProcedureType bootstrap(CsvLine line) throws IllegalArgumentException {
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String uuid = line.getUuid();
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String name = line.getName();
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ProcedureType type = null;
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if (StringUtils.isNotBlank(uuid)) {
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type = procedureService.getProcedureTypeByUuid(uuid);
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} else if (StringUtils.isNotBlank(name)) {
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List<ProcedureType> exactMatches = new ArrayList<ProcedureType>();
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List<ProcedureType> raw = procedureService.getProcedureTypesByName(name);
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if (raw != null) {
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for (ProcedureType candidate : raw) {
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if (name.equals(candidate.getName())) {
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exactMatches.add(candidate);
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}
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}
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}
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if (exactMatches.size() > 1) {
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throw new IllegalArgumentException(
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exactMatches.size() + " procedure types match name '" + name + "'; provide a Uuid to disambiguate.");
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}
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if (!exactMatches.isEmpty()) {
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type = exactMatches.get(0);
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}
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}
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if (type != null) {
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return type;
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}
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type = new ProcedureType();
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if (StringUtils.isNotBlank(uuid)) {
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type.setUuid(uuid);
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}
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return type;
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}
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@Override
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public ProcedureType save(ProcedureType instance) {
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return procedureService.saveProcedureType(instance);
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}
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}

‎api-2.8/src/main/java/org/openmrs/module/initializer/api/procedure/ProcedureTypesLoader.java‎

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package org.openmrs.module.initializer.api.procedure;
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import org.openmrs.annotation.OpenmrsProfile;
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import org.openmrs.module.emrapi.procedure.ProcedureType;
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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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@OpenmrsProfile(modules = { "emrapi:3.4.* - 9.*" })
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@Component
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public class ProcedureTypesLoader extends BaseCsvLoader<ProcedureType, ProcedureTypesCsvParser> {
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@Autowired
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public void setParser(ProcedureTypesCsvParser parser) {
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this.parser = parser;
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}
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}

‎api-2.8/src/test/java/org/openmrs/module/initializer/DomainBaseModuleContextSensitive_2_8_Test.java‎

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package org.openmrs.module.initializer;
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import java.io.File;
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import org.openmrs.module.Module;
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import org.openmrs.module.ModuleFactory;
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public abstract class DomainBaseModuleContextSensitive_2_8_Test extends DomainBaseModuleContextSensitiveTest {
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@Override
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public void initModules() {
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Module mod = new Module("", "emrapi", "", "", "", "3.4.0", "");
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mod.setFile(new File(""));
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ModuleFactory.getStartedModulesMap().put(mod.getModuleId(), mod);
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}
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}

‎api-2.8/src/test/java/org/openmrs/module/initializer/api/lineprocessor/ProcedureTypeLineProcessorTest.java‎

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package org.openmrs.module.initializer.api.lineprocessor;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertNull;
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import org.junit.Test;
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import org.openmrs.module.emrapi.procedure.ProcedureType;
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import org.openmrs.module.initializer.api.CsvLine;
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import org.openmrs.module.initializer.api.procedure.ProcedureTypeLineProcessor;
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public class ProcedureTypeLineProcessorTest {
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private final ProcedureTypeLineProcessor processor = new ProcedureTypeLineProcessor();
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@Test
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public void shouldPopulateNameAndDescription() {
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String[] headers = { "Uuid", "Name", "Description" };
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String[] line = { "9d9aa7c1-2e0e-4b1e-8b57-7e6f1a0b1234", "Appendectomy", "Surgical removal of the appendix" };
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ProcedureType type = processor.fill(new ProcedureType(), new CsvLine(headers, line));
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assertEquals("Appendectomy", type.getName());
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assertEquals("Surgical removal of the appendix", type.getDescription());
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}
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@Test
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public void shouldAllowMissingDescription() {
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String[] headers = { "Uuid", "Name", "Description" };
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String[] line = { "9d9aa7c1-2e0e-4b1e-8b57-7e6f1a0b1234", "Cholecystectomy", null };
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ProcedureType type = processor.fill(new ProcedureType(), new CsvLine(headers, line));
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assertEquals("Cholecystectomy", type.getName());
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assertNull(type.getDescription());
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}
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@Test(expected = IllegalArgumentException.class)
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public void shouldThrowWhenNameIsNull() {
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String[] headers = { "Uuid", "Name", "Description" };
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String[] line = { "9d9aa7c1-2e0e-4b1e-8b57-7e6f1a0b1234", null, "Description without a name" };
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processor.fill(new ProcedureType(), new CsvLine(headers, line));
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}
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@Test(expected = IllegalArgumentException.class)
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public void shouldThrowWhenNameIsBlank() {
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String[] headers = { "Uuid", "Name", "Description" };
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String[] line = { "9d9aa7c1-2e0e-4b1e-8b57-7e6f1a0b1234", "", "Description without a name" };
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processor.fill(new ProcedureType(), new CsvLine(headers, line));
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}
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}

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