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Release Notes: June 2017

Posted by KateN on 19 Jun 2017 (0)


June 19, 2017

Improvements

  • FireCloud is now upgraded to Cromwell version 27. For notes on the new version of Cromwell, read here
  • In the Launch Analysis page, you can now click anywhere in the table row to select an entity, regardless of what columns are visible.
  • When you try to set an invalid namespace on a config output, you will receive an error message now instead of a blank modal.
  • When a new user receives an email invitation to a workspace, they can now click the "Sign up" link, register, and be taken directly to the workspace that the invitation was sent for.

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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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Release notes: June 12, 2017

Posted by KateN on 12 Jun 2017 (0)


Fixes

  • Clicking the Timing diagram for an aborted workflow now correctly renders the diagram. Previously it threw a javascript error.
  • FireCloud's email system is back and functional. It will now properly send workspace sharing emails to both existing users and new users.
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Release notes: June 8, 2017

Posted by KateN on 6 Jun 2017 (0)


Improvements

  • The TCGA controlled access Authorization Domain has been renamed from dbGapAuthorizedUsers to TCGA-dbGaP-Authorized. This change will allow us to support multiple distinct dbGaP-mediated datasets in the future.
  • If you navigated to the second (or later) page of the workspaces list and applied a text 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.
  • We have improved the messaging shown when you link your NIH account to FireCloud but do not have authorization to see any protected NIH datasets. Previously, we would display the error "Failed to link NIH account". This was incorrect. In the event that you don't have access to a protected dataset, we will display instructions for checking your credentials with the NIH.

Fixes

  • Previously you would need to refresh the page in order to see new workspace attributes you just imported. Now you will see these display with their new values after importing
  • When you cancel editing a method configuration, the information on the page will revert to its original state before you made any edits. Previously there were some fields that would keep the edited info until you refreshed the page.
  • If you remove all data from an entity column, the column will now no longer display. Previously it would display the header for the column with no data filled in.
  • Clicking outside of dropdown menus now causes them to be dismissed.
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Release notes: June 1, 2017

Posted by KateN on 25 May 2017 (0)


New Features

  • In the Methods Repository, you can now create a new snapshot of an existing method if you have OWNER permission on at least one previous snapshot. If you are creating a brand-new method (e.g. no previous snapshot exists), the previous behavior applies: you need OWNER permission on the target namespace.
  • A workspace is shared with you, and it uses a group you are not a part of as its Authorization Domain. You are now able to request access to the group from the workspaces list. This will send an email to the admins of the group letting them know you would like to be added as a member of their group.

Improvements

  • In the Monitor tab when looking at a run's details, there is an ID associated with the call which contains JES level metadata. Previously you would have to look up the ID on gcloud, but now you can simply click the link ID and be shown the JES-level metadata.
  • On the Methods Repository detail page (i.e. inside a method or config), the "Permissions" and "Redact" buttons are now disabled if you do not have permissions to use them.
  • FireCloud now uses a single Cromwell instance. Previously we used two Cromwell instances, and if your first call was run on Cromwell #1 and the second call was run on Cromwell #2, the cached call would not be recognized and the job would run again.

Fixes

  • Fixed a bug where users with no billing projects were unable to share workspaces.
  • Fixed a bug where importing an empty TSV gave you an error. Now it doesn't!
  • Due to a bug, links to other entities within an entity's metadata were not displayed in the data table. This has been fixed.
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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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Release notes: May 16, 2017

Posted by KateN on 12 May 2017 (0)


New Features

  • You can now save incomplete metadata when cataloging a dataset for Library. You still cannot publish that dataset until the metadata is complete.

Improvements

  • When a Workflow fails, you will see the details of the workflow or call failure in the Monitor tab. (screenshot right)
  • You will no longer see a Workflow Timing diagram when the Workflow has no Calls, as this was blank anyways.
  • Clicking the Methods Repository link in the top navigation now returns you to the Methods Repository home page if you are within a method.

Fixes

  • Fixed a rare bug where users with the permission to share a workspace were unable to share.
  • If you search in the Methods Repository, click on a method, then hit your browser's back button, you will now be taken back to your original search. Previously the search was lost.
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Release notes: May 10, 2017

Posted by KateN on 10 May 2017 (0)


New Features

  • You can now set Authorization Domains when creating a workspace to prevent users from accidentally sharing data with unauthorized users. Read more about them here.
  • You now have the ability to create & manage groups in the user menu.
    • Create a lab group for your lab to make sharing data with all members easier
    • Use a group as an Authorization Domain to ensure data isn't shared outside your lab.
  • You can now set email notification preferences in FireCloud on the workspace page using the bell icon in the top right. You can also push a notification to all users of a workspace to give a heads-up that data was added or changed using an API endpoint. There is no user interface for this yet.
  • You can now create a new method by cloning an existing workflow. Within the workflow's detail page in the methods repository, there is a Clone... button. Cloning brings up the usual Create Method dialog, but with synopsis, description, and wdl pre-populated from the old method, and "_copy" added to the name.

Fixes

  • We found a vulnerability to a cross-site scripting attack vector in the Library search suggestions. This has been fixed, and the search box is no longer vulnerable.
  • When importing TSV files where a quoted field included tab characters, we used to parse those tabs as separate columns. e.g. "This has tabs" would parse as 3 separate columns. This has now been fixed so you see a single column containing all the text in your quotation marks.
  • Uncaught JavaScript errors will now be displayed to you in a popup. Before, these were not displayed at all, making errors difficult to diagnose.
  • Previously, if you navigated to page 2 or higher of Library search results, left Library, and then returned to Library, you were correctly returned to the page you were on. However, the left-hand facets did not populate. This has been fixed, and facets now populate regardless of which page you're on.
  • A hotfix for Cromwell version 26 has been incorporated. It now retries on more Google errors and fixes the timing diagram for pre-empted jobs.
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Release notes: May 4, 2017

Posted by KateN on 1 May 2017 (0)


New Features

  • When importing new WDLs, the Method Repo will now validate your WDL syntax against the currently deployed version of Cromwell
  • FireCloud now supports Cromwell version 26. Along with this comes better retrying on failed calls, and if/then/else statements.
  • A new workspace specific role, "Catalog", can now be granted to users who need to edit library metadata related to a workspace and do no have write access to the workspace itself. Owners of workspace or FC admins can grant "Catalog" permissions to specific users via the API.
  • Library related permissions have been reworked. Specifically, having a "Curator" role is now only required to publish or unpublish a workspace in the Data Library.
  • Warning banners will now show at the top of the page when FireCloud is experiencing service issues.

Fixes

  • If you typed plain text in front of your link to your google bucket (e.g. BLAHgs://), Firecloud would try to trim the display to remove the plain text. We no longer do that.
  • You were previously warned twice about including personally identifiable infomation from the Import Workspace Attributes screen. We now only warn you once.
  • Previously, email links to workspaces would not work. Now, email links will take you directly to the workspace, as intended.
  • There was an issue with FireCloud's usage of Google APIs which caused slowness and errors throughout the app. This is now resolved.
  • When you clicked on a link in the Data Use Limitations section to view said limitations, the link would not work. It now works, and you can download the data use letters as before.
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