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Release Notes: October 2017

Posted by KateN on 3 Oct 2017 (4)


October 16, 2017 (estimated)

New Features

A new UI for the Methods Repository has been released!

  • The Methods Repository page now only lists methods. Configurations based on those methods are now accessible via the Method's detail view.

  • The Methods detail view shows all snapshots at once - use the dropdown to switch between snapshots and compare them.

  • Export an existing Configuration to a workspace, or use a blank configuration.
  • You will be able to export any configurations that are compatible (i.e. have the same inputs and outputs) with the method snapshot of interest, even if the configuration was originally created based on a different method snapshot.

Improvements

  • A Method Configuration in a workspace will now only let you set the root entity type to a type that exists in your workspace.
  • If you are in the filter box for a table and have entered text to search on, hitting escape will clear the search rather than closing the dialog as it did previously.
  • When you redact a snapshot of a method from the Methods Repository, you will now be warned that you will also remove all associated configurations from the repository.
  • The GA4GH's DUO ontology has now been integrated into the Library.

Bug Fixes

  • Fixed a bug where attempting to delete workspace attributes would occasionally delete the wrong row.
  • Fixed a bug where editing a workspace method configuration to point to a different method snapshot could cause the configuration to be unusable.
  • Using escape key to close the export method config modal was throwing a javascript error; this is now fixed.

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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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An update to method naming rules

Posted by KateN on 27 Jun 2017 (0)


To improve the consistency and reliability of FireCloud, an upcoming release (6/29/17) introduces naming rules for Methods and Method Namespaces. When creating or editing, only letters (A-Z, a-z), numbers (0-9), underscores (_), dashes (-), and periods (.) will be allowed.

All existing methods will continue to run. A small number of users may need to apply the following workarounds:

  • If you want to edit a method with an unsupported name, you should instead clone it to create a new method with a supported name.
  • If you have methods in an unsupported namespace, you should create a new namespace and clone your methods to it.
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Release notes: June 2017

Posted by KateN on 19 Jun 2017 (0)


June 29, 2017

Improvements

  • When creating or editing methods or method namespaces, you will be restricted to using only letters (A-Z, a-z), numbers (0-9), underscores (_), dashes (-), and periods (.). For more information on why we are doing this, as well as the effect this may have on you going forward, please read here.

Bug Fixes

  • Fixed a bug where right-clicking to download workspace files could fail with an authorization error.

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