Trunk 6264 concept reference range initialization

README.md

@@ -161,6 +161,7 @@ This is the list of currently supported domains in their loading order:
 1. [AMPATH Forms Translations (JSON files)](readme/ampathformstranslations.md)
 1. [HTML Forms (XML files)](readme/htmlforms.md)
 1. [Disposition Config (json file)](readme/dispositions.md)
+1. [Concept Reference Ranges (CSV files)](readme/conceptreferenceranges.md)
 
 ## Try it out
 Build the master branch and install the built OMOD to your OpenMRS instance:
@@ -208,6 +209,7 @@ See the [documentation on Initializer's logging properties](readme/rtprops.md#lo
 * Ampath forms translation files will now generate checksums.
 * Enhancement to ensure that when an Ampath forms file is loaded, a new resource with the existing Ampath forms translations is created.
 * Added support for 'billing' (billableservices, paymentmodes, cashpoints) domains.
+* Added support for 'conceptreferencerange' domain.
 
 #### Version 2.7.0
 * Added support for 'queues' domain.

api-2.2/src/test/java/org/openmrs/module/initializer/api/AttributeTypesLoaderTest2_2.java

@@ -2,6 +2,7 @@
 
 import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.text.IsEmptyString.isEmptyOrNullString;
+import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertThat;
 import static org.openmrs.module.initializer.api.AttributeTypesLoaderTest.assertCustomDatatype;
 
@@ -46,7 +47,7 @@ public void load_shouldLoadAccordingToCsvFiles() {
 			Assert.assertEquals("Program Efficiency Score", attType.getName());
 			Assert.assertEquals("Metric of the program efficiency", attType.getDescription());
 			Assert.assertThat(attType.getMinOccurs(), is(0));
-			Assert.assertThat(attType.getMaxOccurs(), is(1));
+			assertNull(attType.getMaxOccurs());
 		}
 
 		// Replay

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

@@ -73,6 +73,7 @@ protected boolean matchesSafely(List<Loader> loaders, Description mismatchDescri
 			exclude.add(Domain.PAYMENT_MODES.getName());
 			exclude.add(Domain.BILLABLE_SERVICES.getName());
 			exclude.add(Domain.CASH_POINTS.getName());
+			exclude.add(Domain.CONCEPT_REFERENCE_RANGES.getName());
 
 			boolean result = true;
 			Set<String> loaderDomains = loaders.stream().map(Loader::getDomainName).collect(Collectors.toSet());

api-2.4/src/main/java/org/openmrs/module/initializer/api/logging/InitializerLogConfigurator2_4.java

@@ -6,11 +6,9 @@
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.core.Appender;
-import org.apache.logging.log4j.core.Filter;
 import org.apache.logging.log4j.core.Layout;
 import org.apache.logging.log4j.core.Logger;
 import org.apache.logging.log4j.core.appender.FileAppender;
-import org.apache.logging.log4j.core.filter.LevelRangeFilter;
 import org.apache.logging.log4j.core.layout.PatternLayout;
 import org.openmrs.annotation.OpenmrsProfile;
 import org.openmrs.module.initializer.InitializerActivator;

api-2.7/pom.xml

@@ -0,0 +1,119 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <groupId>org.openmrs.module</groupId>
+        <artifactId>initializer</artifactId>
+        <version>2.8.0-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>initializer-api-2.7</artifactId>
+    <packaging>jar</packaging>
+    <name>Initializer API 2.7</name>
+    <description>API 2.7 project for Initializer</description>
+
+    <properties>
+        <openmrsPlatformVersion>${openmrsVersion2.7}</openmrsPlatformVersion>
+        <datafilterVersion>2.2.0</datafilterVersion>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.openmrs.test</groupId>
+            <artifactId>openmrs-test</artifactId>
+            <type>pom</type>
+            <version>${openmrsPlatformVersion}</version>
+            <scope>test</scope>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.powermock</groupId>
+                    <artifactId>powermock-api-mockito2</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.13.2</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api-2.5</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api-2.4</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api-2.4</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api-2.3</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api-2.3</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api-2.2</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.parent.groupId}</groupId>
+            <artifactId>${project.parent.artifactId}-api-2.2</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>org.openmrs.module</groupId>
+            <artifactId>datafilter-api</artifactId>
+            <version>${datafilterVersion}</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+</project>

api-2.7/src/main/java/org/openmrs/module/initializer/api/conceptreferencerange/ConceptReferenceRangeCsvParser.java

@@ -0,0 +1,49 @@
+package org.openmrs.module.initializer.api.conceptreferencerange;
+
+import org.apache.commons.lang3.StringUtils;
+import org.openmrs.ConceptReferenceRange;
+import org.openmrs.module.initializer.Domain;
+import org.openmrs.module.initializer.api.BaseLineProcessor;
+import org.openmrs.module.initializer.api.CsvLine;
+import org.openmrs.module.initializer.api.CsvParser;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+@Component
+public class ConceptReferenceRangeCsvParser extends CsvParser<ConceptReferenceRange, BaseLineProcessor<ConceptReferenceRange>> {
+
+	private ConceptReferenceRangeService conceptReferenceRangeService;
+
+	@Autowired
+	public ConceptReferenceRangeCsvParser(ConceptReferenceRangeLineProcessor processor,
+	    ConceptReferenceRangeService conceptReferenceRangeService) {
+		super(processor);
+		this.conceptReferenceRangeService = conceptReferenceRangeService;
+	}
+
+	@Override
+	public Domain getDomain() {
+		return Domain.CONCEPT_REFERENCE_RANGES;
+	}
+
+	@Override
+	public ConceptReferenceRange bootstrap(CsvLine line) throws IllegalArgumentException {
+		String uuid = line.getUuid();
+
+		ConceptReferenceRange referenceRange = conceptReferenceRangeService.getConceptReferenceRangeByUuid(uuid);
+
+		if (referenceRange == null) {
+			referenceRange = new ConceptReferenceRange();
+			if (!StringUtils.isEmpty(uuid)) {
+				referenceRange.setUuid(uuid);
+			}
+		}
+
+		return referenceRange;
+	}
+
+	@Override
+	public ConceptReferenceRange save(ConceptReferenceRange instance) {
+		return conceptReferenceRangeService.saveReferenceRange(instance);
+	}
+}

api-2.7/src/main/java/org/openmrs/module/initializer/api/conceptreferencerange/ConceptReferenceRangeLineProcessor.java

@@ -0,0 +1,67 @@
+package org.openmrs.module.initializer.api.conceptreferencerange;
+
+import org.openmrs.ConceptNumeric;
+import org.openmrs.ConceptReferenceRange;
+import org.openmrs.api.ConceptService;
+import org.openmrs.module.initializer.api.BaseLineProcessor;
+import org.openmrs.module.initializer.api.CsvLine;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.stereotype.Component;
+
+@Component("initializer.conceptReferenceRangeLineProcessor")
+public class ConceptReferenceRangeLineProcessor extends BaseLineProcessor<ConceptReferenceRange> {
+
+	private final String HEADER_CONCEPT_NUMERIC_UUID = "Concept Numeric Uuid";
+
+	private final String HEADER_AH = "Absolute high";
+
+	private final String HEADER_CH = "Critical high";
+
+	private final String HEADER_NH = "Normal high";
+
+	private final String HEADER_AL = "Absolute low";
+
+	private final String HEADER_CL = "Critical low";
+
+	private final String HEADER_NL = "Normal low";
+
+	private final String HEADER_CRITERIA = "Criteria";
+
+	private ConceptService conceptService;
+
+	private final ConceptReferenceRangeService conceptReferenceRangeService;
+
+	@Autowired
+	public ConceptReferenceRangeLineProcessor(@Qualifier("conceptService") ConceptService conceptService,
+	    ConceptReferenceRangeService conceptReferenceRangeService) {
+		this.conceptService = conceptService;
+		this.conceptReferenceRangeService = conceptReferenceRangeService;
+	}
+
+	public ConceptReferenceRange fill(ConceptReferenceRange referenceRange, CsvLine line) throws IllegalArgumentException {
+		//		ConceptNumeric conceptNumeric = conceptService.getConceptNumericByUuid(line.get(HEADER_CONCEPT_NUMERIC_UUID));
+		ConceptNumeric conceptNumeric = conceptReferenceRangeService
+		        .getConceptNumericByUuid(line.get(HEADER_CONCEPT_NUMERIC_UUID));
+
+		if (conceptNumeric == null) {
+			throw new IllegalArgumentException(
+			        "No concept numeric found for '" + line.get(HEADER_CONCEPT_NUMERIC_UUID) + "'");
+		}
+
+		if (referenceRange == null) {
+			referenceRange = new ConceptReferenceRange();
+		}
+
+		referenceRange.setHiAbsolute(line.getDouble(HEADER_AH));
+		referenceRange.setHiCritical(line.getDouble(HEADER_CH));
+		referenceRange.setHiNormal(line.getDouble(HEADER_NH));
+		referenceRange.setLowAbsolute(line.getDouble(HEADER_AL));
+		referenceRange.setLowCritical(line.getDouble(HEADER_CL));
+		referenceRange.setLowNormal(line.getDouble(HEADER_NL));
+		referenceRange.setConceptNumeric(conceptNumeric);
+		referenceRange.setCriteria(line.getString(HEADER_CRITERIA));
+
+		return referenceRange;
+	}
+}

api-2.7/src/main/java/org/openmrs/module/initializer/api/conceptreferencerange/ConceptReferenceRangeLoader.java

@@ -0,0 +1,21 @@
+package org.openmrs.module.initializer.api.conceptreferencerange;
+
+import org.openmrs.ConceptReferenceRange;
+import org.openmrs.module.initializer.api.loaders.BaseCsvLoader;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.io.File;
+
+@Component
+public class ConceptReferenceRangeLoader extends BaseCsvLoader<ConceptReferenceRange, ConceptReferenceRangeCsvParser> {
+
+	@Autowired
+	public void setParser(ConceptReferenceRangeCsvParser parser) {
+		this.parser = parser;
+	}
+
+	@Override
+	protected void preload(File file) {
+	}
+}

api-2.7/src/main/java/org/openmrs/module/initializer/api/conceptreferencerange/ConceptReferenceRangeService.java

@@ -0,0 +1,59 @@
+package org.openmrs.module.initializer.api.conceptreferencerange;
+
+import org.openmrs.ConceptNumeric;
+import org.openmrs.ConceptReferenceRange;
+import org.openmrs.annotation.OpenmrsProfile;
+import org.openmrs.api.ConceptService;
+import org.openmrs.api.OpenmrsService;
+import org.openmrs.api.context.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+
+@OpenmrsProfile(openmrsPlatformVersion = "[2.7.0 - 2.7.*]")
+public class ConceptReferenceRangeService implements OpenmrsService {
+
+	@Autowired
+	private final ConceptService conceptService;
+
+	@Autowired
+	public ConceptReferenceRangeService(@Qualifier("conceptService") ConceptService conceptService) {
+		this.conceptService = conceptService;
+	}
+
+	/**
+	 * Gets an <code>ConceptReferenceRange</code> by uuid.
+	 * 
+	 * @param uuid uuid of the <code>ConceptReferenceRange</code>
+	 * @return conceptReferenceRange or <code>null</code>
+	 */
+	public ConceptReferenceRange getConceptReferenceRangeByUuid(String uuid) {
+		return Context.getConceptService().getConceptReferenceRangeByUuid(uuid);
+	}
+
+	/**
+	 * Saves a <code>ConceptReferenceRange</code>.
+	 * 
+	 * @param referenceRange the <code>ConceptReferenceRange</code> to be saved
+	 * @return the saved <code>ConceptReferenceRange</code>
+	 */
+	public ConceptReferenceRange saveReferenceRange(ConceptReferenceRange referenceRange) {
+		return Context.getConceptService().saveConceptReferenceRange(referenceRange);
+	}
+
+	/**
+	 * Gets a {@link ConceptNumeric} by uuid.
+	 * 
+	 * @param uuid uuid of the {@link ConceptNumeric}
+	 */
+	public ConceptNumeric getConceptNumericByUuid(String uuid) {
+		return Context.getConceptService().getConceptNumericByUuid(uuid);
+	}
+
+	@Override
+	public void onStartup() {
+	}
+
+	@Override
+	public void onShutdown() {
+	}
+}