Update cicd_process.yml

.github/workflows/cicd_process.yml

@@ -1,11 +1,11 @@
 name: deploy to prod 8600
 on:
   push:
-    branches: [ master ]
+    branches: [ 2.x ]
 jobs:
-
   build:
-    name: Deploy
+    name: deploying to 2.x instance
+    if: github.ref == 'refs/heads/2.x'
     runs-on: ubuntu-latest
     steps:
     - name: executing remote connection
@@ -23,7 +23,7 @@ jobs:
           sudo chown -R cicd2:cicd2 openmrs-module-kenyaemr
           git config --global --add safe.directory /apps/github-workflows/kenyaemr-modules/openmrs-module-kenyaemr
           cd /apps/github-workflows/kenyaemr-modules/openmrs-module-kenyaemr
-          git clone https://github.com/palladiumkenya/openmrs-module-kenyaemr.git /apps/github-workflows/kenyaemr-modules/openmrs-module-kenyaemr
+          git clone -b 2.x https://github.com/palladiumkenya/openmrs-module-kenyaemr.git /apps/github-workflows/kenyaemr-modules/openmrs-module-kenyaemr
           sudo chown -R cicd2:cicd2 /apps/github-workflows/kenyaemr-modules/openmrs-module-kenyaemr
           git status
           mvn license:format
@@ -35,3 +35,35 @@ jobs:
           sudo chmod 755 /var/lib/OpenMRS/modules/*.omod
           sudo systemctl stop tomcat
           sudo systemctl start tomcat
+
+  dev_server_deployment:
+    name: deploying to 3.x dev instance
+    if: github.ref == 'refs/heads/master'
+    runs-on: ubuntu-latest
+    steps:
+    - name: executing remote connection
+      uses: appleboy/ssh-action@master
+      with:
+        host: ${{ secrets.CICD_HOST }}
+        username: ${{ secrets.CICD_USERNAME }}
+        key: ${{ secrets.CICD_SECRET }}
+        port: ${{ secrets.PORT }}
+        command_timeout: 200m
+        script: |
+          cd /apps/githubworkflows/kenyaemr-modules
+          sudo rm -rf openmrs-module-kenyaemr
+          sudo mkdir openmrs-module-kenyaemr
+          sudo chown -R cicd:cicd openmrs-module-kenyaemr
+          git config --global --add safe.directory /apps/githubworkflows/kenyaemr-modules/openmrs-module-kenyaemr
+          cd /apps/githubworkflows/kenyaemr-modules/openmrs-module-kenyaemr
+          git clone -b master https://github.com/palladiumkenya/openmrs-module-kenyaemr.git .
+          git status
+          mvn license:format
+          sudo mvn clean install -DskipTests
+          sudo rm -rf /var/lib/OpenMRS/modules/kenyaemr-*.omod
+          sudo cp -r /apps/githubworkflows/kenyaemr-modules/openmrs-module-kenyaemr/omod/target/kenyaemr-*.omod /var/lib/OpenMRS/modules/
+          sudo chown -R tomcat:tomcat /var/lib/OpenMRS/modules/
+          sudo chmod +r /var/lib/OpenMRS/modules/*.omod
+          sudo chmod 755 /var/lib/OpenMRS/modules/*.omod
+          sudo service tomcat9 restart 
+

.github/workflows/maven_deploy_cicd.yml

@@ -4,7 +4,7 @@ on:
   # Manually triggered workflow using the "Run workflow" button
   workflow_dispatch:
   push:
-    branches: [ master ]
+    branches: [ master,openmrs-2.6.x-upgrade ]
 
 jobs:
   publish:

api/pom.xml

@@ -14,11 +14,11 @@
 	<parent>
 		<groupId>org.openmrs.module</groupId>
 		<artifactId>kenyaemr</artifactId>
-		<version>18.7.2-SNAPSHOT</version>
+		<version>18.8.0</version>
 	</parent>
 
 	<artifactId>kenyaemr-api</artifactId>
-    <version>18.7.2-SNAPSHOT</version>
+    <version>18.8.0</version>
 	<packaging>jar</packaging>
 	<name>KenyaEMR Module API</name>
 	<description>API project for KenyaEMR Module</description>

api/src/main/distro/metadata/identifierTypes.xml

@@ -29,4 +29,5 @@
 	<ref key="ALIEN_ID_NUMBER" uuid="1c7d0e5b-2068-4816-a643-8de83ab65fbf" />
 	<ref key="DRIVING_LICENSE" uuid="ca125004-e8af-445d-9436-a43684150f8b" />
 	<ref key="RECENCY_TESTING_ID" uuid="fd52829a-75d2-4732-8e43-4bff8e5b4f1a" />
+	<ref key="SOCIAL_HEALTH_INSURANCE_NUMBER" uuid="52c3c0c3-05b8-4b26-930e-2a6a54e14c90" />
 </refs>

api/src/main/java/org/openmrs/module/kenyaemr/calculation/library/hiv/NeedsNewVLOrderCalculation.java

@@ -60,7 +60,7 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj
             if (vlOrders.size() > 0) {
                 Integer latestVlOrder = Collections.max(vlOrders);
                 if (dueForVl.contains(ptId) && orderService.getOrder(latestVlOrder).isVoided()
-                        && (orderService.getOrder(latestVlOrder).getVoidReason().equalsIgnoreCase("Sample not taken")
+                && orderService.getOrder(latestVlOrder).getVoidReason() != null && (orderService.getOrder(latestVlOrder).getVoidReason().equalsIgnoreCase("Sample not taken")
                         || orderService.getOrder(latestVlOrder).getVoidReason().equalsIgnoreCase("Collect new sample")
                         || orderService.getOrder(latestVlOrder).getVoidReason().equalsIgnoreCase("Sample rejected")
                         || orderService.getOrder(latestVlOrder).getVoidReason().equalsIgnoreCase("No reagents"))) {

api/src/main/java/org/openmrs/module/kenyaemr/calculation/library/surveillance/EligibleForCholeraCalculation.java

@@ -49,8 +49,8 @@ public String getFlagMessage() {
         return "Suspected Cholera case";
     }
 
-    Integer VOMITING = 122983;
-    Integer DIARRHEA = 142412;
+    Integer VOMITING = 122983;   
+	Integer WATERY_DIARRHEA = 161887;
     Integer SCREENING_QUESTION = 5219;
 
     @Override
@@ -71,7 +71,7 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj
                 Encounter lastGreenCardEnc = EmrUtils.lastEncounter(patient, greenCardEncType, greenCardForm);   //last greencard followup form
                 ConceptService cs = Context.getConceptService();
                 Concept vomitingResult = cs.getConcept(VOMITING);
-                Concept diarrheaResult = cs.getConcept(DIARRHEA);
+                Concept diarrheaResult = cs.getConcept(WATERY_DIARRHEA);
                 Concept screeningQuestion = cs.getConcept(SCREENING_QUESTION);
                 boolean patientVomitClinicalEncResult = lastClinicalEncounter != null ? EmrUtils.encounterThatPassCodedAnswer(lastClinicalEncounter, screeningQuestion, vomitingResult) : false;
                 boolean patientDiarrheaClinicalEncResult = lastClinicalEncounter != null ? EmrUtils.encounterThatPassCodedAnswer(lastClinicalEncounter, screeningQuestion, diarrheaResult) : false;
@@ -115,4 +115,4 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj
 
         return ret;
     }
-}
+}

api/src/main/java/org/openmrs/module/kenyaemr/calculation/library/surveillance/EligibleForDysenteryCalculation.java

@@ -47,7 +47,7 @@ public class EligibleForDysenteryCalculation extends AbstractPatientCalculation
     public String getFlagMessage() {
         return "Suspected Dysentery case";
     }
-    Integer BLOOD_IN_STOOL = 132494;
+    Integer BLOOD_IN_STOOL = 117671;
     Integer DIARRHEA = 142412;
     Integer SCREENING_QUESTION = 5219;
 
@@ -110,4 +110,4 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj
         }
         return ret;
     }
-}
+}

api/src/main/java/org/openmrs/module/kenyaemr/calculation/library/surveillance/EligibleForHaemorrhagicCalculation.java

@@ -62,7 +62,7 @@ public String getFlagMessage() {
         return "Suspected Haemorrhagic Fever";
     }
     Integer FEVER = 140238;
-    Integer BLEEDING_TENDENCIES = 159339;  
+    Integer BLEEDING_TENDENCIES = 162628;  
     Integer SCREENING_QUESTION = 5219;
 
     @Override

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

@@ -0,0 +1,71 @@
+/**
+ * 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.openmrs.api.APIException;
+import org.openmrs.api.context.Context;
+import org.openmrs.module.kenyacore.chore.AbstractChore;
+import org.springframework.stereotype.Component;
+
+import java.io.PrintWriter;
+
+@Component("kenyaemr.chore.migratePatientAllergiesFromObs")
+public class MigratePatientAllergiesFromObs extends AbstractChore {
+    @Override
+    public void perform(PrintWriter printWriter) throws APIException {
+        String migrateAllergies = "insert into allergy (allergy_id, patient_id, severity_concept_id, coded_allergen, non_coded_allergen, allergen_type,\n" +
+                "                     comments, creator, date_created, changed_by, date_changed, voided, voided_by, date_voided,\n" +
+                "                     void_reason, uuid, form_namespace_and_path, encounter_id)  \n" +
+                "select null,o1.person_id,cn4.concept_id, case when cn1.concept_id is not null then cn1.concept_id else cn2.concept_id end,\n" +
+                "    case when cn1.concept_id is not null then cn1.name else cn2.name end,\n" +
+                "    case when cn2.concept_id is not null then 'Medication' else 'other' end,null,o1.creator,o1.date_created,null,null,o1.voided,\n" +
+                "    o1.voided_by,o1.date_voided,reaction.obs_id,o1.uuid,null,null\n" +
+                "    from obs o1\n" +
+                "    left join (select * from obs where concept_id = 160643) allergen1\n" +
+                "    on (o1.obs_group_id = allergen1.obs_group_id)\n" +
+                "    LEFT JOIN concept_name cn1\n" +
+                "    ON ( cn1.concept_id = allergen1.value_coded )\n" +
+                "    left join (select * from obs where concept_id = 1193) allergen2\n" +
+                "    on (o1.obs_group_id = allergen2.obs_group_id)\n" +
+                "    LEFT JOIN concept_name cn2\n" +
+                "    ON ( cn2.concept_id = allergen2.value_coded )\n" +
+                "    left join (select * from obs where concept_id = 159935) reaction\n" +
+                "    on (o1.obs_group_id = reaction.obs_group_id)\n" +
+                "    LEFT JOIN concept_name cn3\n" +
+                "    ON ( cn3.concept_id = reaction.value_coded )\n" +
+                "    left join (select * from obs where concept_id = 162760) severity\n" +
+                "    on (o1.obs_group_id = severity.obs_group_id)\n" +
+                "    LEFT JOIN concept_name cn4\n" +
+                "    ON ( cn4.concept_id = severity.value_coded )\n" +
+                "    where (allergen1.value_coded != 1066 or allergen2.value_coded != 1066)\n" +
+                "    AND o1.obs_group_id IS NOT NULL AND o1.concept_id in (160643,159935,162760,1193)  \n" +
+                " group by o1.person_id, o1.obs_group_id;";
+
+        String migrateAllergyReactions = "insert into allergy_reaction (allergy_reaction_id, allergy_id, reaction_concept_id, reaction_non_coded, uuid) \n" +
+                "select null,allergy_id, cn3.concept_id, cn3.name,reaction.uuid\n" +
+                "    from obs o1\n" +
+                "    left join (select * from obs where concept_id = 159935) reaction\n" +
+                "    on (o1.obs_group_id = reaction.obs_group_id)\n" +
+                "    LEFT JOIN concept_name cn3\n" +
+                "    ON ( cn3.concept_id = reaction.value_coded )\n" +
+                "    inner join allergy al on al.void_reason = reaction.obs_id\n" +
+                "    where o1.obs_group_id IS NOT NULL AND o1.concept_id in (159935) \n" +
+                " group by o1.person_id, o1.obs_group_id;";
+
+        String removeJoinColumn = "update allergy set void_reason = null;";
+
+        Context.getAdministrationService().executeSQL(migrateAllergies, false);
+        Context.getAdministrationService().executeSQL(migrateAllergyReactions, false);
+        Context.getAdministrationService().executeSQL(removeJoinColumn, false);
+
+
+        printWriter.println("Completed migrating patients allergies");
+    }
+}

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

@@ -0,0 +1,50 @@
+/**
+ * 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.openmrs.api.APIException;
+import org.openmrs.api.context.Context;
+import org.openmrs.module.kenyacore.chore.AbstractChore;
+import org.springframework.stereotype.Component;
+
+import java.io.PrintWriter;
+
+@Component("kenyaemr.chore.migratePatientConditionsFromObs")
+public class MigratePatientConditionsFromObs extends AbstractChore {
+    @Override
+    public void perform(PrintWriter printWriter) throws APIException {
+        String migrateConditions = "insert into conditions (condition_id, additional_detail, previous_version, condition_coded, condition_non_coded,\n" +
+                "                        condition_coded_name, clinical_status, verification_status, onset_date, date_created, voided,\n" +
+                "                        date_voided, void_reason, uuid, creator, voided_by, changed_by, patient_id, end_date,\n" +
+                "                        date_changed, encounter_id, form_namespace_and_path)  \n" +
+                "select null, null, null,cn1.concept_id,null,cn1.concept_id , 'INACTIVE', 'PROVISIONAL',t2.value_datetime, o1.obs_datetime,\n" +
+                "        0, null,null,o1.uuid,o1.creator,null,null,o1.person_id,null,null,null,null\n" +
+                "    from obs o1\n" +
+                "    left join (select * from obs where concept_id = 1284) t1\n" +
+                "    on (o1.obs_group_id = t1.obs_group_id)\n" +
+                "    LEFT JOIN concept_name cn1\n" +
+                "    ON ( cn1.concept_id = t1.value_coded )\n" +
+                "    left join (select * from obs where concept_id = 159948) t2\n" +
+                "    on (o1.obs_group_id = t2.obs_group_id)\n" +
+                "    left join (select * from obs where concept_id = 166937) t3\n" +
+                "    on (o1.obs_group_id = t3.obs_group_id)\n" +
+                "    LEFT JOIN concept_name cn3\n" +
+                "    ON ( cn3.concept_id = t3.value_coded )\n" +
+                "    where o1.obs_group_id is not null and o1.concept_id in (1284,159948,166937)\n" +
+                "    and t1.concept_id is not null  \n" +
+                " group by o1.person_id, o1.obs_group_id;";
+
+
+        Context.getAdministrationService().executeSQL(migrateConditions, false);
+
+
+        printWriter.println("Completed migrating conditions");
+    }
+}

api/src/main/java/org/openmrs/module/kenyaemr/metadata/CommonMetadata.java

@@ -39,6 +39,8 @@
 @Component
 public class CommonMetadata extends AbstractMetadataBundle {
 
+	public static final String GP_CLIENT_VERIFICATION_USE_EMR_PROXY = "kenyaemr.client.registry.use.emr.proxy"; 
+	public static final String GP_CLIENT_VERIFICATION_EMR_VERIFICATION_PROXY_URL = "kenyaemr.client.registry.emr.verification.proxy.url";
 	public static final String GP_CLIENT_VERIFICATION_GET_END_POINT = "kenyaemr.client.registry.get.api";
 	public static final String GP_CLIENT_VERIFICATION_POST_END_POINT = "kenyaemr.client.registry.post.api";
 	public static final String GP_CLIENT_VERIFICATION_API_TOKEN = "kenyaemr.client.registry.api.token";
@@ -62,8 +64,10 @@ public static final class _EncounterType {
 		public static final String HIV_SELF_TEST = "8b706d42-b4ae-4b3b-bd83-b14f15294362";
 		public static final String VMMC_PROCEDURE = "35c6fcc2-960b-11ec-b909-0242ac120002" ;
 		public static final String GAD_7 = "899d64ad-be13-4071-a879-2153847206b7";
+		public static final String MAT_CLINICAL_ENCOUNTER = "c3518485-ee22-4a47-b6d4-6d0e8f297b02";
 		public static final String ILI_SURVEILLANCE = "f60910c7-2edd-4d93-813c-0e57095f892f";
 		public static final String SARI_SURVEILLANCE = "76d55715-88cc-4851-b5e0-09136426fd46";
+		public static final String PROCEDURE_RESULTS = "99a7a6ba-59f4-484e-880d-01cbeaead62f";
 	}
 
 	public static final class _Form {
@@ -112,6 +116,7 @@ public static final class _PatientIdentifierType {
 		public static final String ALIEN_ID_NUMBER = Metadata.IdentifierType.ALIEN_ID_NUMBER;
 		public static final String DRIVING_LICENSE = Metadata.IdentifierType.DRIVING_LICENSE;
 		public static final String RECENCY_TESTING_ID = Metadata.IdentifierType.RECENCY_TESTING_ID;
+		public static final String SOCIAL_HEALTH_INSURANCE_NUMBER = Metadata.IdentifierType.SOCIAL_HEALTH_INSURANCE_NUMBER;
 	}
 
 	public static final class _PersonAttributeType {
@@ -188,8 +193,10 @@ public void install() {
 		install(encounterType("Cervical cancer screening", "Cervical cancer screening", _EncounterType.CACX_SCREENING));
 		install(encounterType("HIV self testing", "Self testing screening", _EncounterType.HIV_SELF_TEST));
 		install(encounterType("Oncology screening", "Oncology screening encounter type", _EncounterType.ONCOLOGY_SCREENING));
+		install(encounterType("MAT Clinical Encounter", "MAT Clinical Encounter", _EncounterType.MAT_CLINICAL_ENCOUNTER));
 		install(encounterType("ILI Surveillance", "ILI Surveillance encounter type", _EncounterType.ILI_SURVEILLANCE));
 		install(encounterType("SARI Surveillance", "SARI Surveillance encounter type", _EncounterType.SARI_SURVEILLANCE));
+		install(encounterType("Procedure Results", "Procedure outcome encounter type", _EncounterType.PROCEDURE_RESULTS));
 
 		install(form("Clinical Encounter", null, _EncounterType.CONSULTATION, "1", _Form.CLINICAL_ENCOUNTER));
 		install(form("Lab Results", null, _EncounterType.LAB_RESULTS, "1", _Form.LAB_RESULTS));
@@ -228,6 +235,12 @@ public void install() {
 		install(globalProperty("client_number_label", "Label for Client Number", "Client Number"));
 		install(globalProperty("clientNumber.enabled", "Switch to show client number", "false"));
 
+		if(Context.getAdministrationService().getGlobalPropertyObject(CommonMetadata.GP_CLIENT_VERIFICATION_USE_EMR_PROXY) == null) {
+			install(globalProperty(GP_CLIENT_VERIFICATION_USE_EMR_PROXY, "Use the EMR backend to proxy NUPI requests (true or false)", "false"));
+		}    
+		if(Context.getAdministrationService().getGlobalPropertyObject(CommonMetadata.GP_CLIENT_VERIFICATION_EMR_VERIFICATION_PROXY_URL) == null) {
+			install(globalProperty(GP_CLIENT_VERIFICATION_EMR_VERIFICATION_PROXY_URL, "The local EMR URL to proxy NUPI verification requests", "http://127.0.0.1:8080/openmrs/ws/rest/v1/kenyaemr/verifynupi"));
+		} 
 		if(Context.getAdministrationService().getGlobalPropertyObject(CommonMetadata.GP_CLIENT_VERIFICATION_GET_END_POINT) == null) {
 			install(globalProperty(GP_CLIENT_VERIFICATION_GET_END_POINT, "A GET API for getting client information at the client registry", "https://afyakenyaapi.health.go.ke/partners/registry/search"));
 		}
@@ -294,6 +307,8 @@ public void install() {
 				null, LocationBehavior.NOT_USED, false, _PatientIdentifierType.DRIVING_LICENSE));
 		install(patientIdentifierType("Recency Testing ID", "Recency Testing ID", "", "Allows for alphanumeric format",
 				null, LocationBehavior.NOT_USED, false, _PatientIdentifierType.RECENCY_TESTING_ID));
+		install(patientIdentifierType("Social Health Insurance Number", "Social Health Insurance Number", "", "Allows for alphanumeric format",
+				null, LocationBehavior.NOT_USED, false, _PatientIdentifierType.SOCIAL_HEALTH_INSURANCE_NUMBER));
 
 
 		install(personAttributeType("Telephone contact", "Telephone contact number",

api/src/main/java/org/openmrs/module/kenyaemr/reporting/Moh705ReportUtils/AutismDiagnosisConstants.java → api/src/main/java/org/openmrs/module/kenyaemr/reporting/MohReportUtils/AutismDiagnosisConstants.java

@@ -7,7 +7,7 @@
  * 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.reporting.Moh705ReportUtils;
+package org.openmrs.module.kenyaemr.reporting.MohReportUtils;
 
 public class AutismDiagnosisConstants {
 

api/src/main/java/org/openmrs/module/kenyaemr/reporting/Moh705ReportUtils/ColumnParameters.java → api/src/main/java/org/openmrs/module/kenyaemr/reporting/MohReportUtils/ColumnParameters.java

@@ -7,7 +7,7 @@
  * 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.reporting.Moh705ReportUtils;
+package org.openmrs.module.kenyaemr.reporting.MohReportUtils;
 
 /**
  * Describes a column in a CohortIndicatorDataSetDefinition

api/src/main/java/org/openmrs/module/kenyaemr/reporting/Moh705ReportUtils/ConvulsiveDiagnosisConstants.java → api/src/main/java/org/openmrs/module/kenyaemr/reporting/MohReportUtils/ConvulsiveDiagnosisConstants.java

@@ -7,7 +7,7 @@
  * 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.reporting.Moh705ReportUtils;
+package org.openmrs.module.kenyaemr.reporting.MohReportUtils;
 
 public class ConvulsiveDiagnosisConstants {
 

api/src/main/java/org/openmrs/module/kenyaemr/reporting/Moh705ReportUtils/DiabetesDiagnosisConstants.java → api/src/main/java/org/openmrs/module/kenyaemr/reporting/MohReportUtils/DiabetesDiagnosisConstants.java

@@ -7,7 +7,7 @@
  * 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.reporting.Moh705ReportUtils;
+package org.openmrs.module.kenyaemr.reporting.MohReportUtils;
 
 public class DiabetesDiagnosisConstants {