Creates custom Github Aciton for cloudos job run (#1)

* Adds README.md

* Adds recommendation for github secrets

.github/workflows/cloudos-ci.yml

@@ -3,11 +3,11 @@ on: [push]
 jobs:
   custom_test:
     runs-on: ubuntu-latest
-    name: Local test with act
+    name: Dry run test for cloudos job run
     steps:
       - name: Checkout
         uses: actions/checkout@v2
-      - name: Echo cloudos command
+      - name: Print cloudos job run command (dry_run set to true)
         uses: ./ # Uses an action in the root directory
         id: cloudos_job_run
         with:
@@ -17,4 +17,5 @@ jobs:
           project_name: 'cloudos-cli-tests'
           workflow_name: 'cgpu/rnatoy'
           nextflow_profile: 'test'
-          cloudos_cli_flags: '--resumable --spot'
+          cloudos_cli_flags: '--resumable --spot'
+          dry_run: 'true'

README.md

@@ -1 +1,121 @@
-# action-custom-action
+# GitHub Action: Run Lifebit CloudOS jobs with cloudos-cli
+
+This github action uses the [`cloudos-cli`](https://github.com/lifebit-ai/cloudos-cli), the official Lifebit CloudOS API client, to launch jobs programmatically using the `cloudos job run` command.
+
+## Example usage
+
+```yaml
+on: [push]
+
+jobs:
+  cloudos_job_run:
+    runs-on: ubuntu-latest
+    name: Submit CloudOS job programmatically
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Echo cloudos command
+        uses: lifebit-ai/[email protected]
+        id: cloudos_job_run
+        with:
+          apikey:  ${{ secrets.CLOUDOS_APIKEY }}
+          cloudos_url: 'https://cloudos.lifebit.ai'
+          workspace_id: ${{ secrets.CLOUDOS_WORKSPACE_ID }}
+          project_name: 'cloudos-cli-tests'
+          workflow_name: 'cgpu/rnatoy'
+          nextflow_profile: 'test'
+          cloudos_cli_flags: '--resumable --spot'
+```
+
+
+## Inputs
+
+### `dry_run`
+
+If set to `'true'` the action only prints the `cloudos job run` command instead of executing it. Secrets are stripped before printing. This mode can be used for testing.
+
+### `apikey`
+
+The Lifebit CloudOS user personal API token.
+
+> :warning: It is highly recommended to use Github Actions Secrets to define this secret variable. Follow the [official Github Actions documentation for reporsitory secrets](https://docs.github.com/en/actions/security-guides/encrypted-secrets#creating-encrypted-secrets-for-a-repository) to set this up for your reporsitory.
+
+
+### `cloudos_url`
+
+The Lifebit CloudOS application hostname without a trailing backslash eg https://cloudos.lifebit.ai
+
+### `workspace_id`
+
+The Lifebit CloudOS workspace id. It Can be found under Settings in the web application. It is recommended to use Github Action repository secrets to set up this variable.
+
+### `project_name`
+
+The Lifebit CloudOS workspace id. It can be created and selected from the Lifebit CloudOS web application user interface under Projects.
+
+### `workflow_name`
+
+The Lifebit CloudOS workflow name. It can be created and selected from the Lifebit CloudOS web application user interface under Pipelines & Tools.
+
+
+### `job_config`
+
+A local file with suffix .config, that includes only a params scope enclosed in curly brackets. The file should contain parameter key:value pairs. For example see: [cloudos/examples/rnatoy.config'](https://github.com/lifebit-ai/cloudos-cli/blob/dev/cloudos/examples/rnatoy.config')
+
+
+### `nextflow_profile`
+
+One or many comma separated strings, indicating the nextflow profile/s to use with your job. Only applicable to Nextflow workflows.'
+
+### `git_commit`
+
+The exact whole 40 character commit hash to run for the selected pipeline. If not specified it defaults to the last commit of the default branch.
+
+### `git_tag`
+
+The version tag of the chosen workflow repository. It must exist in the repository
+
+
+### `job_name`
+
+A name to assign to the job run.
+
+### `instance_type`
+
+The type of AWS EC2 instance to use as master node for the job eg c5.xlarge
+
+### `instance_disk`
+
+Disk storage in GB to be used for the master node vm.
+
+
+### `storage_mode`
+
+The storage mode to use. Available options: [regular,lustre]. Regular is EBS.
+
+### `lustre_size`
+
+The lustre storage to be used when --storage-mode=lustre, in GB. It should be 1200 or a multiple of it.'
+
+### `wait_time`
+
+Max time to wait (in seconds) to job completion
+
+### `wdl_mainfile`
+
+For WDL workflows, which mainFile (.wdl) is configured to use (string). This is defined when the WDL repository is imported under Pipelines & Tools using the Lifebit CloudOS web application user interface.
+
+### `wdl_importsfile`
+
+For WDL workflows, which importsFile (.zip) is configured to use (string). This is defined when the WDL repository is imported under Pipelines & Tools using the Lifebit CloudOS web application user interface.
+
+### `cromwell_token`
+
+Specific Cromwell server authentication token. Only required for WDL jobs.
+
+### `repository_platform`
+
+Name of the repository platform of the workflow. Default=github.
+### `cloudos_cli_flag`
+
+Additional cloudos-cli flags, space separated eg `'--spot --resumable'`. Available options: `[--spot, --batch, --resumable, --verbose, --wait-completion]`

action.yaml

@@ -26,7 +26,6 @@ inputs:
   nextflow_profile:
     description: 'One or many comma separated strings, indicating the nextflow profile/s to use with your job. Only applicable to Nextflow workflows.'
     required: false
-    default: 'standard'
   git_commit:
     description: 'The exact whole 40 character commit hash to run for the selected pipeline. If not specified it defaults to the last commit of the default branch.'
     required: false
@@ -40,23 +39,18 @@ inputs:
   instance_type:
     description: 'The type of AWS EC2 instance to use as master node for the job eg c5.xlarge'
     required: false
-    default: 'c5.xlarge'
   instance_disk:
     description: 'Disk storage in GB to be used for the master node vm.'
     required: false
-    default: '500'
   storage_mode:
     description: 'The storage mode to use. Available options: [regular,lustre]. Regular is EBS.'
     required: false
-    default: 'regular'
   lustre_size:
     description: 'The lustre storage to be used when --storage-mode=lustre, in GB. It should be 1200 or a multiple of it.'
     required: false
-    default: '1200'
   wait_time:
     description: 'Max time to wait (in seconds) to job completion'
     required: false
-    default: '3600'
   wdl_mainfile:
     description: 'For WDL workflows, which mainFile (.wdl) is configured to use (string). This is defined when the WDL repository is imported under Pipelines & Tools using the Lifebit CloudOS web application user interface.'
     required: false
@@ -73,6 +67,10 @@ inputs:
     description: 'Additional cloudos-cli flags, space separated eg "--spot --resumable". Available options: [--spot, --batch, --resumable, --verbose, --wait-completion]'
     required: false
     default: ''
+  dry_run:
+    description: 'Mode of execution for the action, by default the API call will be sent. Set to dry_run: true if you only want to print the command (strips secrets before printing).'
+    required: false
+    default: ''
 runs:
   using: 'docker'
   image: 'Dockerfile'
@@ -96,4 +94,5 @@ runs:
     - ${{ inputs.wdl_importsfile }}
     - ${{ inputs.cromwell_token }}
     - ${{ inputs.repository_platform }}
-    - ${{ inputs.cloudos_cli_flags}}
+    - ${{ inputs.cloudos_cli_flags}}
+    - ${{ inputs.dry_run}}

entrypoint.sh

@@ -25,5 +25,5 @@ if [[ ${INPUT_CROMWELL_TOKEN} ]];      then CLOUDOS_RUN_CMD+=" --cromwell-token
 if [[ ${INPUT_REPOSITORY_PLATFORM} ]]; then CLOUDOS_RUN_CMD+=" --repository-platform ${INPUT_REPOSITORY_PLATFORM}" ; fi
 if [[ ${INPUT_CLOUDOS_CLI_FLAGS} ]];   then CLOUDOS_RUN_CMD+=" ${INPUT_CLOUDOS_CLI_FLAGS}" ; fi
 
-$CLOUDOS_RUN_CMD
+if [[ ${INPUT_DRY_RUN} != 'true' ]]; then $CLOUDOS_RUN_CMD ; fi
 printf '%s\n' "${CLOUDOS_RUN_CMD//$INPUT_APIKEY/}"