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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 (0)


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.

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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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This is a heads-up that we are actively working on reorganizing the documentation to make it more accessible, as a prelude to building new documentation on topics not currently covered. As part of this reorganization, many small articles will be renamed and moved to different sections, and the large monolithic articles such as "FireCloud Basics" in the Help Topics section will be broken down into more digestible topical documents. A "Quickstart" guide will also be added in the near future to provide a path of minimal effort for new users to get started with FireCloud.

In addition, I want to highlight that we are moving the documentation that covers cancer analysis-specific materials, such as the list of Best Practice workflows and TCGA reference files, to a dedicated section called Cancer Genome Analysis. We believe this will make it easier to find relevant materials depending on whether you're trying to figure out how to use FireCloud features in general versus looking for cancer analysis-specific guidance. We expect to add additional such analysis categories as FireCloud's userbase grows to encompass analysis use cases beyond cancer.

We will do our best to minimize disruption during this period, but there will inevitably be some breaking changes, which will ultimately be for the better. If you have trouble finding content that you previously used or bookmarked, just post a comment in this thread and we'll point you to the new form or location of the content you're looking for.

Thanks for your patience! We welcome your feedback and questions in the comments below.

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This week is the big Boston-based biotech conference and trade show, Bio-IT World, and we're excited to demo FireCloud to the assembled hordes of biotech and biomedical professionals. Specifically, our good friends at Google Cloud will be hosting us at their booth in the Exhibit Hall (booth 261), Boston Seaport, at the following times:

Tuesday, May 23

  • 5:00 - 7:00pm / Welcome Reception

Wednesday, May 24

  • 9:50 - 10:50am / Coffee Break
  • 3:25 - 4:00pm / Refreshment Break
  • 5:30 - 6:30pm / 15th Anniversary Celebration & Best of Show Awards

Thursday, May 25

  • 9:45 - 10:30am / Coffee Break
  • 1:20 - 1:55pm / Dessert Refreshment Break

So if you were already planning to attend the conference, make sure to swing by during one of those times! We can walk you through performing basic operations in FireCloud if you're new to the platform, and in general we'll do our best to answer your most burning questions on any FireCloud topic. Also we promise to keep the cringe-worthy puns to a minimum.

And keep in mind, if you're local and biotech-curious but hesitant to shell out the cash for a full ticket, you can get a free pass to the Exhibit Hall that allows you to come see us for the low, low price of no money at all.

See you there!

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Release notes: May 18, 2017

Posted by KateN on 18 May 2017 (0)


This week's release is entirely UI (User Interface) changes. These changes are designed to make your experience using FireCloud much more straight forward.

Improvements

  • In a previous release, we began alerting you of Javascript errors. However, the information provided was not helpful. It was also too noisy to be useful so the alert has been shut off.
  • The Sharing... link previously found in the main body of the Summary page of a Workspace is now a Share... button in the left panel of buttons.
  • After previewing a file for upload, you can change the file, select it again, and the preview will reflect the changes you made
  • Workflow inputs and outputs are now shown in tables.
  • Workspace attributes are in consistent order whether viewing or editing. Previously they switched their order seemingly arbitrarily.
  • Workspace clones have "_copy" appended to the name by default.
  • The UI will prevent you from entering more than 80 characters in the synopsis field of the method creation dialog. Previously entering >80 characters would fail without telling you why.
  • Page in background no longer scrolls when dialog is open.
  • When monitoring a running workflow, the Abort button was not very bold on the page. The button is now red and shows its icon.
  • The entity viewer now has a close button, and a back button if another entity has been clicked within it. (see screenshot to the right)
  • A 'View' link has been added to the Monitor table to make it clearer what you click to view your workflow details.
  • In the Analysis tab of your workspace, the 'Select Tracks' button used to be in the same row as all the other tab headers. It is now within Analysis tab.
  • Buttons and links that spawn dialogs now have ellipses at the end of them. (e.g. Clone...) Buttons that just spawn 'are you sure?' style confirmations do not.
  • Readers of workspaces no longer see the config edit button. Previously they could see and click on it, but it would throw an error when they tried to save changes.
  • Links which will open a page in a new window now have an icon to indicate that.
  • Unknown statuses of workflows are now show as unknown rather than defaulting to error. (e.g. if you clicked on a workflow run just after launching it and it hasn't quite started yet.)
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