diff --git a/README.md b/README.md index 025d23e2..34012bcd 100644 --- a/README.md +++ b/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) \ No newline at end of file diff --git a/distro/pom.xml b/distro/pom.xml index fc5b6884..4f93aa67 100644 --- a/distro/pom.xml +++ b/distro/pom.xml @@ -5,7 +5,7 @@ bahmni org.openmrs.distro - 0.94-SNAPSHOT + 1.1.1 4.0.0 @@ -83,6 +83,11 @@ bahmnicore-omod ${bahmniCoreVersion} + + org.bahmni.module + bahmni-ipd-omod + ${bahmniIpdVersion} + org.bahmni.module openelis-atomfeed-client-omod @@ -166,6 +171,13 @@ calculation-omod ${calculationVersion} + + + org.bahmni.module + medication-administration-omod + ${medicationAdministrationVersion} + + org.openmrs.module metadatamapping-omod @@ -184,6 +196,7 @@ owa-omod ${owaVersion} + org.openmrs event-omod @@ -302,27 +315,17 @@ openconceptlab-omod ${openConceptLabVersion} + org.openmrs.module initializer-omod ${initializerModuleVersion} + org.openmrs.module reportingcompatibility-omod - ${reportingcompatibilityVersion} - - - - org.bahmni.module - medication-administration-omod - ${medicationAdministrationVersion} - - - - org.bahmni.module - bahmni-ipd-omod - ${bahmniIpdVersion} + ${reportingCompatibilityVersion} diff --git a/openmrs-module-bahmni.configuration/pom.xml b/openmrs-module-bahmni.configuration/pom.xml index c9054b46..1ac0b601 100644 --- a/openmrs-module-bahmni.configuration/pom.xml +++ b/openmrs-module-bahmni.configuration/pom.xml @@ -5,7 +5,7 @@ bahmni org.openmrs.distro - 0.94-SNAPSHOT + 1.1.1 4.0.0 @@ -16,7 +16,7 @@ UTF-8 - 2.5.10 + 2.5.12 ${project.parent.artifactId} ${project.parent.name} ${project.parent.version} diff --git a/package/.appversion b/package/.appversion index afaf360d..8cfbc905 100644 --- a/package/.appversion +++ b/package/.appversion @@ -1 +1 @@ -1.0.0 \ No newline at end of file +1.1.1 \ No newline at end of file diff --git a/package/docker/openmrs/bahmni_startup.sh b/package/docker/openmrs/bahmni_startup.sh old mode 100644 new mode 100755 diff --git a/package/docker/openmrs/templates/appointment.properties.template b/package/docker/openmrs/templates/appointment.properties.template new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/package/docker/openmrs/templates/appointment.properties.template @@ -0,0 +1 @@ + diff --git a/package/docker/openmrs/update_elis_host_port.sh b/package/docker/openmrs/update_elis_host_port.sh new file mode 100755 index 00000000..1db09e93 --- /dev/null +++ b/package/docker/openmrs/update_elis_host_port.sh @@ -0,0 +1,14 @@ +#!/bin/bash +set +e + +run_sql() { + mysql -N -s --host="${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 diff --git a/package/helm/openmrs/templates/configMap.yaml b/package/helm/openmrs/templates/configMap.yaml index 6d020cad..8c74de17 100644 --- a/package/helm/openmrs/templates/configMap.yaml +++ b/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 }}" diff --git a/package/helm/openmrs/templates/deployment.yaml b/package/helm/openmrs/templates/deployment.yaml index 568af315..14463d4d 100644 --- a/package/helm/openmrs/templates/deployment.yaml +++ b/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 diff --git a/package/helm/openmrs/templates/hpa.yaml b/package/helm/openmrs/templates/hpa.yaml index 18d71e7c..5df81b52 100644 --- a/package/helm/openmrs/templates/hpa.yaml +++ b/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 }} diff --git a/package/helm/openmrs/templates/volumes/bahmni-uploaded-files.yaml b/package/helm/openmrs/templates/volumes/bahmni-uploaded-files.yaml new file mode 100644 index 00000000..15894078 --- /dev/null +++ b/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 }} diff --git a/package/helm/openmrs/values.yaml b/package/helm/openmrs/values.yaml index cd55537b..b4a856da 100644 --- a/package/helm/openmrs/values.yaml +++ b/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: {} diff --git a/package/resources/add_hibernate_properties.sh b/package/resources/add_hibernate_properties.sh new file mode 100644 index 00000000..d33519c6 --- /dev/null +++ b/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 diff --git a/package/resources/fhir-export-anonymise-config.json b/package/resources/fhir-export-anonymise-config.json new file mode 100644 index 00000000..d0bd4574 --- /dev/null +++ b/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" + } +} \ No newline at end of file diff --git a/pom.xml b/pom.xml index 78557b18..9a63710a 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.openmrs.distro bahmni - 0.94-SNAPSHOT + 1.1.1 openmrs-module-bahmni.configuration distro