Problem with display of workspaces and faceted search

birgerbirger Member, Broadie, CGA-mod ✭✭✭

(It is unclear whether these issues appeared with the latest Sept 7 release or preceded that release.)

I log into FireCloud with a google account that has been linked to an eRA commons account. Under that eRA commons account I'm authorized to access TCGA and TARGET controlled access data.

In FireCloud there are currently 33 open access hg19 TCGA workspaces, 33 controlled access hg19 TCGA workspaces, 33 open access hg38 TCGA workspaces, 33 controlled access hg38 workspaces, 5 open access hg38 TARGET workspaces and 5 controlled access hg38 TARGET workspaces. The open access workspaces are shared (READER level privileges) with [email protected]; the controlled access TCGA workspaces are shared (READER level privileges) with [email protected]; the controlled access TARGET workspaces are shared (READER level privileges) with [email protected] The TCGA workspaces have been published in the data library; the TARGET workspaces have not.

With no faceted search boxes checked, under the Public Workspaces tab, I see the open access workspaces. Under the My Workspaces tab, I see the Controlled access workspaces. The controlled access workspaces should not be in the My Workspaces tab - they are readable by ALL firecloud users that are dbGaP authorized (and have linked their firecloud account to their eRA Commons account.

When I check the TCGA protected access faceted search box, I still see both the TCGA and TARGET controlled access workspaces under the My Workspaces tab. TCGA protected access is distinct from TARGET protected access. You probably need a separate facet checkbox for TARGET, or change the faceted check box's label from TARGET to "TARGET and TCGA". When only the TCGA protected access faceted search box is checked, I also still see the TARGET and TCGA open access workspaces under the Public Workspaces tab - this is a definite bug.

When I check only the TCGA open access faceted search box, I see neither the controlled access TARGET/TCGA workspaces under the My Workspaces tab, nor the open access TARGET/TCGA workspaces under the public workspaces tab. This is a bug.

Bottom line, the faceted search for open and controlled access workspaces is confusing and buggy.

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    @birger Thanks for this in-depth report. I've walked through the experience and I am seeing the same bugs with TCGA (not Target since I don't have access). However, I am raising bugs for all these issues and will follow up with when we can get a fix into a release.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    @birger Thank you for your report! You should see a fix go through for this in our next release, which is currently planned for early this week.

  • birgerbirger Member, Broadie, CGA-mod ✭✭✭

    The release notes for the October 3 release stated this problem was fixed, but most of the reported issues remain. The open access TCGA and TARGET workspaces show up in the Public workspaces tab and the controlled access TCGA and TARGET workspaces show up in the My Workspaces tab. Although the controlled access workspaces are restricted to members of their respective Authorization Domains, they are still public workspaces and should appear on the Public workspaces tag. Also, TARGET data is different from TCGA data.; you either need to change the labels in your faceted search box (TCGA controlled access to TCGA and TARGET controlled access) or have separate check boxes for TARGET and TCGA.

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    @moran Can you comment more on your plans for this?

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    @birger Are you still experiencing this issue? I'd like to follow up to see if a solution was reached.

Sign In or Register to comment.