Release Notes: November 2017

Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin
edited December 2017 in FireCloud Announcements

Nov 21, 2017

New Features

  • The Data Library catalog now has a new feature that allows to "Filter by Research Purpose". Clicking the link will pop up a modal that allows to select among six Data Use fields to search on. This algorithm is powered by the Data Use Oversight System (DUOS) matching algorithm which uses the GA4GH Consent Codes and Data Use Ontology for matching. More information about the development of DUOS and its pilot study is found here.
  • Consent codes and catalogued workspace tags are now columns in the Data Library page. You can search on these as you would any other column.
  • Disease selection for data use limitation in the catalog wizard now only allows diseases in the ontology. You can select multiple diseases.
  • The API endpoint to PUT library metadata now supports an optional "validate" query parameter. Validation is always enabled for published datasets and is now controlled by the query parameter for unpublished datasets. This allows API users to receive validation feedback for their payloads.
  • When cataloging a dataset, you now have the option to specify a custom message to users when they request access. This message has full markdown support.
  • When cataloging a workspace for the library, if using the questionnaire to determine data use limitations, a primary category (GRU, HMB, or DS) is now required.

Improvements

  • We've added a new IRB question for the Data Use Restriction Questionnaire: "Requester must provide documentation of local IRB/REC approval."

Bug Fixes

  • Display icon next to a new billing project of "pending" status if the project is still waiting on an item prior to finalization. Previously, there was no indication that the status was pending.
  • If you updated a method configuration to a new snapshot which had additional inputs or outputs compared to the previous snapshot, editing the values of those inputs and outputs could fail to save. This is now fixed.
  • When you enter illegal characters when editing a Method Configuration name, you will now see a warning message and not be allowed to save.

November 15, 2017

New Features

  • FireCloud's Method Repository now supports WDLs with HTTP imports referencing the URL of other public methods in the FC repository. Read about using these import statements here.
  • A submissionsCount API endpoint has been added to Orchestration.

Improvements

  • FireCloud has been upgraded to use Cromwell 29 (specifically, 29_hotfix). For more information on that release, please read here.
  • In the Method Repository, when viewing the table of a method's configurations, each configuration's compatibility with the selected method version is shown. Configurations which are incompatible due to a change in the inputs/outputs are shown with a warning icon. Previously, incompatible configurations were not shown at all.

Bug Fixes

  • Fixed an issue that caused the Export to Workspace dialog to enter an unusable state if a blank method name is specified.
  • Fixed an issue where the Export to Workspace dialog allowed the user to specify an invalid method name, leaving the method in an unusable state in the destination workspace.
  • Fixed a bug where going to the Data Library and quickly navigating away could cause a JavaScript error.
  • New columns created by importing metadata or running analysis will now show in data table regardless of local preferences or workspace defaults. Previously some outputs would fail to display in your Data tab due to these preferences & defaults.
  • Fixed an issue that could cause the preview pane of the Data tab to display the wrong entity.

November 1, 2017

New Features

  • Expanded our Methods Repository API to support multiple GA4GH Tool Registry Schema APIs. Documentation can be found on our swagger page: https://api.firecloud.org/#/GA4GH_Tool_Registry
  • Queue status: We moved workflow queue status from the main page header to the Workflow Monitor page, and added a manual refresh button so that you can see your updated queue status. Because FireCloud now makes many fewer queue status requests, it will be more responsive.

Improvements

  • Visible performance improvements when using all parts of the app.
  • Increased the speed at which workspaces get created.

Bugs

  • Can compute: If you change a Writer to a Reader in a workspace, the "can compute" permissions checkbox should be unchecked in the UI. There was a bug with the checkbox where you couldn't save the updated permission and this has been fixed.
  • The "Create New Workspace" button is disabled when you do not have a billing project available to use. Now, a modal will direct you to create a billing project if you do not have one and want to create a workspace.
  • Filtering in the workspace data tab did not find results after analysis completed. Now Filtering in the data tab should work in all cases.
Post edited by KateN on
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Comments

  • dheimandheiman Member, Broadie ✭✭

    Hi @Tiffany_at_Broad, this is fantastic, but what exactly IS the URL path to a method's WDL in the method repository? Is it https://portal.firecloud.org/#methods/<method namespace>/<method>/<snapshot> or something more involved? That is not listed at the link you've given.

    Thanks!

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin
    edited December 2017

    The format looks like this and the items starred should be replaced:
    https://api.firecloud.org/ga4gh/v1/tools/*methods_from_Tiffany_at_Broad%3AConvert_Cram_To_Bam*/versions/*13*/plain-WDL/descriptor

    • methods_from_Tiffany_at_Broad%3AConvert_Cram_To_Bam = namespace + %3A + name of FC method
    • 13 = snapshot ID

    Note: It says ga4gh because it is compliant with the ga4gh api spec, but it all comes from the methods repo.

    You can also type your public method info into the Swagger here and have the url returned to you.

    Post edited by Tiffany_at_Broad on
  • dheimandheiman Member, Broadie ✭✭

    Awesome, thanks!

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