Merge branch 'master' into ContactPointMap-impl

ibacher · web-flow · commit 88cc7792b34a · 2024-05-20T16:23:22.000-04:00
diff --git a/README.md b/README.md
@@ -197,10 +197,11 @@ See the [documentation on Initializer's logging properties](readme/rtprops.md#lo
 ## Releases notes
 
 #### Version 2.7.0
+* Added support for 'fhircontactpointmap' domain.
 * Added support for 'queues' domain.
 * Added support for 'addresshierarchy' domain.
 * Fix for Liquibase Loader to ensure compatibility with OpenMRS versions 2.5.5+
-* Added support for 'fhircontactpointmap' domain.
+* Fix for OCL Loader to ensure it throws an Exception if the OCL import fails
 
 #### Version 2.6.0
 * Added support for 'cohorttypes' and 'cohortattributetypes' domains.
diff --git a/api-2.3/src/main/java/org/openmrs/module/initializer/api/queues/QueueLineProcessor.java b/api-2.3/src/main/java/org/openmrs/module/initializer/api/queues/QueueLineProcessor.java
@@ -19,6 +19,10 @@ public class QueueLineProcessor extends BaseLineProcessor<Queue> {
 	
 	protected static String HEADER_SERVICE = "service";
 	
+	protected static String HEADER_STATUS_CONCEPT_SET = "status concept set";
+	
+	protected static String HEADER_PRIORITY_CONCEPT_SET = "priority concept set";
+	
 	protected static String HEADER_LOCATION = "location";
 	
 	private final ConceptService conceptService;
@@ -45,6 +49,22 @@ public Queue fill(Queue queue, CsvLine line) throws IllegalArgumentException {
 				queue.setService(null);
 			}
 		}
+		if (line.containsHeader(HEADER_STATUS_CONCEPT_SET)) {
+			String statusConceptSet = line.getString(HEADER_STATUS_CONCEPT_SET);
+			if (StringUtils.isNotBlank(statusConceptSet)) {
+				queue.setStatusConceptSet(Utils.fetchConcept(statusConceptSet, conceptService));
+			} else {
+				queue.setStatusConceptSet(null);
+			}
+		}
+		if (line.containsHeader(HEADER_PRIORITY_CONCEPT_SET)) {
+			String priorityConceptSet = line.getString(HEADER_PRIORITY_CONCEPT_SET);
+			if (StringUtils.isNotBlank(priorityConceptSet)) {
+				queue.setPriorityConceptSet(Utils.fetchConcept(priorityConceptSet, conceptService));
+			} else {
+				queue.setPriorityConceptSet(null);
+			}
+		}
 		if (line.containsHeader(HEADER_LOCATION)) {
 			String location = line.getString(HEADER_LOCATION);
 			if (StringUtils.isNotBlank(location)) {
diff --git a/api-2.3/src/test/java/org/openmrs/module/initializer/api/queues/QueueLoaderIntegrationTest.java b/api-2.3/src/test/java/org/openmrs/module/initializer/api/queues/QueueLoaderIntegrationTest.java
@@ -65,5 +65,16 @@ public void load_shouldLoadAccordingToCsvFiles() throws Exception {
 			Assert.assertEquals(2001, queue.getService().getConceptId().intValue());
 			Assert.assertEquals(3, queue.getLocation().getLocationId().intValue());
 		}
+		// Queue with statuses
+		{
+			Queue queue = queueService.getQueueByUuid("4856c1c1-c9b3-4a7e-8669-4220051ab640").orElse(null);
+			Assert.assertNotNull(queue);
+			Assert.assertEquals("Triage Queue", queue.getName());
+			Assert.assertEquals("Queue with custom statuses", queue.getDescription());
+			Assert.assertEquals(2001, queue.getService().getConceptId().intValue());
+			Assert.assertEquals(2003, queue.getStatusConceptSet().getConceptId().intValue());
+			Assert.assertEquals("Triage queue priorities", queue.getPriorityConceptSet().getName().getName());
+			Assert.assertEquals("Xanadu", queue.getLocation().getName());
+		}
 	}
 }
diff --git a/api-2.3/src/test/resources/testAppDataDir/configuration/queues/queues.csv b/api-2.3/src/test/resources/testAppDataDir/configuration/queues/queues.csv
@@ -1,3 +1,4 @@
-Uuid,Void/Retire,Name,Description,Service,Location
-2a0e0eee-6888-11ee-ab8d-0242ac120002,,Revised Queue,Revised Description,68b910bd-298c-4ecf-a632-661ae2f446op,Xanadu
-288db1cc-688a-11ee-ab8d-0242ac120002,,New Queue,New Description,Triage,167ce20c-4785-4285-9119-d197268f7f4a
+Uuid,Void/Retire,Name,Description,Service,Status Concept Set,Priority Concept Set,Location
+2a0e0eee-6888-11ee-ab8d-0242ac120002,,Revised Queue,Revised Description,68b910bd-298c-4ecf-a632-661ae2f446op,,,Xanadu
+288db1cc-688a-11ee-ab8d-0242ac120002,,New Queue,New Description,Triage,,,167ce20c-4785-4285-9119-d197268f7f4a
+4856c1c1-c9b3-4a7e-8669-4220051ab640,,Triage Queue,Queue with custom statuses,67b910bd-298c-4ecf-a632-661ae2f446op,1d2a73ca-20aa-4218-b4d2-043024a9156e,24932838-60ca-44e8-840f-4184b368643c,Xanadu
diff --git a/api/src/main/java/org/openmrs/module/initializer/api/c/ConceptNumericLineProcessor.java b/api/src/main/java/org/openmrs/module/initializer/api/c/ConceptNumericLineProcessor.java
@@ -42,10 +42,15 @@ public Concept fill(Concept instance, CsvLine line) throws IllegalArgumentExcept
 			return instance;
 		}
 		
-		ConceptNumeric cn = new ConceptNumeric(instance);
+		ConceptNumeric cn = null;
 		if (instance.getId() != null) { // below overrides any other processors work, so this one should be called first
 			cn = conceptService.getConceptNumeric(instance.getId());
 		}
+		
+		if (cn == null) {
+			cn = new ConceptNumeric(instance);
+		}
+		
 		cn.setDatatype(conceptService.getConceptDatatypeByName(DATATYPE_NUMERIC));
 		
 		cn.setHiAbsolute(line.getDouble(HEADER_AH));
diff --git a/api/src/main/java/org/openmrs/module/initializer/api/loaders/OpenConceptLabLoader.java b/api/src/main/java/org/openmrs/module/initializer/api/loaders/OpenConceptLabLoader.java
@@ -1,13 +1,16 @@
 package org.openmrs.module.initializer.api.loaders;
 
-import java.io.File;
-import java.util.zip.ZipFile;
-
+import org.apache.commons.lang.StringUtils;
 import org.openmrs.annotation.OpenmrsProfile;
 import org.openmrs.api.context.Context;
 import org.openmrs.module.initializer.Domain;
+import org.openmrs.module.openconceptlab.Import;
+import org.openmrs.module.openconceptlab.ImportService;
 import org.openmrs.module.openconceptlab.importer.Importer;
 
+import java.io.File;
+import java.util.zip.ZipFile;
+
 @OpenmrsProfile(modules = { "openconceptlab:1.2.9" })
 public class OpenConceptLabLoader extends BaseFileLoader {
 	
@@ -25,7 +28,29 @@ protected String getFileExtension() {
 	protected void load(File file) throws Exception {
 		ZipFile zip = new ZipFile(file);
 		Importer importer = Context.getRegisteredComponent("openconceptlab.importer", Importer.class);
+		ImportService importService = Context.getService(ImportService.class);
+		
+		Import lastImport = importService.getLastImport();
+		log.debug("Starting OCL importer");
 		importer.run(zip);
+		Import oclImport = importService.getLastImport();
+		
+		// Import failed to start.  This can happen another import is already currently running
+		if (oclImport == null || oclImport.equals(lastImport)) {
+			throw new IllegalStateException("OCL import did not start successfully");
+		}
+		
+		// Import detected errors
+		if (StringUtils.isNotBlank(oclImport.getErrorMessage())) {
+			throw new IllegalStateException(oclImport.getErrorMessage());
+		}
+		
+		// Import never stopped
+		if (!oclImport.isStopped()) {
+			throw new IllegalStateException("OCL import did not complete successfully");
+		}
+		
+		log.debug("OCL import completed successfully: " + oclImport.getLocalDateStopped());
 	}
 	
 }
diff --git a/api/src/test/java/org/openmrs/module/initializer/api/c/ConceptNumericLineProcessorTest.java b/api/src/test/java/org/openmrs/module/initializer/api/c/ConceptNumericLineProcessorTest.java
@@ -1,7 +1,9 @@
 package org.openmrs.module.initializer.api.c;
 
 import static org.mockito.Matchers.any;
+import static org.mockito.Mockito.atLeast;
 import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
 import org.junit.Assert;
@@ -89,4 +91,22 @@ public void fill_shouldFailWhenCannotParse() {
 		ConceptNumericLineProcessor p = new ConceptNumericLineProcessor(cs);
 		p.fill(new Concept(), new CsvLine(headerLine, line));
 	}
+	
+	@Test
+	public void fill_shouldOverrideProvidedDataType() {
+		
+		// Setup
+		when(cs.getConceptNumeric(any(Integer.class))).thenReturn(null);
+		String[] headerLine = { "Data type", "Absolute low" };
+		String[] line = { "Numeric", "11.11" };
+		
+		// Replay
+		ConceptNumericLineProcessor p = new ConceptNumericLineProcessor(cs);
+		ConceptNumeric cn = (ConceptNumeric) p.fill(new Concept(1), new CsvLine(headerLine, line));
+		
+		// Verify
+		verify(cs, atLeast(1)).getConceptNumeric(any(Integer.class));
+		Assert.assertEquals(ConceptNumericLineProcessor.DATATYPE_NUMERIC, cn.getDatatype().getName());
+		Assert.assertEquals(0, cn.getLowAbsolute().compareTo(11.11));
+	}
 }
diff --git a/api/src/test/resources/testdata/test-queues.xml b/api/src/test/resources/testdata/test-queues.xml
@@ -4,9 +4,13 @@
   <concept concept_id="2000" retired="false" is_set="true" creator="1" date_created="2022-02-02 14:31:00.0" uuid="907eba27-2b38-43e8-91a9-4dfe3956a35t"/>
   <concept concept_id="2001" retired="false" is_set="false" creator="1" date_created="2022-02-02 14:40:00.0" uuid="67b910bd-298c-4ecf-a632-661ae2f446op"/>
   <concept concept_id="2002" retired="false" is_set="false" creator="1" date_created="2022-03-08 15:40:00.0" uuid="68b910bd-298c-4ecf-a632-661ae2f446op"/>
+  <concept concept_id="2003" retired="false" is_set="false" creator="1" date_created="2024-01-16 15:40:00.0" uuid="1d2a73ca-20aa-4218-b4d2-043024a9156e"/>
+  <concept concept_id="2004" retired="false" is_set="false" creator="1" date_created="2024-01-18 05:40:00.0" uuid="24932838-60ca-44e8-840f-4184b368643c"/>
   <concept_name concept_name_id="893" concept_id="2000" name="Queue Service" locale="en" creator="1" date_created="2022-02-02 14:40:00.0" voided="0" uuid="9cp62348-5bf2-4050-b824-0aa009436ed6" concept_name_type="FULLY_SPECIFIED" locale_preferred="0"/>
   <concept_name concept_name_id="210" concept_id="2001" name="Triage" locale="en" creator="1" date_created="2022-02-02 14:40:00.0" voided="0" uuid="9i667348-5bf2-4050-b824-0aa009436kl0" concept_name_type="FULLY_SPECIFIED" locale_preferred="0"/>
   <concept_name concept_name_id="211" concept_id="2002" name="Consultation" locale="en" creator="1" date_created="2022-02-02 14:40:00.0" voided="0" uuid="5t747348-5bf2-4050-b824-0aa009436kl0" concept_name_type="FULLY_SPECIFIED" locale_preferred="0"/>
+  <concept_name concept_name_id="212" concept_id="2003" name="Triage statuses" locale="en" creator="1" date_created="2024-01-15 14:40:00.0" voided="0" uuid="9b6d5a44-47b0-4ed2-873b-5b317721ca9a" concept_name_type="FULLY_SPECIFIED" locale_preferred="0"/>
+  <concept_name concept_name_id="213" concept_id="2004" name="Triage queue priorities" locale="en" creator="1" date_created="2024-01-16 14:40:00.0" voided="0" uuid="9f2af84d-5e4c-43d9-bdde-fea4a3f15744" concept_name_type="FULLY_SPECIFIED" locale_preferred="0"/>
   <concept_set concept_set_id="389000" concept_set="2000" concept_id="2001" sort_weight="0" date_created="2022-02-02 14:40:00.0" creator="1" uuid="470b910bd-298c-4ecf-a632-661ae2f886bf"/>
   <concept_set concept_set_id="389001" concept_set="2000" concept_id="2002" sort_weight="0" date_created="2022-03-08 15:50:00.0" creator="1" uuid="380b910bd-298c-4ecf-a632-661ae2f886bf"/>
 
diff --git a/pom.xml b/pom.xml
@@ -75,7 +75,7 @@
 
         <!-- Modules compatibility > Core 2.3.0 -->
         <datafilterVersion>1.0.0</datafilterVersion>
-        <queueVersion>1.0.0-SNAPSHOT</queueVersion>
+        <queueVersion>2.1.0</queueVersion>
 
         <!-- For Validator -->
         <reportingVersion>1.19.0</reportingVersion>
diff --git a/readme/queues.md b/readme/queues.md
@@ -7,9 +7,9 @@ queues/
 ```
 There is currently only one format for the queue CSV line, here are the possible headers with a sample data set:
 
-| <sub>Uuid</sub>                                 | <sub>Void/Retire</sub> | <sub>Name</sub>                        | <sub>Description</sub>   | <sub>Service</sub>            | <sub>Location</sub>           |
-|--------------------------------------|-------------|-----------------------------|---------------|--------------------|--------------------|
-| <sub>32176576-1652-4835-8736-826eb0237482</sub> |             | <sub>Clinical Consultation Queue</sub> | <sub>Consult Queue</sub> | <sub>Outpatient Service</sub> | <sub>Outpatient Clinic</sub>| |
+| <sub>Uuid</sub>                                 | <sub>Void/Retire</sub> | <sub>Name</sub>                        | <sub>Description</sub>   | <sub>Service</sub>            | <sub>Status Concept Set</sub>            | <sub>Priority Concept Set</sub>   | <sub>Location</sub>           |
+|--------------------------------------|-------------|-----------------------------|---------------|--------------------|--------------------|-----------------------------------|--------------------|
+| <sub>32176576-1652-4835-8736-826eb0237482</sub> |             | <sub>Clinical Consultation Queue</sub> | <sub>Consult Queue</sub> | <sub>Outpatient Service</sub> |<sub>Queue entry statuses</sub> | <sub>Queue entry priorities</sub> | <sub>Outpatient Clinic</sub>| |
 
 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.
 
@@ -25,11 +25,17 @@ A description is optional and will populate the queue description
 ###### Header `Service`
 This is a reference (UUID, same as mapping or name) to an existing concept that defines the service associated with this queue.
 
+###### Header `Status Concept Set`
+This is a reference (UUID, same as mapping or name) to an existing concept set that defines the queue statuses that could be assigned to the entries in this queue.
+
+###### Header `Priority Concept Set`
+This is a reference (UUID, same as mapping or name) to an existing concept set that defines the queue priorities that could be assigned to the entries in this queue.
+
 ###### Header `Location`
 This is a reference (UUID or name) to an existing location that defines the location associated with this queue.
 
 #### Requirements
-* The [queue module](https://github.com/openmrs/openmrs-module-queue) must be installed
+* The [queue module](https://github.com/openmrs/openmrs-module-queue) version 2.1 or higher must be installed
 * The OpenMRS version must be 2.3 or higher
 
 #### Further examples:

Original file line number	Diff line number	Diff line change
`@@ -65,5 +65,16 @@ public void load_shouldLoadAccordingToCsvFiles() throws Exception {`
`65`	`65`	`Assert.assertEquals(2001, queue.getService().getConceptId().intValue());`
`66`	`66`	`Assert.assertEquals(3, queue.getLocation().getLocationId().intValue());`
`67`	`67`	`}`
	`68`	`+ // Queue with statuses`
	`69`	`+ {`
	`70`	`+ Queue queue = queueService.getQueueByUuid("4856c1c1-c9b3-4a7e-8669-4220051ab640").orElse(null);`
	`71`	`+ Assert.assertNotNull(queue);`
	`72`	`+ Assert.assertEquals("Triage Queue", queue.getName());`
	`73`	`+ Assert.assertEquals("Queue with custom statuses", queue.getDescription());`
	`74`	`+ Assert.assertEquals(2001, queue.getService().getConceptId().intValue());`
	`75`	`+ Assert.assertEquals(2003, queue.getStatusConceptSet().getConceptId().intValue());`
	`76`	`+ Assert.assertEquals("Triage queue priorities", queue.getPriorityConceptSet().getName().getName());`
	`77`	`+ Assert.assertEquals("Xanadu", queue.getLocation().getName());`
	`78`	`+ }`
`68`	`79`	`}`
`69`	`80`	`}`