Arvados

Story

Resolved

Closed

Rejected

Sprint Impediments

3824

[Crunch] crunch-job should create task execution environment inside docker container, not on worker host.

Tom Clegg

impediments

-c-a

3859

[Crunch] Job lock method to fix race condition with multiple instances of crunch-dispatch

Peter Amstutz

impediments

-c-a

3899

[Crunch] crunch-job and Workbench use the new job state attribute (see #3898) instead of paying attention to (and updating) running and success flags.

Peter Amstutz

impediments

-c-a

4188

[OPS] Automatically upload arvados/jobs image to docker registry as part of Jenkins docker build step.

Ward Vandewege

impediments

-c-a

4044 4044 Tom Clegg Tom Clegg 3 Crunch 52 Crunch [Crunch] job spawns tasks but never runs them, gets stuck waiting for first task to end, even though it has already ended. Resolved Resolved 3 1.0 1.0 1.0 4044 36 3 78 1 1.0	4130 4130 Review 4044-crunchstat-wait Peter Amstutz 47 0 4044 3 36 -c-a 5
4091 4091 Radhika Chippada Radhika Chippada 72 [Workbench] Add tests for undertested parts of Workbench, including infinite scroll. Resolved Resolved 3 1.0 1.0 1.0 4091 36 72 78 6 1.0	4326 4326 Review branch: 4091-test-infinite-scrolling I think infinite scrolling is working now. Tom Clegg 3 0 4091 3 36 -c-a 5 4328 4328 Data collections tab for a project displaying all object types. It would be easiest to see this in action in bcosc's Home project. Radhika Chippada 72 0 4091 3 36 -c-a 5 4329 4329 Sort order created_at being ignored by the server Radhika Chippada 72 0 4091 3 36 -c-a 5
4297 4297 Tom Clegg Tom Clegg 3 Crunch 52 Crunch [Crunch] crunch-dispatch eats way too much cpu Resolved Resolved 3 0.5 0.5 0.5 4297 36 3 78 1 0.5	4323 4323 Review 4297-dispatch-load Tom Clegg 3 0 4297 3 36 -c-a 5
4064 4064 Crunch 52 Crunch [Crunch] Typoed "output_of" value in pipeline leaves a job stuck in the queue Resolved Resolved 3 0.5 0.5 0.5 4064 36 78 1 0.5		4171 4171 [Crunch] arv-run-pipeline-instance should detect bad "output_of" values and fail the pipeline 0 4064 5 36 -c-a 5
4134 4134 Radhika Chippada Radhika Chippada 72 [Support] fix bugs and write tests (second half) Resolved Resolved 3 5.0 5.0 5.0 4134 36 72 78 3 5.0
3813 3813 [Workbench] add link to pipeline instance from job view page Resolved Resolved 3 0.5 0.5 0.5 3813 36 78 2 0.5
4015 4015 Tim Pierce Tim Pierce 44 Workbench 56 Workbench [Workbench] Collection chooser should be filling in portable_data_hash as well as collection uuid when used to pick pipeline inputs. Resolved Resolved 3 0.5 0.5 0.5 4015 36 44 78 1 0.5	4304 4304 Review 4015-collection-chooser-portable-data-hash Ready for review @ commit:87b2e5d, including tests and updated fixtures. Tim Pierce 44 0 4015 3 36 -c-a 5 4210 4210 populate portable_data_hash in the collection chooser Tim Pierce 44 0 4015 3 36 -c-a 5
4285 4285 Radhika Chippada Radhika Chippada 72 [Workbench] Not found error when the view or download icons are clicked for a file in a subdir of a collection. Resolved Resolved 3 0.5 0.5 0.5 4285 36 72 78 1 0.5	4319 4319 Review branch: 4285-view-download-collection-subdir-files Radhika Chippada 72 0 4285 3 36 -c-a 5
4313 4313 Tim Pierce Tim Pierce 44 Tests 59 Tests [Tests] remove stale *.pyc files between Jenkins tests Resolved Resolved 3 0.5 0.5 0.5 4313 36 44 78 1 0.5
4051 4051 [Workbench] Pipeline component display order should be controlled by sort_order attributes if present. Rejected Rejected 6 0.5 0.5 0.5 4051 36 78 2 0.5
3699 3699 Tim Pierce Tim Pierce 44 SDKs 54 SDKs [SDKs] Copy a pipeline instance, along with its input and output data, from one arvados instance to another Resolved Resolved 3 1.0 1.0 1.0 3699 36 44 78 6 1.0	3742 3742 arv-copy works on collections Tim Pierce 44 0 3699 3 36 -c-a 5 3744 3744 arv-copy works on pipeline instances Tim Pierce 44 0 3699 3 36 -c-a 5 3743 3743 arv-copy works on docker images Tim Pierce 44 0 3699 3 36 -c-a 5 3758 3758 arv-copy works on git repos Tim Pierce 44 0 3699 3 36 -c-a 5 3838 3838 Review 3699-arv-copy Peter Amstutz 47 0 3699 3 36 -c-a 5 3784 3784 arv-copy works on pipeline templates Tim Pierce 44 0 3699 3 36 -c-a 5 3759 3759 arv-copy authenticates to multiple Arvados instances * Looks in @$HOME/.config/arvados/${instance}.conf@ for authentication settings. * Prompts user for ARVADOS_API_HOST, ARVADOS_API_TOKEN, ARVADOS_API_HOST_INSECURE if this file does not exist. Tim Pierce 44 0 3699 3 36 -c-a 5
4295 4295 Peter Amstutz Peter Amstutz 47 [API] Improve websocket efficiency Resolved Resolved 3 0.5 0.5 0.5 4295 36 47 78 1 0.5	4301 4301 Review 4295-efficient-websockets Peter Amstutz 47 0 4295 3 36 -c-a 5
4195 4195 Radhika Chippada Radhika Chippada 72 Documentation 58 Documentation [Documentation] Fix Workbench pipeline tutorial Resolved Resolved 3 0.5 0.5 0.5 4195 36 72 78 1 0.5	4280 4280 Review branch: 4195-pipeline-tutorial Branch ready for review. The tutorial needed update to match the latest dashboard, where "Add new project" button is no longer present in the dashboard. Radhika Chippada 72 0 4195 3 36 -c-a 5
4228 4228 Radhika Chippada Radhika Chippada 72 Workbench 56 Workbench [Workbench (probably)] Cannot create new collection with selected files in shared pipeline directory. Resolved Resolved 3 0.5 0.5 0.5 4228 36 72 78 1 0.5	4287 4287 Review branch: 4228-collection-subdir-files Radhika Chippada 72 0 4228 3 36 -c-a 5
4266 4266 Tom Clegg Tom Clegg 3 Crunch 52 Crunch [Crunch] crunch-dispatch should process logs efficiently, particularly while throwing away excessive log data. Resolved Resolved 3 0.5 0.5 0.5 4266 36 3 78 1 0.5	4272 4272 Review 4266-log-performance Tom Clegg 3 0 4266 3 36 -c-a 5 4267 4267 Optimize ruby code Tom Clegg 3 0 4266 3 36 -c-a 5
4058 4058 Peter Amstutz Peter Amstutz 47 [Workbench] "Show portable data hash" page should show the kind of content that relates to PDH instead of trying to be a mostly-functional "show collection" page. Resolved Resolved 3 1.0 1.0 1.0 4058 36 47 78 1 1.0	4263 4263 Review 4058-workbench-collection-redirect Peter Amstutz 47 0 4058 3 36 -c-a 5 4149 4149 Redirect when there is a single collection, show a "menu" page when there is more than one collection Peter Amstutz 47 0 4058 3 36 -c-a 5 4150 4150 Add tests Peter Amstutz 47 0 4058 3 36 -c-a 5
4026 4026 Radhika Chippada Radhika Chippada 72 [Workbench] "Move to project..." button should be displayed to an admin user even if the sub-project is in another user's Home project. Resolved Resolved 3 0.5 0.5 0.5 4026 36 72 78 1 0.5	4261 4261 Review branch: 4026-project-move-admin Branch ready for review. Radhika Chippada 72 0 4026 3 36 -c-a 5
4227 4227 Radhika Chippada Radhika Chippada 72 Workbench 56 Workbench [Workbench] Pipeline elapsed time is misformatted Resolved Resolved 3 0.5 0.5 0.5 4227 36 72 78 1 0.5	4277 4277 Review branch: 4227-date-display Radhika Chippada 72 0 4227 3 36 -c-a 5
3826 3826 Tom Clegg Tom Clegg 3 Crunch 52 Crunch [Crunch] Display network activity in crunchstat Resolved Resolved 3 2.0 2.0 2.0 3826 36 3 78 6 2.0	4198 4198 Review 3826-crunchstat-netstats Tom Clegg 3 0 3826 3 36 -c-a 5 4181 4181 Collect container-level network stats Tom Clegg 3 0 3826 3 36 -c-a 5 4225 4225 Review 3826-crunchstat-netstats -- esp for language issues (Supplement Brett's review, just because both Brett and I are relatively new to Go) Tim Pierce 44 0 3826 3 36 -c-a 5 4152 4152 Talk to Ward Tom Clegg 3 0 3826 3 36 -c-a 5
4054 4054 Radhika Chippada Radhika Chippada 72 [Workbench] In the project sharing tab, show email addresses alongside full names. Resolved Resolved 3 0.5 0.5 0.5 4054 36 72 78 1 0.5	4260 4260 Review branch: 4054-sharing-email Branch ready for review. Radhika Chippada 72 0 4054 3 36 -c-a 5
3787 3787 Peter Amstutz Peter Amstutz 47 Documentation 58 Documentation [Documentation] Add a section in the User Guide about how to create, upload, and use a custom docker image Resolved Resolved 3 0.5 0.5 0.5 3787 36 47 78 3 0.5	4224 4224 Review 3787-docker-docs Peter Amstutz 47 0 3787 3 36 -c-a 5 4147 4147 Write new documentation page Peter Amstutz 47 0 3787 3 36 -c-a 5
4062 4062 Radhika Chippada Radhika Chippada 72 [Workbench] Infinite scrolling in the 'Jobs and pipelines' tab should not keep repeating the same list over and over again Resolved Resolved 3 0.5 0.5 0.5 4062 36 72 78 1 0.5	4226 4226 Review 4062-infinite-scroll-repeat-issue (this addresses 4062 and 4091) Also see 4062-infinite-scroll-repeat-TC branch Radhika Chippada 72 0 4062 3 36 -c-a 5
4068 4068 Radhika Chippada Radhika Chippada 72 Workbench 56 Workbench [Workbench] the /manage_account account page does not show all repositories a user has access to Rejected Rejected 6 0.5 0.5 0.5 4068 36 72 78 1 0.5
4133 4133 Brett Smith Brett Smith 79 [Support] fix bugs and write tests (first half) Resolved Resolved 3 5.0 5.0 5.0 4133 36 79 78 3 5.0	4086 4086 [Crunch] Not enough memory to run GATK I'm trying to parallelize gatk haplotype caller to run on multiple cores using the -nct tag in jobs/qr1hi-8i9sb-zs7g4zo303dhdnu, but run into this error: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java. Looking it up, most people say to play with the -Xmx command to allocate more, but 4g should be sufficient for the job, but maybe theres some underlying factors as well. Brett Smith 79 High 5 0 4133 3 36 -c-a 5 4189 4189 [Workbench] Manage access doesn't give full access to projects I currently have manage access to projects/qr1hi-j7d0g-834hs5rnunpn6y6. I am able to do most things but run into some problems. This is also a problem for me: #4182 but it is not a huge deal right now. Here, you can see that I can edit descriptions, project names, etc. in both the main and sub projects. But I cannot edit data collection names, pipeline instances, etc. !383340ae000ebd8e05e387954d0f0e4d.png! !c3cd99f4c30f704cf39eda97159a3e62.png! Here, I'm trying to run lobSTR v3 pipeline in the lobSTR v3 project and I get a weird run page where I cannot edit anything such as the instance name, description, inputs, etc. !f1489b76c3047a36528a87c337014dd7.png! !fb74ed8f2d369435930d3ba53a5111e2.png! I expected to have full handle on all editing text and inputs. Brett Smith 79 0 4133 3 35 -c-a 5 4202 4202 Review 4189-workbench-project-admin-attr-editing-wip Brett Smith 79 0 4133 3 35 -c-a 5
4200 4200 Crunch 52 Crunch [Crunch] Notify user, cancel pipeline when it cannot run because a parameter is the output_of a nonexistent component Closed Closed 5 0.5 0.5 0.5 4200 36 78 1 0.5
4083 4083 Peter Amstutz Peter Amstutz 47 [SDKs] Add "import _strptime" to work around potential Python bug. Resolved Resolved 3 0.5 0.5 0.5 4083 36 47 78 1 0.5	4252 4252 Review 4083-import-strptime Peter Amstutz 47 0 4083 3 36 -c-a 5 4151 4151 Figure out what uses strptime and fix them Peter Amstutz 47 0 4083 3 36 -c-a 5
4229 4229 Tom Clegg Tom Clegg 3 Keep 53 Keep [Keep] Add missing Close() calls Resolved Resolved 3 0.5 0.5 0.5 4229 36 3 78 1 0.5	4240 4240 Review 4229-close-files Peter Amstutz 47 0 4229 3 36 -c-a 5
4219 4219 Tom Clegg Tom Clegg 3 Keep 53 Keep [Keep] keepstore should not fail permission signature verification just because extra hints are present in URL. Resolved Resolved 3 0.5 0.5 0.5 4219 36 3 78 1 0.5	4220 4220 Ignore extra hints when checking signatures. Write tests. Tom Clegg 3 0 4219 3 36 -c-a 5 4221 4221 Review 4219-verify-with-hints Tim Pierce 44 0 4219 3 36 -c-a 5
4188 4188 Ward Vandewege Ward Vandewege 1 [OPS] Automatically upload arvados/jobs image to docker registry as part of Jenkins docker build step. Resolved Resolved 3 0.5 0.5 0.5 4188 36 1 78 3 0.5
3692 3692 Peter Amstutz Peter Amstutz 47 API 57 API [API] Eventbus filters parameter should use implicit AND (like REST filters) instead of implicit OR. Resolved Resolved 3 0.5 0.5 0.5 3692 36 47 78 1 0.5	4179 4179 Review 3692-event-bus-fix-and Peter Amstutz 47 0 3692 3 36 -c-a 5 4176 4176 Write test Peter Amstutz 47 0 3692 3 36 -c-a 5 4177 4177 Fix it Peter Amstutz 47 0 3692 3 36 -c-a 5
3656 3656 Peter Amstutz Peter Amstutz 47 [SDKs] "arv create object_type" should create a new object and then open it like "arv edit" does now. Resolved Resolved 3 0.5 0.5 0.5 3656 36 47 78 6 0.5	4170 4170 Review 3656-arv-create Peter Amstutz 47 0 3656 3 36 -c-a 5 4148 4148 Implement 'arv create' Peter Amstutz 47 0 3656 3 36 -c-a 5
4126 4126 Radhika Chippada Radhika Chippada 72 SDKs 54 SDKs [SDKs] Parameter in pipeline runner is missing Resolved Resolved 3 0.5 0.5 0.5 4126 36 72 78 1 0.5	4178 4178 Review 4126-preserve-parameter-hash Peter Amstutz 47 0 4126 3 36 -c-a 5
4102 4102 [Keep] Fix FUSE test suite so it does not need to be updated every time a new collection fixture is added to apiserver Rejected Rejected 6 0.5 0.5 0.5 4102 36 78 1 0.5
4196 4196 [SDKs] arv-keepdocker needs to stop using `docker pull -t` Resolved Resolved 3 0.5 0.5 0.5 4196 36 78 1 0.5
4239 4239 Brett Smith Brett Smith 79 SDKs 54 SDKs [SDKs] Python SDK doesn't work with apiclient 1.3 Resolved Resolved 3 0.5 0.5 0.5 4239 36 79 78 1 0.5
4249 4249 Workbench 56 Workbench [Workbench] Can't view/download files that are retrievable from arv-get Resolved Resolved 3 0.5 0.5 0.5 4249 36 78 1 0.5