Release Notes: August 2017

Posted by KateN on 4 Aug 2017 (2)


August 29, 2017

New Features

  • Enable blank output expressions for Method Configs. The outputs of the associated workflows will not be written back to the data model.
    • The UI will complain that a blank output expression is not valid. This will be corrected in the near future.
  • The Data Library now supports filtering on tags, just like Workspaces.
  • The Workspace table is now split into two tabs: "My Workspaces", showing everything that has been explicitly shared with you, and "Public Workspaces", showing workspaces that have been shared with the All Users group. If a workspace fits both criteria, it will show up in both tabs. -The Data Library and Method Repository pages have been restyled to match the new Workspaces page design.

Improvements

  • Improved filtering, sorting, and pagination performance on the workspace table, especially with a large number of workspaces.
  • Loading image previews were slow, and you couldn't see the full image until after the preview had fully loaded so image previews are no longer displayed in the workspace data table. Previews are no longer displayed for common image file extensions. This lets you choose to open the full image whenever you want, without having to wait for the preview to load.
  • TSV metadata downloads are much faster, when the TSV contains a large number of entities.

Bug Fixes

  • If you left the default entity type of Launch Analysis empty, then the table would get stuck with an infinite spinner. This no longer occurs.
  • The Create Method popup said that you need docker digests for call caching to work. This is incorrect, so the message has been removed.
  • The Data Library's discoverable-by feature has been fixed in a few places:
    • When a workspace is cloned, the new workspace defaults the discoverable by setting to all users.
    • When library attributes were modified and discoverable by was not set to a specific group, it was being set to no groups and the dataset was no longer visible in the library. This has been fixed so it will still be discoverable by all users.
    • Changing the discoverable-by setting back to all users was not being saved, but it is saved now.
  • Fixed an issue that allowed users to create duplicate method configurations inside their workspace.

August 14, 2017

New Features

  • One-Click Sharing:
    • When sharing a method config (in the method repo) with new users, a permissions check is made on the underlying method. If you have owner permissions on the method, you are prompted to give access to new users. If you do not have owner permissions on the method, you are notified that the new users will need to request access from an owner.
    • When sharing a workspace with users, there's a permissions check against the methods referred to by the workspace's method configurations. For all non-public methods:
      1. For methods owned by the sharer, the sharer is prompted to grant read access to any new users lacking that access
      2. For methods not owned by the sharer, the sharer is notified that the new users may lack access
  • When creating a new group, you can enter a group name with 50 or fewer characters. You may only use alphanumeric characters, underscores, or dashes. If the name is invalid, you will get an error message informing you so.
  • The evaluate endpoint is now available in the orchestration API.

Improvements

  • When editing a method config, the autocomplete used to autocomplete ALL data attributes all the time. Now, you will only see autocompletes from the currently selected root entity type. The autocomplete values change whenever you change the entity type.

Bug Fixes

  • When you use swagger for any endpoint that posts to methods or configs, and have error/malformed input you will now receive a descriptive error. (Before you got a "No Response" error.)
  • Groups added to billing projects will now be properly displayed; previously an incorrect name was displayed in some cases.

August 8, 2017

New Features

  • Enable user access to an imported method in one click: When importing a private method/config into a workspace, the permissions of that method/config and the workspace are checked.
    • If you have "grant" access on the workspace and "owner" access to the method, and there are users of the workspace who do not have access to the method, you will get a popup asking if you want to grant access to those users.
    • If you lack either of the two permissions ("grant" on workspace or "owner" on method), you are notified that some workspace users might not have access to the method and would need to get access from the method owner(s), who are listed.
  • Authorization Domains may now contain multiple groups. Users must be a part of each group in the Authorization Domain to view the workspace.
  • Consent, Ontology, and Google have been added to the orchestration status report in the API

Improvements

  • Previews now do not show for bam/bai files, as they were gibberish and slow to load. If the file is over 100MB we now also provide the gsutil command for downloading (as an alternative to downloading through the browser), as well as a link to information about the gsutil tool
  • Adding users or groups to workspaces is no longer case-sensitive. (The user and group names will still display with original casing)

Bug Fixes

  • When you created, then redacted a method in the method repository, you were forbidden from re-creating the method. This has been fixed and you can now re-create the method as expected.
  • Fixed an issue that caused workflow outputs to not be written back to the data model.
  • If you navigated to the second (or later) page of a the workflows table within a submission, and selected a status-button filter that did not return very many items, you could end up with no results displayed. Now, we jump back to the first page to avoid confusion.
  • You can now sort the workspaces list by access level; this function was broken previously.
  • When you download TSVs and check the "All" button, the download will now contain all columns, as expected.

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YingLiu


HI, How to download the workflow pipeline scripts ? like QC_Workflow,Mutect_Workflow etc . I wanna convert these pipeline into shell scripts . thank you !

Fri 4 Aug 2017

YingLiu


> @YingLiu said: > HI, How to download the workflow pipeline scripts ? > like QC_Workflow,Mutect_Workflow etc . > I wanna convert these pipeline into shell scripts . > thank you ! > @KateN

Fri 4 Aug 2017



Fri 4 Aug 2017


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