Problems with GitHub App

Dockstore
1

Hello,

I’m having some trouble with the GitHub app and sync. We had similar problems when first adding the repo in May, but they went away without any clear reason. I updated the .dockstore.yml for the first time yesterday, and GitHub App Logs shows a list of errors. I started with the documentation templates for example, and I’ve linted the file to check that it’s proper yaml. dockstore yaml validate produces the same output as the GitHub App Logs, but it’s just not clear what’s wrong from these messages.

User williamrowell: Error handling push event for repository PacificBiosciences/HiFI-human-WGS-WDL and reference refs/heads/main
Error reading .dockstore.yml: Cannot create property=workflows for JavaBean=io.dockstore.common.yaml.DockstoreYaml12@7073d1da
 in 'string', line 2, column 1:
    version: 1.2
    ^
Cannot create property=filters for JavaBean=io.dockstore.common.yaml.YamlWorkflow@7ef6156b
 in 'string', line 15, column 5:
      - name: HiFi-human-WGS-WDL
        ^
Cannot create property=branches for JavaBean=io.dockstore.common.yaml.Filters@54584a75
 in 'string', line 68, column 7:
          branches: /develop/
          ^
No single argument constructor found for interface java.util.List
 in 'string', line 68, column 17:
          branches: /develop/
                    ^

 in 'string', line 68, column 7:
          branches: /develop/
          ^

 in 'string', line 15, column 3:
      - name: HiFi-human-WGS-WDL
      ^

Terminated processing of .dockstore.yml.

One added note here, and hope I’m not burying the lede, but we did rename the GitHub repo. Would this cause any problems like this?

Thanks

2

Hello,

In your .dockstore.yml, the type of the branches and and tags properties on lines 68 and 69 is array. So you need to have either:

filters:
    branches: 
        - /develop/
    tags:
        - /v.*/

or, using the bracket syntax:

filters:
    branches: [ /develop/ ]
    tags: [ /v.*/ ]

Our error message is not very friendly, and I can see how the docs are confusing as well. I’ve created a ticket to improve this.

3

Thanks for the help and the future clarification in the documents!