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

3706

[SDKs] Remove fallback-to-keep warning from python SDK if block hash has a permission signature

Tom Clegg

impediments

-c-a

4461 4461 Ward Vandewege Ward Vandewege 1 [OPS] Replace dnsmasq with unbound Resolved Resolved 3 1.0 1.0 1.0 4461 36 1 79 1 1.0	4585 4585 add code to puppet Ward Vandewege 1 0 4461 3 36 -c-a 5 4586 4586 deploy on our installations Ward Vandewege 1 0 4461 3 36 -c-a 5
4348 4348 Tim Pierce Tim Pierce 44 [Support] fix bugs and write tests (second half) Resolved Resolved 3 5.0 5.0 5.0 4348 36 44 79 3 5.0	4352 4352 fix bugs, write tests Tim Pierce 44 0 4348 3 36 -c-a 5
3382 3382 Phil Hodgson Phil Hodgson 80 Workbench 56 Workbench [Workbench] When specifying inputs for new pipeline instance, parameters should not disappear from Inputs tab after a value is chosen. Resolved Resolved 3 0.5 0.5 0.5 3382 36 80 79 1 0.5	4485 4485 Review 3382 Branch: 3382-always-show-inputs Phil Hodgson 80 0 3382 3 36 -c-a 5 4484 4484 Correct conditions for whether input parameters should be displayed Phil Hodgson 80 0 3382 3 36 -c-a 5
4250 4250 Radhika Chippada Radhika Chippada 72 [Documentation] (recurring) Refresh user documentation Resolved Resolved 3 1.0 1.0 1.0 4250 36 72 79 2 1.0	4565 4565 Review branch: 4250-doc-updates Radhika Chippada 72 0 4250 3 36 -c-a 5
4380 4380 Brett Smith Brett Smith 79 Node Manager 66 Node Manager [Node Manager] Should drain nodes via SLURM before terminating them Resolved Resolved 3 1.0 1.0 1.0 4380 36 79 79 1 1.0	4496 4496 Review 4380-node-manager-computenode-reorg-wip Tim Pierce 44 0 4380 3 36 -c-a 5 4519 4519 Review 4380-node-manager-slurm-drain-wip Brett Smith 79 0 4380 3 36 -c-a 5
4363 4363 Tom Clegg Tom Clegg 3 Keep 53 Keep [Keep] arv-mount should not munge filenames unless required by POSIX Resolved Resolved 3 0.5 0.5 0.5 4363 36 3 79 1 0.5	4365 4365 Ensure posix-incompatible filenames do not cause I/O errors (add tests) Tom Clegg 3 0 4363 3 36 -c-a 5 4375 4375 Add tests Tom Clegg 3 0 4363 3 36 -c-a 5 4364 4364 Ensure posix-allowed filenames are not altered by arv-mount (add tests) Tom Clegg 3 0 4363 3 36 -c-a 5 4510 4510 Test some utf8 characters Tom Clegg 3 0 4363 3 36 -c-a 5 4517 4517 Review 4363-less-filename-munging Brett Smith 79 0 4363 3 36 -c-a 5
4552 4552 Tom Clegg Tom Clegg 3 API 57 API [API] Fix permission error due to stripped signatures when ensure_unique_name behavior is invoked during collections.create Resolved Resolved 3 0.5 0.5 0.5 4552 36 3 79 1 0.5	4554 4554 Add test Tom Clegg 3 0 4552 3 36 -c-a 5 4555 4555 Fix Tom Clegg 3 0 4552 3 36 -c-a 5 4568 4568 Review 4552-collection-unique-name Tom Clegg 3 0 4552 3 36 -c-a 5 4569 4569 Tidy up collection signing Move signing logic out of controller into model Tom Clegg 3 0 4552 3 36 -c-a 5
4194 4194 Radhika Chippada Radhika Chippada 72 Keep 53 Keep [Keep] consistent logging for keepstore requests Resolved Resolved 3 2.5 2.5 2.5 4194 36 72 79 2 2.5	4542 4542 Review branch: 4194-keep-logging Tim Pierce 44 0 4194 3 36 -c-a 5
4470 4470 Tom Clegg Tom Clegg 3 Crunch 52 Crunch [Crunch] tmpdir not writable running jobs in Docker Resolved Resolved 3 0.5 0.5 0.5 4470 36 3 79 1 0.5	4556 4556 Confirm fixed by 3824 Tom Clegg 3 0 4470 3 36 -c-a 5
3465 3465 Peter Amstutz Peter Amstutz 47 [SSO] Research requirements to upgrade SSO codebase to use oauth2 (or openid connect) Resolved Resolved 3 3.0 3.0 3.0 3465 36 47 79 1 3.0	4379 4379 Talk to Ward about what this involves Peter Amstutz 47 0 3465 3 36 -c-a 5 4429 4429 Document authentication dance between Workbench, API, SSO and external identity provider Peter Amstutz 47 0 3465 3 36 -c-a 5
4251 4251 Ward Vandewege Ward Vandewege 1 [Documentation] (recurring) Write blog post in first three days of sprint Resolved Resolved 3 0.5 0.5 0.5 4251 36 1 79 2 0.5	4356 4356 write blog post Ward Vandewege 1 0 4251 3 36 -c-a 5
4024 4024 Radhika Chippada Radhika Chippada 72 Workbench 56 Workbench [Workbench] PipelineInstances#index should scroll down to show older pipelines, and should have a search box (similar to the "pipelines" tab on the "show project" page) Resolved Resolved 3 2.0 2.0 2.0 4024 36 72 79 2 2.0	4331 4331 Add infinite scrolling to pipeline_instances page. Radhika Chippada 72 0 4024 3 36 -c-a 5 4463 4463 Add search filter to pipeline_instances page Radhika Chippada 72 0 4024 3 36 -c-a 5 4386 4386 Review branch: 4024-pipeline-instances-scroll This branch addresses adding infinite scrolling to recently finished pipelines panel in the dashboard. Radhika Chippada 72 0 4024 3 36 -c-a 5 4498 4498 Fix double-load after fwd/back Tom Clegg 3 0 4024 3 36 -c-a 5 4466 4466 Scrolling when search filter is used Radhika Chippada 72 0 4024 3 36 -c-a 5
3824 3824 Tom Clegg Tom Clegg 3 Crunch 52 Crunch [Crunch] crunch-job should create task execution environment inside docker container, not on worker host. Resolved Resolved 3 2.0 2.0 2.0 3824 36 3 79 1 2.0	4549 4549 Review 3824-task-work Peter Amstutz 47 0 3824 3 36 -c-a 5 4283 4283 Make test case Tom Clegg 3 0 3824 3 36 -c-a 5 4282 4282 Create/setup task temp dirs at runtime Tom Clegg 3 0 3824 3 36 -c-a 5 4548 4548 Make sure JOB_TMP and TASK_TMP are writable by crunch user Tom Clegg 3 0 3824 3 36 -c-a 5 4325 4325 Review 3824-crunch-container-setup Tom Clegg 3 0 3824 3 36 -c-a 5 4153 4153 Talk to Ward Tom Clegg 3 0 3824 3 36 -c-a 5 4550 4550 Review 3824-docker-fixes (lower priority than 3824-task-work) Ward Vandewege 1 0 3824 3 36 -c-a 5
4535 4535 [API] Configuration option to set advertised hostname Resolved Resolved 3 4535 36 79 1	4537 4537 Review 4535-configure-api-host-url Ward Vandewege 1 0 4535 3 36 -c-a 5
4388 4388 Brett Smith Brett Smith 79 SDKs 54 SDKs [SDKs] Manifest#each_line should not crash when encountering a blank line in a manifest. Resolved Resolved 3 0.5 0.5 0.5 4388 36 79 79 1 0.5	4541 4541 Review 4388-workbench-update Tom Clegg 3 0 4388 3 36 -c-a 5
4395 4395 Ward Vandewege Ward Vandewege 1 [SDKs] sdk/go/keepclient race condition Resolved Resolved 3 0.5 0.5 0.5 4395 36 1 79 1 0.5
4474 4474 [Node Manager] Node manager shut down node in middle of job Resolved Resolved 3 4474 36 79 1
4482 4482 [Crunch] Diagnostics failure "user not found on host" Resolved Resolved 3 4482 36 79 1
3177 3177 Radhika Chippada Radhika Chippada 72 Workbench 56 Workbench [Workbench] File chooser dialog (replace remaining use of clippy) Resolved Resolved 3 2.0 2.0 2.0 3177 36 72 79 6 2.0	4445 4445 Review branch: 3177-collection-choose-files Radhika Chippada 72 0 3177 3 36 -c-a 5
2853 2853 Tom Clegg Tom Clegg 3 Keep 53 Keep [Keep] Use rendezvous hashing to assign blocks to servers in Go and Python SDKs Resolved Resolved 3 2.0 2.0 2.0 2853 36 3 79 6 2.0	4492 4492 Fix tests that expect old probe order Tom Clegg 3 0 2853 3 36 -c-a 5 4491 4491 Replace shuffling in Go SDK Tom Clegg 3 0 2853 3 36 -c-a 5 4490 4490 Replace shuffling in Python SDK Tom Clegg 3 0 2853 3 36 -c-a 5 4495 4495 Review 2853-rendezvous Tom Clegg 3 0 2853 3 36 -c-a 5
4486 4486 [Documentation] document the arv cli tool Resolved Resolved 3 0.5 0.5 0.5 4486 36 79 2 0.5
4316 4316 Brett Smith Brett Smith 79 Review 3603-pysdk-file-api-wip Resolved Resolved 3 0.5 0.5 0.5 4316 36 79 79 6 0.5
3400 3400 Peter Amstutz Peter Amstutz 47 SDKs 54 SDKs [Workbench] Rails client library should offer an "all pages" mode for queries that return pages of lists Resolved Resolved 3 1.0 1.0 1.0 3400 36 47 79 1 1.0	4418 4418 Write tests Peter Amstutz 47 0 3400 3 36 -c-a 5 4417 4417 ArvadosResourceList returns exactly @limit items unless there are fewer that that available, regardless of underlying paging from API server Peter Amstutz 47 0 3400 3 36 -c-a 5 4441 4441 Review 3400-workbench-all-items Peter Amstutz 47 0 3400 3 36 -c-a 5 4381 4381 ArvadosResourceList returns all items unless @limit is non-nil Peter Amstutz 47 0 3400 3 36 -c-a 5
4434 4434 Tom Clegg Tom Clegg 3 API 57 API [API] Test suite should not depend on a particular database collation config. Resolved Resolved 3 4434 36 3 79 1	4435 4435 Review 4434-collation Tom Clegg 3 0 4434 3 36 -c-a 5
3857 3857 Tim Pierce Tim Pierce 44 SDKs 54 SDKs [SDKs] Python KeepClient should use different timeouts for different operations Resolved Resolved 3 1.0 1.0 1.0 3857 36 44 79 1 1.0	3916 3916 Testing Tim Pierce 44 0 3857 3 36 -c-a 5 3915 3915 Implement timeout configuration settings Tim Pierce 44 0 3857 3 36 -c-a 5 4444 4444 Review 3857-python-sdk-timeouts Available for review at commit:3993ba4 Some notes: * This change replaces httplib2 with the requests module in every call where the SDK issues a request to Keep. * It does _not_ explicitly implement or test multiple connection timeouts. Doing so just means issuing a timeout parameter that is a (connection_timeout, read_timeout) parameter, e.g. <pre> client = arvados.KeepClient(api_client=api, timeout=(2, 20)) </pre> Tim Pierce 44 0 3857 3 36 -c-a 5 3914 3914 Study httplib2 and other docs Research to identify options for setting timeout settings Tim Pierce 44 0 3857 3 36 -c-a 5
4294 4294 Tim Pierce Tim Pierce 44 Node Manager 66 Node Manager [Node Manager] Add support for min_nodes configuration value Resolved Resolved 3 1.0 1.0 1.0 4294 36 44 79 6 1.0	4355 4355 min_nodes tests Tim Pierce 44 0 4294 3 36 -c-a 5 4483 4483 Review 4294-node-manager-min-nodes Tim Pierce 44 0 4294 3 36 -c-a 5 4354 4354 decline node shutdown if it brings the number of nodes lower than min_nodes Tim Pierce 44 0 4294 3 36 -c-a 5 4353 4353 spin up a new node if node list is less than min_nodes Tim Pierce 44 0 4294 3 36 -c-a 5
4347 4347 Brett Smith Brett Smith 79 [Support] fix bugs and write tests (first half) Resolved Resolved 3 5.0 5.0 5.0 4347 36 79 79 3 5.0
4084 4084 Peter Amstutz Peter Amstutz 47 Workbench 56 Workbench [Workbench] Pipeline instance Log pane should not get refreshed (it already stays up-to-date by itself) Resolved Resolved 3 1.0 1.0 1.0 4084 36 47 79 1 1.0	4413 4413 Compress tab panes back to a single level Tom Clegg 3 0 4084 3 36 -c-a 5 4154 4154 Investigate Peter Amstutz 47 0 4084 3 36 -c-a 5 4428 4428 Review 4084-log-pane-refresh-TC Peter Amstutz 47 0 4084 3 36 -c-a 5 4155 4155 Write tests Peter Amstutz 47 0 4084 3 36 -c-a 5 4290 4290 Review 4084-log-pane-refresh Tom Clegg 3 0 4084 3 36 -c-a 5
4402 4402 SDKs 54 SDKs [SDKs] CollectionWriter.write_directory_tree(...,max_manifest_depth=0) should produce a single stream. Closed Closed 5 0.5 0.5 0.5 4402 36 79 1 0.5
4408 4408 Brett Smith Brett Smith 79 Workbench 56 Workbench [Workbench] Anonymous collection download links should not redirect to login path. Resolved Resolved 3 0.5 0.5 0.5 4408 36 79 79 1 0.5	4448 4448 Review 4408-collection-sharing-login-fix-wip Radhika Chippada 72 0 4408 3 36 -c-a 5
4334 4334 Peter Amstutz Peter Amstutz 47 Crunch 52 Crunch [Crunch] crunch-dispatch should not allocate Jobs to nodes in the idle* SLURM state Resolved Resolved 3 1.0 1.0 1.0 4334 36 47 79 1 1.0	4450 4450 Review 4334-idle-star-is-down 0 4334 3 36 -c-a 5 4376 4376 Diagnose and fix Peter Amstutz 47 0 4334 3 36 -c-a 5
4088 4088 Tim Pierce Tim Pierce 44 Workbench 56 Workbench [Workbench] On collections#show page, filter displayed files by filename regexp, and add a "select all" / "deselect all" button. Resolved Resolved 3 1.0 1.0 1.0 4088 36 44 79 2 1.0	4206 4206 write workbench tests Tim Pierce 44 0 4088 3 36 -c-a 5 4384 4384 Review 4088-collection-show-files-filter Tim Pierce 44 0 4088 3 36 -c-a 5 4205 4205 Add "select all" / "deselect all" buttons to app/views/collections/_show_files.html.erb Tim Pierce 44 0 4088 3 36 -c-a 5 4332 4332 Review 4088-collection-show-files-filter Tim Pierce 44 0 4088 3 36 -c-a 5 4204 4204 Add regex box and filter to app/views/collections/_show_files.html.erb Tim Pierce 44 0 4088 3 36 -c-a 5
4310 4310 Peter Amstutz Peter Amstutz 47 Crunch 52 Crunch [Crunch] crunch-dispatch --jobs locking is broken Resolved Resolved 3 0.5 0.5 0.5 4310 36 47 79 1 0.5	4459 4459 Review 4310-lock-before-fail Peter Amstutz 47 0 4310 3 36 -c-a 5 4447 4447 Review 4310-git-tag-race Peter Amstutz 47 0 4310 3 36 -c-a 5 4374 4374 Diagnose and fix Peter Amstutz 47 0 4310 3 36 -c-a 5
4383 4383 Ward Vandewege Ward Vandewege 1 [Docker] upload all docker containers to docker repository, and then add a script to download and run them in one go Resolved Resolved 3 0.5 0.5 0.5 4383 36 1 79 2 0.5	4405 4405 add a feature to auto-admin the first user who signs in for a new installation Ward Vandewege 1 0 4383 3 36 -c-a 5 4430 4430 review 4383-easy-install Ward Vandewege 1 0 4383 3 36 -c-a 5
4389 4389 Tom Clegg Tom Clegg 3 Workbench 56 Workbench [Workbench] Fix infinite loop in ApplicationController#project_breadcrumbs Resolved Resolved 3 0.5 0.5 0.5 4389 36 3 79 1 0.5	4390 4390 Review 4389-breadcrumbs-infinite-loop Tim Pierce 44 0 4389 3 36 -c-a 5 4593 4593 Fix Tom Clegg 3 0 4389 3 36 -c-a 5
3609 3609 Peter Amstutz Peter Amstutz 47 SDKs 54 SDKs [SDKs] arv-run wrapper to interactively submit 'run-command' jobs Resolved Resolved 3 2.0 2.0 2.0 3609 36 47 79 6 2.0	3731 3731 Add pipe support to run-command Peter Amstutz 47 0 3609 3 36 -c-a 5 4168 4168 Talk to awz about his vision for this tool Peter Amstutz 47 0 3609 3 36 -c-a 5 3733 3733 Write wrapper Peter Amstutz 47 0 3609 3 36 -c-a 5 4183 4183 Review 3609-arv-ws Peter Amstutz 47 0 3609 3 36 -c-a 5 3729 3729 Design command line Peter Amstutz 47 0 3609 3 36 -c-a 5 4241 4241 Review 3609-arv-run Tim Pierce 44 0 3609 3 36 -c-a 5
4432 4432 SDKs 54 SDKs [SDKs] When copying pipeline instances using arv-copy, the component jobs get re-arranged Closed Closed 5 4432 36 79 1
4357 4357 Brett Smith Brett Smith 79 Node Manager 66 Node Manager [Node Manager] Should spin up more nodes (up to max_nodes) when up nodes are busy Resolved Resolved 3 1.0 1.0 1.0 4357 36 79 79 1 1.0	4370 4370 Review 4357-node-manager-busy-nodes-wip Brett Smith 79 0 4357 3 36 -c-a 5
4185 4185 Tom Clegg Tom Clegg 3 Crunch 52 Crunch [Crunch] crunchstat memory reports seem suspect for multithreaded programs Resolved Resolved 3 0.5 0.5 0.5 4185 36 3 79 1 0.5	4372 4372 Find out whether current stats make sense to users Tom Clegg 3 0 4185 3 36 -c-a 5
4303 4303 Brett Smith Brett Smith 79 Crunch 52 Crunch [Crunch] Output of job gets stuck at collate step Resolved Resolved 3 0.5 0.5 0.5 4303 36 79 79 1 0.5	4385 4385 Review 4303-crunch-retry-logging-wip Peter Amstutz 47 0 4303 3 36 -c-a 5
4406 4406 Deployment 60 Deployment [Docker] Default arvdock doesn't start sso server container, but also assumes that it exists by linking it to the API container Resolved Resolved 3 4406 36 79 1
4412 4412 Brett Smith Brett Smith 79 SDKs 54 SDKs [SDKs] arv edit fails under Ruby 2.1.4 Resolved Resolved 3 0.5 0.5 0.5 4412 36 79 79 1 0.5
4031 4031 Peter Amstutz Peter Amstutz 47 Workbench 56 Workbench [Workbench] Nodes should be connected via input=output in provenance/used by graphs Resolved Resolved 3 1.0 1.0 1.0 4031 36 47 79 1 1.0	4333 4333 Review 4031-fix-graph-connections Peter Amstutz 47 0 4031 3 36 -c-a 5 4143 4143 Write tests Peter Amstutz 47 0 4031 3 36 -c-a 5 4142 4142 Diagnose and fix Peter Amstutz 47 0 4031 3 36 -c-a 5
3618 3618 Phil Hodgson Phil Hodgson 80 [Workbench] In project view, sort results in the collections (and other) tab by clicking column headings. Resolved Resolved 3 2.0 2.0 2.0 3618 36 80 79 2 2.0	4320 4320 Remember sort order when switching tabs Or, I would propose, at least when using the Browser back (as in #3634), using URL rewriting that would include the specified ordering. Phil Hodgson 80 0 3618 3 36 -c-a 5 4107 4107 Make it possible to order by a specified column Right now assumptions are made in both Workbench and the API about how ordering works, and it would appear that the API can't be told to use a specific column from a specific table. This needs to be mastered, and may require API modifications (TBD). Phil Hodgson 80 0 3618 3 36 -c-a 5 4108 4108 Add UI elements for sorting by column header Phil Hodgson 80 0 3618 3 36 -c-a 5 4173 4173 Review 3618 Branch 3618-column-ordering Phil Hodgson 80 0 3618 3 36 -c-a 5
3706 3706 Tom Clegg Tom Clegg 3 SDKs 54 SDKs [SDKs] Remove fallback-to-keep warning from python SDK if block hash has a permission signature Resolved Resolved 3 0.5 0.5 0.5 3706 36 3 79 6 0.5	4367 4367 Review 3706-keep-warning Tom Clegg 3 0 3706 3 36 -c-a 5 4346 4346 Write tests Tom Clegg 3 0 3706 3 36 -c-a 5 4345 4345 Do not warn unless both methods fail Tom Clegg 3 0 3706 3 36 -c-a 5
4391 4391 Workbench 56 Workbench [Workbench] Selection clip does not show list of selected items in drop down Closed Closed 5 4391 36 79 1
4040 4040 Tim Pierce Tim Pierce 44 Tests 59 Tests [Tests] FUSE mount test suite should not fail just because new collection fixtures have been added Resolved Resolved 3 0.5 0.5 0.5 4040 36 44 79 1 0.5	4351 4351 Review 4040-fuse-tests Radhika Chippada 72 0 4040 3 36 -c-a 5 4207 4207 Add fixtures exclusively for testing FUSE mounts Tim Pierce 44 0 4040 3 36 -c-a 5
4359 4359 Tom Clegg Tom Clegg 3 [Workbench] Clean up project paging after #4091 bug fixes Resolved Resolved 3 0.5 0.5 0.5 4359 36 3 79 6 0.5	4362 4362 Review 4359-project-paging Tom Clegg 3 0 4359 3 36 -c-a 5 4361 4361 Remove overlapping uuids using filters Tom Clegg 3 0 4359 3 36 -c-a 5 4360 4360 Use inequality operators instead of adding/subtracting 1 second from timestamps Tom Clegg 3 0 4359 3 36 -c-a 5
4369 4369 Brett Smith Brett Smith 79 Crunch 52 Crunch [Crunch] Unexpected backward incompatibility in run-command Closed Closed 5 4369 36 79 79 1
4307 4307 Brett Smith Brett Smith 79 [Workbench] Pipeline instance name text should be editable after the instance starts Resolved Resolved 3 0.5 0.5 0.5 4307 36 79 79 1 0.5
4013 4013 SDKs 54 SDKs [SDKs] Pipeline instance logging emits misleading warning: API server did not return Collection "...." Closed Closed 5 0.5 0.5 0.5 4013 36 79 3 0.5
4493 4493 Crunch 52 Crunch [Crunch] job fails with Docker error "Engine is shutdown" Resolved Resolved 3 4493 36 79 1
4522 4522 Workbench 56 Workbench [Workbench] qr1hi /collections page error "HTTPClient::ReceiveTimeoutError error connecting to API server" Rejected Rejected 6 4522 36 79 1