dockstore / write_api_service Goto Github PK

Implementation of tool-registry-schema with experimental write API support

Home Page: https://github.com/ga4gh/tool-registry-schemas

License: Apache License 2.0

Java 92.59% HTML 7.41%

write_api_service's Introduction

The Write-API allows developer to automatically create GitHub and Quay repositories for any tool encapsulated in Docker and described with a CWL descriptor on behalf of the user. It implements the proposed GA4GH Write API

This contains two parts:

The Write API web service that handles creation of GitHub and Quay repositories
The client that interacts with the web service and handles publishing of tools to Dockstore.

See their respective READMEs in the write-api-client and write-api-service directories for more details.

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write_api_service's Issues

Change secondary files to a list

Currently secondary files takes a single string as an input. Thus, it will only push one file to GitHub. In many cases, there will be multiple secondary files. Changing secondary files to a list of strings will allow multiple files to be pushed.

Message unclear on Dockerfile create without valid credentials

Expected

If the webservice does not have a correct quay.io token, we should see something like the following

$ java -jar target/write-api-client-0.1-alpha.0-SNAPSHOT-shaded.jar --config ~/.dockstore/write_api_client.properties  add --Dockerfile Dockerfile --cwl-file Dockstore.cwl
14:18:07.065 [main] INFO io.dockstore.client.cli.Add - Handling add...
14:18:09.598 [main] INFO io.dockstore.client.cli.Add - Created repository on git.
14:18:11.814 [main] INFO io.dockstore.client.cli.Add - Created branch, tag, and release on git.
14:18:17.039 [main] ERROR io.dockstore.client.cli.Add - Could not create Dockerfile: {"code":403,"message":"Web service does not have permission to create quay.io repo  (ID 0dadbb28c0adc651)."}

instead we see

$ java -jar target/write-api-client-0.1-alpha.0-SNAPSHOT-shaded.jar --config ~/.dockstore/write_api_client.properties  add --Dockerfile Dockerfile --cwl-file Dockstore.cwl
14:18:07.065 [main] INFO io.dockstore.client.cli.Add - Handling add...
14:18:09.598 [main] INFO io.dockstore.client.cli.Add - Created repository on git.
14:18:11.814 [main] INFO io.dockstore.client.cli.Add - Created branch, tag, and release on git.
14:18:17.039 [main] ERROR io.dockstore.client.cli.Add - Could not create Dockerfile: {"code":500,"message":"There was an error processing your request. It has been logged (ID 0dadbb28c0adc651)."}

Verbosity for mvn clean install

Notify tester that the test is going to wait for 5 mins.

Add command error

Sometimes (1/500 chance, currently nondeterministic), the 'Add' command will create a GitHub repository with no README file. As a result, no files can be added to that repository, no branches can be created. The repository is unusable.

Show default version in Check help message

It is unclear which version is checked when no version is specified. Either change it so --version is required or show default version.

Comb through readmes for missing content and broken links

Example the link after https://github.com/dockstore/write_api_service/tree/develop/write-api-service#usage is broken, there is still documentation that says "(Document line of test to change here)"

Document how to create properties files

Out of the box, running mvn clean install fails and it isn't clear from the root readme how to fix it.
Clearly list steps needed to get this to run (i.e. create tokens and place then in X file)

Release and merge to develop

As we move toward a general release, we're going to need a tag + release + merge to develop.
Hubflow may help for this

Document how to get quay.io tokens easily

Mentioned in stand-up, an easier way to create quay.io tokens.
Please document in https://github.com/dockstore/write_api_service/tree/develop/write-api-service#usage or in addition to #9

Move Integration Tests Out Of ClientTest.java

Separate Integration Tests and Unit tests by moving the integration tests out of ClientTest.java . This allows different maven profiles.

Create news blog item in the UI

Create a new item in the blog for the UI,
announce the new write API, why you would use it rather than the UI or talking to the swagger UI (e.g. it creates repos and quay.io images for you).

Odd usage alignment

Usage: client [options] [command] [command options]
  Options:
    --config
      Config file location.
      Default: /home/dyuen/.dockstore/write.api.config.properties
    --help
      Prints help for the client.
      Default: false
  Commands:
    add      Add the Dockerfile and CWL file(s) using the write API.
      Usage: add [options]
        Options:
        * --Dockerfile
            The Dockerfile to upload
        * --cwl-file
            The cwl descriptor to upload
          --cwl-secondary-file
            The optional secondary cwl descriptor to upload
          --help
            Prints help for the add command
            Default: false
          --version
            The version of the tool to upload to

    publish      Publish tool to dockstore using the output of the 'add' 
            command. 
      Usage: publish [options]
        Options:
          --help
            Prints help for the publish command.
            Default: false
        * --tool
            The json output from the 'add' command.

Note that "Add the Dockerfile" and "Publish tool to dockstore" seem misaligned

Dockstore-ui's Write-API Conversion Process Outdated

Change Dockstore-ui's Write-API Conversion Process because it is outdated. It still includes organization and repository in the properties file and the help usage is also outdated (it doesn't include the check command and also id in the other command).

Is the id fixed in the config file?

It isn't clear how to create new repos
The interface

$ java -jar target/write-api-client-0.1-alpha.0-SNAPSHOT-shaded.jar --config ~/.dockstore/write_api_client.properties 
14:13:04.303 [main] WARN io.dockstore.client.cli.Client - Expecting 'publish' or 'add' command
Usage: client [options] [command] [command options]
  Options:
    --config
      Config file location.
      Default: /home/dyuen/.dockstore/write.api.config.properties
    --help
      Prints help for the client.
      Default: false
  Commands:
    add      Add the Dockerfile and CWL file(s) using the write API.
      Usage: add [options]
        Options:
        * --Dockerfile
            The Dockerfile to upload
        * --cwl-file
            The cwl descriptor to upload
          --cwl-secondary-file
            The optional secondary cwl descriptor to upload
          --help
            Prints help for the add command
            Default: false
          --version
            The version of the tool to upload to

    publish      Publish tool to dockstore using the output of the 'add' 
            command. 
      Usage: publish [options]
        Options:
          --help
            Prints help for the publish command.
            Default: false
        * --tool
            The json output from the 'add' command.

does not match the specification. In particular, the command-line tool in the specification https://wiki.oicr.on.ca/display/SOFTENG/Dockstore+Write+API+%28Paste-bin+service%29+Specification has an "id" field that allows a user to specify the organization and repository that is created to house the documents.

It looks like the config file has these values hard-coded.

Add a badge linking to travis-ci

Markdown code available at https://travis-ci.org/dockstore/write_api_service

Increase Verbosity for Publish Command

When using the publish command for a tool whose Dockerfile hasn't finished building on Quay.io, the client will sleep for a while waiting for the image to be built. However, no output is displayed to the user.