cmwl_pipeline

Dependencies:

• Java 11
• Scala 2.12.9
• SBT 1.3.4

Getting Started

Installation

required dependencies installation

Install Java 11 JDK, Scala 2.12.9, the Scala build tool

docker installation

To install Docker and docker-compose CLI, run the scripts/install-docker.sh script.

Compiling

To compile from the command line, use the command below:

    sbt compile

Running Locally

To run the application, use the following command:

    sbt run

Running the Tests

The tree below reflects how unit tests and integration tests are separated by different directories.

  -src
    |_it   // Here, you add new tests which load application context
    |      // and connect to datasources deployed on staging.
    |
    |_test // Here, you add pure unit tests which cover one or several specific
           // `cromwell.pipeline.components` and have no dependencies on infrastructure.

Running Unit Tests Locally

Use the command below to run unit tests:

    sbt test

Running Integration Tests Locally

To run the integration test suit, execute the following command:

sbt it:test

Finding unused dependencies

To show unused dependencies list, execute the following command:

sbt unusedCompileDependencies

Finding undeclared dependencies

This task executes while building To show undeclared dependencies list, execute the following command:

sbt undeclaredCompileDependencies

Default configuration can be overloaded in application.properties file located in the same directory as service jar

Build With

• SBT Build and dependency management
• AkkaHTTP Asynchronous, streaming-first HTTP server and client
• Slick Database query and access library
• Liquibase Migrations
• Circee JSON processing
• ScalaTest Unit-testing framework
• ScalaMock Unit-testing framework

Run cromwell on aws instance

In order to run the cromwell project on aws instance. It is necessary to be connected to the EPAM vpn and select the Russia gateway (vpn-ru.epam.com).

Run the workflows through swagger

Once that you're connected, follow this link to try/execute the services through the swagger interface.

Run the next workflows:

• POST /api/workflows/{version} and fill the next two options
  • For the workflowSource file option select the cromwell-saample/hello.wdl file that was created before.
  • For the workflowInouts file option select the cromwell-saample/input.json file. Submit the request, and a response like the below will be returned.

{
  "id": "56e252bc-c83a-46e0-b311-9bc26f0038f8", 
  "status": "Submitted" 
}

• GET /api/workflows/{version}/{id}/status copy the id returned by the previous response
  • For the id paste the id that was copied. Submit the request, and a response like the below will be returned.

{
  "status": "Succeeded", 
  "id": "56e252bc-c83a-46e0-b311-9bc26f0038f8" 
} 

Run the workflows through curl, postman or another client

Run the next commands

• curl -X POST "http://ec2-54-218-82-67.us-west-2.compute.amazonaws.com/api/workflows/v1" -H "accept: application/json" -H "Content-Type: multipart/form-data" -F "[email protected]" -F [email protected];type=application/json
  • A response with the workflow id will be returned.
• curl -X GET "http://ec2-54-218-82-67.us-west-2.compute.amazonaws.com/api/workflows/v1/{workflow_id}}/status" -H "accept: application/json"
  • Replace the workflow_id with the id returned by the previous response.
  • A response with the workflow status will be returned.

Run Cromwell Pipeline in the Docker (Local)

• Create .env file with environment variables from .env.example file in the root folder
• Run sbt clean docker:publishLocal for creating Pipeline docker image using the local Docker server
• Run docker-compose up for running all docker containers or docker run -d --name cmwl_pipeline -p 8080:8080 cmwl_pipeline:0.1 for running only Pipeline
• Use http://localhost:8080 address for sending request

Run Pipeline and all services in Docker locally

• You can use existing .env.example file or create your own to provide environmental variables.
• Run sbt clean portal/docker:publishLocal for creating Pipeline docker image using the local Docker server.
• Run docker-compose --env-file .env.example up for starting docker images of Pipeline, Gitlab, Postgres and Mongo.
• If you want to run IntelliJ, just comment out Pipeline in docker-compose and provide correct env variables to IntelliJ run configuration.
• Other elements could be removed from docker-compose in a similar fashion
• If you are experiencing a problem with logging in into gitlab(password issue), you should uncomment line 58 in docker-compose.yml file, delete all volumes and docker images + containers, and run docker-compose up again. After everything is up and running, try logging in with root as login name and initial_root_password.

File upload process in Cromwell Pipeline

Step 1: WDL file validation

For validation WDL file send POST request
to address <cromwell_pipeline_url>/files/validation
with header Authorization <auth_token>
and request body:

{
    "content": "<file_content>"
}

• Instead of <cromwell_pipeline_url> insert the application URL
• Instead of <auth_token> insert the authorization token
• Instead of <file_content> insert the content from cromwell-sample/hello.wdl file

If validation succeed, response OK with HTTP status 200 will be returned.

Step 2: Create project (if doesn't exist)

To create project send POST request
to address <cromwell_pipeline_url>/projects
with header Authorization <auth_token>
and request body:

{
    "name": "<project_name>"
}

• Instead of <cromwell_pipeline_url> insert the application URL
• Instead of <auth_token> insert the authorization token
• Instead of <project_name> insert the name of new project

If creation succeed, response OK with HTTP status 200 will be returned.

Get project by name (if exists)

To get project by name send GET request
to address <cromwell_pipeline_url>/projects?name=<project_name>
with header Authorization <auth_token>

• Instead of <cromwell_pipeline_url> insert the application URL
• Instead of <auth_token> insert the authorization token

If project exists, response OK with HTTP status 200, and the following response body will be returned:

{
    "projectId": "<project_id>",
    "ownerId": "<owner_id>",
    "name": "<project_name>",
    "active": true,
    "repositoryId": <repository_id>,
    "visibility": "<visibility>"
}

Step 3: Upload file to project

To upload file into existing project send POST request
to address <cromwell_pipeline_url>/files
with header Authorization <auth_token>
and request body:

{
    "projectId": "<project_id>",
    "projectFile": {
        "path": "<file_name>",
        "content": "<file_content>"
    }
}

• Instead of <cromwell_pipeline_url> insert the application URL
• Instead of <auth_token> insert the authorization token
• Instead of <project_id> insert the project id from response in Step 2 (Get project by name)
• Instead of <file_name> insert the file name ("hello.wdl")
• Instead of <file_content> insert the content from cromwell-sample/hello.wdl file

If uploading succeed, response OK with HTTP status 200, and the following response body will be returned:

{
    "file_path": "<file_name>",
    "branch": "master"
}

Step 4: Build project configuration by project

To build project configuration by project send POST request
to address <cromwell_pipeline_url>/files/configurations
with header Authorization <auth_token>
and request body:

{
    "projectId": "<project_id>",
    "projectFilePath": "<file_name>",
}

• Instead of <cromwell_pipeline_url> insert the application URL
• Instead of <auth_token> insert the authorization token
• Instead of <project_id> insert the id of project, which configuration you want to build
• Instead of <file_name> insert the file name ("hello.wdl")

If building succeed, response OK with HTTP status 200, and the following response body will be returned:

{
    "projectId": "<project_id>",
    "active": true,
    "projectFileConfigurations": [
        {
            "path": "<file_name>",
            "inputs": [
                {
                    "name": "forkjoin.grep.float",
                    "typedValue": {
                        "_type": "Float"
                    }
                },
                {
                    "name": "forkjoin.grep.pattern",
                    "typedValue": {
                        "_type": "String"
                    }
                }
            ]
        }
    ]
}

Step 5: Add configuration to project

To add configuration to the project send PUT request
to address <cromwell_pipeline_url>/configurations
with header Authorization <auth_token>
and request body (JSON from response in Step 4):

{
    "projectId": "<project_id>",
    "active": true,
    "projectFileConfigurations": [
        {
            "path": "<file_name>",
            "inputs": [
                {
                    "name": "forkjoin.grep.float",
                    "typedValue": {
                        "_type": "Float"
                    }
                },
                {
                    "name": "forkjoin.grep.pattern",
                    "typedValue": {
                        "_type": "String"
                    }
                }
            ]
        }
    ]
}

If adding succeed, response OK with HTTP status 200 will be returned.

Developer Guide

https://kb.epam.com/display/EPMLSTR/Cromwell+Developer+Guide