Merge branch 'main' into feat/postgres-tuning

Author: arran-standish

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                                    |
+<table><thead><tr><th width="243">Variable Name</th><th width="95">Type</th><th width="180">Relevance</th><th width="112">Required</th><th>Default</th></tr></thead><tbody><tr><td>JS_REPORT_LICENSE_KEY</td><td>String</td><td>Service license key</td><td>Yes</td><td></td></tr><tr><td>JS_REPORT</td><td>String</td><td>Jsreport service password</td><td>No</td><td>dev_password_only</td></tr><tr><td>JS_REPORT_USERNAME</td><td>String</td><td>Jsreport service username</td><td>No</td><td>admin</td></tr><tr><td>JS_REPORT_SECRET</td><td>String</td><td>Secret password for the authentication of a cookie session related to the extension used in Jsreport</td><td>No</td><td>dev_secret_only</td></tr><tr><td>ES_HOSTS</td><td>String</td><td>Elasticsearch connection string</td><td>No</td><td>analytics-datastore-elastic-search:9200</td></tr><tr><td>ES_PASSWORD</td><td>String</td><td>Elasticsearch password (for request authentication)</td><td>No</td><td>dev_password_only</td></tr><tr><td>ES_USERNAME</td><td>String</td><td>Elasticsearch username (for request authentication</td><td>No</td><td>elastic</td></tr><tr><td>JS_REPORT_INSTANCES</td><td>Number</td><td>Number of service replicas</td><td>No</td><td>1</td></tr><tr><td>JS_REPORT_SSL</td><td>Boolean</td><td>SSL protocol requirement</td><td>No</td><td>false</td></tr><tr><td>JS_REPORT_CONFIG_FILE</td><td>String</td><td>Path to the service import file</td><td>No</td><td>export.jsrexport </td></tr><tr><td>JS_REPORT_DEV_MOUNT</td><td>Boolean</td><td>Dev mount mode enabling flag</td><td>No</td><td>false</td></tr><tr><td>JS_REPORT_PACKAGE_PATH</td><td>String</td><td>Local path to package</td><td>Yes if <code>JS_REPORT_DEV_MOUNT</code> is set to true</td><td></td></tr><tr><td>JS_REPORT_CPU_LIMIT</td><td>Number</td><td>CPU usage limit</td><td>No</td><td>0</td></tr><tr><td>JS_REPORT_MEMORY_LIMIT</td><td>String</td><td>RAM usage limit</td><td>No</td><td>3G</td></tr><tr><td>JS_REPORT_CPU_RESERVE</td><td>Number</td><td>Reserved CPU</td><td>No</td><td>0.05</td></tr><tr><td>JS_REPORT_MEMORY_RESERVE</td><td>String</td><td>Reserved RAM</td><td>No</td><td>500M</td></tr></tbody></table>

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                 |
+<table><thead><tr><th width="263">Variable Name</th><th width="96">Type</th><th width="171">Relevance</th><th width="102">Required</th><th>Default</th></tr></thead><tbody><tr><td>ES_KIBANA<em>_</em>SYSTEM</td><td>String</td><td>ElasticSearch auth username</td><td>Yes</td><td></td></tr><tr><td>KIBANA_INSTANCES</td><td>Number</td><td>Number of service replicas </td><td>No</td><td>1</td></tr><tr><td>KIBANA_YML<em>_</em>CONFIG</td><td>String</td><td>Path to the service configuration file</td><td>No</td><td>kibana-kibana.yml </td></tr><tr><td>KIBANA_USERNAME</td><td>String</td><td>Service username</td><td>No</td><td>elastic</td></tr><tr><td>KIBANA_PASSWORD</td><td>String</td><td>Service password</td><td>No</td><td>dev_password_only</td></tr><tr><td>KIBANA_SSL</td><td>Boolean</td><td>SSL protocol requirement</td><td>No</td><td>True</td></tr><tr><td>KIBANA_CONFIG<em>_</em>FILE</td><td>String</td><td>Path to the dashboard import file</td><td>No</td><td>kibana-export.ndjson</td></tr><tr><td>KIBANA_MEMORY<em>_</em>LIMIT</td><td>String</td><td>RAM usage limit</td><td>No</td><td>3G</td></tr><tr><td>KIBANA_MEMORY<em>_</em>RESERVE</td><td>String</td><td>Reserved RAM</td><td>No</td><td>500M</td></tr></tbody></table>

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 `<tag_name>` 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/<tag_name>/config.yaml`&#x20;
+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/<tag_name>/config.yaml`&#x20;
 
 {% hint style="info" %}
 &#x20;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/<tag_name>/.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).

documentation/SUMMARY.md

@@ -2,7 +2,11 @@
 
 * [OpenHIM Platform](README.md)
 * [Getting Started](<README (1).md>)
-* [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)

documentation/development.md renamed to 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](<README (1).md>).
+* 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/).
 
 ##

documentation/config-importing.md renamed to documentation/development/config-importing.md

@@ -5,5 +5,5 @@ description: >-
   describes the details of these packages.
 ---
 
-# Packages
+# 📦 Packages