diff --git a/docs/packages/dashboard-visualiser-js-report/environment-variables.md b/docs/packages/dashboard-visualiser-js-report/environment-variables.md index 3b2afe94..ea41d076 100644 --- a/docs/packages/dashboard-visualiser-js-report/environment-variables.md +++ b/docs/packages/dashboard-visualiser-js-report/environment-variables.md @@ -6,21 +6,4 @@ description: Listed in this page are all environment variables needed to run Jsr -| Variable Name | Type | Relevance | Required | Default | -| --------------------------- | ------- | ---------------------------------------------------------------------------------------------------- | ------------------------------------------- | --------------------------------------- | -| JS\_REPORT\_LICENSE\_KEY | String | Service license key | Yes | | -| JS\_REPORT | String | Jsreport service password | No | dev\_password\_only | -| JS\_REPORT\_USERNAME | String | Jsreport service username | No | admin | -| JS\_REPORT\_SECRET | String | Secret password for the authentication of a cookie session related to the extension used in Jsreport | No | dev\_secret\_only | -| ES\_HOSTS | String | Elasticsearch connection string | No | analytics-datastore-elastic-search:9200 | -| ES\_PASSWORD | String | Elasticsearch password (for request authentication) | No | dev\_password\_only | -| ES\_USERNAME | String | Elasticsearch username (for request authentication | No | elastic | -| JS\_REPORT\_INSTANCES | Number | Number of service replicas | No | 1 | -| JS\_REPORT\_SSL | Boolean | SSL protocol requirement | No | false | -| JS\_REPORT\_CONFIG\_FILE | String | Path to the service import file | No | export.jsrexport | -| JS\_REPORT\_DEV\_MOUNT | Boolean | Dev mount mode enabling flag | No | false | -| JS\_REPORT\_PACKAGE\_PATH | String | Local path to package | Yes if `JS_REPORT_DEV_MOUNT` is set to true | | -| JS\_REPORT\_CPU\_LIMIT | Number | CPU usage limit | No | 0 | -| JS\_REPORT\_MEMORY\_LIMIT | String | RAM usage limit | No | 3G | -| JS\_REPORT\_CPU\_RESERVE | Number | Reserved CPU | No | 0.05 | -| JS\_REPORT\_MEMORY\_RESERVE | String | Reserved RAM | No | 500M | +
Variable NameTypeRelevanceRequiredDefault
JS_REPORT_LICENSE_KEYStringService license keyYes
JS_REPORTStringJsreport service passwordNodev_password_only
JS_REPORT_USERNAMEStringJsreport service usernameNoadmin
JS_REPORT_SECRETStringSecret password for the authentication of a cookie session related to the extension used in JsreportNodev_secret_only
ES_HOSTSStringElasticsearch connection stringNoanalytics-datastore-elastic-search:9200
ES_PASSWORDStringElasticsearch password (for request authentication)Nodev_password_only
ES_USERNAMEStringElasticsearch username (for request authenticationNoelastic
JS_REPORT_INSTANCESNumberNumber of service replicasNo1
JS_REPORT_SSLBooleanSSL protocol requirementNofalse
JS_REPORT_CONFIG_FILEStringPath to the service import fileNoexport.jsrexport
JS_REPORT_DEV_MOUNTBooleanDev mount mode enabling flagNofalse
JS_REPORT_PACKAGE_PATHStringLocal path to packageYes if JS_REPORT_DEV_MOUNT is set to true
JS_REPORT_CPU_LIMITNumberCPU usage limitNo0
JS_REPORT_MEMORY_LIMITStringRAM usage limitNo3G
JS_REPORT_CPU_RESERVENumberReserved CPUNo0.05
JS_REPORT_MEMORY_RESERVEStringReserved RAMNo500M
diff --git a/docs/packages/dashboard-visualiser-kibana/environment-variables.md b/docs/packages/dashboard-visualiser-kibana/environment-variables.md index 3220bde7..bbdba3e9 100644 --- a/docs/packages/dashboard-visualiser-kibana/environment-variables.md +++ b/docs/packages/dashboard-visualiser-kibana/environment-variables.md @@ -4,16 +4,4 @@ description: Listed in this page are all environment variables needed to run Kib # Environment Variables - - -| Variable Name | Type | Relevance | Required | Default | -| ------------------------- | ------- | -------------------------------------- | -------- | -------------------- | -| ES\_KIBANA_\__SYSTEM | String | ElasticSearch auth username | Yes | | -| KIBANA\_INSTANCES | Number | Number of service replicas | No | 1 | -| KIBANA\_YML_\__CONFIG | String | Path to the service configuration file | No | kibana-kibana.yml | -| KIBANA\_USERNAME | String | Service username | No | elastic | -| KIBANA\_PASSWORD | String | Service password | No | dev\_password\_only | -| KIBANA\_SSL | Boolean | SSL protocol requirement | No | True | -| KIBANA\_CONFIG_\__FILE | String | Path to the dashboard import file | No | kibana-export.ndjson | -| KIBANA\_MEMORY_\__LIMIT | String | RAM usage limit | No | 3G | -| KIBANA\_MEMORY_\__RESERVE | String | Reserved RAM | No | 500M | +
Variable NameTypeRelevanceRequiredDefault
ES_KIBANA_SYSTEMStringElasticSearch auth usernameYes
KIBANA_INSTANCESNumberNumber of service replicas No1
KIBANA_YML_CONFIGStringPath to the service configuration fileNokibana-kibana.yml
KIBANA_USERNAMEStringService usernameNoelastic
KIBANA_PASSWORDStringService passwordNodev_password_only
KIBANA_SSLBooleanSSL protocol requirementNoTrue
KIBANA_CONFIG_FILEStringPath to the dashboard import fileNokibana-export.ndjson
KIBANA_MEMORY_LIMITStringRAM usage limitNo3G
KIBANA_MEMORY_RESERVEStringReserved RAMNo500M
diff --git a/documentation/README (1).md b/documentation/README (1).md index 42df9367..be323358 100644 --- a/documentation/README (1).md +++ b/documentation/README (1).md @@ -20,7 +20,7 @@ The following tools are needed to run/deploy platform: 1. Once Docker is installed initialise Docker Swarm: `docker swarm init` 2. Download the [Instant OpenHIE 2 binary](https://jembi.gitbook.io/instant-v2/getting-started). Once you are able to execute the instant executable, return here. 3. Go to the OpenHIM Platform [https://github.com/jembi/platform/releases/latest](https://github.com/jembi/platform/releases/latest) page and use the `` for the following steps. -4. Download the latest OpenHIM Platform config file which configures Instant OpenHIE v2 to use openHIM Platform packages: `wget https://raw.githubusercontent.com/jembi/platform//config.yaml` +4. Download the latest OpenHIM Platform config file which configures Instant OpenHIE v2 to use OpenHIM Platform packages: `wget https://raw.githubusercontent.com/jembi/platform//config.yaml` {% hint style="info" %} e.g. `wget https://raw.githubusercontent.com/jembi/platform/2.3.0/config.yaml` @@ -29,4 +29,8 @@ The following tools are needed to run/deploy platform: 5. Download the latest environment variable file, which sets configuration options for OpenHIM Platform packages: `wget https://raw.githubusercontent.com/jembi/platform//.env.local` 6. Launch some OpenHIM Platform packages, e.g. `./instant package init --name interoperability-layer-openhim --name message-bus-kafka --env-file .env.local --dev` This launches the OpenHIM and Kafka packages in dev mode (which exposes service ports for development purposes) using the config supplied in the env var file. -Next, you might want to browse the packages available in OpenHIM Platform. Each package's documentation lists the variables used to configure them. For more information on how to start stop and destroy packages using the command line, see the [Instant OpenHIE 2 CLI docs](https://jembi.gitbook.io/instant-v2/cli). +Next, you might want to browse the [recipes](recipes/) available in OpenHIM Platform. Each recipe bundles a set of packages and configuration to setup an HIE for a particular purpose. + +Alternatively you can also browse the individual set of [packages](packages/) that OpenHIM Platform offers. Each package's documentation lists the environment variables used to configure them. + +For more information on how to start stop and destroy packages using the command line, see the [Instant OpenHIE 2 CLI docs](https://jembi.gitbook.io/instant-v2/cli). diff --git a/documentation/SUMMARY.md b/documentation/SUMMARY.md index 5ab5d3bc..ebc6a855 100644 --- a/documentation/SUMMARY.md +++ b/documentation/SUMMARY.md @@ -2,7 +2,11 @@ * [OpenHIM Platform](README.md) * [Getting Started]() -* [Packages](packages/README.md) +* [📜 Recipes](recipes/README.md) + * [Central Data Repository with Data Warehousing](recipes/central-data-repository-with-data-warehousing.md) + * [Central Data repository (no reporting)](recipes/central-data-repository-no-reporting.md) + * [Master Patient Index](recipes/master-patient-index.md) +* [📦 Packages](packages/README.md) * [Interoperability Layer Openhim](packages/interoperability-layer-openhim/README.md) * [Local Development](packages/interoperability-layer-openhim/local-development.md) * [Environment Variables](packages/interoperability-layer-openhim/environment-variables.md) @@ -48,12 +52,12 @@ * [Reverse Proxy Nginx](packages/reverse-proxy-nginx/README.md) * [Local Development](packages/reverse-proxy-nginx/local-development.md) * [Environment Variables](packages/reverse-proxy-nginx/environment-variables.md) -* [Development](development.md) * [Provisioning remote servers](provisioning-up-remote-servers/README.md) * [Ansible](provisioning-up-remote-servers/ansible.md) * [Terraform](provisioning-up-remote-servers/terraform.md) -* [Config Importing](config-importing.md) * [Resource Allocations](resource-allocations.md) +* [Development](development/README.md) + * [Config Importing](development/config-importing.md) * [Disaster Recovery Process](disaster-recovery-process/README.md) * [Elasticsearch](disaster-recovery-process/elasticsearch.md) * [HAPI FHIR Data](disaster-recovery-process/hapi-fhir-data.md) diff --git a/documentation/development.md b/documentation/development/README.md similarity index 89% rename from documentation/development.md rename to documentation/development/README.md index 2602744e..3593d20b 100644 --- a/documentation/development.md +++ b/documentation/development/README.md @@ -2,7 +2,7 @@ ## Adding Packages -* The Go Cli runs all services from the `jembi/platform` docker image. When adding new packages or updating existing packages to Platform you will need to build/update your local `jembi/platform` image. [How to build the image](). +* The Go Cli runs all services from the `jembi/platform` docker image. When adding new packages or updating existing packages to Platform you will need to build/update your local `jembi/platform` image. [How to build the image](<../README (1).md>). * As you add new packages to the platform remember to list them in the `config.yml` file - otherwise the added package will not be detected by the [platform-cli tool](http://127.0.0.1:5000/o/lTiMw1wKTVQEjepxV4ou/s/TwrbQZir3ZdvejunAFia/). ## diff --git a/documentation/config-importing.md b/documentation/development/config-importing.md similarity index 100% rename from documentation/config-importing.md rename to documentation/development/config-importing.md diff --git a/documentation/packages/README.md b/documentation/packages/README.md index 284e919b..6fbcac9b 100644 --- a/documentation/packages/README.md +++ b/documentation/packages/README.md @@ -5,5 +5,5 @@ description: >- describes the details of these packages. --- -# Packages +# 📦 Packages diff --git a/documentation/packages/analytics-datastore-elasticsearch/environment-variables.md b/documentation/packages/analytics-datastore-elasticsearch/environment-variables.md index 8072cde5..9db1f011 100644 --- a/documentation/packages/analytics-datastore-elasticsearch/environment-variables.md +++ b/documentation/packages/analytics-datastore-elasticsearch/environment-variables.md @@ -6,17 +6,4 @@ description: >- # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| ---------------------------- | ------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------- | ---------------------------------- | -| ES\_ELASTIC | String | Elasticsearch super-user password | Yes | dev\_password\_only | -| ES\_KIBANA\_SYSTEM | String | The password for the user Kibana used to connect and communicate with Elasticsearch | Yes | dev\_password\_only | -| ES\_LOGSTASH\_SYSTEM | String | The password for the user Logstash used to map and transform the data before storing it in Elasticsearch | Yes | dev\_password\_only | -| ES\_BEATS\_SYSTEM | String | The password for the user the Beats use when storing monitoring information in Elasticsearch | Yes | dev\_password\_only | -| ES\_REMOTE\_MONITORING\_USER | String | The password for the user Metricbeat used when collecting and storing monitoring information in Elasticsearch. It has the remote\_monitoring\_agent and remote\_monitoring\_collector built-in roles | Yes | dev\_password\_only | -| ES\_APM\_SYSTEM | String | The password for the user of the APM server used when storing monitoring information in Elasticsearch | Yes | dev\_password\_only | -| ES\_LEADER\_NODE | String |

Specify the leader service name (the service name in case single mode and the leader service name in case cluster mode)

This is used for the config importer. Specifying the service name to initialize the mapping inside Elasticsearch

| Yes | analytics-datastore-elastic-search | -| ES\_HEAP\_SIZE | String |

The heap size is the amount of RAM allocated to the Java Virtual Machine of a node in Elasticsearch

It should be set -Xms and -Xmx to the same value (50% of the total available RAM to a maximum of 31GB)

| No | -Xms2048m -Xmx2048m | -| ES\_SSL | Boolean | This variable is used only for the config importer of Elasticsearch (internal connection between docker services the elastic and the importer) | No | false | -| ES\_MEMORY\_LIMIT | String | RAM usage limit of Elasticsearch service | No | 3G | -| ES\_MEMORY\_RESERVE | String | Reserved RAM for Elasticsearch service | No | 500M | -| ES\_PATH\_REPO | String | The path to the repository in the container to store Elasticsearch backup snapshots | No | /backups/elasticsearch | +
Variable NameTypeRelevanceRequiredDefault
ES_ELASTICStringElasticsearch super-user passwordYesdev_password_only
ES_KIBANA_SYSTEMStringThe password for the user Kibana used to connect and communicate with ElasticsearchYesdev_password_only
ES_LOGSTASH_SYSTEMStringThe password for the user Logstash used to map and transform the data before storing it in ElasticsearchYesdev_password_only
ES_BEATS_SYSTEMStringThe password for the user the Beats use when storing monitoring information in ElasticsearchYesdev_password_only
ES_REMOTE_MONITORING_USERStringThe password for the user Metricbeat used when collecting and storing monitoring information in Elasticsearch. It has the remote_monitoring_agent and remote_monitoring_collector built-in rolesYesdev_password_only
ES_APM_SYSTEMStringThe password for the user of the APM server used when storing monitoring information in ElasticsearchYesdev_password_only
ES_LEADER_NODEString

Specify the leader service name (the service name in case single mode and the leader service name in case cluster mode)

This is used for the config importer. Specifying the service name to initialize the mapping inside Elasticsearch

Yesanalytics-datastore-elastic-search
ES_HEAP_SIZEString

The heap size is the amount of RAM allocated to the Java Virtual Machine of a node in Elasticsearch

It should be set -Xms and -Xmx to the same value (50% of the total available RAM to a maximum of 31GB)

No-Xms2048m -Xmx2048m
ES_SSLBooleanThis variable is used only for the config importer of Elasticsearch (internal connection between docker services the elastic and the importer)Nofalse
ES_MEMORY_LIMITStringRAM usage limit of Elasticsearch serviceNo3G
ES_MEMORY_RESERVEStringReserved RAM for Elasticsearch serviceNo500M
ES_PATH_REPOStringThe path to the repository in the container to store Elasticsearch backup snapshotsNo/backups/elasticsearch
diff --git a/documentation/packages/client-registry-santempi/environment-variables.md b/documentation/packages/client-registry-santempi/environment-variables.md index dd3d60f1..3036629a 100644 --- a/documentation/packages/client-registry-santempi/environment-variables.md +++ b/documentation/packages/client-registry-santempi/environment-variables.md @@ -4,15 +4,7 @@ description: Listed in this page are all environment variables needed to run Kib # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| ----------------------------------- | ------ | ------------------------------------------------- | -------- | ---------------------------------------------- | -| SANTEMPI\_INSTANCES | Number | Number of service replicas | No | 1 | -| SANTEMPI\_MAIN\_CONNECTION\_STRING | String | Connection string to SanteMPI | No | _Check below table_ | -| SANTEMPI\_AUDIT\_CONNECTION\_STRING | String | Audit connection string to SanteMPI | No | _Check below table_ | -| SANTEMPI\_POSTGRESQL\_PASSWORD | String | SanteMPI postgreSQL password | No | SanteDB123 | -| SANTEMPI\_POSTGRESQL\_USERNAME | String | SanteMPI postgreSQL username | No | santempi | -| SANTEMPI\_REPMGR\_PRIMARY\_HOST | String | SanteMPI postgreSQL replicas manager primary host | No | santempi-psql-1 | -| SANTEMPI\_REPMGR\_PARTNER\_NODES | String | SanteMPI postgreSQL replicas manager nodes hosts | Yes | santempi-psql-1,santempi-psql-2,santempi-psql- | +
Variable NameTypeRelevanceRequiredDefault
SANTEMPI_INSTANCESNumberNumber of service replicas No1
SANTEMPI_MAIN_CONNECTION_STRINGStringConnection string to SanteMPINoCheck below table
SANTEMPI_AUDIT_CONNECTION_STRINGStringAudit connection string to SanteMPINoCheck below table
SANTEMPI_POSTGRESQL_PASSWORDStringSanteMPI postgreSQL passwordNoSanteDB123
SANTEMPI_POSTGRESQL_USERNAMEStringSanteMPI postgreSQL usernameNosantempi
SANTEMPI_REPMGR_PRIMARY_HOSTStringSanteMPI postgreSQL replicas manager primary hostNosantempi-psql-1
SANTEMPI_REPMGR_PARTNER_NODESStringSanteMPI postgreSQL replicas manager nodes hostsYessantempi-psql-1,santempi-psql-2,santempi-psql-
### Note diff --git a/documentation/packages/dashboard-visualiser-superset/environment-variables.md b/documentation/packages/dashboard-visualiser-superset/environment-variables.md index a1d68a54..35ce9c76 100644 --- a/documentation/packages/dashboard-visualiser-superset/environment-variables.md +++ b/documentation/packages/dashboard-visualiser-superset/environment-variables.md @@ -4,14 +4,4 @@ description: Listed in this page are all environment variables needed to run Sup # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| ----------------------- | ------- | --------------------------------- | -------- | ------------------- | -| SUPERSET\_USERNAME | String | Service username | No | admin | -| SUPERSET\_FIRSTNAME | String | Admin account first name | No | SUPERSET | -| SUPERSET\_LASTNAME | String | Admin account last name | No | ADMIN | -| SUPERSET\_EMAIL | String | Admin account email address | No | admin@superset.com | -| SUPERSET\_PASSWORD | String | Admin account password | No | admin | -| SUPERSET\_API\_USERNAME | String | Service username | No | admin | -| SUPERSET\_API\_PASSWORD | String | Service password | No | admin | -| SUPERSET\_SSL | Boolean | SSL protocol requirement | No | False | -| CONFIG_\__FILE | String | Path to the dashboard import file | No | superset-export.zip | +
Variable NameTypeRelevanceRequiredDefault
SUPERSET_USERNAMEStringService usernameNoadmin
SUPERSET_FIRSTNAMEStringAdmin account first nameNoSUPERSET
SUPERSET_LASTNAMEStringAdmin account last name NoADMIN
SUPERSET_EMAILStringAdmin account email address Noadmin@superset.com
SUPERSET_PASSWORDStringAdmin account password Noadmin
SUPERSET_API_USERNAMEStringService username Noadmin
SUPERSET_API_PASSWORDStringService password Noadmin
SUPERSET_SSLBooleanSSL protocol requirementNoFalse
CONFIG_FILEStringPath to the dashboard import fileNosuperset-export.zip
diff --git a/documentation/packages/data-mapper-logstash/environment-variables.md b/documentation/packages/data-mapper-logstash/environment-variables.md index b34252fd..46c16ec9 100644 --- a/documentation/packages/data-mapper-logstash/environment-variables.md +++ b/documentation/packages/data-mapper-logstash/environment-variables.md @@ -6,14 +6,4 @@ description: Listed in this page are all environment variables needed to run Log -| Variable Name | Type | Relevance | Required | Default | -| ------------------------- | ------- | -------------------------------------------------------------------------------------------------- | ----------------------------------- | --------------------------------------- | -| LOGSTASH\_INSTANCES | Number | Number of service replicas | No | 1 | -| LOGSTASH\_DEV\_MOUNT | Boolean | DEV mount mode enabling flag | No | false | -| LOGSTASH\_PACKAGE\_PATH | String | Logstash package absolute path | yes if `LOGSTASH_DEV_MOUNT` is true | | -| LS\_JAVA\_OPTS | String | JVM heap size, it should be no less than 4GB and no more than 8GB (maximum of 50-75% of total RAM) | No | -Xmx2g -Xms2g | -| ES\_ELASTIC | String | ElasticSearch Logstash user password | Yes | dev\_password\_only | -| ES\_HOSTS | String | Elasticsearch connection string | Yes | analytics-datastore-elastic-search:9200 | -| KIBANA\_SSL | Boolean | SSL protocol requirement | No | True | -| LOGSTASH\_MEMORY\_LIMIT | String | RAM usage limit | No | 3G | -| LOGSTASH\_MEMORY\_RESERVE | String | Reserved RAM | No | 500M | +
Variable NameTypeRelevanceRequiredDefault
LOGSTASH_INSTANCESNumberNumber of service replicas No1
LOGSTASH_DEV_MOUNTBooleanDEV mount mode enabling flagNofalse
LOGSTASH_PACKAGE_PATHStringLogstash package absolute pathyes if LOGSTASH_DEV_MOUNT is true
LS_JAVA_OPTSStringJVM heap size, it should be no less than 4GB and no more than 8GB (maximum of 50-75% of total RAM)No-Xmx2g -Xms2g
ES_ELASTICStringElasticSearch Logstash user passwordYesdev_password_only
ES_HOSTSStringElasticsearch connection stringYesanalytics-datastore-elastic-search:9200
KIBANA_SSLBooleanSSL protocol requirementNoTrue
LOGSTASH_MEMORY_LIMITStringRAM usage limitNo3G
LOGSTASH_MEMORY_RESERVEStringReserved RAMNo500M
diff --git a/documentation/packages/fhir-datastore-hapi-fhir/environment-variables.md b/documentation/packages/fhir-datastore-hapi-fhir/environment-variables.md index 9a3d8074..beeaa277 100644 --- a/documentation/packages/fhir-datastore-hapi-fhir/environment-variables.md +++ b/documentation/packages/fhir-datastore-hapi-fhir/environment-variables.md @@ -6,21 +6,4 @@ description: >- # Environment Variables -| Variable Name | Type | Revelance | Required | Default | -| ----------------------------- | ------ | ----------------------------------------------------------------- | -------- | --------------- | -| REPMGR\_PRIMARY\_HOST | String | Service name of the primary replication manager host (PostgreSQL) | No | postgres-1 | -| REPMGR\_PARTNER\_NODES | String | Service names of the replicas of PostgreSQL | Yes | postgres-1 | -| POSTGRES\_REPLICA\_SET | String | PostgreSQL replica set (host and port of the replicas) | Yes | postgres-1:5432 | -| HAPI\_FHIR\_CPU\_LIMIT | Number | CPU limit usage for hapi-fhir service | No | 0 (unlimited) | -| HAPI\_FHIR\_CPU\_RESERVE | Number | Reserved CPU usage for hapi-fhir service | No | 0.05 | -| HAPI\_FHIR\_MEMORY\_LIMIT | String | RAM limit usage for hapi-fhir service | No | 3G | -| HAPI\_FHIR\_MEMORY\_RESERVE | String | Reserved RAM usage for hapi-fhir service | No | 500M | -| HF\_POSTGRES\_CPU\_LIMIT | Number | CPU limit usage for postgreSQL service | No | 0 (unlimited) | -| HF\_POSTGRES\_CPU\_RESERVE | Number | Reserved CPU usage for postgreSQL service | No | 0.05 | -| HF\_POSTGRES\_MEMORY\_LIMIT | String | RAM limit usage for postgreSQL service | No | 3G | -| HF\_POSTGRES\_MEMORY\_RESERVE | String | Reserved RAM usage for hapi-fhir service | No | 500M | -| HAPI\_FHIR\_INSTANCES | Number | Number of hapi-fhir service replicas | No | 1 | -| HF\_POSTGRESQL\_USERNAME | String | Hapi-fhir PostgreSQL username | Yes | admin | -| HF\_POSTGRESQL\_PASSWORD | String | Hapi-fhir PostgreSQL password | Yes | instant101 | -| HF\_POSTGRESQL\_DATABASE | String | Hapi-fhir PostgreSQL database | No | hapi | -| REPMGR\_PASSWORD | Strign | hapi-fhir PostgreSQL Replication Manager username | Yes | | +
Variable NameTypeRevelanceRequiredDefault
REPMGR_PRIMARY_HOSTStringService name of the primary replication manager host (PostgreSQL)Nopostgres-1
REPMGR_PARTNER_NODESStringService names of the replicas of PostgreSQLYespostgres-1
POSTGRES_REPLICA_SETStringPostgreSQL replica set (host and port of the replicas)Yespostgres-1:5432
HAPI_FHIR_CPU_LIMITNumberCPU limit usage for hapi-fhir serviceNo0 (unlimited)
HAPI_FHIR_CPU_RESERVENumberReserved CPU usage for hapi-fhir serviceNo0.05
HAPI_FHIR_MEMORY_LIMITStringRAM limit usage for hapi-fhir serviceNo3G
HAPI_FHIR_MEMORY_RESERVEStringReserved RAM usage for hapi-fhir serviceNo500M
HF_POSTGRES_CPU_LIMITNumberCPU limit usage for postgreSQL serviceNo0 (unlimited)
HF_POSTGRES_CPU_RESERVENumberReserved CPU usage for postgreSQL serviceNo0.05
HF_POSTGRES_MEMORY_LIMITStringRAM limit usage for postgreSQL serviceNo3G
HF_POSTGRES_MEMORY_RESERVEStringReserved RAM usage for hapi-fhir serviceNo500M
HAPI_FHIR_INSTANCESNumberNumber of hapi-fhir service replicas No1
HF_POSTGRESQL_USERNAMEStringHapi-fhir PostgreSQL usernameYesadmin
HF_POSTGRESQL_PASSWORDStringHapi-fhir PostgreSQL passwordYesinstant101
HF_POSTGRESQL_DATABASEStringHapi-fhir PostgreSQL databaseNohapi
REPMGR_PASSWORDStrignhapi-fhir PostgreSQL Replication Manager username Yes
diff --git a/documentation/packages/interoperability-layer-openhim/environment-variables.md b/documentation/packages/interoperability-layer-openhim/environment-variables.md index c50b040a..53d19225 100644 --- a/documentation/packages/interoperability-layer-openhim/environment-variables.md +++ b/documentation/packages/interoperability-layer-openhim/environment-variables.md @@ -6,24 +6,4 @@ description: >- # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| --------------------------------- | ------ | --------------------------------------- | -------- | ------------------------------- | -| OPENHIM\_CORE\_MEDIATOR\_HOSTNAME | String | Hostname of the Openhim mediator | Yes | localhost | -| OPENHIM\_MEDIATOR\_API\_PORT | Number | Port of the Openhim mediator | Yes | 8080 | -| OPENHIM\_CORE\_INSTANCES | Number | Number of openhim-core instances | No | 1 | -| OPENHIM\_CONSOLE\_INSTANCES | String | Number of openhim-console instances | No | 1 | -| OPENHIM\_MONGO\_URL | String | MongoDB connection string | Yes | mongodb://mongo-1:27017/openhim | -| OPENHIM\_MONGO\_ATNAURL | String | ??????????? | Yes | mongodb://mongo-1:27017/openhim | -| OPENHIM\_CPU\_LIMIT | Number | CPU limit usage for openhim-core | No | 0 | -| OPENHIM\_CPU\_RESERVE | Number | Reserverd CPU usage for openhim-core | No | 0.05 | -| OPENHIM\_MEMORY\_LIMIT | String | RAM usage limit for openhim-core | No | 3G | -| OPENHIM\_MEMORY\_RESERVE | String | Reserved RAM for openhim-core | No | 500M | -| OPENHIM\_CONSOLE\_CPU\_LIMIT | Number | CPU limit usage for openhim-console | No | 0 | -| OPENHIM\_CONSOLE\_CPU\_RESERVE | Number | Reserverd CPU usage for openhim-console | No | 0.05 | -| OPENHIM\_CONSOLE\_MEMORY\_LIMIT | String | RAM usage limit for openhim-console | No | 2G | -| OPENHIM\_CONSOLE\_MEMORY\_RESERVE | String | Reserved RAM for openhim-console | No | 500M | -| OPENHIM\_MONGO\_CPU\_LIMIT | Number | CPU limit usage for mongo | No | 0 | -| OPENHIM\_MONGO\_CPU\_RESERVE | Number | Reserverd CPU usage for mongo | No | 0.05 | -| OPENHIM\_MONGO\_MEMORY\_LIMIT | String | RAM usage limit for mongo | No | 3G | -| OPENHIM\_MONGO\_MEMORY\_RESERVE | String | Reserved RAM for mongo | No | 500M | -| MONGO\_SET\_COUNT | Number | Number of instances of Mongo | YES | 1 | +
Variable NameTypeRelevanceRequiredDefault
OPENHIM_CORE_MEDIATOR_HOSTNAMEStringHostname of the Openhim mediatorYeslocalhost
OPENHIM_MEDIATOR_API_PORTNumberPort of the Openhim mediatorYes8080
OPENHIM_CORE_INSTANCESNumberNumber of openhim-core instancesNo1
OPENHIM_CONSOLE_INSTANCESStringNumber of openhim-console instancesNo1
OPENHIM_MONGO_URLStringMongoDB connection stringYesmongodb://mongo-1:27017/openhim
OPENHIM_MONGO_ATNAURLString???????????Yesmongodb://mongo-1:27017/openhim
OPENHIM_CPU_LIMITNumberCPU limit usage for openhim-coreNo0
OPENHIM_CPU_RESERVENumberReserverd CPU usage for openhim-coreNo0.05
OPENHIM_MEMORY_LIMITStringRAM usage limit for openhim-coreNo3G
OPENHIM_MEMORY_RESERVEStringReserved RAM for openhim-coreNo500M
OPENHIM_CONSOLE_CPU_LIMITNumberCPU limit usage for openhim-consoleNo0
OPENHIM_CONSOLE_CPU_RESERVENumberReserverd CPU usage for openhim-consoleNo0.05
OPENHIM_CONSOLE_MEMORY_LIMITStringRAM usage limit for openhim-consoleNo2G
OPENHIM_CONSOLE_MEMORY_RESERVEStringReserved RAM for openhim-consoleNo500M
OPENHIM_MONGO_CPU_LIMITNumberCPU limit usage for mongoNo0
OPENHIM_MONGO_CPU_RESERVENumberReserverd CPU usage for mongoNo0.05
OPENHIM_MONGO_MEMORY_LIMITStringRAM usage limit for mongoNo3G
OPENHIM_MONGO_MEMORY_RESERVEStringReserved RAM for mongoNo500M
MONGO_SET_COUNTNumberNumber of instances of MongoYES1
diff --git a/documentation/packages/kafka-mapper-consumer/environment-variables.md b/documentation/packages/kafka-mapper-consumer/environment-variables.md index 13af9960..71e06e28 100644 --- a/documentation/packages/kafka-mapper-consumer/environment-variables.md +++ b/documentation/packages/kafka-mapper-consumer/environment-variables.md @@ -8,9 +8,4 @@ description: >- -| Variable Name | Type | Relevance | Required | Default | -| ---------------- | ------ | ------------------- | -------- | ------------------------------ | -| KAFKA\_HOST | String | Kafka hostname | No | kafka | -| KAFKA\_PORT | Number | Kafka port | No | 9092 | -| CLICKHOUSE\_HOST | String | Clickhouse hostname | No | analytics-datastore-clickhouse | -| CLICKHOUSE\_PORT | String | Clickhouse port | No | 8123 | +
Variable NameTypeRelevanceRequiredDefault
KAFKA_HOSTStringKafka hostnameNokafka
KAFKA_PORTNumberKafka portNo9092
CLICKHOUSE_HOSTStringClickhouse hostnameNoanalytics-datastore-clickhouse
CLICKHOUSE_PORTStringClickhouse portNo8123
diff --git a/documentation/packages/kafka-unbundler-consumer/environment-variables.md b/documentation/packages/kafka-unbundler-consumer/environment-variables.md index be17c79e..493461b8 100644 --- a/documentation/packages/kafka-unbundler-consumer/environment-variables.md +++ b/documentation/packages/kafka-unbundler-consumer/environment-variables.md @@ -4,7 +4,4 @@ description: A kafka processor to unbundle resources into their own kafka topics # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| ------------- | ------ | -------------- | -------- | ------- | -| KAFKA\_HOST | String | Kafka hostname | No | kafka | -| KAFKA\_PORT | Number | Kafka port | No | 9092 | +
Variable NameTypeRelevanceRequiredDefault
KAFKA_HOSTStringKafka hostnameNokafka
KAFKA_PORTNumberKafka portNo9092
diff --git a/documentation/packages/message-bus-helper-hapi-proxy/environment-variables.md b/documentation/packages/message-bus-helper-hapi-proxy/environment-variables.md index 7b2f4a91..9dd2c1a8 100644 --- a/documentation/packages/message-bus-helper-hapi-proxy/environment-variables.md +++ b/documentation/packages/message-bus-helper-hapi-proxy/environment-variables.md @@ -4,13 +4,4 @@ description: Listed in this page are all environment variables needed to run Hap # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| ------------------------------ | ------ | -------------------------------------- | -------- | -------------------------- | -| HAPI\_SERVER\_URL | String | Hapi-fhir server URL | No | http://hapi-fhir:8080/fhir | -| KAFKA\_BOOTSTRAP\_SERVERS | String | Kafka server | No | kafka:9092 | -| HAPI\_SERVER\_VALIDATE\_FORMAT | String | Path to the service configuration file | No | kibana-kibana.yml | -| HAPI\_PROXY\_INSTANCES | Number | Number of instances of hapi-proxy | No | 1 | -| HAPI\_PROXY\_CPU\_LIMIT | Number | CPU usage limit | No | 0 | -| HAPI\_PROXY\_CPU\_RESERVE | Number | Reserved CPU usage | No | 0.05 | -| HAPI\_PROXY\_MEMORY\_LIMIT | String | RAM usage limit | No | 3G | -| HAPI\_PROXY\_MEMORY\_RESERVE | String | Reserved RAM | No | 500M | +
Variable NameTypeRelevanceRequiredDefault
HAPI_SERVER_URLStringHapi-fhir server URLNohttp://hapi-fhir:8080/fhir
KAFKA_BOOTSTRAP_SERVERSStringKafka serverNokafka:9092
HAPI_SERVER_VALIDATE_FORMATStringPath to the service configuration fileNokibana-kibana.yml
HAPI_PROXY_INSTANCESNumberNumber of instances of hapi-proxyNo1
HAPI_PROXY_CPU_LIMITNumberCPU usage limitNo0
HAPI_PROXY_CPU_RESERVENumberReserved CPU usageNo0.05
HAPI_PROXY_MEMORY_LIMITStringRAM usage limitNo3G
HAPI_PROXY_MEMORY_RESERVEStringReserved RAMNo500M
diff --git a/documentation/packages/message-bus-kafka/environment-variables.md b/documentation/packages/message-bus-kafka/environment-variables.md index db5368e9..79ad9377 100644 --- a/documentation/packages/message-bus-kafka/environment-variables.md +++ b/documentation/packages/message-bus-kafka/environment-variables.md @@ -6,27 +6,5 @@ description: >- # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| -------------------------- | ------ | ---------------- | -------- | ------- | -| KAFKA\_INSTANCES | Number | Service replicas | No | 1 | -| KAFKA\_CPU\_LIMIT | Number | CPU usage limit | No | 0 | -| KAFKA\_CPU\_RESERVE | Number | Reserved CPU | No | 0.05 | -| KAFKA\_MEMORY\_LIMIT | String | RAM usage limit | No | 3G | -| KAFKA\_MEMORY\_RESERVE | String | Reserved RAM | No | 500M | -| KAFKA\_TOPICS | String | Kafka topics | Yes | | -| | | | | | -| ZOOKEEPER\_CPU\_LIMIT | Number | CPU usage limit | No | 0 | -| ZOOKEEPER\_CPU\_RESERVE | Number | Reserved CPU | No | 0.05 | -| ZOOKEEPER\_MEMORY\_LIMIT | String | RAM usage limit | No | 3G | -| ZOOKEEPER\_MEMORY\_RESERVE | String | Reserved RAM | No | 500M | -| | | | | | -| KMINION\_CPU\_LIMIT | Number | CPU usage limit | No | 0 | -| KMINION\_CPU\_RESERVE | Number | Reserved CPU | No | 0.05 | -| KMINION\_MEMORY\_LIMIT | String | RAM usage limit | No | 3G | -| KMINION\_MEMORY\_RESERVE | String | Reserved RAM | No | 500M | -| | | | | | -| KAFDROP\_CPU\_LIMIT | Number | CPU usage limit | No | 0 | -| KAFDROP\_CPU\_RESERVE | Number | Reserved CPU | No | 0.05 | -| KAFDROP\_MEMORY\_LIMIT | String | RAM usage limit | No | 3G | -| KAFDROP\_MEMORY\_RESERVE | String | Reserved RAM | No | 500M | +
Variable NameTypeRelevanceRequiredDefault
KAFKA_INSTANCESNumberService replicasNo1
KAFKA_CPU_LIMITNumberCPU usage limitNo0
KAFKA_CPU_RESERVENumberReserved CPUNo0.05
KAFKA_MEMORY_LIMITStringRAM usage limitNo3G
KAFKA_MEMORY_RESERVEStringReserved RAMNo500M
KAFKA_TOPICSStringKafka topicsYes
ZOOKEEPER_CPU_LIMITNumberCPU usage limitNo0
ZOOKEEPER_CPU_RESERVENumberReserved CPUNo0.05
ZOOKEEPER_MEMORY_LIMITStringRAM usage limitNo3G
ZOOKEEPER_MEMORY_RESERVEStringReserved RAMNo500M
KMINION_CPU_LIMITNumberCPU usage limitNo0
KMINION_CPU_RESERVENumberReserved CPUNo0.05
KMINION_MEMORY_LIMITStringRAM usage limitNo3G
KMINION_MEMORY_RESERVEStringReserved RAMNo500M
KAFDROP_CPU_LIMITNumberCPU usage limitNo0
KAFDROP_CPU_RESERVENumberReserved CPUNo0.05
KAFDROP_MEMORY_LIMITStringRAM usage limitNo3G
KAFDROP_MEMORY_RESERVEStringReserved RAMNo500M
diff --git a/documentation/packages/monitoring/environment-variables.md b/documentation/packages/monitoring/environment-variables.md index 2c09a916..c20483f0 100644 --- a/documentation/packages/monitoring/environment-variables.md +++ b/documentation/packages/monitoring/environment-variables.md @@ -6,7 +6,4 @@ description: >- # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| ----------------------------- | ------ | --------------------------- | -------- | ------------------- | -| GF\_SECURITY\_ADMIN\_USER | String | Username of Grafana service | No | admin | -| GF\_SECURITY\_ADMIN\_PASSWORD | String | Password of Grafana service | No | dev\_password\_only | +
Variable NameTypeRelevanceRequiredDefault
GF_SECURITY_ADMIN_USERStringUsername of Grafana serviceNoadmin
GF_SECURITY_ADMIN_PASSWORDStringPassword of Grafana serviceNodev_password_only
diff --git a/documentation/packages/reverse-proxy-nginx/environment-variables.md b/documentation/packages/reverse-proxy-nginx/environment-variables.md index 8aaa9a31..0c34bbd2 100644 --- a/documentation/packages/reverse-proxy-nginx/environment-variables.md +++ b/documentation/packages/reverse-proxy-nginx/environment-variables.md @@ -6,14 +6,4 @@ description: >- # Environment Variables -| Variable Name | Type | Relevance | Required | Default | -| ------------------------- | ------ | ------------------------------------------------- | -------- | --------- | -| DOMAIN\_NAME | String | Domain name | Yes | localhost | -| SUBDOMAINS | String | Subdomain names | Yes | | -| RENEWAL\_EMAIL | String | Renewal email | Yes | | -| REVERSE\_PROXY\_INSTANCES | Number | Number of instances | No | 1 | -| STAGING | String | Generate fake or real certificate (true for fake) | No | false | -| NGINX\_CPU\_LIMIT | Number | CPU usage limit | No | 0 | -| NGINX\_CPU\_RESERVE | Number | Reserved CPU | No | 0.05 | -| NGINX\_MEMORY\_LIMIT | String | RAM usage limit | No | 3G | -| NGINX\_MEMORY\_RESERVE | String | Reserved RAM | No | 500M | +
Variable NameTypeRelevanceRequiredDefault
DOMAIN_NAMEStringDomain nameYeslocalhost
SUBDOMAINSStringSubdomain namesYes
RENEWAL_EMAILStringRenewal emailYes
REVERSE_PROXY_INSTANCESNumberNumber of instancesNo1
STAGINGStringGenerate fake or real certificate (true for fake)Nofalse
NGINX_CPU_LIMITNumberCPU usage limitNo0
NGINX_CPU_RESERVENumberReserved CPUNo0.05
NGINX_MEMORY_LIMITStringRAM usage limitNo3G
NGINX_MEMORY_RESERVEStringReserved RAMNo500M
diff --git a/documentation/recipes/README.md b/documentation/recipes/README.md new file mode 100644 index 00000000..5382f24f --- /dev/null +++ b/documentation/recipes/README.md @@ -0,0 +1,13 @@ +--- +description: Pre-defined recipes for common use cases +--- + +# 📜 Recipes + +OpenHIM platform comes bundles with a set of generic packages that can be deployed and configured to support a number of different use cases. To help users of OpenHIM Platform get started with something they can make use of immediately, a number of default OpenHIM Platform reciepes are provided. These help you get started with everything you need setup and configured for a particular use case. + +We current support the following default recipes: + + + +
Central Data Repository with Data WarehouseA FHIR-based Shared Health record linked to an MPI for linking and matching patient demographics and a default reporting pipeline to transform and visualise FHIR data.central-data-repository-with-data-warehousing.md
Central Data RepositoryA FHIR-based Shared Health record linked to an MPI for linking and matching patient demographics. No reporting is include but all FHIR data is pushed to Kafka for external system to use.central-data-repository-no-reporting.md
Master Patient IndexA master patient index setup using JeMPI. it also includes OpenHIM as the API gateway providing security, a mapping mediator to allow FHIR-based communication with JeMPI and Keycloak to support user management.master-patient-index.md
diff --git a/documentation/recipes/central-data-repository-no-reporting.md b/documentation/recipes/central-data-repository-no-reporting.md new file mode 100644 index 00000000..9e5b1677 --- /dev/null +++ b/documentation/recipes/central-data-repository-no-reporting.md @@ -0,0 +1,20 @@ +# Central Data repository (no reporting) + +{% hint style="warning" %} +Note: This recipe is in a pre-release alpha stage. It's usable but do so at your own risk. +{% endhint %} + +This recipe sets up an HIE that does the following: + +* Accept FHIR bundles submitted securely through an IOL (OpenHIM) +* Stores Clinical FHIR data to a FHIR store (HAPI FHIR) +* Stores Patient Demographic data to an MPI (JeMPI) +* Pushes FHIR resources to Kafka for other external systems to use + +To launch this package in dev mode copy and paste this into your terminal in a new folder (ensure you have the [instant CLI installed](https://jembi.gitbook.io/instant-v2/getting-started/quick-start)): + +```bash +wget https://raw.githubusercontent.com/jembi/platform/recipes/cdr.env && \ +wget https://raw.githubusercontent.com/jembi/platform/recipes/config.yaml && \ +instant package init -p cdr --dev +``` diff --git a/documentation/recipes/central-data-repository-with-data-warehousing.md b/documentation/recipes/central-data-repository-with-data-warehousing.md new file mode 100644 index 00000000..86b34df9 --- /dev/null +++ b/documentation/recipes/central-data-repository-with-data-warehousing.md @@ -0,0 +1,49 @@ +# Central Data Repository with Data Warehousing + + + +{% hint style="warning" %} +Note: This recipe is in a pre-release alpha stage. It's usable but do so at your own risk. +{% endhint %} + +This recipe sets up an HIE that does the following: + +* Accept FHIR bundles submitted securely through an IOL (OpenHIM) +* Stores Clinical FHIR data to a FHIR store (HAPI FHIR) +* Stores Patient Demographic data to an MPI (JeMPI) +* Pushes FHIR resources to Kafka for the reporting pipeline (and other systems) to use +* Pulls FHIR data out of Kafka and maps it to flattened tables in the Data Warehouse (Clickhouse) +* Allows for the Data Warehouse data to be visualised via a BI tool (Apache Superset) + +To launch this package in dev mode copy and paste this into your terminal in a new folder (ensure you have the [instant CLI installed](https://jembi.gitbook.io/instant-v2/getting-started/quick-start)): + +```bash +wget https://raw.githubusercontent.com/jembi/platform/recipes/cdr-dw.env && \ +wget https://raw.githubusercontent.com/jembi/platform/recipes/config.yaml && \ +instant package init -p cdr-dw --dev +``` + +## Services + +When deployed in `--dev` mode the location of the UIs will be as follows: + +| Service | URL | Auth | +| -------- | -------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------- | +| OpenHIM | [http://localhost:9000/](http://localhost:9000/) |

Test SSO user:
u: test p: dev_password_only

| +| JeMPI | [http://localhost:3033/](http://localhost:3033/) |

Test SSO user:
u: test p: dev_password_only

| +| Superset | [http://localhost:8089/](http://localhost:8089/) |

Test SSO user:
u: test p: dev_password_only

| +| Grafana | [http://localhost:3000/](http://localhost:3000/) |

Test SSO user:
u: test p: dev_password_only

| +| Keycloak | [http://localhost:9088/admin/master/console/#/platform-realm](http://localhost:9088/admin/master/console/#/platform-realm) | u: admin p: dev\_password\_only | + +Extra UIs only exposed in `--dev` mode: + +| Service | URL | Auth | +| --------- | ------------------------------------------------ | ---- | +| Kafdrop | [http://localhost:9013/](http://localhost:9013/) | none | +| HAPI FHIR | [http://localhost:3447/](http://localhost:3447/) | none | + +## Example use + +Use the following example postman collection to see interaction you cna have with the system and see how the system reacts. + +{% embed url="https://www.postman.com/jembi-platform/workspace/jembi-public/collection/23372581-055117db-6827-43d8-bc50-86f06f5a54c6?action=share&creator=23372581" %} diff --git a/documentation/recipes/master-patient-index.md b/documentation/recipes/master-patient-index.md new file mode 100644 index 00000000..4f99ec4b --- /dev/null +++ b/documentation/recipes/master-patient-index.md @@ -0,0 +1,15 @@ +# Master Patient Index + +{% hint style="warning" %} +Note: This recipe is in a pre-release alpha stage. It's usable but do so at your own risk. +{% endhint %} + +This recipe sets up an HIE that deploys JeMPI behind the OpenHIM with a mapping mediator configured to allow for FHIR-based communication with JeMPI. It also deploys Keycloak for user management and authentication. + +To launch this package in dev mode copy and paste this into your terminal in a new folder (ensure you have the [instant CLI installed](https://jembi.gitbook.io/instant-v2/getting-started/quick-start)): + +```bash +wget https://raw.githubusercontent.com/jembi/platform/recipes/mpi.env && \ +wget https://raw.githubusercontent.com/jembi/platform/recipes/config.yaml && \ +instant package init -p mpi --dev +```