Galaxy Middleware API

This API is implemented in order to integrate the MIP front-end with Galaxy through a RestAPI.

Requirements

• Deploy Project

  • Application Server(i.e. Tomcat)

• Build Project

  • Java8
  • Gradle

Dependencies:

1. Galaxy has to be installed (https://github.com/madgik/galaxy/tree/master/Docker_Build_Scripts).
2. After installing Galaxy an API key should be created:
   • Enter Galaxy from the browser.
   • Select the "User" Drop Down menu, on the navigation bar.
   • Select the "Preferences" option.
   • Select the "Manage API Key" option.
   • "Create a new key"
   • Copy the key so we can use it in the next step.

Deploy:

Use the following command after changing the appropriate variables:

• "galaxyUrl" should be replaces by the url of the server that has Galaxy installed.
• "galaxyApiKey" should be replaced by the API key created in Galaxy.
• "galaxyReverseProxyPassword" has to be the same as the password given when installing Galaxy.
• "jwtSecret" has to be the same as in the HBPMedical/portal-backend.
• Change the tag name of the docker "galaxy_middleware_api" image to the version you want to install.

docker run -d -e jwtSecret='1234567890' -e jwtIssuer='mip.humanbrainproject.eu' -e galaxyURL='http://88.197.53.100:8090/' -e galaxyApiKey='1234541541351' -e galaxyReverseProxyUsername='admin' -e galaxyReverseProxyPassword='password' -p 8091:8080 hbpmip/galaxy_middleware_api:v0.3.1

If you want, you can save all the environmental variables and use the following instructions to deploy:

1. You can follow this template to create the env.list file :

   jwtSecret=theJwtSecret
   jwtIssuer=theJwtIssuer
   galaxyURL=YourGalaxyURL
   galaxyApiKey=YourGalaxyApiKey
   galaxyReverseProxyUsername=admin
   galaxyReverseProxyPassword=password
   

2. Run the docker image:

   docker run -d --env-file env.list -p 8091:8080 hbpmip/galaxy_middleware_api:v0.3.1

You can use the api from the following endpoint http://localhost:PORT/Galaxy_Middleware_API-1.0.0-SNAPSHOT/api/getWorkflows

Test:

Generate a JWT token with HMAC512 security. Then update jwtToken variable in Postman and test the API calls.

Building the docker image:

If you want to create a new image of Galaxy_Middleware_API you can follow these instructions:

1. In the project directory :

   gradle clean

2. In the project directory :

   gradle war

3. docker build -t hbpmip/galaxy_middleware_api .