Update branch with master changes

README.md

@@ -4,3 +4,6 @@ openmrs-distro-bahmni
 `./mvnw clean deploy` command to create artifacts.
 
 This command will attempt to upload & publish artifacts to https://bahmnirepo.thoughtworks.com (maven repository). You will need authorization to upload (your public key needs to be on the server). 
+
+This distribution also includes [FHIR CDSS module](https://github.com/Bahmni/openmrs-module-cdss) and [FHIR Terminology Service Module](https://github.com/Bahmni/openmrs-module-snomed) along with other modules bundled with standard Bahmni.
+More details can be found [here](https://bahmni.atlassian.net/wiki/spaces/BAH/pages/3132686337/SNOMED+FHIR+Terminology+Server+Integration+with+Bahmni)

distro/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>bahmni</artifactId>
         <groupId>org.openmrs.distro</groupId>
-        <version>0.94-SNAPSHOT</version>
+        <version>1.1.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -83,6 +83,11 @@
             <artifactId>bahmnicore-omod</artifactId>
             <version>${bahmniCoreVersion}</version>
         </dependency>
+        <dependency>
+            <groupId>org.bahmni.module</groupId>
+            <artifactId>bahmni-ipd-omod</artifactId>
+            <version>${bahmniIpdVersion}</version>
+        </dependency>
         <dependency>
             <groupId>org.bahmni.module</groupId>
             <artifactId>openelis-atomfeed-client-omod</artifactId>
@@ -166,6 +171,13 @@
             <artifactId>calculation-omod</artifactId>
             <version>${calculationVersion}</version>
         </dependency>
+
+        <dependency>
+            <groupId>org.bahmni.module</groupId>
+            <artifactId>medication-administration-omod</artifactId>
+            <version>${medicationAdministrationVersion}</version>
+        </dependency>
+
         <dependency>
             <groupId>org.openmrs.module</groupId>
             <artifactId>metadatamapping-omod</artifactId>
@@ -184,6 +196,7 @@
             <artifactId>owa-omod</artifactId>
             <version>${owaVersion}</version>
         </dependency>
+
          <dependency>
             <groupId>org.openmrs</groupId>
             <artifactId>event-omod</artifactId>
@@ -302,27 +315,17 @@
           <artifactId>openconceptlab-omod</artifactId>
           <version>${openConceptLabVersion}</version>
         </dependency>
+
         <dependency>
             <groupId>org.openmrs.module</groupId>
             <artifactId>initializer-omod</artifactId>
             <version>${initializerModuleVersion}</version>
         </dependency>
+
         <dependency>
             <groupId>org.openmrs.module</groupId>
             <artifactId>reportingcompatibility-omod</artifactId>
-            <version>${reportingcompatibilityVersion}</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.bahmni.module</groupId>
-            <artifactId>medication-administration-omod</artifactId>
-            <version>${medicationAdministrationVersion}</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.bahmni.module</groupId>
-            <artifactId>bahmni-ipd-omod</artifactId>
-            <version>${bahmniIpdVersion}</version>
+            <version>${reportingCompatibilityVersion}</version>
         </dependency>
         <!-- end -->
     </dependencies>

openmrs-module-bahmni.configuration/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>bahmni</artifactId>
         <groupId>org.openmrs.distro</groupId>
-        <version>0.94-SNAPSHOT</version>
+        <version>1.1.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -16,7 +16,7 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <openMRSVersion>2.5.10</openMRSVersion>
+        <openMRSVersion>2.5.12</openMRSVersion>
         <MODULE_ID>${project.parent.artifactId}</MODULE_ID>
         <MODULE_NAME>${project.parent.name}</MODULE_NAME>
         <MODULE_VERSION>${project.parent.version}</MODULE_VERSION>

package/.appversion

@@ -1 +1 @@
-1.0.0
+1.1.1

package/docker/openmrs/templates/appointment.properties.template

@@ -0,0 +1 @@
+

package/docker/openmrs/update_elis_host_port.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+set +e
+
+run_sql() {
+  mysql -N -s --host="${OMRS_DB_HOSTNAME}" --user="${OMRS_DB_USERNAME}" --password="${OMRS_DB_PASSWORD}" "${OMRS_DB_NAME}" -e "$1"
+}
+
+if [ $(run_sql "select count(*) from information_schema.tables where table_schema='${OMRS_DB_NAME}' and table_name='markers';") -gt 0 ]
+then
+    echo "Updating OpenELIS Host Port in markers and failed_events table"
+    run_sql "update markers set feed_uri_for_last_read_entry = concat('http://${OPENELIS_HOST}:${OPENELIS_PORT}/openelis/ws/feed/patient',substring(feed_uri_for_last_read_entry, (LENGTH(feed_uri_for_last_read_entry) - LOCATE('/', REVERSE(feed_uri_for_last_read_entry)))+1) ) where feed_uri like '%openelis/ws/feed/patient/recent';"
+    run_sql "update markers set feed_uri = 'http://${OPENELIS_HOST}:${OPENELIS_PORT}/openelis/ws/feed/patient/recent' where feed_uri like '%openelis/ws/feed/patient/recent';"
+    run_sql "update failed_events set feed_uri = 'http://${OPENELIS_HOST}:${OPENELIS_PORT}/openelis/ws/feed/patient/recent' where feed_uri like '%openelis/ws/feed/patient/recent';"
+fi

package/helm/openmrs/templates/configMap.yaml

@@ -22,3 +22,5 @@ data:
   MAIL_SMTP_PORT: "{{ .Values.config.MAIL_SMTP_PORT }}"
   MAIL_SMTP_HOST: "{{ .Values.config.MAIL_SMTP_HOST }}"
   OMRS_DOCKER_ENV: "{{ .Values.config.OMRS_DOCKER_ENV }}"
+  TZ: "{{ .Values.global.TZ }}"
+  OMRS_C3P0_MAX_SIZE: "{{ .Values.config.OMRS_C3P0_MAX_SIZE }}"

package/helm/openmrs/templates/deployment.yaml

@@ -78,6 +78,8 @@ spec:
               name: bahmni-config
             - mountPath: /home/bahmni/uploaded_results
               name: bahmni-uploaded-results
+            - mountPath: /home/bahmni/uploaded-files
+              name: bahmni-uploaded-files
       restartPolicy: Always
       volumes:
       #   - name: openmrs-data
@@ -101,3 +103,6 @@ spec:
         - name: bahmni-uploaded-results
           persistentVolumeClaim:
             claimName: bahmni-uploaded-results-pvc
+        - name: bahmni-uploaded-files
+          persistentVolumeClaim:
+            claimName: bahmni-uploaded-files-pvc

package/helm/openmrs/templates/hpa.yaml

@@ -1,5 +1,5 @@
 {{- if .Values.autoscaling.enabled }}
-apiVersion: autoscaling/v2beta1
+apiVersion: autoscaling/v2
 kind: HorizontalPodAutoscaler
 metadata:
   name: {{ .Chart.Name }}
@@ -18,12 +18,16 @@ spec:
     - type: Resource
       resource:
         name: cpu
-        targetAverageUtilization: {{ .Values.autoscaling.targetCPUUtilizationPercentage }}
+        target:
+          type: Utilization
+          averageUtilization: {{ .Values.autoscaling.targetCPUUtilizationPercentage }}
     {{- end }}
     {{- if .Values.autoscaling.targetMemoryUtilizationPercentage }}
     - type: Resource
       resource:
         name: memory
-        targetAverageUtilization: {{ .Values.autoscaling.targetMemoryUtilizationPercentage }}
+        target:
+          type: Utilization
+          averageUtilization: {{ .Values.autoscaling.targetMemoryUtilizationPercentage }}
     {{- end }}
 {{- end }}

package/helm/openmrs/templates/volumes/bahmni-uploaded-files.yaml

@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  labels:
+    app: {{ .Chart.Name }}
+    environment: {{ .Values.metadata.labels.environment }}
+  name: bahmni-uploaded-files-pvc
+spec:
+  storageClassName: {{ .Values.global.storageClass }}
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+      storage: {{ .Values.volumes.uploadedFiles.capacity }}

package/helm/openmrs/values.yaml

@@ -7,6 +7,7 @@ global:
   nodeSelector: {}
   affinity: {}
   tolerations: {}
+  TZ: "UTC"
 
 metadata:
   labels:
@@ -42,6 +43,7 @@ config:
   MAIL_SMTP_PORT: ""
   MAIL_SMTP_HOST: ""
   OMRS_DOCKER_ENV: 'false'
+  OMRS_C3P0_MAX_SIZE: 50
 
 secrets:
   OMRS_DB_HOSTNAME: ""
@@ -74,6 +76,8 @@ volumes:
     capacity: "1Gi"
   uploadedResults:
     capacity: "2Gi"
+  uploadedFiles:
+    capacity: "2Gi"
 nodeSelector: {}
 affinity: {}
 tolerations: {}

package/resources/add_hibernate_properties.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+set -e
+
+sed '/module.allow_web_admin/a\
+c3p0.max_size=${OMRS_C3P0_MAX_SIZE}' ./startup-init.sh > ./startup-init-temp.sh
+
+rm ./startup-init.sh
+mv ./startup-init-temp.sh ./startup-init.sh

package/resources/fhir-export-anonymise-config.json

@@ -0,0 +1,91 @@
+{
+  "resources": {
+    "patient": [
+      {
+        "fieldName": "id",
+        "method": "correlate"
+      },
+      {
+        "fieldName": "identifier",
+        "method": "redact"
+      },
+      {
+        "fieldName": "address",
+        "method": "redact"
+      },
+      {
+        "fieldName": "name",
+        "method": "redact"
+      },
+      {
+        "fieldName": "telecom",
+        "method": "redact"
+      },
+      {
+        "fieldName": "birthDate",
+        "method": "firstOfMonth"
+      },
+      {
+        "fieldName": "deceasedDateTime",
+        "method": "firstOfMonth"
+      }
+    ],
+    "condition": [
+      {
+        "fieldName": "subject",
+        "method": "correlate"
+      },
+      {
+        "fieldName": "encounter",
+        "method": "redact"
+      },
+      {
+        "fieldName": "recorder",
+        "method": "redact"
+      },
+      {
+        "fieldName": "recordedDate",
+        "method": "redact"
+      }
+    ],
+    "medicationRequest": [
+      {
+        "fieldName": "subject",
+        "method": "correlate"
+      },
+      {
+        "fieldName": "priority",
+        "method": "redact"
+      },
+      {
+        "fieldName": "authoredOn",
+        "method": "redact"
+      },
+      {
+        "fieldName": "requester",
+        "method": "redact"
+      },
+      {
+        "fieldName": "dosageInstruction",
+        "method": "redact"
+      },
+      {
+        "fieldName": "encounter",
+        "method": "redact"
+      }
+    ],
+    "serviceRequest": [
+      {
+        "fieldName": "subject",
+        "method": "correlate"
+      },
+      {
+        "fieldName": "encounter",
+        "method": "redact"
+      }
+    ]
+  },
+  "parameters": {
+    "oneWayHashSalt": "Bahmni123"
+  }
+}

pom.xml

@@ -5,7 +5,7 @@
 
 	<groupId>org.openmrs.distro</groupId>
 	<artifactId>bahmni</artifactId>
-	<version>0.94-SNAPSHOT</version>
+	<version>1.1.1</version>
     <modules>
         <module>openmrs-module-bahmni.configuration</module>
         <module>distro</module>