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michaelloosenmichaelloosen
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Merge branch 'main' into PLAT-400-cluster-clikhouse
2 parents 2ed8e5d + 77ce93c commit 44f248d

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16 files changed

+147
-43
lines changed

16 files changed

+147
-43
lines changed

‎analytics-datastore-elastic-search/importer/docker-compose.config.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -26,4 +26,4 @@ configs:
2626
file: ./fhir-enrich-reports.json
2727
name: fhir-enrich-reports.json-${fhir_enrich_reports_json_DIGEST:?err}
2828
labels:
29-
name: elastic-search
29+
name: elasticsearch

‎analytics-datastore-elastic-search/swarm.sh‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ import_elastic_index() {
3434
log info "Importing Elasticsearch index mapping"
3535
config::set_config_digests "${COMPOSE_FILE_PATH}"/importer/docker-compose.config.yml
3636
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/importer/docker-compose.config.yml instant" "Failed to start elastic search config importer"
37-
config::remove_stale_service_configs "${COMPOSE_FILE_PATH}"/importer/docker-compose.config.yml "elastic-search"
37+
config::remove_stale_service_configs "${COMPOSE_FILE_PATH}"/importer/docker-compose.config.yml "elasticsearch"
3838
config::remove_config_importer elastic-search-config-importer
3939
}
4040

@@ -161,7 +161,7 @@ elif [[ "$ACTION" == "destroy" ]]; then
161161
fi
162162

163163
docker::try_remove_volume es-data
164-
docker::prune_configs "elastic-search"
164+
docker::prune_configs "elasticsearch"
165165
else
166166
log error "Valid options are: init, up, down, or destroy"
167167
fi

‎client-registry-santempi/package-metadata.json‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
"description": "A patient matching and deduplicater for the platform",
55
"type": "infrastructure",
66
"version": "0.0.1",
7-
"dependencies": ["reverse-proxy-nginx"],
7+
"dependencies": [],
88
"environmentVariables": {
99
"STATEFUL_NODES": "single",
1010
"SANTEMPI_INSTANCES": "1",

‎client-registry-santempi/swarm.sh‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -34,43 +34,43 @@ await_postgres_start() {
3434
main() {
3535
if [ "${STATEFUL_NODES}" == "cluster" ]; then
3636
log info "Running Client Registry SanteMPI package in Cluster node mode"
37-
local POSTGRES_CLUSTER_COMPOSE_PARAM="-c ${COMPOSE_FILE_PATH}/docker-compose-postgres.cluster.yml"
37+
local postgres_cluster_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose-postgres.cluster.yml"
3838
else
3939
log info "Running Client Registry SanteMPI package in Single node mode"
40-
local POSTGRES_CLUSTER_COMPOSE_PARAM=""
40+
local postgres_cluster_compose_param=""
4141
fi
4242

4343
if [ "$MODE" == "dev" ]; then
4444
log info "Running Client Registry SanteMPI package in DEV mode"
45-
local POSTGRES_DEV_COMPOSE_PARAM="-c ${COMPOSE_FILE_PATH}/docker-compose-postgres.dev.yml"
46-
local SANTE_MPI_DEV_COMPOSE_PARAM="-c ${COMPOSE_FILE_PATH}/docker-compose.dev.yml"
45+
local postgres_dev_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose-postgres.dev.yml"
46+
local sante_mpi_dev_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose.dev.yml"
4747
else
4848
log info "Running Client Registry SanteMPI package in PROD mode"
49-
local POSTGRES_DEV_COMPOSE_PARAM=""
50-
local SANTE_MPI_DEV_COMPOSE_PARAM=""
49+
local postgres_dev_compose_param=""
50+
local sante_mpi_dev_compose_param=""
5151
fi
5252

5353
if [ "$ACTION" == "init" ]; then
54-
try "docker stack deploy -c $COMPOSE_FILE_PATH/docker-compose-postgres.yml $POSTGRES_CLUSTER_COMPOSE_PARAM $POSTGRES_DEV_COMPOSE_PARAM instant" "Failed to deploy SanteMPI Postgres"
54+
try "docker stack deploy -c $COMPOSE_FILE_PATH/docker-compose-postgres.yml $postgres_cluster_compose_param $postgres_dev_compose_param instant" "Failed to deploy SanteMPI Postgres"
5555

5656
await_postgres_start
5757

58-
try "docker stack deploy -c "$COMPOSE_FILE_PATH"/docker-compose.yml $SANTE_MPI_DEV_COMPOSE_PARAM instant" "Failed to deploy SanteMPI"
58+
try "docker stack deploy -c ""$COMPOSE_FILE_PATH""/docker-compose.yml $sante_mpi_dev_compose_param instant" "Failed to deploy SanteMPI"
5959
elif [ "$ACTION" == "up" ]; then
60-
try "docker stack deploy -c $COMPOSE_FILE_PATH/docker-compose-postgres.yml $POSTGRES_CLUSTER_COMPOSE_PARAM $POSTGRES_DEV_COMPOSE_PARAM instant" "Failed to stand up SanteMPI Postgres"
60+
try "docker stack deploy -c $COMPOSE_FILE_PATH/docker-compose-postgres.yml $postgres_cluster_compose_param $postgres_dev_compose_param instant" "Failed to stand up SanteMPI Postgres"
6161

6262
await_postgres_start
6363

64-
try "docker stack deploy -c "$COMPOSE_FILE_PATH"/docker-compose.yml $SANTE_MPI_DEV_COMPOSE_PARAM instant" "Failed to stand up SanteMPI"
64+
try "docker stack deploy -c ""$COMPOSE_FILE_PATH""/docker-compose.yml $sante_mpi_dev_compose_param instant" "Failed to stand up SanteMPI"
6565
elif [ "$ACTION" == "down" ]; then
66-
try "docker service scale instant_santedb-mpi=0 instant_santempi-psql-1=0" "Failed to scale down santeMPI"
66+
try "docker service scale instant_santedb-mpi=0 instant_santedb-www=0 instant_santempi-psql-1=0" "Failed to scale down santeMPI"
6767

6868
if [ "$STATEFUL_NODES" == "cluster" ]; then
6969
try "docker service scale instant_santempi-psql-2=0 instant_santempi-psql-3=0" "Failed to scale down santeMPI postgres replicas"
7070
fi
7171

7272
elif [ "$ACTION" == "destroy" ]; then
73-
docker::service_destroy santedb-www
73+
docker::service_destroy santedb-www
7474
docker::service_destroy santedb-mpi
7575
docker::service_destroy santempi-psql-1
7676
docker::try_remove_volume santedb-data

‎config.yml‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -38,3 +38,5 @@ packages:
3838
name: Dashboard Visualiser Superset
3939
- id: monitoring
4040
name: Monitoring package
41+
- id: mpi-mediator
42+
name: OpenHIM-Sante Mediator

‎data-mapper-logstash/package-metadata.json‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,6 @@
1515
"LOGSTASH_MEMORY_LIMIT": "3G",
1616
"LOGSTASH_MEMORY_RESERVE": "500M",
1717
"ES_ELASTIC": "dev_password_only",
18-
"ES_HOSTS": "analytics-datastore-elastic-search:9200"
18+
"ES_HOSTS": "\"analytics-datastore-elastic-search:9200\""
1919
}
2020
}

‎data-mapper-logstash/swarm.sh‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -26,10 +26,10 @@ inject_pipeline_elastic_hosts() {
2626

2727
if [[ "$MODE" == "dev" ]]; then
2828
log info "Running Data Mapper Logstash package in DEV mode"
29-
LogstashDevComposeParam="-c ${COMPOSE_FILE_PATH}/docker-compose.dev.yml"
29+
logstash_dev_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose.dev.yml"
3030
else
3131
log info "Running Data Mapper Logstash package in PROD mode"
32-
LogstashDevComposeParam=""
32+
logstash_dev_compose_param=""
3333
fi
3434

3535
if [[ "$LOGSTASH_DEV_MOUNT" == "true" ]]; then
@@ -39,9 +39,9 @@ if [[ "$LOGSTASH_DEV_MOUNT" == "true" ]]; then
3939
fi
4040

4141
log info "Running Data Mapper Logstash package with dev mount"
42-
LogstashDevMountComposeParam="-c ${COMPOSE_FILE_PATH}/docker-compose.dev-mnt.yml"
42+
logstash_dev_mount_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose.dev-mnt.yml"
4343
else
44-
LogstashDevMountComposeParam=""
44+
logstash_dev_mount_compose_param=""
4545
fi
4646

4747
if [[ "${ACTION}" == "init" ]] || [[ "${ACTION}" == "up" ]]; then
@@ -57,9 +57,9 @@ if [[ "${ACTION}" == "init" ]] || [[ "${ACTION}" == "up" ]]; then
5757
config::set_config_digests "${COMPOSE_FILE_PATH}"/docker-compose.yml
5858

5959
config::generate_service_configs data-mapper-logstash /usr/share/logstash "${COMPOSE_FILE_PATH}/pipeline" "${COMPOSE_FILE_PATH}" logstash
60-
LogstashTempComposeParam="-c ${COMPOSE_FILE_PATH}/docker-compose.tmp.yml"
60+
logstash_temp_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose.tmp.yml"
6161

62-
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose.yml $LogstashDevComposeParam $LogstashDevMountComposeParam $LogstashTempComposeParam instant" "Failed to deploy Data Mapper Logstash"
62+
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose.yml $logstash_dev_compose_param $logstash_dev_mount_compose_param $logstash_temp_compose_param instant" "Failed to deploy Data Mapper Logstash"
6363

6464
docker::await_container_startup data-mapper-logstash
6565
docker::await_container_status data-mapper-logstash Running

‎fhir-datastore-hapi-fhir/swarm.sh‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -33,34 +33,34 @@ await_postgres_start() {
3333

3434
if [ "${STATEFUL_NODES}" == "cluster" ]; then
3535
log info "Running FHIR Datastore HAPI FHIR package in Cluster node mode"
36-
postgresClusterComposeParam="-c ${COMPOSE_FILE_PATH}/docker-compose-postgres.cluster.yml"
36+
postgres_cluster_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose-postgres.cluster.yml"
3737
else
3838
log info "Running FHIR Datastore HAPI FHIR package in Single node mode"
39-
postgresClusterComposeParam=""
39+
postgres_cluster_compose_param=""
4040
fi
4141

4242
if [ "${MODE}" == "dev" ]; then
4343
log info "Running FHIR Datastore HAPI FHIR package in DEV mode"
44-
postgresDevComposeParam="-c ${COMPOSE_FILE_PATH}/docker-compose-postgres.dev.yml"
45-
hapiFhirDevComposeParam="-c ${COMPOSE_FILE_PATH}/docker-compose.dev.yml"
44+
postgres_dev_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose-postgres.dev.yml"
45+
hapi_fhir_dev_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose.dev.yml"
4646
else
4747
log info "Running FHIR Datastore HAPI FHIR package in PROD mode"
48-
postgresDevComposeParam=""
49-
hapiFhirDevComposeParam=""
48+
postgres_dev_compose_param=""
49+
hapi_fhir_dev_compose_param=""
5050
fi
5151

5252
if [ "${ACTION}" == "init" ]; then
53-
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose-postgres.yml $postgresClusterComposeParam $postgresDevComposeParam instant" "Failed to deploy FHIR Datastore HAPI FHIR Postgres"
53+
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose-postgres.yml $postgres_cluster_compose_param $postgres_dev_compose_param instant" "Failed to deploy FHIR Datastore HAPI FHIR Postgres"
5454

5555
await_postgres_start
5656

57-
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose.yml $hapiFhirDevComposeParam instant" "Failed to deploy FHIR Datastore HAPI FHIR"
57+
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose.yml $hapi_fhir_dev_compose_param instant" "Failed to deploy FHIR Datastore HAPI FHIR"
5858
elif [ "${ACTION}" == "up" ]; then
59-
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose-postgres.yml $postgresClusterComposeParam $postgresDevComposeParam instant" "Failed to stand up hapi-fhir postgres"
59+
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose-postgres.yml $postgres_cluster_compose_param $postgres_dev_compose_param instant" "Failed to stand up hapi-fhir postgres"
6060

6161
await_postgres_start
6262

63-
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose.yml $hapiFhirDevComposeParam instant" "Failed to stand up hapi-fhir"
63+
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose.yml $hapi_fhir_dev_compose_param instant" "Failed to stand up hapi-fhir"
6464
elif [ "${ACTION}" == "down" ]; then
6565
try "docker service scale instant_hapi-fhir=0 instant_postgres-1=0" "Failed to scale down hapi-fhir"
6666

‎job-scheduler-ofelia/swarm.sh‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,9 +8,8 @@ COMPOSE_FILE_PATH=$(
88
)
99
readonly COMPOSE_FILE_PATH
1010

11+
# Import libraries
1112
ROOT_PATH="${COMPOSE_FILE_PATH}/.."
12-
readonly ROOT_PATH
13-
1413
. "${ROOT_PATH}/utils/config-utils.sh"
1514
. "${ROOT_PATH}/utils/docker-utils.sh"
1615
. "${ROOT_PATH}/utils/log.sh"
@@ -29,6 +28,8 @@ main() {
2928
try "docker service scale instant_job-scheduler-ofelia=0" "Failed to scale down job-scheduler-ofelia"
3029
elif [[ "${ACTION}" == "destroy" ]]; then
3130
docker::service_destroy job-scheduler-ofelia
31+
32+
docker::prune_configs "ofelia"
3233
else
3334
log error "Valid options are: init, up, down, or destroy"
3435
fi

‎message-bus-kafka/swarm.sh‎

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -13,27 +13,26 @@ ROOT_PATH="${COMPOSE_FILE_PATH}/.."
1313
. "${ROOT_PATH}/utils/docker-utils.sh"
1414
. "${ROOT_PATH}/utils/log.sh"
1515

16-
1716
if [[ $STATEFUL_NODES == "cluster" ]]; then
1817
log info "Running Message Bus Kafka package in Cluster node mode"
19-
kafkaClusterComposeParam="-c ${COMPOSE_FILE_PATH}/docker-compose.cluster.yml"
18+
kafka_cluster_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose.cluster.yml"
2019
else
2120
log info "Running Message Bus Kafka package in Single node mode"
22-
kafkaClusterComposeParam=""
21+
kafka_cluster_compose_param=""
2322
fi
2423

2524
if [[ "${MODE}" == "dev" ]]; then
2625
log info "Running Message Bus Kafka package in DEV mode"
27-
kafkaDevComposeParam="-c ${COMPOSE_FILE_PATH}/docker-compose.dev.yml"
26+
kafka_dev_compose_param="-c ${COMPOSE_FILE_PATH}/docker-compose.dev.yml"
2827
else
2928
log info "Running Message Bus Kafka package in PROD mode"
30-
kafkaDevComposeParam=""
29+
kafka_dev_compose_param=""
3130
fi
3231

3332
if [[ "${ACTION}" == "init" ]] || [[ "${ACTION}" == "up" ]]; then
3433
config::set_config_digests "${COMPOSE_FILE_PATH}"/importer/docker-compose.config.yml
3534

36-
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose.yml $kafkaClusterComposeParam $kafkaDevComposeParam instant" "Failed to deploy Message Bus Kafka"
35+
try "docker stack deploy -c ${COMPOSE_FILE_PATH}/docker-compose.yml $kafka_cluster_compose_param $kafka_dev_compose_param instant" "Failed to deploy Message Bus Kafka"
3736

3837
config::await_service_running "kafka" "${COMPOSE_FILE_PATH}"/docker-compose.await-helper.yml "${KAFKA_INSTANCES}"
3938

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