Dockstore Yaml Command Line Validator Tool

Description

The Dockstore Yaml Command Line Validator Tool is used to verify that a dict .dockstore.yml file is valid for use in Dockstore and that all referenced files are present.

The Dockstore Yaml Command Line Validator Tool is particularly helpful when you are trying to sync a GitHub repository with Dockstore by adding a dict .dockstore.yml to the root or .github directory of the repository. As you can verify that dict .dockstore.yml is valid before pushing, and it can help you to determine why your repository is not syncing with Dockstore.

The Dockstore Yaml Command Line Validator Tool will first determine if dict .dockstore.yml is a valid yaml file and display the following if dict .dockstore.yml is a valid yaml file (but not necessarily valid for use in Dockstore),

path/to/.dockstore.yml is a valid yaml file

If dict .dockstore.yml is not a valid yaml file the following will be displayed along with an error message explaining why dict .dockstore.yml is not a valid yaml file,

path/to/.dockstore.yml is not a valid yaml file

Next, the Dockstore Yaml Command Line Validator Tool will determine if dict .dockstore.yml is valid for use in Dockstore, if it is it will display this message,

path/to/.dockstore.yml is a valid dockstore yaml file and all required files are present

If dict .dockstore.yml is not a valid for use in Dockstore the Dockstore Yaml Command Line Validator Tool will display a helpful error message, such as,

Your file structure has the following errors:
path/to/dockstore.cwl.json does not exist

or,

path/to/.dockstore.yml has the following errors:
Unknown property: 'primaryDescriptorath'. Did you mean: 'primaryDescriptorPath'?

Usage

The Dockstore Yaml Command Line Validator Tool can be used with the following command in the dict Dockstore CLI,

dockstore yaml validate --path directory/of/.dockstore.yml

Path Parameter

The --path parameter must be set to the directory that contains dict .dockstore.yml, but must not include dict .dockstore.yml. For example,

path/to/my/awesome/workflow

is acceptable, however

path/to/my/awesome/workflow/.dockstore.yml

is not acceptable.

The --path parameter can be either an absolute or relative directory. Therefore, the following are valid uses of the Dockstore Yaml Command Line Validator Tool,

dockstore yaml validate --path .
dockstore yaml validate --path directory/of/.dockstore.yml
dockstore yaml validate --path ../../path/to/service
dockstore yaml validate --path ~/path/to/workflow
dockstore yaml validate --path /usr/jdoe/dockstore/workflow

Please note that all files referenced in dict .dockstore.yml, are checked relative to the path parameter, unless the path parameter ends in .github, in this case all files referenced in dict .dockstore.yml are checked relative to the parent of the path parameter.

For example if ./my/awesome/workflow/.dockstore.yml contained the following,

testParameterFiles:
  - /dockstore.wdl.json

and you selected ./my/awesome/workflow as the path parameter, then the Dockstore Yaml Command Line Validator Tool would check that the file ./my/awesome/workflow/dockstore.wdl.json exists.

However, if ./my/fantastic/workflow/.github/.dockstore.yml contained the following,

testParameterFiles:
  - /workflow.cwl.json

and you selected ./my/fantastic/workflow/.github as the path parameter, then the Dockstore Yaml Command Line Validator Tool would check that the file ./my/fantastic/workflow/workflow.cwl.json exists.