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Release Notes: December 2017

Posted by KateN on 6 Dec 2017 (0)


December 14, 2017

Improvements

  • Improved reliability when creating billing projects

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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 Validation is always enabled for published datasets and is now controlled by the query parameter for unpublished datasets.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.

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Release Notes: October 2017

Posted by KateN on 3 Oct 2017 (4)


October 20, 2017

New Features

  • Users can now specify a snapshot comment when creating or editing a method in the Method Repository. The comment appears in the method config tab of a workspace, when importing/exporting methods, and when viewing a method in the Repository.

Improvements

  • Now we explicitly state in the user interface that group functionality cannot be used in the Methods Repository. We are working on supporting this.

Bug Fixes

  • Two-dimensional Array entity attributes (e.g. [[1,2,3],[4,5,6],[7,8,9]]) can now be bound to two-dimensional array WDL inputs (e.g. Array[Array[Int]]).
  • Fixed an issue where after updating the owners of a method or method configuration inside the Method Repository, the new list of owners was not displayed until the page was refreshed.

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The National Cancer Institute (NCI) funded the beginning development of FireCloud and two other genetic analysis cloud platforms. NCI started a pilot program that offered free credits ranging from $300, $1000, and $10,000 to give researchers a risk-free trial to compute on these platforms.

The NCI’s Cloud credit pilot was highly popular with around 164 researchers issued FireCloud credit and has been a great vehicle for getting users into the system. As the pilot comes to an end on September 27th, we are trying to make it easy for you to continue using the system and save your data. We have included instructions and individual contacts who can help you through the transition.


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Release Notes: September 2017

Posted by KateN on 7 Sep 2017 (0)


September 26, 2017

New Features

  • Featured Workspaces: The Workspaces page has a new tab, "Featured Workspaces," where the Firecloud Communications Team will highlight workshop workspaces and tutorial workspaces loaded with popular method configurations.

Improvements

  • Methods Repository: FireCloud now validates your WDL when using the "Edit..." functionality on a method.
  • Methods Repository: Method configuration detail pages in the Repository now show their inputs and outputs. The method configuration edit page (inside a workspace) has also been updated to use this new design.

Bug Fixes

  • Data Library: Users need the ability to unpublish a workspace from the Data Library before they are allowed to delete it. This bug fix prevents workspace owners who do not have "catalog" permissions from deleting a published workspace.
  • APIs: Fixed a bug where calling GET submission/outputs in the FireCloud Swagger gave an error.

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This is a notification intended for anyone who uses the APIs to interact with FireCloud. If you don't know what that is, you don't need to worry about it. If you'd like to be notified of any future API changes by email, please join the new API users mailing list.

TL;DR: Changes will be made to the following endpoints in the next release (likely arriving on 23 August 2017) :

PUT /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/{configNamespace}/{configName}
POST /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/{configNamespace}/{configName}/rename

These endpoints create and edit method configurations that have been imported into a workspace. A diff of the Swagger description will be posted once the release is out. Read on below the fold for a more detailed description of how these endpoints' behaviours will change.


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Updates from the Methods Repo

Posted by KateN on 17 Aug 2017 (0)


We know that many of you have been struggling with developing and evolving pipelines via FireCloud due to challenges in managing access to multiple versions in our system; you have to manage access to each “version” (snapshot) of your method independently. It’s thanks to your feedback and patience we continue to evolve our Methods Repository.

We would like to highlight a few improvements to Methods’ management we included during Spring 2017:

  1. Clone a method. This allows you to avoid typing in documentation/synopsis and the WDL when you just want to make edits, or start a new Method based on another.
  2. Edit a method. Start a new snapshot of the same method with pre-populated documentation/synopsis/WDL and access control list. Note that in the foreseen future, changes you apply to the access control list or other metadata would only apply to the new saved version.
  3. Synchronizing access between workspace users, methods and their configuration in one-click. In the current model, the access for each object in managed independently. This is a pain. We know that and dislike it too. Now, when you import a method as a configuration into a workspace, FireCloud will ask you if you would like to allow other users of this workspace to run this method and will update all permission for you accordingly. We are working towards a more permanent solution, but this one-click feature will save you time and headaches now.
  4. Auto-complete when wiring a configuration with the data model in the Workplace. We now provide an autocomplete displaying the custom attributes on entities in every workspace when you fill out inputs and outputs of a Method Configuration. See figure below.
  5. Import a configuration directly from another Workspace (without the need to “publish” it in the Method Repository).

What’s coming next?

  1. New UI/UX for the Method Repository that integrates versions and configuration of the same method into one UI component for ease of finding methods.
  2. The ability to reuse method configurations with multiple method’s versions (no longer limited to the snapshot the configuration was created for).
  3. Updates to the Methods Repository UI with a section for Featured methods. We look forward to your contributions!
  4. Public tags on Methods and the ability to search on tags.
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A breaking change was introduced in the API by this morning's release. This does not affect the web UI.

The create workspace endpoint has a new required field, authorizationDomain, which was previously optional. This refers to the Authorization Domain security feature, which enables you to set boundaries on workspace sharing permissions. If you do not want to assign an authorization domain to the workspace you are creating, you can set the field to "authorizationDomain": [].

Please accept our apologies for this unanticipated breaking change. We will review our procedures to ensure that breaking changes are not allowed to happen without advance notification and sufficient justification for the inconvenience caused to FireCloud API users.

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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.

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Release Notes: July 2017

Posted by KateN on 10 Jul 2017 (1)


July 26 2017

Improvements

  • To prevent you from accidentally deleting a group, you will now see a confirmation pop-up after you hit delete.
  • When a page is taking a long time to load, you will now see a visual indication that it is still working on loading; sometimes large pages, like the Data Library, would appear to hang while they worked on loading all the data.
  • You will notice that data tables now have shorter load times due to backend improvements.
  • We've reduced the time it takes for workflow monitoring to appear in the UI after submission.

Bug Fixes

  • You can now download large TSVs. Previously, users were encountering errors when downloading the TSVs with >1000 entities.
  • When you try to delete a group and it is being used in a workspace, you now get an error message telling you why you can't delete. Previously you would see no message and the group would not be deleted.
  • When you resize multiple columns in your Data Model table, sometimes the text would overlap. This has now been fixed, and resizing columns works as expected.

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