Trunk 6264 concept reference range initialization

README.md

@@ -159,6 +159,7 @@ This is the list of currently supported domains in their loading order:
 1. [AMPATH Forms (JSON files)](readme/ampathforms.md)
 1. [AMPATH Forms Translations (JSON files)](readme/ampathformstranslations.md)
 1. [HTML Forms (XML files)](readme/htmlforms.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:
@@ -206,6 +207,7 @@ 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/src/main/java/org/openmrs/module/initializer/Domain.java

@@ -26,6 +26,7 @@ public enum Domain {
 	OCL,
 	CONCEPTS,
 	CONCEPT_SETS,
+	CONCEPT_REFERENCE_RANGE,
 	BILLABLE_SERVICES,
 	PAYMENT_MODES,
 	CASH_POINTS,

api/src/main/java/org/openmrs/module/initializer/api/c/ConceptReferenceRangeCsvParser.java

@@ -0,0 +1,51 @@
+package org.openmrs.module.initializer.api.c;
+
+import org.apache.commons.lang3.StringUtils;
+import org.openmrs.ConceptReferenceRange;
+import org.openmrs.api.ConceptService;
+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.beans.factory.annotation.Qualifier;
+import org.springframework.stereotype.Component;
+
+@Component
+public class ConceptReferenceRangeCsvParser extends CsvParser<ConceptReferenceRange, BaseLineProcessor<ConceptReferenceRange>> {
+
+	private final ConceptService conceptService;
+
+	@Autowired
+	public ConceptReferenceRangeCsvParser(@Qualifier("conceptService") ConceptService conceptService,
+	    ConceptReferenceRangeLineProcessor processor) {
+		super(processor);
+		this.conceptService = conceptService;
+	}
+
+	@Override
+	public Domain getDomain() {
+		return Domain.CONCEPT_REFERENCE_RANGE;
+	}
+
+	@Override
+	public ConceptReferenceRange bootstrap(CsvLine line) throws IllegalArgumentException {
+		String uuid = line.getUuid();
+
+		ConceptReferenceRange referenceRange = conceptService.getConceptReferenceRangeByUuid(uuid);
+
+		if (referenceRange == null) {
+			referenceRange = new ConceptReferenceRange();
+			if (!StringUtils.isEmpty(uuid)) {
+				referenceRange.setUuid(uuid);
+			}
+		}
+
+		return referenceRange;
+	}
+
+	@Override
+	public ConceptReferenceRange save(ConceptReferenceRange instance) {
+		return conceptService.saveConceptReferenceRange(instance);
+	}
+}

api/src/main/java/org/openmrs/module/initializer/api/c/ConceptReferenceRangeLineProcessor.java

@@ -0,0 +1,61 @@
+package org.openmrs.module.initializer.api.c;
+
+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;
+
+	@Autowired
+	public ConceptReferenceRangeLineProcessor(@Qualifier("conceptService") ConceptService conceptService) {
+		this.conceptService = conceptService;
+	}
+
+	public ConceptReferenceRange fill(ConceptReferenceRange referenceRange, CsvLine line) throws IllegalArgumentException {
+		ConceptNumeric conceptNumeric = conceptService.getConceptNumericByUuid(line.get(HEADER_CONCEPT_NUMERIC_UUID));
+
+		if (conceptNumeric == null) { // below overrides any other processors work, so this one should be called first
+			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/src/main/java/org/openmrs/module/initializer/api/c/ConceptReferenceRangeLoader.java

@@ -0,0 +1,21 @@
+package org.openmrs.module.initializer.api.c;
+
+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/src/test/java/org/openmrs/module/initializer/api/ConceptReferenceRangeIntegrationTest.java

@@ -0,0 +1,30 @@
+package org.openmrs.module.initializer.api;
+
+import org.junit.Assert;
+import org.junit.jupiter.api.Test;
+import org.openmrs.ConceptReferenceRange;
+import org.openmrs.api.ConceptService;
+import org.openmrs.module.initializer.DomainBaseModuleContextSensitiveTest;
+import org.openmrs.module.initializer.api.c.ConceptReferenceRangeLoader;
+import org.springframework.beans.factory.annotation.Autowired;
+
+public class ConceptReferenceRangeIntegrationTest extends DomainBaseModuleContextSensitiveTest {
+
+	@Autowired
+	private ConceptService conceptService;
+
+	@Autowired
+	private ConceptReferenceRangeLoader conceptReferenceRangeLoader;
+
+	@Test
+	public void load_shouldLoadConceptReferenceRangeFromCsvFiles() {
+		conceptReferenceRangeLoader.load();
+
+		{
+			ConceptReferenceRange referenceRange = conceptService
+			        .getConceptReferenceRangeByUuid("239c1904-15ff-45e1-ac9d-d83afb637926");
+			Assert.assertNotNull(referenceRange);
+			Assert.assertEquals(Double.valueOf("70"), referenceRange.getLowAbsolute());
+		}
+	}
+}

api/src/test/resources/testAppDataDir/configuration/concepts/concept_referenceranges.csv

@@ -0,0 +1,4 @@
+Uuid,Concept Numeric Uuid,Absolute low,Critical low,Normal low,Normal high,Critical high,Absolute high,Criteria
+bc059100-4ace-4af5-afbf-2da7f3a34acf,30247229-052c-400b-a823-cb66b1c506c7,-100.5,-85.7,-50.3,45.1,78,98.8, $patient.getAge() > 3
+930e1fb4-490d-45fe-a137-0cd941c76124,,-100.5,-85.7,-50.3,45.1,78,98.8, $patient.getAge() < 10
+b5a7b296-e500-4a2c-ab2e-eb012ed9ae1e,,60,70,80,120,130,150, $fn.getCurrentHour() > 2

pom.xml

@@ -58,6 +58,7 @@
         <openmrsVersion2.3>2.3.6</openmrsVersion2.3>
         <openmrsVersion2.4>2.4.5</openmrsVersion2.4>
         <openmrsVersion2.5>2.5.5</openmrsVersion2.5>
+        <openmrsVersion2.7>2.7.0-SNAPSHOT</openmrsVersion2.7>
 
         <openmrsPlatformVersion>${openmrsVersion2.1}</openmrsPlatformVersion>
 

readme/conceptreferenceranges.md

@@ -0,0 +1,49 @@
+## Domain 'conceptreferenceranges'
+
+The **conceptreferenceranges** subfolder contains CSV configuration files that help manage ConceptReferenceRange entity.
+
+This is a possible example of how the configuration subfolder may look like:
+
+```bash
+concepts/
+  └── concepts_referenceranges.csv
+```
+
+Here is a sample CSV:
+
+| Uuid                                 | Concept Numeric Uuid | Absolute low                     | Critical low                                    | Normal low                      | Normal high | Absolute high | Absolute high | Criteria | 
+|--------------------------------------|-|----------------------------------|-------------------------------------------------|---------------------------------|------------------------------------|-|-------------------------| - |
+| bc059100-4ace-4af5-afbf-2da7f3a34acf | 3f8f0ab7-c240-4b68-8951-bb7020be01f6 | 60                               | 70                                              | 80                              | 120 | 130 | 150                     | $patient.getAge() > 3 |
+
+
+Summery of the set of available headers.
+
+###### Header `Uuid`
+Uuid of the conceptReferenceRange entity.
+
+###### Header `Concept Numeric Uuid` *(mandatory)*
+UUID of ConceptNumeric.
+
+###### Header `Absolute low` *(mandatory)*
+Absolute low of referenceRange.
+
+###### Header `Critical low` *(mandatory)*
+Critical low of referenceRange.
+
+###### Header `Normal low` *(mandatory)*
+Normal low of referenceRange.
+
+###### Header `Normal high`
+Normal high of referenceRange.
+
+###### Header `Critical high`
+Critical high of referenceRange.
+
+###### Header `Absolute high` *(mandatory)*
+Absolute high of referenceRange.
+
+###### Header `Criteria` *(mandatory)*
+Criteria.
+
+#### Further examples:
+Please look at the test configuration folder for sample import files for all domains, see [here](../api/src/test/resources/testAppDataDir/configuration).