Arvados

Story

Resolved

Closed

Sprint Impediments

2769 2769 Tim Pierce Tim Pierce 44 Keep 53 Keep [Keep] Keep supports DELETE requests Resolved Resolved 3 3.0 3.0 3.0 2769 36 44 70 6 3.0	3273 3273 Add configuration flags for DELETE. Tom Clegg 3 0 2769 3 36 -c-a 5 3271 3271 Implement DELETE request * Verify user's adminhood * Verify token Tim Pierce 44 0 2769 3 36 -c-a 5 3422 3422 Review 2769-keep-delete-request Review @ commit:b9d9b77 This branch implements basic DELETE support for Keep: The DeleteHandler method implements DELETE requests for Keep, checking that the user is authorized to issue DELETE and then deleting the requested block from local volumes. * CanDelete checks that the user with the given token is authorized to delete blocks from Keep. * MockVolume and UnixVolume objects provide a Delete method for deleting a block from that volume. * TestDeleteHandler tests: Unauthenticated requests Requests from a non-admin user Requests from a non-admin user for a nonexistent block Requests from a non-admin user for an existing block Misha Zatsman 82 0 2769 3 36 -c-a 5 3533 3533 Review 2769-disable-delete-flag Peter Amstutz 47 0 2769 3 36 -c-a 5
3235 3235 Tom Clegg Tom Clegg 3 Workbench 56 Workbench [Workbench] Site-wide search from top nav Resolved Resolved 3 3.0 3.0 3.0 3235 36 3 70 6 3.0	3294 3294 Top nav "search" button opens a collection chooser Chooser action button is "open" Tom Clegg 3 0 3235 3 36 -c-a 5 3305 3305 Turn off "projects" drop-down in chooser unless requested by caller Tom Clegg 3 0 3235 3 36 -c-a 5 3295 3295 Make a chooser modal that shows multiple types Tom Clegg 3 0 3235 3 36 -c-a 5 3376 3376 Test/fix infinite scroll Tom Clegg 3 0 3235 3 36 -c-a 5 3377 3377 Hide object type separators when no objects of that type are displayed Tom Clegg 3 0 3235 3 36 -c-a 5 3389 3389 Fix up "filter by project" dropdown * Menu appears in the wrong place (left side of dialog) in Firefox * Use currently selected project (if applicable) as dropdown heading Tom Clegg 3 0 3235 3 36 -c-a 5 3396 3396 Show only projects, not groups (and fix section heading) Tom Clegg 3 0 3235 3 36 -c-a 5 3395 3395 Show selected project in project-filter dropdown title Tom Clegg 3 0 3235 3 36 -c-a 5 3390 3390 Bring up search dialog by pasting uuid into top nav Tom Clegg 3 0 3235 3 36 -c-a 5 3399 3399 Special case for pasting UUID Tom Clegg 3 0 3235 3 36 -c-a 5 3398 3398 Trigger search update on keyup paste change Tom Clegg 3 0 3235 3 36 -c-a 5 3420 3420 Search modal bugs Observed in iceweasel (which might not be relevant): * Filter doesn't apply when modal first appears; waits for keyup * Collections in "My Project" don't appear in results (even with names) * "My Project" itself doesn't appear in results ** Last two could be triggered by having many subprojects in My Project Tom Clegg 3 0 3235 3 36 -c-a 5 3447 3447 Individual files in search preview should not be clickable: you can't do anything with them after selecting. Tom Clegg 3 0 3235 3 36 -c-a 5 3267 3267 Review 3235 Radhika Chippada 72 0 3235 3 36 -c-a 5	3306 3306 Replace preview pane with an "expand/collapse" button that shows details (e.g., collection contents) inline with the list of items Tom Clegg 3 0 3235 5 36 -c-a 5
3415 3415 Brett Smith Brett Smith 79 SDKs 54 SDKs [SDKs] Report the server-provided error message when API calls fail in Python SDK Resolved Resolved 3 0.5 0.5 0.5 3415 36 79 70 1 0.5	3478 3478 Review 3415-py-sdk-api-errors-wip Brett Smith 79 0 3415 3 36 -c-a 5
3320 3320 Peter Amstutz Peter Amstutz 47 Sample Pipelines 55 Sample Pipelines [Sample Pipelines] Assist pipeline porting efforts in the science team Resolved Resolved 3 3.0 3.0 3.0 3320 36 47 70 3 3.0	3323 3323 Help Bryan Peter Amstutz 47 0 3320 3 36 -c-a 5
3463 3463 Ward Vandewege Ward Vandewege 1 Workbench 56 Workbench [workbench] add e-mail address to the user list in the sharing dialog Resolved Resolved 3 0.5 0.5 0.5 3463 36 1 70 2 0.5	3464 3464 review #3463 Tom Clegg 3 0 3463 3 36 -c-a 5
3444 3444 Tom Clegg Tom Clegg 3 API 57 API [API] Get rid of obsolete "folder" usage in API and Workbench (after 249979c is merged) Resolved Resolved 3 3444 36 3 70 1	3494 3494 Review 3444-no-folders Tom Clegg 3 0 3444 3 36 -c-a 5
3263 3263 Radhika Chippada Radhika Chippada 72 [Support] Curate bug reports Resolved Resolved 3 2.0 2.0 2.0 3263 36 72 70 3 2.0	3264 3264 Curate bugs during the first half of the sprint Brett Smith 79 0 3263 3 36 -c-a 5 3265 3265 Curate bugs during the second half of the sprint Radhika Chippada 72 0 3263 3 36 -c-a 5
3372 3372 Peter Amstutz Peter Amstutz 47 Sample Pipelines 55 Sample Pipelines [Sample pipelines] Add title and description fields to user-provided input parameters in sample pipelines Resolved Resolved 3 0.5 0.5 0.5 3372 36 47 70 1 0.5	3471 3471 Add title and search_for for GATK pipeline inputs. Peter Amstutz 47 0 3372 3 36 -c-a 5 3492 3492 Add title and description fields to pipeline template schema doc Peter Amstutz 47 0 3372 3 36 -c-a 5
3057 3057 Peter Amstutz Peter Amstutz 47 Sample Pipelines 55 Sample Pipelines [Sample pipelines] Example pipelines should have link_name for all of the default inputs (samtools etc) Resolved Resolved 3 1.0 1.0 1.0 3057 36 47 70 6 1.0	3495 3495 Add link_name to GATK3 pipeline Peter Amstutz 47 0 3057 3 36 -c-a 5
3232 3232 Peter Amstutz Peter Amstutz 47 [Documentation] Rearrange doc site so "run a sample pipeline in Workbench" comes before any vm/repo/terminal instructions. Resolved Resolved 3 0.5 0.5 0.5 3232 36 47 70 6 0.5	3392 3392 Review 3232-user-guide-updates The scope of the changes are well beyond this story but very much needed. Radhika Chippada 72 0 3232 3 36 -c-a 5 3325 3325 Split documentation into separate Workbench and CLI sections Peter Amstutz 47 0 3232 3 36 -c-a 5
3234 3234 Radhika Chippada Radhika Chippada 72 [Documentation] Update tutorials to match current code. Resolved Resolved 3 1.0 1.0 1.0 3234 36 72 70 6 1.0	3404 3404 [Tutorial] Update "Getting an API token" section to point to the new "manage account" page Also update any other references to the current user's API tokens to point to the manage account page. Radhika Chippada 72 0 3234 3 36 -c-a 5
3466 3466 Peter Amstutz Peter Amstutz 47 Keep 53 Keep arv-get failing to download entire file from a collection. Resolved Resolved 3 3466 36 47 70 1
3442 3442 Peter Amstutz Peter Amstutz 47 API 57 API Can re-use job where the job is readable but the output collection isn't. Resolved Resolved 3 0.5 0.5 0.5 3442 36 47 70 1 0.5	3449 3449 Review 3442-no-reuse-job-when-output-unreadable Tim Pierce 44 0 3442 3 36 -c-a 5
3443 3443 Peter Amstutz Peter Amstutz 47 API 57 API [API] Read permissions for collections should be obtainable via name links Resolved Resolved 3 0.5 0.5 0.5 3443 36 47 70 1 0.5	3450 3450 Review 3443-read-collections-from-name-links Tim Pierce 44 0 3443 3 36 -c-a 5
3363 3363 Ward Vandewege Ward Vandewege 1 [Docker] quick fix for SSO - google openid has been deprecated, default to using Curoverse SSO server Resolved Resolved 3 1.0 1.0 1.0 3363 36 1 70 1 1.0
3370 3370 Peter Amstutz Peter Amstutz 47 Crunch 52 Crunch [Crunch] Job fails with "KeyError: 'CRUNCH_SRC'" Resolved Resolved 3 0.5 0.5 0.5 3370 36 47 70 1 0.5	3451 3451 Verify Abram's problem is fixed Peter Amstutz 47 0 3370 3 36 -c-a 5
3129 3129 Workbench 56 Workbench [Workbench] Show API token copy-and-paste block in a pop-up accessible from every page Resolved Resolved 3 1.0 1.0 1.0 3129 36 70 2 1.0
2985 2985 Radhika Chippada Radhika Chippada 72 [Workbench] Workbench usability and feature improvements Resolved Resolved 3 1.0 1.0 1.0 2985 36 72 70 6 1.0	3158 3158 Review 2985-shared-projects-descriptions Review for commit commit:ae7e9e24: Project descriptions in the "My Projects" and "Projects shared with me" panels are displayed inline next to the project name, not in a tooltip. Tim Pierce 44 0 2985 3 36 -c-a 5 3055 3055 Add explanatory text to the examples on the "Advanced" tab Tim Pierce 44 0 2985 3 36 -c-a 5 3064 3064 Show loading spinner when waiting for infinite scroll request Tim Pierce 44 0 2985 3 36 -c-a 5 3059 3059 Indicate difference between "queued" and "nothing submitted yet" jobs on pipeline instance status page * "Queued" = one or more jobs exist for this pipeline, but none have been started yet * "Not submitted" = no jobs have been created yet. Tim Pierce 44 0 2985 3 36 -c-a 5 3116 3116 Review 2985-workbench-ui Review changes for 2985-workbench-ui: * commit:892e6e0 (distinguish between queued and unstarted jobs, fixes #3059) * commit:74bf191 (display pipeline instance status in project summary page, fixes #3056) Tim Pierce 44 0 2985 3 36 -c-a 5 3056 3056 Display state of a pipeline instance shown in folder contents view. Tim Pierce 44 0 2985 3 36 -c-a 5 3083 3083 List of my/shared projects should show project descriptions in the list, instead of tooltips Tim Pierce 44 0 2985 3 36 -c-a 5 3065 3065 Add "Move to a different project..." action to the selection dropdown on the project page (bring up folder chooser, just like the "move project..." button) (Leave "copy" aside, for a separate story) Radhika Chippada 72 0 2985 3 36 -c-a 5 3379 3379 Review 2985-selection-button-move-copy 2985-selection-button-move-copy is ready for review. This branch implements the "move" operation. Radhika Chippada 72 0 2985 3 36 -c-a 5
3193 3193 Radhika Chippada Radhika Chippada 72 Workbench 56 Workbench [Workbench] Regular user should view VMs and repositories, and manage tokens and SSH keys, on an approachable "access" page instead of relying on the generic "view/edit items" pages. Resolved Resolved 3 3.0 3.0 3.0 3193 36 72 70 6 3.0	3215 3215 Arvados does not tell you your SSH login name I found out that there is no way to know your SSH login username form "My account" page. Ward Vandewege 1 0 3193 3 36 -c-a 5 3357 3357 Review 3193-manage-account Peter Amstutz 47 0 3193 3 36 -c-a 5 3194 3194 [Blocker] Clarify requirements/implementation Tom Clegg 3 0 3193 3 36 -c-a 5
3016 3016 Radhika Chippada Radhika Chippada 72 [Workbench] Pipeline template can specify a search string to restrict choices shown in collection chooser dialog Resolved Resolved 3 1.0 1.0 1.0 3016 36 72 70 6 1.0	3394 3394 Pass the search string from template to the input chooser popup Radhika Chippada 72 0 3016 3 36 -c-a 5 3424 3424 Update the schema doc Radhika Chippada 72 0 3016 3 36 -c-a 5 3423 3423 Review 3016-pipeline-template-search-string Branch is ready for review. user/tutorials/tutorial-firstscript.html is still not updated (waiting for branch 3232 to be merged into master). Tom Clegg 3 0 3016 3 36 -c-a 5	3393 3393 Update build a pipeline template documentation Update the schema doc and build a pipeline template documentation with an additional search attribute related details. Radhika Chippada 72 0 3016 5 36 -c-a 5
3425 3425 Tom Clegg Tom Clegg 3 Crunch 52 Crunch [Crunch] Task outputs chopped at 4KB. Resolved Resolved 3 3425 36 3 70 1	3426 3426 Review 3425-truncated-output Peter Amstutz 47 0 3425 3 36 -c-a 5
3349 3349 [Documentation] Update install docs Resolved Resolved 3 0.5 0.5 0.5 3349 36 70 6 0.5	3350 3350 Review 3349-install-docs Peter Amstutz 47 0 3349 3 36 -c-a 5
3219 3219 Ward Vandewege Ward Vandewege 1 [Docker] further docker image improvements Resolved Resolved 3 1.0 1.0 1.0 3219 36 1 70 2 1.0	3331 3331 add crunch-dispatch Ward Vandewege 1 0 3219 3 36 -c-a 5 3330 3330 add compute nodes Ward Vandewege 1 0 3219 3 36 -c-a 5 3337 3337 review 3219-further-docker-improvements Ward Vandewege 1 0 3219 3 36 -c-a 5 3332 3332 add local git trees Ward Vandewege 1 0 3219 3 36 -c-a 5 3253 3253 add shell image Ward Vandewege 1 0 3219 3 36 -c-a 5
3351 3351 Tom Clegg Tom Clegg 3 [SDK] arv-put hangs during remote upload Resolved Resolved 3 3351 36 3 70 1	3374 3374 Test patched Python package Abram Connelly 99 0 3351 3 36 -c-a 5 3375 3375 Review 3351-keep-timeout Radhika Chippada 72 0 3351 3 36 -c-a 5
3138 3138 Radhika Chippada Radhika Chippada 72 [Workbench] UI improvements: Persistent top nav between pages Resolved Resolved 3 2.0 2.0 2.0 3138 36 72 70 6 2.0	3310 3310 Review branch: 3138-wiselinks Radhika Chippada 72 0 3138 3 36 -c-a 5 3345 3345 Remove all uses of :footer_js from workbench Instead, use techniques like @$(document).on('ready',function(){...})@ to trigger the use of code in static @app/assets/javascripts/*.js@ files at the right time. Radhika Chippada 72 0 3138 3 36 -c-a 5
3286 3286 Tom Clegg Tom Clegg 3 Workbench 56 Workbench [Workbench] "Home" icon next to "Projects" dropdown should link to dashboard, instead of opening the projects dropdown. Resolved Resolved 3 0.5 0.5 0.5 3286 36 3 70 1 0.5	3366 3366 Review 3286-home-button Ward Vandewege 1 0 3286 3 36 -c-a 5 3364 3364 Split home button and projects dropdown Tom Clegg 3 0 3286 3 36 -c-a 5
3200 3200 Brett Smith Brett Smith 79 Workbench 56 Workbench [Workbench] Improve AJAX error reporting Resolved Resolved 3 1.0 1.0 1.0 3200 36 79 70 1 1.0	3322 3322 Review 3200-ajax-error-handling-wip Brett Smith 79 0 3200 3 36 -c-a 5 3251 3251 When updating parameters on the pipeline instance page, AJAX errors result in "loading forever" behavior instead of displaying an error message Brett Smith 79 0 3200 3 36 -c-a 5 3276 3276 Tab load failure should result in an error message and a "reload" button in the tab pane. Brett Smith 79 0 3200 3 36 -c-a 5 3207 3207 Error while adding public_key to a new authorized key Brett Smith 79 0 3200 3 36 -c-a 5
2044 2044 Brett Smith Brett Smith 79 [Workbench] interface lets users share a project folder with other users on this instance Resolved Resolved 3 1.0 1.0 1.0 2044 36 79 70 6 1.0	2665 2665 API server lets all known users list basic information about other users Brett Smith 79 0 2044 3 36 -c-a 5 3217 3217 Review 2044-api-users-index-wip Radhika Chippada 72 0 2044 3 36 -c-a 5 2749 2749 Workbench has interface to share folders between users of instance Tom says: ”hopefully sooner rather than later -- none of the Javascript or Workbench-server support will be specific to Groups. (But if it makes the difference between getting it done or not, "only groups are essential for this story" is the rule.)” Brett Smith 79 0 2044 3 36 -c-a 5 3238 3238 Review 2044-workbench-project-sharing-wip Brett Smith 79 0 2044 3 36 -c-a 5
3140 3140 Radhika Chippada Radhika Chippada 72 [Workbench] UI enhancements: Split project contents into separate tabs and clean up "contents" partial Resolved Resolved 3 1.0 1.0 1.0 3140 36 72 70 6 1.0	3181 3181 Review branch 3140-project-content-tabs Tim Pierce 44 0 3140 3 36 -c-a 5 3277 3277 Review latest 3140-project-content-tabs Radhika Chippada 72 0 3140 3 36 -c-a 5
3072 3072 Tim Pierce Tim Pierce 44 [Workbench] Showing the empty collection in Workbench gives an error page Resolved Resolved 3 0.5 0.5 0.5 3072 36 44 70 1 0.5	3237 3237 Review 3072-empty-collection-bugfix Changes at commit:a96adab2a: Added empty collection (owned by the anonymous group) to test fixtures and to @db/seeds.rb@. API integration tests: in @permissions_test.rb@, test that the active user can read objects in the anonymous group, even when there are no explicit permission links on that group or objects in it. Workbench integration tests: added a test to confirm that a non-admin user can get the empty collection. Cleanup code: @User.can?@ now takes either a uuid or an object for the target. Tim Pierce 44 0 3072 3 36 -c-a 5
3170 3170 Tom Clegg Tom Clegg 3 Workbench 56 Workbench [Workbench] Automatic reloading of pipeline instance page interferes with ajax loading of tabs - should just reload the components tab, not the whole page. Resolved Resolved 3 1.0 1.0 1.0 3170 36 3 70 1 1.0	3292 3292 Clean up tab loading javascript Tom Clegg 3 0 3170 3 36 -c-a 5 3293 3293 Modify periodic refresh to load only tab content, not page. Tom Clegg 3 0 3170 3 36 -c-a 5 3291 3291 Review 3170-refresh-tab-pane Radhika Chippada 72 0 3170 3 36 -c-a 5
3182 3182 Tom Clegg Tom Clegg 3 Tests 59 Tests [Tests] UsersTest#test_setup_the_active_user test fails too much. Resolved Resolved 3 1.0 1.0 1.0 3182 36 3 70 1 1.0
3214 3214 Tom Clegg Tom Clegg 3 [API] Unprivileged user can create subprojects under projects they do not own (but cannot modify the subproject once created) Resolved Resolved 3 1.0 1.0 1.0 3214 36 3 70 1 1.0	3290 3290 Review 3214-permission-to-use-owner-uuid Tom Clegg 3 0 3214 3 36 -c-a 5
3124 3124 Brett Smith Brett Smith 79 API 57 API [API] Job creation 'filters' chokes on invalid commit hash Resolved Resolved 3 1.0 1.0 1.0 3124 36 79 70 1 1.0
3252 3252 Brett Smith Brett Smith 79 [Documentation] Instructions for installing/using arv-put without root access Resolved Resolved 3 0.5 0.5 0.5 3252 36 79 70 6 0.5	3288 3288 Review 3252-py-sdk-install-docs-wip Ward Vandewege 1 0 3252 3 36 -c-a 5
3160 3160 Radhika Chippada Radhika Chippada 72 Workbench 56 Workbench [Workbench] When copying an unnamed pipeline instance, use a blank name instead of "Copy of unnamed pipeline". Resolved Resolved 3 0.5 0.5 0.5 3160 36 72 70 1 0.5	3289 3289 Review 3160-copy-unnamed-pipeline Just one statement changed. Tom Clegg 3 0 3160 3 36 -c-a 5
3132 3132 [Keep] Putting data into Keep tutorial: not able to add the VCF data to keep Resolved Resolved 3 1.0 1.0 1.0 3132 36 70 1 1.0
3270 3270 Ward Vandewege Ward Vandewege 1 Deployment 60 Deployment [Workbench] Set up infrastructure for user experiments Resolved Resolved 3 1.0 1.0 1.0 3270 36 1 70 6 1.0