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workspace listed in API listing but not in UI? Publish allowed me to see it ! is this right?

esalinasesalinas BroadMember, Broadie ✭✭✭

I have a workspace TCGA_BRCA_ControlledAccess_V1-0_DATA_wgs_10_pairs
in project/namespace broad-firecloud-benchmark

I'm able to see this in the API listing (see attached PDF) when I visit the swagger page.

I'm able to see in when I use fissfc:

wm8b1-75c:wgs_wdl_cmp esalinas$ /usr/local/bin/fissfc space_info -w TCGA_BRCA_ControlledAccess_V1-0_DATA_wgs_10_pairs -p broad-firecloud-benchmark|head -11
{
  "workspaceSubmissionStats": {
    "lastSuccessDate": "2017-02-16T10:14:42.160Z",
    "lastFailureDate": "2017-02-14T14:42:43.291Z",
    "runningSubmissionsCount": 0
  },
  "accessLevel": "PROJECT_OWNER",
  "owners": ["[email protected]"],
  "workspace": {
    "workspaceId": "6e92fceb-ef44-4648-a5b0-71cacc0248eb",
    "name": "TCGA_BRCA_ControlledAccess_V1-0_DATA_wgs_10_pairs",

I'm also able to list the bucket contents:

wm8b1-75c:wgs_wdl_cmp esalinas$ gsutil ls gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb|head
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/10a7883c-975c-4d44-a80d-6bee90713758/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/120acd57-5ea9-43b4-849c-0f5f3d04756f/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/2c075e39-39e5-426e-b55a-f0d2b144c2d6/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/727dc7b1-02b3-4eed-acc0-b9bbe446c8d6/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/9fd8c5ac-c708-427e-b020-65c6691845d3/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/aadd08ee-0074-4fbc-92a7-3dbafc11c34d/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/b4c08c2f-ac36-45c2-87e3-8e0a98b1676c/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/b9948486-47e6-4556-b351-ddecc82ed55a/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/c646970d-8935-4ad7-a361-754f1b983f2e/
gs://fc-6e92fceb-ef44-4648-a5b0-71cacc0248eb/ca23703e-4ac2-404b-891e-a7fb275fc054/
wm8b1-75c:wgs_wdl_cmp esalinas$ 

But when I search for the workspace ("using search term "wgs" as a search term which is a substring of the workspace name) I don't see the workspace listed (see attached PDF).

If I type in the entire workspace name "TCGA_BRCA_ControlledAccess_V1-0_DATA_wgs_10_pairs" as the search term I see "No workspaces to display." Further more, I note that I have "All" selected, not "Complete", etc. the workspace

So I scrolled over to the "Include..." box and clicked the box next to "Published" and once I did that the workspace appeared in the UI.
Is my workspace "Published"? I don't recall having "Published" it. What does "Published" mean? Is this behavior correct behavior?

Best Answer

Answers

  • davidandavidan Portland, MEMember, Broadie
    edited February 2017

    Hi Eddie - did you by any chance clone your TCGA_BRCA_ControlledAccess_V1-0_DATA_wgs_10_pairs workspace from a pre-existing workspace? If you did clone it, is your previous workspace published in Library? Thanks for the info - this will help to debug the issue.

  • esalinasesalinas BroadMember, Broadie ✭✭✭
    edited February 2017

    HI @davidan yes, I did clone my workspace from TCGA_BRCA_ControlledAccess_V1-0_DATA which is both a pre-existing workspace and an "official TGCA controlled access workspace" I have guessed that the "Published" flag/tag/checkbox is inherited/propagated from the source of the clone. The source of the clone (which is "TCGA_BRCA_ControlledAccess_V1-0_DATA" as I mentioned) I believe is part of the Library.

  • davidandavidan Portland, MEMember, Broadie

    Eddie - yes. We are currently tracking an issue (GAWB-1585 if you want to follow along) in which cloned workspaces partially inherit the published status of the workspace from which they are cloned. The new workspace will NOT be present in Library, but for the purposes of the "Include..." filter on the workspace listing and the summary page of the workspace, it will act as if it was published.

    The quick fix for this is to unpublish the workspace from its summary page, assuming you have permission to do so or can ask someone with permission to do it for you. Since it's not actually published into Library, this won't change anything in Library, but it will reset that workspace's published status. The longer-term solution is of course to wait for the issue to be fixed!

  • esalinasesalinas BroadMember, Broadie ✭✭✭

    @davidan you wrote:

    The quick fix for this is to unpublish the workspace from its summary page, assuming you have permission to do so or can ask someone with permission to do it for you. Since it's not actually published into Library, this won't change anything in Library, but it will reset that workspace's published status. The longer-term solution is of course to wait for the issue to be fixed!

    Assuming I do I have permission, would I see a button on the summary tab for my workspace TCGA_BRCA_ControlledAccess_V1-0_DATA_wgs_10_pairs that says "Unpublish" ? I don't see such a button so I guess I don't have permission. Right now since it's not in the library I guess it's not critical.

  • esalinasesalinas BroadMember, Broadie ✭✭✭

    Thanks for the update

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