{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/dockstore/issues/224","repository_url":"https://api.github.com/repos/ga4gh/dockstore","labels_url":"https://api.github.com/repos/ga4gh/dockstore/issues/224/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/dockstore/issues/224/comments","events_url":"https://api.github.com/repos/ga4gh/dockstore/issues/224/events","html_url":"https://github.com/ga4gh/dockstore/issues/224","id":153802162,"number":224,"title":"When refreshing tools with non-default paths, refresh uses the default paths rather than non-default for each version","user":{"login":"denis-yuen","id":1730679,"avatar_url":"https://avatars.githubusercontent.com/u/1730679?v=3","gravatar_id":"","url":"https://api.github.com/users/denis-yuen","html_url":"https://github.com/denis-yuen","followers_url":"https://api.github.com/users/denis-yuen/followers","following_url":"https://api.github.com/users/denis-yuen/following{/other_user}","gists_url":"https://api.github.com/users/denis-yuen/gists{/gist_id}","starred_url":"https://api.github.com/users/denis-yuen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/denis-yuen/subscriptions","organizations_url":"https://api.github.com/users/denis-yuen/orgs","repos_url":"https://api.github.com/users/denis-yuen/repos","events_url":"https://api.github.com/users/denis-yuen/events{/privacy}","received_events_url":"https://api.github.com/users/denis-yuen/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ga4gh/dockstore/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/ga4gh/dockstore/labels/web%20service","name":"web service","color":"bfdadc"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-05-09T15:23:23Z","updated_at":"2016-05-10T06:11:42Z","closed_at":null,"body":"Refresh behaviour is not quite correct. When refreshing, even if a particular version uses a non-default path (say /delly_docker/Dockstore.cwl rather than /Dockstore.cwl), the grabbing of descriptors uses the default \r\nhttps://github.com/ga4gh/dockstore/blob/develop/dockstore-webservice/src/main/java/io/dockstore/webservice/helpers/Helper.java#L241\r\n\r\nThis causes descriptors to be not returned when reporting on CWL and Dockerfiles in the client.\r\n\r\nWorkaround: modify the default path to match the real paths in the source code repo\r\nAccomplish this with the command `dockstore updateContainer --entry quay.io/pancancer/pcawg_delly_workflow --cwl-path /delly_docker/Dockstore.cwl --dockerfile-path /delly_docker/Dockerfile`\r\ni.e. \r\n```\r\ndefault_cwl_path\": \"/Dockstore.cwl\",\r\n\"default_wdl_path\": \"/Dockstore.wdl\",\r\n```\r\nshould be \r\n```\r\ndefault_cwl_path\": \"/delly_docker/Dockstore.cwl\",\r\n\"default_wdl_path\": \"/delly_docker/Dockstore.wdl\",\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/ga4gh/dockstore/issues/comments/218067699","html_url":"https://github.com/ga4gh/dockstore/issues/224#issuecomment-218067699","issue_url":"https://api.github.com/repos/ga4gh/dockstore/issues/224","id":218067699,"user":{"login":"briandoconnor","id":1730584,"avatar_url":"https://avatars.githubusercontent.com/u/1730584?v=3","gravatar_id":"","url":"https://api.github.com/users/briandoconnor","html_url":"https://github.com/briandoconnor","followers_url":"https://api.github.com/users/briandoconnor/followers","following_url":"https://api.github.com/users/briandoconnor/following{/other_user}","gists_url":"https://api.github.com/users/briandoconnor/gists{/gist_id}","starred_url":"https://api.github.com/users/briandoconnor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/briandoconnor/subscriptions","organizations_url":"https://api.github.com/users/briandoconnor/orgs","repos_url":"https://api.github.com/users/briandoconnor/repos","events_url":"https://api.github.com/users/briandoconnor/events{/privacy}","received_events_url":"https://api.github.com/users/briandoconnor/received_events","type":"User","site_admin":false},"created_at":"2016-05-10T06:11:42Z","updated_at":"2016-05-10T06:11:42Z","body":"Actually, this is strange.  the pcawg_delly_workflow no longer shows up in my pancancer organization:\r\n\r\n![image](https://cloud.githubusercontent.com/assets/1730584/15136982/6288dee8-163b-11e6-956e-aa4c887da99c.png)\r\n"}}