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# Project Tracker Status Priority Subject Assigned To Updated % Done Hours
12893 Arvados Bug Duplicate Normal [Crunch2] Logs should be saved to disk when container is cancelled 01/10/2018 02:46 PM

11822 Arvados Bug Duplicate Normal [API] Add recursive and include_trash params missing from discovery doc 06/07/2017 06:52 PM

10568 Arvados Bug Duplicate Normal crunchstat-summary should look for child jobs in "components" field of job record 01/04/2017 10:29 PM

10521 Arvados Bug Duplicate Normal [SDKs] [CLI] "arv collection list" retrieves manifest_text even if not explicitly selected 11/11/2016 04:36 PM

8907 Arvados Bug Duplicate Normal [SSO] package should not depend on postgresql 04/07/2016 06:17 PM

6943 Arvados Bug Duplicate Normal [Git hosting] arvados-git-httpd should return 4xx, not 5xx, for authentication errors 08/11/2015 05:30 PM

4505 Arvados Feature Duplicate Normal [SDKs] "arv get {uuid}" outputs JSON representation of given object 11/09/2015 03:31 AM

14611 Arvados Story Duplicate Normal [Epic] Site-wide search for text, filenames, data 02/20/2019 08:31 PM

16457 Arvados Bug Rejected Normal [ws] websocket server should obey TLS.Insecure config when connecting to controller, but doesn't Lucas Di Pentima 06/17/2020 03:32 PM

10120 Arvados Bug Rejected Normal [Crunch] crunch-dispatch log throttling should not apply to its own stderr 02/18/2022 03:15 PM

8151 Arvados Bug Rejected Normal [crunchstat-summary] jobs with tasks_per_node>1 need node size recommendations adjusted 03/15/2019 04:53 AM

4841 Arvados Bug Rejected Normal [Workbench] When using "Run pipeline" button at the top of project A, the pipeline template chooser should start out showing project A, not "All projects". 09/11/2019 02:53 PM

4102 Arvados Bug Rejected Normal [Keep] Fix FUSE test suite so it does not need to be updated every time a new collection fixture is added to apiserver 10/08/2014 07:43 PM

3418 Arvados Bug Rejected Normal [Crunch] crunch-job ignores task sequence 03/09/2017 09:40 PM

3077 Arvados Bug Rejected Normal Add migration to convert remaining non-root collection owner_uuids to name links Tom Clegg 08/26/2014 11:28 AM

2814 Arvados Bug Rejected Normal Editables cannot be edited twice in a row without refreshing page. 05/22/2014 11:10 AM

2508 Arvados Bug Rejected Normal Sasha gets "fiddlesticks" error when logging in to qr1hi. Tom Clegg 04/13/2014 04:13 PM

13646 Arvados Feature Rejected Normal [API] Rails API server loads cluster configuration file 02/13/2019 04:12 PM

10267 Arvados Feature Rejected Normal Permission-monitoring service keeps a flattened permissions table up to date 02/15/2017 08:29 PM

7847 Arvados Feature Rejected Normal [SDKs] Update run-command to use arv-mount --mount-tmp instead of staging directory 07/07/2021 06:35 PM

5944 Arvados Feature Rejected Normal [Workbench] Syntax highlighting for repository-browsing 05/07/2015 07:21 PM

475 GET-Evidence Feature Rejected Normal add “user manager” (control membership in groups: admin, curator, lab member) Tom Clegg 03/02/2022 04:03 PM

435 GET-Evidence Support Rejected Normal Work with Carlos et al. to integrate BioNotate annotations into GET-Evidence Tom Clegg 03/02/2022 04:02 PM

6957 Arvados Story Rejected Normal [SSO] Move sso-provider into arvados tree 01/15/2020 09:16 PM

3150 Arvados Story Rejected Normal [API] Add "trash" behavior for all object types, instead of literal rdbms "delete" 03/09/2017 09:35 PM

2992 Arvados Story Rejected Normal [Workbench] Support "display_order" (integer) key for pipeline template components. Obey when rendering pipeline summary/details in Workbench. 03/13/2019 06:50 AM

2877 Arvados Story Rejected Normal Script looks for CGI data in a specified folder, scrapes header comments in the files, and adds/updates metadata objects accordingly (e.g., provenance links with properties). 05/16/2017 06:08 PM

2874 Arvados Story Rejected Normal Add/move/display collection name links in Workbench, rather than collection uuids Tim Pierce 06/06/2014 01:42 PM

2524 Arvados Story Rejected Normal [Sample clients] Third party can generate a "ready to ingest" event using an API token scoped to a specific project. 03/15/2017 11:12 PM

2523 Arvados Story Rejected Normal [Sample clients] Ingestor utility responds to "ready to ingest" events by copying the specified files from staging directory to Keep and storing the collection in the specified group. Peter Amstutz 03/07/2017 06:16 PM

2028 Arvados Story Rejected Normal [SDKs] Python SDK supports Django model/manager style usage Tom Morris 12/13/2016 07:47 PM

14224 Arvados Workbench 2 Bug Closed Normal [Bug][Running a workflow] Correct shell quoting in command modal Michał Kłobukowski 10/02/2018 03:06 PM

13368 Arvados Bug Closed Normal [API] Add "authorizations" table 12/18/2019 09:21 PM

12594 Arvados Bug Closed Normal [crunch1] crunchrunner should report "signal: SIGKILL" instead of "exit code -1" if command exits via signal 02/12/2020 02:27 PM

12296 Arvados Bug Closed Normal [API] [Node Manager] [Docs] Fix recommendations and explanations for various max-nodes configs 02/11/2020 09:03 PM

12251 Arvados Bug Closed Normal [API] Strict checks for "@@" filter operand 08/12/2021 08:04 PM

12010 Arvados Bug Closed Normal [keep-web] tests hang Tom Clegg 08/02/2017 06:46 PM

10282 Arvados Bug Closed Normal [Go programs]Warn or error when unrecognized keys appear in config files 05/22/2019 04:38 PM

10040 Arvados Bug Closed Normal [Workbench] ContainerRequest#show crashes "undefined method `each' for nil:NilClass" 12/19/2019 03:22 PM

10007 Arvados Bug Closed Normal [Workbench] Retrieve all log content directly from API instead of pre-rendering in Rails 12/19/2019 03:21 PM

9496 Arvados Bug Closed Normal [API] Ensure 'items_available' and 'items' (in list responses) both reflect the same database state 01/29/2020 03:07 PM

9429 Arvados Bug Closed Normal [API] Docker image name resolution should not disqualify a well-formed tag link merely because an older badly-formed link exists with the same name and target 01/29/2020 03:04 PM

8710 Tapestry Bug Closed Normal Check UserFiles too when checking for Datasets that are ready to publish 04/09/2016 05:21 PM

8283 Arvados Bug Closed Normal [Crunch] crunch-dispatch should run git as www-data, not root 01/18/2020 12:42 AM

7853 Arvados Bug Closed Normal [Data Manager] Behave appropriately when multiple keepstore nodes share a single storage volume 02/15/2017 09:28 PM

7180 Arvados Bug Closed Normal [Keep] [SDKs] Logic about which services to try should not reference service_type 01/15/2020 08:29 PM

6933 Arvados Bug Closed Normal [Documentation] Use the same example/demo users and domain names throughout 01/15/2020 08:05 PM

6753 Arvados Bug Closed Normal [API] Asset pipeline does not work unless config/environments/production.rb is present at buildtime and runtime 01/31/2022 04:26 PM

6690 Arvados Bug Closed Normal [Deployment] Better strategy for keeping Ruby up-to-date (both RVM and manual installs lag behind) 01/15/2020 07:59 PM

5850 Arvados Bug Closed Normal All clients authenticate directly against SSO server without going through API server 02/13/2019 06:04 PM

5233 Arvados Bug Closed Normal [Tests] Eliminate system globals in test suites 03/11/2022 09:43 PM

5162 Arvados Bug Closed Normal [Crunch] crunch-dispatch should use the API instead of running in the API server's rails environment. 02/13/2018 08:51 PM

4553 Arvados Bug Closed Normal [Docker] Compute node records should get created automatically by build/run scripts 05/16/2017 06:15 PM

4529 Arvados Bug Closed Normal [SDKs] Ensure Python and Go SDKs in a given situation always choose either proxies or disks, never some of each. 03/09/2017 09:51 PM

4402 Arvados Bug Closed Normal [SDKs] CollectionWriter.write_directory_tree(...,max_manifest_depth=0) should produce a single stream. 11/07/2014 07:08 PM

4222 Arvados Bug Closed Normal [Keep] Rename -enforce-permissions to -bypass-read-permissions with default=false; let data manager functions work irrespective of this flag. 03/09/2017 09:51 PM

4132 Arvados Bug Closed Normal [Workbench] Add unit test infrastructure (and some examples) for JavaScript assets 03/09/2017 09:50 PM

4028 Arvados Bug Closed Normal [Crunch] Task stdout appearing in job logs should be labeled "stdout" instead of "stderr" 03/09/2017 09:45 PM

3954 Arvados Bug Closed Normal [API] permission_to_update should prohibit all changes to content-addressable attributes of a job record after the job has started. 03/09/2017 09:44 PM

3910 Arvados Bug Closed Normal [SDKs] Client libraries should retry failed API requests after errors like Gateway Timeout (part 2) 03/10/2017 06:41 PM

3638 Arvados Bug Closed Normal [Workbench] [Draft] When moving a job or pipeline between projects, outputs and logs should move too. 01/03/2020 08:46 PM

3556 Arvados Bug Closed Normal [Documentation] Avoid using the term "parallel" when referring to Crunch concurrency features 03/09/2017 09:40 PM

3555 Arvados Bug Closed Normal [API] Rename nondeterministic to impure 03/09/2017 09:40 PM

3419 Arvados Bug Closed Normal [SDKs] Perl client library should retry failed API requests after errors like Gateway Timeout 03/15/2017 11:13 PM

3416 Arvados Bug Closed Normal [API] Clean up exception raise/rescue usage, use 4xx and 5xx appropriately 06/29/2020 06:32 PM

3386 Arvados Bug Closed Normal [Documentation] Crunch script can exit 111 to indicate transient failure (i.e., try running the task again up to N times) 03/09/2017 09:40 PM

3385 Arvados Bug Closed Normal [Workbench] Clarify in the log viewer the difference between tasks that failed, and tasks that were cancelled (because some other task failed, or the job itself was cancelled). 01/03/2020 04:30 PM

3371 Arvados Bug Closed Normal [SDK] arv-put network timeout should be configurable at runtime with --timeout argument 01/03/2020 04:30 PM

3369 Arvados Bug Closed Normal [Documentation] CLI usage page should help you install the CLI tools on your workstation 01/03/2020 04:30 PM

3353 Arvados Bug Closed Normal [SDK] "arv keep less" uses Perl client library 01/03/2020 04:30 PM

3352 Arvados Bug Closed Normal [SDK] After ^C, arv-put sometimes exits but leaves processes/threads behind that keep the resume file locked, preventing retrying the aborted arv-put. 03/10/2017 06:40 PM

3346 Arvados Bug Closed Normal ActiveRecord::SaveFailed exception does not include useful error message if AuthorizedKey#permission_to_set_authorized_user_uuid fails during @object.save! 01/03/2020 04:29 PM

3262 Arvados Bug Closed Normal [Documentation] Describe how to run tramp in emacs. Tom Clegg 03/10/2017 06:40 PM

3172 Arvados Bug Closed Normal [Workbench] Moving a pipeline instance from a private project to a shared project does not also effectively share the component jobs. 06/29/2020 06:30 PM

3166 Arvados Bug Closed Normal [Workbench] Generic "attributes" tab renders uuid as a link to the object, with object type as link text, instead of actually showing the uuid. 03/10/2017 06:40 PM

3086 Arvados Bug Closed Normal AJAX behaves strangely if login token expires 06/29/2020 06:25 PM

480 GET-Evidence Bug Closed High NA12878 has no chr:pos on CYP2C9-R144C Tom Clegg 02/15/2011 03:17 PM

12958 Arvados Feature Closed Normal [Federation] Workbench login chooser 03/01/2019 07:33 PM

12566 Arvados Feature Closed Normal [arv-mount] --unmount should sync/wait and unmount gracefully unless otherwise specified 02/12/2020 02:26 PM

11646 Arvados Feature Closed Normal [keepstore] Support X-Keep-Desired-Classes header 05/08/2018 12:58 PM

10141 Arvados Feature Closed Normal [Packaging] Include sample config file (/etc/arvados/foo/foo.example.yml) with each configurable package 09/11/2019 02:55 PM

8701 Tapestry Feature Closed Normal Arvados job/pipeline generates ClinVar HTML report from VCF Abram Connelly 04/14/2016 03:55 PM

8700 Tapestry Feature Closed Normal Arvados job/pipeline generates GET-Evidence HTML report from VCF Abram Connelly 04/14/2016 03:55 PM

8626 Arvados Feature Closed Normal [Keep] Configurable free space target for each volume -- don't delete blocks when that much free space is already available 01/18/2020 12:56 AM

7240 Arvados Feature Closed Normal [Keep] keep-rsync should support "verify-existing" flag 01/15/2020 08:31 PM

6667 Arvados Feature Closed Normal [SDKs] Support HTTP proxy configuration using env vars 01/15/2020 08:01 PM

6611 Arvados Feature Closed Normal [Data Manager] Act on pull lists for underreplicated blocks 01/18/2017 07:10 AM

5540 Arvados Feature Closed Normal [Crunch] Contain all job/task containers in a memory-limiting cgroup 01/23/2018 05:06 PM

5414 Arvados Feature Closed Normal [Keep] Use data stored remotely (not in local keepstore) Tom Clegg 02/13/2019 06:04 PM

5413 Arvados Feature Closed Normal [DRAFT] [API/SSO] Use externally-defined (e.g., LDAP) groups as permission groups 10/07/2020 03:43 PM

5237 Arvados Feature Closed Normal [Workbench] Pipeline re-run dialog should offer docker image choices (latest/same), similar to script version choices 03/11/2022 09:45 PM

4735 Arvados Feature Closed Normal [Workbench] Add "manage tokens" section on account page 01/15/2020 07:01 PM

4561 Arvados Feature Closed Normal [SDKs] Refactor run-command so it can be used as an SDK by scripts in a git tree 03/11/2022 09:44 PM

3987 Arvados Feature Closed Normal [Docker] Run a 5-second diagnostic suite after bringing up docker containers. 03/10/2017 06:41 PM

3955 Arvados Feature Closed Normal [Workbench] Render runtime-formatted timestamps as "8:00 am" or "Sep 23" etc depending on how recent. 03/10/2017 06:41 PM

3923 Arvados Feature Closed Normal [Workbench] Use web notifications to alert user when pipelines finish 03/10/2017 06:41 PM

3874 Arvados Feature Closed Normal [Crunch] "Resume job" API: clone a job and all of its tasks, reset failed tasks to "todo" state 01/15/2020 06:59 PM

3768 Arvados Feature Closed Normal [SDKs] Speculatively pre-fetch data blocks while reading from a collection. 03/09/2017 09:43 PM

3760 Arvados Feature Closed Normal [Workbench] When referencing an object that is not readable (e.g., deleted or no longer readable) the link should not be clickable and a tooltip(?) should explain why. 01/03/2020 08:48 PM

3445 Arvados Feature Closed Normal [Workbench] Improve chooser preview for collections, and add previews for objects that don't have any yet (pipeline instances, templates, jobs, projects) 06/29/2020 06:32 PM

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