Story Resolved Rejected
Sprint Impediments
3678
Review multiple-dispatch
Ward Vandewege
1
0
3
impediments
-c-a
5
3342
3342
Peter Amstutz
[Crunch] Pipeline outputs not added to current project.
Resolved
1.0
3342
36
47
73
1
1.0
3708
Review 3342-pipeline-output-current-project
Peter Amstutz
47
0
3342
3
36
-c-a
5
3414
3414
Tim Pierce
[Keep] Keep Server accepts list of blocks to pull from other servers
Resolved
2.0
3414
36
44
73
6
2.0
3697
Review 3414-keep-pull-handler
Tom Clegg
3
0
3414
3
36
-c-a
5
3650
Implement PullHandler
Tim Pierce
44
0
3414
3
36
-c-a
5
3339
3339
Radhika Chippada
[Workbench] Project descriptions on the dashboard should be truncated at the first paragraph break.
Resolved
0.5
3339
36
72
73
1
0.5
3713
Review 3339-truncate-project-descriptions
Radhika Chippada
72
0
3339
3
36
-c-a
5
3680
Update project description display in dashboard to display textile formatted description
Radhika Chippada
72
0
3339
3
36
-c-a
5
3681
Truncate project description display in dashboard at the first textile line break
Radhika Chippada
72
0
3339
3
36
-c-a
5
3505
3505
Tom Clegg
[Sample pipelines] Support science team
Resolved
2.0
3505
36
3
73
3
2.0
3587
Review 3505-virtual-work-dir
Peter Amstutz
47
0
3505
3
36
-c-a
5
3506
Help Sally/Brian/Abram
Tom Clegg
3
0
3505
3
36
-c-a
5
3149
3149
Tom Clegg
[Workbench] Workbench infinite scroll and filter system should do filtering on server side instead of client side.
Resolved
3.0
3149
36
3
73
6
3.0
3671
Propagate search query to workbench when requesting rows in infinite scroll
Tom Clegg
3
0
3149
3
36
-c-a
5
3672
Propagate search query from workbench to api server
Tom Clegg
3
0
3149
3
36
-c-a
5
3673
Clear results and refresh from server if search query is dirty and idle for 250ms
Tom Clegg
3
0
3149
3
36
-c-a
5
3674
Review 3149-filter-any (improve filter support in API)
Tom Clegg
3
0
3149
3
36
-c-a
5
3675
Review 3149-server-side-search
Tom Clegg
3
0
3149
3
36
-c-a
5
3660
3660
Tom Clegg
[Workbench] Project action buttons (add subproject, add data) should appear when project is writable, even if not managed/owned by current user.
Resolved
0.5
3660
36
3
73
1
0.5
3667
Review 3660-project-editable
Tom Clegg
3
0
3660
3
36
-c-a
5
3666
Fix "is it editable?" detection for top buttons on project page
Tom Clegg
3
0
3660
3
36
-c-a
5
3136
3136
Peter Amstutz
[Crunch] Job state is stale in Workbench pipeline instance views, if the job's state changes after the pipeline instance stops.
Resolved
1.0
3136
36
47
73
1
1.0
3327
Fix workbench display to only use the actual jobs and ignore denormalized copy of job data in components.
Peter Amstutz
47
0
3136
3
36
-c-a
5
3676
Review 3136-stale-pipeline-instance-display
Brett Smith
79
0
3136
3
36
-c-a
5
3649
3649
[Crunch] 'Pipeline_instances' page shows job running when it has failed
Rejected
1.0
3649
36
73
1
1.0
3036
3036
Peter Amstutz
[API] Use regular uuids instead of content hashes to identify collections
Resolved
5.0
3036
36
47
73
6
5.0
3502
Document expectations for content addressing
Peter Amstutz
47
0
3036
3
36
-c-a
5
3503
Document intended behavior and design for projects, collections and permissions
Peter Amstutz
47
0
3036
3
36
-c-a
5
3581
Update workbench
Peter Amstutz
47
0
3036
3
36
-c-a
5
3509
Links to collections in workbench render the "name" field sensibly
Peter Amstutz
47
0
3036
3
36
-c-a
5
3579
Update test fixtures
Peter Amstutz
47
0
3036
3
36
-c-a
5
3632
Review 3036-collection-uuids
Peter Amstutz
47
0
3036
3
36
-c-a
5
3580
Update tests
Peter Amstutz
47
0
3036
3
36
-c-a
5
3578
Write db migration
Peter Amstutz
47
0
3036
3
36
-c-a
5
3354
3354
Phil Hodgson
[Workbench] Render description attributes as textile
Resolved
1.0
3354
36
80
73
6
1.0
2917
Render description as textile
0
3354
3
36
-c-a
5
3522
Add textile extension for detecting Arvados links
0
3354
3
36
-c-a
5
3569
Review 3354
Phil Hodgson
80
0
3354
3
36
-c-a
5
3627
3627
Tom Clegg
[Workbench] Projects that are writable, but have root owner != current_user, cannot be selected as a destination in "Move selected items..." chooser.
Resolved
0.5
3627
36
3
73
1
0.5
3575
[Workbench] "Home" project should have hover highlight like other projects
Tom Clegg
3
0
3627
3
36
-c-a
5
3668
Confirm fixed by 3660 branch
Tom Clegg
3
0
3627
3
36
-c-a
5
3670
Review 3627-selectable-projects
Peter Amstutz
47
0
3627
3
36
-c-a
5
3669
Grey out unselectable projects in the chooser
Tom Clegg
3
0
3627
3
36
-c-a
5
3620
3620
Radhika Chippada
[Workbench] Display system menu (gear menu) only to admin users.
Resolved
0.5
3620
36
72
73
6
0.5
3689
Review 3620-admin-only-gear-menu
Brett Smith
79
0
3620
3
36
-c-a
5
3642
3642
Radhika Chippada
[Workbench] Search box should not be displayed in top-nav for non-active users.
Resolved
0.5
3642
36
72
73
1
0.5
3690
Review 3642-search-for-active-only
Brett Smith
79
0
3642
3
36
-c-a
5
3112
3112
Radhika Chippada
[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.
Resolved
2.0
3112
36
72
73
6
2.0
3268
version detail
Radhika Chippada
72
0
3112
3
36
-c-a
5
3431
[Workbench] We need a link / page to contact support in our topnav.
Radhika Chippada
72
0
3112
3
36
-c-a
5
3574
Add source_version to api server config
Radhika Chippada
72
0
3112
3
36
-c-a
5
3596
Add source_version and report email to workbench config
Radhika Chippada
72
0
3112
3
36
-c-a
5
3597
Add Report Issue Mailer to workbench
Radhika Chippada
72
0
3112
3
36
-c-a
5
3598
Add report issue popup
Radhika Chippada
72
0
3112
3
36
-c-a
5
3599
Update workbench filter chaining to allow report issue popup and action propagation for no user, inactive user cases.
Radhika Chippada
72
0
3112
3
36
-c-a
5
3600
Add integration tests for the new report issue links
Radhika Chippada
72
0
3112
3
36
-c-a
5
3601
Add "report issue" button to 404 error page
Radhika Chippada
72
0
3112
3
36
-c-a
5
3602
Perform the "report issue" action using ajax
Radhika Chippada
72
0
3112
3
36
-c-a
5
3606
Add "report issue" button to fiddlesticks error page
Radhika Chippada
72
0
3112
3
36
-c-a
5
3608
Review branch: 3112-report-bug
Brett Smith
79
0
3112
3
36
-c-a
5
3171
3171
Tom Clegg
[API] Modify permission model to allow users to see a subset of other users, according to group permissions/membership.
Resolved
2.0
3171
36
3
73
6
2.0
3563
Write tests
Tom Clegg
3
0
3171
3
36
-c-a
5
3562
Change permission model
Tom Clegg
3
0
3171
3
36
-c-a
5
3653
Review 3171-group-membership
Tom Clegg
3
0
3171
3
36
-c-a
5
3564
Design appropriate "join group" interface
Tom Clegg
3
0
3171
3
36
-c-a
5
3565
Implement admin "add user to group" and "create/rename groups" interface
Tom Clegg
3
0
3171
3
36
-c-a
5
3665
Review 3171-admin-groups
Peter Amstutz
47
0
3171
3
36
-c-a
5
3504
3504
Peter Amstutz
[SDKs] Clients are compatible with #3036
Resolved
2.0
3504
36
47
73
6
2.0
3631
Review 3504-clients-compatible-with-3036
Peter Amstutz
47
0
3504
3
36
-c-a
5
3507
Update clients to permit arvados uuids for Collections
Peter Amstutz
47
0
3504
3
36
-c-a
5
3520
Review 3036-mutable-collections
Peter Amstutz
47
0
3504
3
36
-c-a
5
3448
3448
Tim Pierce
[Keep] storage server records (and reports in index) the timestamp of the most recent PUT operation for each block.
Resolved
2.0
3448
36
44
73
2
2.0
3647
Add timestamp support to PUT and DELETE
Tim Pierce
44
0
3448
3
36
-c-a
5
3683
Review 3448-keep-put-timestamps
Tim Pierce
44
0
3448
3
36
-c-a
5
3153
3153
Radhika Chippada
[API] Configuration option to automatically set up users (VM, repository, invite)
Resolved
3.0
3153
36
72
73
6
3.0
3643
Review branch: 3153-auto-setup-user
Tom Clegg
3
0
3153
3
36
-c-a
5
3183
3183
Radhika Chippada
[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.
Resolved
0.5
3183
36
72
73
1
0.5
3326
Fix it
Radhika Chippada
72
0
3183
3
36
-c-a
5
3623
Review branch: 3188-remove-selected-button
Tom Clegg
3
0
3183
3
36
-c-a
5
3148
3148
[Workbench] "Recent jobs and pipelines" doesn't actually show the most recent jobs and pipelines
Resolved
1.0
3148
36
73
1
1.0
2800
2800
Brett Smith
[Crunch] Remove global state in Python SDK
Resolved
1.0
2800
36
79
73
1
1.0
3621
Review 2800-pgs branch
Tom Clegg
3
0
2800
3
36
-c-a
5
3639
Review 2800-pysdk-no-global-keep-client-wip
Peter Amstutz
47
0
2800
3
36
-c-a
5
3344
3344
Brett Smith
[Workbench] Cannot [figure out how to] rename a collection created by arv-put with no --name provided.
Resolved
1.0
3344
36
79
73
1
1.0
3610
3610
Tom Clegg
[Workbench] pipeline_instances#show's Components tab clobbers the websocket log viewer when replacing the components table.
Resolved
0.5
3610
36
3
73
1
0.5
3636
Review 3610-pipeline-log-refresh
0
3610
3
36
-c-a
5
3635
Stop clobbering live listener with tab-load event every time it hears an event.
Tom Clegg
3
0
3610
3
36
-c-a
5
3441
3441
Peter Amstutz
[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.
Resolved
0.5
3441
36
47
73
1
0.5
3510
Fix warnings
Peter Amstutz
47
0
3441
3
36
-c-a
5
3614
Review 3441-python-keep-log-level
Peter Amstutz
47
0
3441
3
36
-c-a
5
3114
3114
Phil Hodgson
[Workbench] Add a "copy this collection to a project" button to collections page
Resolved
0.5
3114
36
80
73
2
0.5
3476
Add button and make it work
Phil Hodgson
80
0
3114
3
36
-c-a
5
3484
Review 3114
Phil Hodgson
80
0
3114
3
36
-c-a
5
3604
3604
Tom Clegg
[Workbench] theming support for login and inactive user page is broken (maybe elsewhere too)
Resolved
0.5
3604
36
3
73
1
0.5
3615
Review 3604-theme-and-new-user-process
Tom Clegg
3
0
3604
3
36
-c-a
5
3612
3612
Tom Clegg
[SDKs] arv-get fails "arvados.errors.NotFoundError: Block not found"
Resolved
0.5
3612
36
3
73
1
0.5
3619
Reproduce
Tom Clegg
3
0
3612
3
36
-c-a
5
3593
3593
Brett Smith
[Workbench] Workbench can't render exceptions
Resolved
0.5
3593
36
79
73
1
0.5
3595
Review 3593-workbench-exception-rendering
Brett Smith
79
0
3593
3
36
-c-a
5
3457
3457
Brett Smith
[SDKs] 'No handlers could be found for logger "arv-get"'
Resolved
0.5
3457
36
79
73
1
0.5
3577
Review 3457-pysdk-logging-wip
Brett Smith
79
0
3457
3
36
-c-a
5
3551
3551
Tom Clegg
[Keep] Clean up source tree layout
Resolved
1.0
3551
36
3
73
1
1.0
3554
Update jenkins script
Tom Clegg
3
0
3551
3
36
-c-a
5
3553
Review 3551-go-layout
Tom Clegg
3
0
3551
3
36
-c-a
5
3552
Clean up source tree, make sure tests and docker work
Tom Clegg
3
0
3551
3
36
-c-a
5
3421
3421
Brett Smith
[Workbench] "Rename collection" button on project page is hidden/inaccessible if the current name is too long and the browser window is too narrow.
Resolved
0.5
3421
36
79
73
1
0.5
3584
Review 3421-wide-project-tables-wip
Brett Smith
79
0
3421
3
36
-c-a
5
3405
3405
Brett Smith
[Workbench] Pipeline runner errors not reported to user.
Resolved
0.5
3405
36
79
73
1
0.5
3582
Review 3405-pipeline-error-logging-wip
Peter Amstutz
47
0
3405
3
36
-c-a
5
3296
3296
Radhika Chippada
[Workbench] Configuration option requires new users to complete a survey/form before using Workbench
Resolved
2.0
3296
36
72
73
6
2.0
3155
redirect regular workbench pages to the "edit profile" page if any required fields (as decided by application.(defaults.)yml) are not filled in.
0
3296
3
36
-c-a
5
3154
Provide an "edit profile" page for editing the current_user.prefs[:profile] hash
0
3296
3
36
-c-a
5
3156
[API] Send e-mail to admin the first time a user's profile data is saved
0
3296
3
36
-c-a
5
3474
Review branch 3296-user-profile
Radhika Chippada
72
0
3296
3
36
-c-a
5
3477
When an admin does "login as" a different user, skip profile check.
0
3296
3
36
-c-a
5
3512
Add a "message" field to config
Radhika Chippada
72
0
3296
3
36
-c-a
5
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.
Radhika Chippada
72
0
3296
3
36
-c-a
5
3531
3531
Tom Clegg
[Workbench] On projects#show, sort {jobs and pipelines} by date instead of listing all jobs before any pipelines.
Resolved
0.5
3531
36
3
73
6
0.5
3558
Interleave jobs and pipelines, sort by created_at only
Tom Clegg
3
0
3531
3
36
-c-a
5
3559
Write tests
Tom Clegg
3
0
3531
3
36
-c-a
5
3561
Review 3531-sort-jobs-with-pipelines
Tom Clegg
3
0
3531
3
36
-c-a
5
3373
3373
Peter Amstutz
[Sample pipelines] Improve SNV pipeline to accept example exome fastq data (2 pairs of reads) as a single input collection.
Resolved
2.0
3373
36
47
73
1
2.0
3488
Review 3373-improve-gatk3-snv-pipeline
Peter Amstutz
47
0
3373
3
36
-c-a
5
3417
Split by read pair, perform parallel alignment, merge bam files
Peter Amstutz
47
0
3373
3
36
-c-a
5
3548
Update pipeline to use arvados repository once merged
Peter Amstutz
47
0
3373
3
36
-c-a
5
3547
Add Haplotype caller
Peter Amstutz
47
0
3373
3
36
-c-a
5
3549
Use GATK 3.2
Peter Amstutz
47
0
3373
3
36
-c-a
5
3412
3412
Brett Smith
[API] Full collection view in list returned by api server
Resolved
1.0
3412
36
79
73
6
1.0
3534
Review 3412-full-collections-index-wip
Brett Smith
79
0
3412
3
36
-c-a
5
3178
3178
Tom Clegg
Discovery document does not publish optional parameters "find_or_create", "filters", "minimum_script_version", and "exclude_script_versions" for the Job "create" method.
Resolved
0.5
3178
36
3
73
1
0.5
3566
Add missing discovery methods
Tom Clegg
3
0
3178
3
36
-c-a
5
3567
Review 3178-discoverable-parameters
Tom Clegg
3
0
3178
3
36
-c-a
5
3572
3572
Tom Clegg
[Crunch] 'arv pipeline run --submit --template ...' does not start pipeline instance
Resolved
0.5
3572
36
3
73
1
0.5
3570
3570
[Crunch] With multiple crunch-dispatch processes, race condition causes job record to have success=false while still running.
Resolved
0.5
3570
36
73
1
0.5
3571
Review 3570-crunch-race
Tom Clegg
3
0
3570
3
36
-c-a
5
3254
3254
Peter Amstutz
[Documentation] Add a "run one of the sample crunch scripts in local/development mode from your VM" tutorial
Resolved
1.0
3254
36
47
73
6
1.0
3275
Split "writing a crunch script" into before-push and after-push stages
Peter Amstutz
47
0
3254
3
36
-c-a
5
3576
3576
Tom Clegg
[API] arv job cancel gets error.
Resolved
0.5
3576
36
3
73
1
0.5
3489
3489
Tom Clegg
[Workbench] Collection chooser starts at "All projects" but doesn't show any collections.
Resolved
0.5
3489
36
3
73
1
0.5
3539
Reproduce problem
Tom Clegg
3
0
3489
3
36
-c-a
5
3544
Indicate preselected project (if any) in chooser instead of always showing "All projects" at first
Tom Clegg
3
0
3489
3
36
-c-a
5
3545
Review 3489-indicate-initial-project-filter
Tom Clegg
3
0
3489
3
36
-c-a
5
3212
3212
Tom Clegg
[Crunch] arv pipeline reuses job results even when --no-reuse is given
Resolved
1.0
3212
36
3
73
1
1.0
3266
Figure out how --no-reuse flag should propagate to crunch-dispatch
Tom Clegg
3
0
3212
3
36
-c-a
5
3557
Review 3212-pipeline-no-reuse
Tom Clegg
3
0
3212
3
36
-c-a
5
3525
3525
Tom Clegg
[API] Users should have manage permission on their own repositories
Resolved
0.5
3525
36
3
73
1
0.5
3526
Review 3525-manage-own-repo
Tom Clegg
3
0
3525
3
36
-c-a
5
3530
Migrate existing repo permissions to can_manage
Tom Clegg
3
0
3525
3
36
-c-a
5
3527
3527
Brett Smith
[Crunch] Remove check for "docker_image_hash" link when job supplies a keep locator for "docker_image" .
Resolved
0.5
3527
36
79
73
6
0.5
3529
Review 3527-infer-docker-hash-wip
Tom Clegg
3
0
3527
3
36
-c-a
5
3499
3499
Tom Clegg
[Workbench] Objects owned directly by user are visible on a "home" project
Resolved
1.0
3499
36
3
73
6
1.0
3516
Update docs
Radhika Chippada
72
0
3499
3
36
-c-a
5
3514
Make groups/{user_uuid}/contents return home project contents
Tom Clegg
3
0
3499
3
36
-c-a
5
3513
Update breadcrumbs to show Home link to projects/user_uuid
Tom Clegg
3
0
3499
3
36
-c-a
5
3515
Make projects#show page behave properly when uuid is a user_uuid
Tom Clegg
3
0
3499
3
36
-c-a
5
3517
Show Home at root of projects tree
Tom Clegg
3
0
3499
3
36
-c-a
5
3524
Review 3499-home-project
Peter Amstutz
47
0
3499
3
36
-c-a
5
3518
arv-put: allow --name without --project-uuid, make up a name if none given
Tom Clegg
3
0
3499
3
36
-c-a
5
3611
Review 3499-home-project-docs-wip
Brett Smith
79
0
3499
3
36
-c-a
5
3496
3496
Tom Clegg
[Workbench] In add pipeline popup, when screen is too narrow, it breaks (second section doesn't work)
Resolved
0.5
3496
36
3
73
1
0.5
3482
3482
Brett Smith
[Crunch] crunch-job prints the wrong output hash in its log messages (hash of manifest with signatures)
Resolved
0.5
3482
36
79
73
1
0.5
3436
3436
Brett Smith
[Workbench] "Share with users" and "Share with groups" popups should not show Projects drop down.
Resolved
0.5
3436
36
79
73
1
0.5
3438
3438
Brett Smith
[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.
Resolved
0.5
3438
36
79
73
1
0.5
3427
3427
Brett Smith
[SDK] arv-put does not resume upload
Resolved
1.0
3427
36
79
73
1
1.0
3388
3388
Brett Smith
[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".
Resolved
0.5
3388
36
79
73
6
0.5
0
-c-a
0
impediments
-c-a
August 28, 2014 09:52:18.2467808723449707 +0000