O3-5907: Added medication side effects domain

README.md

@@ -78,6 +78,7 @@ configuration/
   ├── locations/
   ├── locationtagmaps/
   ├── locationtags/
+  ├── medicationsideeffects/
   ├── messageproperties/
   ├── metadatasetmembers/ 
   ├── metadatasets/ 
@@ -160,6 +161,7 @@ This is the list of currently supported domains in their loading order:
 1. [Identifier Sources (CSV files)](readme/idgen.md)
 1. [Autogeneration Options (CSV files)](readme/autogenerationoptions.md)
 1. [Drugs (CSV files)](readme/drugs.md)
+1. [Medication Side Effects (CSV files)](readme/medicationsideeffects.md)
 1. [Order Frequencies (CSV files)](readme/freqs.md)
 1. [Order Types (CSV files)](readme/ordertypes.md)
 1. [Bahmni Appointment Specialities (CSV files)](readme/appointmentspecialities.md)

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

@@ -74,6 +74,7 @@ protected boolean matchesSafely(List<Loader> loaders, Description mismatchDescri
 			exclude.add(Domain.BILLABLE_SERVICES.getName());
 			exclude.add(Domain.CASH_POINTS.getName());
 			exclude.add(Domain.CASHIER_ITEM_PRICES.getName());
+			exclude.add(Domain.MEDICATION_SIDE_EFFECTS.getName());
 			exclude.add(Domain.CONCEPT_REFERENCE_RANGE.getName());
 			exclude.add(Domain.FLAGS.getName());
 			exclude.add(Domain.FLAG_PRIORITIES.getName());

api-2.4/pom.xml

@@ -86,6 +86,13 @@
             <version>${billingVersion}</version>
             <scope>provided</scope>
         </dependency>
+
+        <dependency>
+            <groupId>org.openmrs.module</groupId>
+            <artifactId>medicationsideeffects-api</artifactId>
+            <version>${medicationsideeffectsVersion}</version>
+            <scope>provided</scope>
+        </dependency>
 
         <dependency>
             <groupId>org.openmrs.module</groupId>

api-2.4/src/main/java/org/openmrs/module/initializer/api/medicationsideeffects/MedicationSideEffectLineProcessor.java

@@ -0,0 +1,83 @@
+/*
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package org.openmrs.module.initializer.api.medicationsideeffects;
+
+import org.apache.commons.lang3.StringUtils;
+import org.openmrs.Concept;
+import org.openmrs.Drug;
+import org.openmrs.annotation.OpenmrsProfile;
+import org.openmrs.api.ConceptService;
+import org.openmrs.module.initializer.api.BaseLineProcessor;
+import org.openmrs.module.initializer.api.CsvLine;
+import org.openmrs.module.medicationsideeffects.model.MedicationSideEffect;
+import org.openmrs.module.medicationsideeffects.model.SideEffectClassification;
+import org.springframework.beans.factory.annotation.Autowired;
+
+@OpenmrsProfile(modules = { "medicationsideeffects:1.0.0 - 9.*" })
+public class MedicationSideEffectLineProcessor extends BaseLineProcessor<MedicationSideEffect> {
+
+	protected static final String HEADER_DRUG_UUID = "Drug Uuid";
+
+	protected static final String HEADER_CLASSIFICATION = "Classification";
+
+	protected static final String HEADER_CONCEPT_UUID = "Side Effect Concept Uuid";
+
+	protected static final String HEADER_SIDE_EFFECT_TEXT = "Side Effect Text";
+
+	protected static final String HEADER_RECOMMENDED_ACTION = "Recommended Action";
+
+	protected static final String HEADER_NOTES = "Notes";
+
+	private final ConceptService conceptService;
+
+	@Autowired
+	public MedicationSideEffectLineProcessor(ConceptService conceptService) {
+		this.conceptService = conceptService;
+	}
+
+	@Override
+	public MedicationSideEffect fill(MedicationSideEffect instance, CsvLine line) throws IllegalArgumentException {
+		String drugUuid = line.get(HEADER_DRUG_UUID, true);
+		Drug drug = conceptService.getDrugByUuid(drugUuid);
+		if (drug == null) {
+			throw new IllegalArgumentException("No drug found for uuid '" + drugUuid + "'");
+		}
+		instance.setDrug(drug);
+
+		String classification = line.get(HEADER_CLASSIFICATION, true);
+		try {
+			instance.setClassification(SideEffectClassification.valueOf(classification.toUpperCase()));
+		}
+		catch (IllegalArgumentException e) {
+			throw new IllegalArgumentException(
+			        "Invalid classification '" + classification + "' (expected common or serious)");
+		}
+
+		String conceptUuid = line.getString(HEADER_CONCEPT_UUID);
+		Concept concept = null;
+		if (StringUtils.isNotBlank(conceptUuid)) {
+			concept = conceptService.getConceptByUuid(conceptUuid);
+			if (concept == null) {
+				throw new IllegalArgumentException("No concept found for uuid '" + conceptUuid + "'");
+			}
+		}
+		instance.setSideEffectConcept(concept);
+
+		instance.setSideEffectText(line.getString(HEADER_SIDE_EFFECT_TEXT));
+		instance.setRecommendedAction(line.getString(HEADER_RECOMMENDED_ACTION));
+		instance.setNotes(line.getString(HEADER_NOTES));
+
+		if (concept == null && StringUtils.isBlank(instance.getSideEffectText())) {
+			throw new IllegalArgumentException("either 'Side Effect Concept Uuid' or 'Side Effect Text' must be provided");
+		}
+
+		return instance;
+	}
+}

api-2.4/src/main/java/org/openmrs/module/initializer/api/medicationsideeffects/MedicationSideEffectsCsvParser.java

@@ -0,0 +1,56 @@
+/*
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package org.openmrs.module.initializer.api.medicationsideeffects;
+
+import org.apache.commons.lang3.StringUtils;
+import org.openmrs.annotation.OpenmrsProfile;
+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.openmrs.module.medicationsideeffects.model.MedicationSideEffect;
+import org.openmrs.module.medicationsideeffects.service.MedicationSideEffectService;
+import org.springframework.beans.factory.annotation.Autowired;
+
+@OpenmrsProfile(modules = { "medicationsideeffects:1.0.0 - 9.*" })
+public class MedicationSideEffectsCsvParser extends CsvParser<MedicationSideEffect, BaseLineProcessor<MedicationSideEffect>> {
+
+	private final MedicationSideEffectService service;
+
+	@Autowired
+	public MedicationSideEffectsCsvParser(MedicationSideEffectService service,
+	    MedicationSideEffectLineProcessor lineProcessor) {
+		super(lineProcessor);
+		this.service = service;
+	}
+
+	@Override
+	public MedicationSideEffect bootstrap(CsvLine line) throws IllegalArgumentException {
+		String uuid = line.getUuid();
+		MedicationSideEffect sideEffect = service.getByUuid(uuid);
+		if (sideEffect == null) {
+			sideEffect = new MedicationSideEffect();
+			if (StringUtils.isNotBlank(uuid)) {
+				sideEffect.setUuid(uuid);
+			}
+		}
+		return sideEffect;
+	}
+
+	@Override
+	public MedicationSideEffect save(MedicationSideEffect instance) {
+		return service.saveMedicationSideEffect(instance);
+	}
+
+	@Override
+	public Domain getDomain() {
+		return Domain.MEDICATION_SIDE_EFFECTS;
+	}
+}

api-2.4/src/main/java/org/openmrs/module/initializer/api/medicationsideeffects/MedicationSideEffectsLoader.java

@@ -0,0 +1,24 @@
+/*
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package org.openmrs.module.initializer.api.medicationsideeffects;
+
+import org.openmrs.annotation.OpenmrsProfile;
+import org.openmrs.module.initializer.api.loaders.BaseCsvLoader;
+import org.openmrs.module.medicationsideeffects.model.MedicationSideEffect;
+import org.springframework.beans.factory.annotation.Autowired;
+
+@OpenmrsProfile(modules = { "medicationsideeffects:1.0.0 - 9.*" })
+public class MedicationSideEffectsLoader extends BaseCsvLoader<MedicationSideEffect, MedicationSideEffectsCsvParser> {
+
+	@Autowired
+	public void setParser(MedicationSideEffectsCsvParser parser) {
+		this.parser = parser;
+	}
+}

api-2.4/src/test/java/org/openmrs/module/initializer/api/DomainBaseModuleContextSensitive_2_4_test.java

@@ -28,6 +28,11 @@ public DomainBaseModuleContextSensitive_2_4_test() {
 			mod.setFile(new File(""));
 			ModuleFactory.getStartedModulesMap().put(mod.getModuleId(), mod);
 		}
+		{
+			Module mod = new Module("", "medicationsideeffects", "", "", "", "1.0.0");
+			mod.setFile(new File(""));
+			ModuleFactory.getStartedModulesMap().put(mod.getModuleId(), mod);
+		}
 	}
 
 	@Override

api-2.4/src/test/java/org/openmrs/module/initializer/api/medicationsideeffects/MedicationSideEffectLineProcessorTest.java

@@ -0,0 +1,97 @@
+/*
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package org.openmrs.module.initializer.api.medicationsideeffects;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.mockito.Mockito.when;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mock;
+import org.mockito.MockitoAnnotations;
+import org.openmrs.Concept;
+import org.openmrs.Drug;
+import org.openmrs.api.ConceptService;
+import org.openmrs.module.initializer.api.CsvLine;
+import org.openmrs.module.medicationsideeffects.model.MedicationSideEffect;
+import org.openmrs.module.medicationsideeffects.model.SideEffectClassification;
+
+public class MedicationSideEffectLineProcessorTest {
+
+	private static final String[] HEADERS = new String[] { "Uuid", "Void/Retire", "Drug Uuid", "Classification",
+	        "Side Effect Concept Uuid", "Side Effect Text", "Recommended Action", "Notes" };
+
+	private static final String DRUG_UUID = "a1a1a1a1-0000-0000-0000-000000000001";
+
+	private static final String CONCEPT_UUID = "b1b1b1b1-0000-0000-0000-000000000001";
+
+	@Mock
+	private ConceptService conceptService;
+
+	private MedicationSideEffectLineProcessor processor;
+
+	private Drug drug;
+
+	@Before
+	public void setUp() {
+		MockitoAnnotations.initMocks(this);
+		processor = new MedicationSideEffectLineProcessor(conceptService);
+		drug = new Drug();
+		drug.setUuid(DRUG_UUID);
+		when(conceptService.getDrugByUuid(DRUG_UUID)).thenReturn(drug);
+	}
+
+	private CsvLine line(String... values) {
+		return new CsvLine(HEADERS, values);
+	}
+
+	@Test
+	public void fill_shouldMapCodedCommonEffect() {
+		Concept concept = new Concept();
+		concept.setUuid(CONCEPT_UUID);
+		when(conceptService.getConceptByUuid(CONCEPT_UUID)).thenReturn(concept);
+
+		MedicationSideEffect result = processor.fill(new MedicationSideEffect(),
+		    line(null, null, DRUG_UUID, "common", CONCEPT_UUID, null, null, "Nausea note"));
+
+		assertEquals(drug, result.getDrug());
+		assertEquals(SideEffectClassification.COMMON, result.getClassification());
+		assertEquals(concept, result.getSideEffectConcept());
+		assertNull(result.getSideEffectText());
+		assertEquals("Nausea note", result.getNotes());
+	}
+
+	@Test
+	public void fill_shouldMapFreeTextSeriousEffect() {
+		MedicationSideEffect result = processor.fill(new MedicationSideEffect(),
+		    line(null, null, DRUG_UUID, "serious", null, "Signs of liver injury", "Seek urgent care", null));
+
+		assertEquals(SideEffectClassification.SERIOUS, result.getClassification());
+		assertNull(result.getSideEffectConcept());
+		assertEquals("Signs of liver injury", result.getSideEffectText());
+		assertEquals("Seek urgent care", result.getRecommendedAction());
+	}
+
+	@Test(expected = IllegalArgumentException.class)
+	public void fill_shouldThrowWhenDrugNotFound() {
+		processor.fill(new MedicationSideEffect(), line(null, null, "missing-drug-uuid", "common", null, "x", null, null));
+	}
+
+	@Test(expected = IllegalArgumentException.class)
+	public void fill_shouldThrowWhenClassificationInvalid() {
+		processor.fill(new MedicationSideEffect(), line(null, null, DRUG_UUID, "moderate", null, "x", null, null));
+	}
+
+	@Test(expected = IllegalArgumentException.class)
+	public void fill_shouldThrowWhenNeitherConceptNorTextProvided() {
+		processor.fill(new MedicationSideEffect(), line(null, null, DRUG_UUID, "common", null, null, null, null));
+	}
+}