Merge pull request #2086 from patryllus/feat/AddingICD11CodeSets

Added a chore to incorporate ICD11 codesets to diagnosis class concepts

api/src/main/java/org/openmrs/module/kenyaemr/chore/AddICD11MappingCodeSetsForDiagnosis.java

@@ -0,0 +1,117 @@
+/**
+ * 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.kenyaemr.chore;
+
+import org.codehaus.jackson.JsonNode;
+import org.codehaus.jackson.map.ObjectMapper;
+import org.codehaus.jackson.node.ArrayNode;
+import org.codehaus.jackson.node.ObjectNode;
+import org.openmrs.api.context.Context;
+import org.openmrs.module.kenyacore.chore.AbstractChore;
+import org.springframework.stereotype.Component;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Iterator;
+
+/**
+ * Update ICD 11 Mappings for Diagnosis
+ * Uses DiagnosisICD10ToICD11Mapper
+ */
+@Component("kenyaemr.chore.AddICD11MappingCodeSetsForDiagnosis")
+public class AddICD11MappingCodeSetsForDiagnosis extends AbstractChore {
+
+	/**
+	 * @see AbstractChore#perform(PrintWriter)
+	 */
+
+	@Override
+	public void perform(PrintWriter out) {
+
+		ObjectMapper mapper = new ObjectMapper();
+		ArrayNode conf = null;
+		try {
+			System.out.println("Retrieving ICD code mapper");
+			conf = (ArrayNode) mapper.readTree(icd11DiagnosisCodeJson());
+			if (conf != null) {
+				System.out.println("ICD code mapper found");
+				for (Iterator<JsonNode> it = conf.iterator(); it.hasNext(); ) {
+					ObjectNode node = (ObjectNode) it.next();
+
+					String conceptId = node.get("ConceptId").asText();
+					String icd11code = node.get("ICD11Code").asText();
+
+					String updateConceptSql = "Insert into concept_reference_map (\n" +
+						"    concept_map_id,\n" +
+						"    creator,\n" +
+						"    date_created,\n" +
+						"    concept_id,\n" +
+						"    uuid,\n" +
+						"    concept_reference_term_id,\n" +
+						"    concept_map_type_id,\n" +
+						"    changed_by,\n" +
+						"    date_changed)\n" +
+						"select null,\n" +
+						"       1,\n" +
+						"       CURDATE(),\n" +
+						"      " + conceptId + ",\n" +
+						"       UUID(),\n" +
+						"       rt.concept_reference_term_id,\n" +
+						"       1,\n" +
+						"       null,\n" +
+						"       null\n" +
+						"from concept_reference_term rt\n" +
+						"left join openmrs.concept_reference_map crm on rt.concept_reference_term_id = crm.concept_reference_term_id\n" +
+						"where rt.code = '" + icd11code + "' and crm.concept_reference_term_id is null;";
+
+					Context.getAdministrationService().executeSQL(updateConceptSql, false);
+
+				}
+			}
+		} catch (IOException e) {
+			out.println("Failed to update ICD 11 codes");
+			throw new RuntimeException(e);
+		}
+		out.println("Successfully updated ICD 11 codes");
+	}
+
+	private static String icd11DiagnosisCodeJson() {
+		String json = "[\n" +
+			"    {\n" +
+			"        \"DiagnosisName\": \"Headache, not elsewhere classified\",\n" +
+			"        \"ConceptId\": \"139084\",\n" +			
+			"        \"ICD11Code\": \"8A8Z\"\n" +
+			"    },\n" +
+			"    {\n" +
+			"        \"DiagnosisName\": \"Malaria due to Plasmodium falciparum\",\n" +
+			"        \"ConceptId\": \"116128\",\n" +		
+			"        \"ICD11Code\": \"1F40\"\n" +
+			"    },\n" +
+			"    {\n" +
+			"        \"DiagnosisName\": \"Typhoid fever\",\n" +
+			"        \"ConceptId\": \"141\",\n" +			
+			"        \"ICD11Code\": \"1A07.Z\"\n" +
+			"    },\n" +
+			"    {\n" +
+			"        \"DiagnosisName\": \"Pneumonia, organism unspecified\",\n" +
+			"        \"ConceptId\": \"114100\",\n" +			
+			"        \"ICD11Code\": \"CA40.Z\"\n" +
+			"    },\n" +
+			"    {\n" +
+			"        \"DiagnosisName\": \"Fever of other or unknown origin\",\n" +
+			"        \"ConceptId\": \"140238\",\n" +		
+			"        \"ICD11Code\": \"MG26\"\n" +
+			"    }\n" +
+			"]";
+		return json;
+	}
+
+
+}