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2014-08-27 Sprint
closed
08/27/2014
100%
166 issues
(
166 closed
— 0 open)
Time tracking
Estimated time
112
.00
hours
Issues by
Tracker
Status
Priority
Author
Assigned To
Category
Bug
33/33
Feature
2/2
Support
1/1
Task
114/114
Idea
16/16
Related issues
Bug #2800
: [Crunch] Remove global state in Python SDK
Actions
Bug #3136
: [Crunch] Job state is stale in Workbench pipeline instance views, if the job's state changes after the pipeline instance stops.
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Bug #3148
: [Workbench] "Recent jobs and pipelines" doesn't actually show the most recent jobs and pipelines
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Bug #3178
: Discovery document does not publish optional parameters "find_or_create", "filters", "minimum_script_version", and "exclude_script_versions" for the Job "create" method.
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Bug #3183
: [Workbench] In project view, when "Remove selected" button is used in the "Selected" dropdown, the dropdown menu stays open until the mouse is clicked somewhere else in the page.
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Bug #3212
: [Crunch] arv pipeline reuses job results even when --no-reuse is given
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Bug #3339
: [Workbench] Project descriptions on the dashboard should be truncated at the first paragraph break.
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Bug #3342
: [Crunch] Pipeline outputs not added to current project.
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Bug #3344
: [Workbench] Cannot [figure out how to] rename a collection created by arv-put with no --name provided.
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Bug #3373
: [Sample pipelines] Improve SNV pipeline to accept example exome fastq data (2 pairs of reads) as a single input collection.
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Bug #3405
: [Workbench] Pipeline runner errors not reported to user.
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Bug #3421
: [Workbench] "Rename collection" button on project page is hidden/inaccessible if the current name is too long and the browser window is too narrow.
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Bug #3427
: [SDK] arv-put does not resume upload
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Bug #3436
: [Workbench] "Share with users" and "Share with groups" popups should not show Projects drop down.
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Bug #3438
: [Workbench] When selecting inputs for a pipeline, title bar of collection chooser dialog should include the title (or, if none, the component/param name) of the relevant script parameter.
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Bug #3441
: [SDKs] arv-put (if not in debug mode) should not print an error message when it gets "503 full" from a server, if it turns out that the block eventually gets written successfully to different servers.
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Bug #3457
: [SDKs] 'No handlers could be found for logger "arv-get"'
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Bug #3482
: [Crunch] crunch-job prints the wrong output hash in its log messages (hash of manifest with signatures)
Actions
Bug #3489
: [Workbench] Collection chooser starts at "All projects" but doesn't show any collections.
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Bug #3496
: [Workbench] In add pipeline popup, when screen is too narrow, it breaks (second section doesn't work)
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Bug #3525
: [API] Users should have manage permission on their own repositories
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Bug #3551
: [Keep] Clean up source tree layout
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Bug #3570
: [Crunch] With multiple crunch-dispatch processes, race condition causes job record to have success=false while still running.
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Bug #3572
: [Crunch] 'arv pipeline run --submit --template ...' does not start pipeline instance
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Bug #3576
: [API] arv job cancel gets error.
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Bug #3593
: [Workbench] Workbench can't render exceptions
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Bug #3604
: [Workbench] theming support for login and inactive user page is broken (maybe elsewhere too)
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Bug #3610
: [Workbench] pipeline_instances#show's Components tab clobbers the websocket log viewer when replacing the components table.
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Bug #3612
: [SDKs] arv-get fails "arvados.errors.NotFoundError: Block not found"
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Bug #3627
: [Workbench] Projects that are writable, but have root owner != current_user, cannot be selected as a destination in "Move selected items..." chooser.
Actions
Bug #3642
: [Workbench] Search box should not be displayed in top-nav for non-active users.
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Bug #3649
: [Crunch] 'Pipeline_instances' page shows job running when it has failed
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Bug #3660
: [Workbench] Project action buttons (add subproject, add data) should appear when project is writable, even if not managed/owned by current user.
Actions
Feature #3114
: [Workbench] Add a "copy this collection to a project" button to collections page
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Feature #3448
: [Keep] storage server records (and reports in index) the timestamp of the most recent PUT operation for each block.
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Support #3505
: [Sample pipelines] Support science team
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Task #2917
: Render description as textile
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Task #3154
: Provide an "edit profile" page for editing the current_user.prefs[:profile] hash
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Task #3155
: redirect regular workbench pages to the "edit profile" page if any required fields (as decided by application.(defaults.)yml) are not filled in.
Actions
Task #3156
: [API] Send e-mail to admin the first time a user's profile data is saved
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Task #3266
: Figure out how --no-reuse flag should propagate to crunch-dispatch
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Task #3268
: version detail
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Task #3275
: Split "writing a crunch script" into before-push and after-push stages
Actions
Task #3326
: Fix it
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Task #3327
: Fix workbench display to only use the actual jobs and ignore denormalized copy of job data in components.
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Task #3417
: Split by read pair, perform parallel alignment, merge bam files
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Task #3431
: [Workbench] We need a link / page to contact support in our topnav.
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Task #3474
: Review branch 3296-user-profile
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Task #3476
: Add button and make it work
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Task #3477
: When an admin does "login as" a different user, skip profile check.
Actions
Task #3484
: Review 3114
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Task #3488
: Review 3373-improve-gatk3-snv-pipeline
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Task #3502
: Document expectations for content addressing
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Task #3503
: Document intended behavior and design for projects, collections and permissions
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Task #3506
: Help Sally/Brian/Abram
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Task #3507
: Update clients to permit arvados uuids for Collections
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Task #3509
: Links to collections in workbench render the "name" field sensibly
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Task #3510
: Fix warnings
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Task #3512
: Add a "message" field to config
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Task #3513
: Update breadcrumbs to show Home link to projects/user_uuid
Actions
Task #3514
: Make groups/{user_uuid}/contents return home project contents
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Task #3515
: Make projects#show page behave properly when uuid is a user_uuid
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Task #3516
: Update docs
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Task #3517
: Show Home at root of projects tree
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Task #3518
: arv-put: allow --name without --project-uuid, make up a name if none given
Actions
Task #3520
: Review 3036-mutable-collections
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Task #3522
: Add textile extension for detecting Arvados links
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Task #3524
: Review 3499-home-project
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Task #3526
: Review 3525-manage-own-repo
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Task #3529
: Review 3527-infer-docker-hash-wip
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Task #3530
: Migrate existing repo permissions to can_manage
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Task #3534
: Review 3412-full-collections-index-wip
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Task #3539
: Reproduce problem
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Task #3544
: Indicate preselected project (if any) in chooser instead of always showing "All projects" at first
Actions
Task #3545
: Review 3489-indicate-initial-project-filter
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Task #3547
: Add Haplotype caller
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Task #3548
: Update pipeline to use arvados repository once merged
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Task #3549
: Use GATK 3.2
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Task #3552
: Clean up source tree, make sure tests and docker work
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Task #3553
: Review 3551-go-layout
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Task #3554
: Update jenkins script
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Task #3557
: Review 3212-pipeline-no-reuse
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Task #3558
: Interleave jobs and pipelines, sort by created_at only
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Task #3559
: Write tests
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Task #3560
: Redirect user back to the profile page after the user fills in all required fields. Include a message saying profile is all set and the user can now access workbench.
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Task #3561
: Review 3531-sort-jobs-with-pipelines
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Task #3562
: Change permission model
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Task #3563
: Write tests
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Task #3564
: Design appropriate "join group" interface
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Task #3565
: Implement admin "add user to group" and "create/rename groups" interface
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Task #3566
: Add missing discovery methods
Actions
Task #3567
: Review 3178-discoverable-parameters
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Task #3569
: Review 3354
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Task #3571
: Review 3570-crunch-race
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Task #3574
: Add source_version to api server config
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Task #3575
: [Workbench] "Home" project should have hover highlight like other projects
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Task #3577
: Review 3457-pysdk-logging-wip
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Task #3578
: Write db migration
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Task #3579
: Update test fixtures
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Task #3580
: Update tests
Actions
Task #3581
: Update workbench
Actions
Task #3582
: Review 3405-pipeline-error-logging-wip
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Task #3584
: Review 3421-wide-project-tables-wip
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Task #3587
: Review 3505-virtual-work-dir
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Task #3595
: Review 3593-workbench-exception-rendering
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Task #3596
: Add source_version and report email to workbench config
Actions
Task #3597
: Add Report Issue Mailer to workbench
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Task #3598
: Add report issue popup
Actions
Task #3599
: Update workbench filter chaining to allow report issue popup and action propagation for no user, inactive user cases.
Actions
Task #3600
: Add integration tests for the new report issue links
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Task #3601
: Add "report issue" button to 404 error page
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Task #3602
: Perform the "report issue" action using ajax
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Task #3606
: Add "report issue" button to fiddlesticks error page
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Task #3608
: Review branch: 3112-report-bug
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Task #3611
: Review 3499-home-project-docs-wip
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Task #3614
: Review 3441-python-keep-log-level
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Task #3615
: Review 3604-theme-and-new-user-process
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Task #3619
: Reproduce
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Task #3621
: Review 2800-pgs branch
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Task #3623
: Review branch: 3188-remove-selected-button
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Task #3631
: Review 3504-clients-compatible-with-3036
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Task #3632
: Review 3036-collection-uuids
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Task #3635
: Stop clobbering live listener with tab-load event every time it hears an event.
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Task #3636
: Review 3610-pipeline-log-refresh
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Task #3639
: Review 2800-pysdk-no-global-keep-client-wip
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Task #3643
: Review branch: 3153-auto-setup-user
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Task #3647
: Add timestamp support to PUT and DELETE
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Task #3650
: Implement PullHandler
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Task #3653
: Review 3171-group-membership
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Task #3665
: Review 3171-admin-groups
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Task #3666
: Fix "is it editable?" detection for top buttons on project page
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Task #3667
: Review 3660-project-editable
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Task #3668
: Confirm fixed by 3660 branch
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Task #3669
: Grey out unselectable projects in the chooser
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Task #3670
: Review 3627-selectable-projects
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Task #3671
: Propagate search query to workbench when requesting rows in infinite scroll
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Task #3672
: Propagate search query from workbench to api server
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Task #3673
: Clear results and refresh from server if search query is dirty and idle for 250ms
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Task #3674
: Review 3149-filter-any (improve filter support in API)
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Task #3675
: Review 3149-server-side-search
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Task #3676
: Review 3136-stale-pipeline-instance-display
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Task #3678
: Review multiple-dispatch
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Task #3680
: Update project description display in dashboard to display textile formatted description
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Task #3681
: Truncate project description display in dashboard at the first textile line break
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Task #3683
: Review 3448-keep-put-timestamps
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Task #3689
: Review 3620-admin-only-gear-menu
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Task #3690
: Review 3642-search-for-active-only
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Task #3697
: Review 3414-keep-pull-handler
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Task #3708
: Review 3342-pipeline-output-current-project
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Task #3713
: Review 3339-truncate-project-descriptions
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Idea #3036
: [API] Use regular uuids instead of content hashes to identify collections
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Idea #3112
: [Workbench] "Report bug on this page" and "Show version detail" buttons on each workbench page (footer or top nav or [?]), and more prominently on error pages.
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Idea #3149
: [Workbench] Workbench infinite scroll and filter system should do filtering on server side instead of client side.
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Idea #3153
: [API] Configuration option to automatically set up users (VM, repository, invite)
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Idea #3171
: [API] Modify permission model to allow users to see a subset of other users, according to group permissions/membership.
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Idea #3254
: [Documentation] Add a "run one of the sample crunch scripts in local/development mode from your VM" tutorial
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Idea #3296
: [Workbench] Configuration option requires new users to complete a survey/form before using Workbench
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Idea #3354
: [Workbench] Render description attributes as textile
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Idea #3388
: [Workbench] "Share with groups" option for a project lists all groups, both user specific like "all users" and projects. It is desirable that this lists only user-specific groups meant to serve as "roles".
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Idea #3412
: [API] Full collection view in list returned by api server
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Idea #3414
: [Keep] Keep Server accepts list of blocks to pull from other servers
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Idea #3499
: [Workbench] Objects owned directly by user are visible on a "home" project
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Idea #3504
: [SDKs] Clients are compatible with #3036
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Idea #3527
: [Crunch] Remove check for "docker_image_hash" link when job supplies a keep locator for "docker_image" .
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Idea #3531
: [Workbench] On projects#show, sort {jobs and pipelines} by date instead of listing all jobs before any pipelines.
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Idea #3620
: [Workbench] Display system menu (gear menu) only to admin users.
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