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# Project Tracker Status Priority Subject Assigned To Updated % Done Hours
489 GET-Evidence Feature Closed Immediate Fix PharmGKB analysis so it matches against all SNPs, not just the nsSNPs Tom Clegg 02/15/2011 03:17 PM

725 GET-Evidence Bug Resolved High evidence.personalgenomes.org/NKX2-5-Glu21Gln has PHP warnings at top Tom Clegg 12/07/2011 07:46 PM

2892 Arvados Bug Resolved High Error page when signing user agreement 05/28/2014 10:10 AM

3047 Arvados Bug Resolved High UrlGenerationError in projects#show Tom Clegg 06/27/2014 11:15 AM

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

487 GET-Evidence Feature Closed High Show full PGP9 and PGP12 genomes on snp.med and GET-E Tom Clegg 02/15/2011 03:17 PM

474 GET-Evidence Feature Closed High Move todo's from http://evidence.personalgenomes.org/status to trac Tom Clegg 02/15/2011 03:17 PM

477 GET-Evidence Feature Closed High Integrate trait-o-matic functionality into GET-Evidence Tom Clegg 02/16/2011 02:25 PM

473 GET-Evidence Feature Closed High Implement auto-scoring mechanism Tom Clegg 02/16/2011 02:21 PM

15921 Arvados Bug Resolved Normal [Workbench2] Remove spurious trailing slash from API endpoints Lucas Di Pentima 12/13/2019 03:10 PM

2484 Arvados Bug Resolved Normal Workbench error when combining existing collections to make a new collection (encountered by Jonathan 2014-03-26) Peter Amstutz 04/16/2014 12:47 PM

11803 Arvados Bug Resolved Normal repositories#get_all_permissions API should not be so slow Tom Clegg 06/21/2017 06:36 PM

14407 Arvados Bug Resolved Normal [Workbench] tests fail on current version of firefox Tom Clegg 11/13/2018 08:53 PM

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

11973 Arvados Bug Resolved Normal [CWL] package-builder fails on schema-salad>=2.6 Tom Clegg 07/17/2017 02:32 PM

3691 Arvados Bug New Normal [Workbench] Suppress "ajax failed" error messages when ajax fails due to browser navigation event. 07/07/2021 06:36 PM

8289 Arvados Bug Resolved Normal [API] Avoid making queries unnecessarily slow by adding superfluous "order by" columns Tom Clegg 02/08/2016 08:11 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

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

14845 Arvados Bug Resolved Normal [controller] Fix flaky test Tom Clegg 03/01/2019 07:33 PM

2893 Arvados Bug Resolved Normal Prevent symbols and fancy Hash subclasses from going in or out of the database in serialized attributes Tom Clegg 05/30/2014 03:53 PM

7719 Arvados Bug Resolved Normal [Keep] Permit -never-delete=false for experimental use Radhika Chippada 11/04/2015 09:28 PM

6318 Arvados Bug New Normal [SDKs] Go SDK locator regexp (and its tests) should agree with the documented format 07/07/2021 06:29 PM

12349 Arvados Bug New Normal [API] Validate container requests "output_path must be in a writable mount" 09/27/2017 04:15 PM

15678 Arvados Bug Resolved Normal arvados-server "version" is incorrect in packaged binaries -- just reports "dev" Tom Clegg 10/08/2019 06:08 PM

14539 Arvados Bug Resolved Normal [SDKs] [arv-mount] Use "." placeholder to persist empty directories Lucas Di Pentima 03/01/2019 06:30 PM

5073 Arvados Bug Resolved Normal [Documentation] List known limitations of docker install at doc.arvados.org/install Tom Clegg 03/10/2015 08:04 PM

6772 Arvados Bug New Normal [API] Should not be necessary to host git repos on the same host as API server 07/07/2021 06:29 PM

15273 Arvados Bug Resolved Normal [API] accept lowercase postgresql connection params 05/23/2019 06:45 PM

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

18290 Arvados Bug Resolved Normal [LSF] Add "/host" to rusage strings Ward Vandewege 10/25/2021 05:26 PM

3720 Arvados Bug Resolved Normal [API] Fetching collection record is very slow when manifest is not small. Brett Smith 09/05/2014 01:55 PM

3099 Arvados Bug Resolved Normal ajax-loader.gif gives 406 Not Acceptable in production mode. Tom Clegg 07/02/2014 05:00 PM

4324 Arvados Bug New Normal [Docker] Fix supervisor.conf to supervise services instead of running init.d start script and hoping everything is OK 07/07/2021 06:35 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

12755 Arvados Bug Resolved Normal Error installing docker-cleaner rpm on centos7 Tom Clegg 01/02/2018 03:37 PM

10794 Arvados Bug New Normal [keepstore] Refactor volume Get/Put funcs to BlockReader/BlockWriter interfaces 07/07/2021 06:21 PM

10880 Arvados Bug Resolved Normal [Tests] Fix flaky test test_callback (tests.test_events.PollClientTestCase) Tom Clegg 01/13/2017 02:55 AM

10298 Arvados Bug New Normal [Crunch2] [API] Accept collection UUID or PDH as container_image in a container request 07/06/2021 09:11 PM

2246 Arvados Bug Resolved Normal Race condition in crunch-job: multiple jobs use the same /tmp/crunch-job/ on head node to check out git trees and make archives. Fix as simple as using git archive --remote? Tom Clegg 04/11/2014 12:59 PM

10777 Arvados Bug Resolved Normal [Crunch2] crunch-run: stop the container and fail if arv-mount dies before the container finishes Tom Clegg 03/01/2017 12:19 AM

6997 Arvados Bug Resolved Normal [Keep] keepstore reboots GCE host under heavy load 01/31/2019 06:50 PM

14745 Arvados Bug Resolved Normal [crunch-dispatch-cloud] Azure cloud driver fixups Eric Biagiotti 03/01/2019 07:33 PM

17878 Arvados Bug New Normal [container shell] confusing error "channel 3: bad ext data" when forwarding tcp traffic into a container with API: false 07/08/2021 05:21 PM

6272 Arvados Bug Resolved Normal [Keep] keepstored index response should have an EOF marker to enable the client to detect an incomplete response. Tom Clegg 06/17/2015 01:12 PM

14488 Arvados Bug New Normal [keepstore] Do not try to trash blocks that were already trashed in previous sweep 07/06/2021 09:09 PM

15819 Arvados Bug Resolved Normal [packages] workbench dev package not being built 01/22/2020 02:52 PM

17522 Arvados Bug Resolved Normal [arv-put] should use binary mode when reading stdin Lucas Di Pentima 11/16/2021 04:48 PM

4752 Arvados Bug Resolved Normal [Docker] Make websockets work, probably by using passenger standalone instead of apache. Peter Amstutz 04/02/2015 07:41 PM

6240 Arvados Bug New Normal [API] "order" params should be rejected or used (not silently ignored) even when they reference columns missing from the "select" param 07/07/2021 06:29 PM

17413 Arvados Bug New Normal [arv-mount] Exit (instead of undefined behavior) after unhandled exception 07/06/2021 09:08 PM

13162 Arvados Bug New Normal [SDKs] Remove arvadosclient and keepclient libraries 07/06/2021 09:10 PM

2243 Arvados Bug Resolved Normal Pipeline instance page H2 should be the instance's name, not the template's name. Tom Clegg 04/11/2014 12:37 AM

3421 Arvados Bug Resolved Normal [Workbench] "Rename collection" button on project page is hidden/inaccessible if the current name is too long and the browser window is too narrow. Brett Smith 08/13/2014 07:04 PM

11148 Arvados Bug New Normal [Crunch2] Propagate dispatch error messages (e.g., sbatch fails) to user via logs/websocket 07/07/2021 05:25 PM

14398 Arvados Bug Resolved Normal [keep-balance] deadlock on index retrieval error Tom Clegg 11/13/2018 08:53 PM

5451 Arvados Bug New Normal [Documentation] Fix Go SDK comments so they look reasonable in godoc 07/07/2021 06:30 PM

14482 Arvados Bug Resolved Normal [SDKs] Handle "." empty directory placeholder in manifests in Ruby SDK Lucas Di Pentima 03/01/2019 06:30 PM

16795 Arvados Bug Resolved Normal [a-d-c] flaky test Tom Clegg 10/07/2020 02:11 AM

14181 Arvados Bug Resolved Normal [keep-web] [Documentation] Increase client_max_body_size for WebDAV requests Tom Clegg 03/01/2019 06:30 PM

5685 Arvados Bug Resolved Normal [SDKs] In Go SDK keepclient, use defaultCollectionReplication as default Want_replicas (instead of always 2) 05/05/2016 02:06 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

12551 Arvados Bug Resolved Normal crunch-job should check errors from open() calls Tom Clegg 11/03/2017 08:17 PM

13427 Arvados Bug Resolved Normal [keep-balance] Handle volumes that are mounted simultaneously by multiple servers Tom Clegg 07/23/2018 06:52 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

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

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

10690 Arvados Bug Resolved Normal "dump config yaml" for Go programs and Rails projects Tom Clegg 01/30/2017 08:01 PM

14804 Arvados Bug Resolved Normal [keepstore] Return 5xx (not 4xx) if block is not found due to transient backend device failure Lucas Di Pentima 03/01/2019 07:33 PM

12959 Arvados Bug Resolved Normal [Federation] Wrong cluster ID shown on multisite search page Tom Clegg 02/14/2018 08:35 PM

4700 Arvados Bug New Normal [Workbench] Websocket client should only subscribe to events about relevant objects, not all events. 07/07/2021 06:31 PM

11968 Arvados Bug Resolved Normal [arvados-ws] Fix crash at startup Tom Clegg 07/14/2017 12:59 AM

18586 Arvados Bug New Normal Remove docs/code for unsupported AsyncPermissionsUpdateInterval 12/14/2021 04:21 PM

16852 Arvados Bug New Normal [keep-balance] replication level distribution should account for volumes' built-in replication 07/06/2021 09:12 PM

17507 Arvados Bug Resolved Normal [keep-web] [s3] Implement NextContinuationToken per ListObjectsV2 API Tom Clegg 06/16/2021 02:07 PM

6934 Arvados Bug Resolved Normal [Authentication] Write tests for pam module and shellinabox config Tom Clegg 08/14/2015 01:11 PM

18803 Arvados Bug Resolved Normal RailsAPI should interpret user identity_url="" to mean null in a create/update request Tom Clegg 03/24/2022 07:28 PM

9996 Arvados Bug Resolved Normal [keep-balance] Stop retrieving collections from API if the run is going to be aborted anyway 09/08/2016 10:45 PM

11190 Arvados Bug Resolved Normal Containers seem to run more than once, which isn't supposed to happen Tom Clegg 04/26/2017 07:20 PM

16830 Arvados Bug New Normal [keep-web] S3 PutObject response should have content MD5 07/06/2021 09:12 PM

16790 Arvados Bug Resolved Normal [keep-web] S3 ListObjects response should not have empty NextMarker field Tom Clegg 10/07/2020 02:11 AM

14475 Arvados Bug Resolved Normal [Controller] POST .../collections/$uuid seems to have broken Workbench integration tests 11/13/2018 09:53 PM

3013 Arvados Bug Resolved Normal Tab pane url is incorrect if the url of the page itself has a query string Peter Amstutz 06/17/2014 09:49 AM

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

17610 Arvados Bug Resolved Normal [API] Federated token scopes are not obeyed if scopes include "GET .../users/current" Tom Clegg 05/13/2021 03:29 PM

11220 Arvados Bug Resolved Normal [SDKs] Fix misleading arv-mount/pysdk error messages by removing obsolete "fetch manifest from Keep" code Tom Clegg 11/03/2017 03:30 PM

7743 Arvados Bug New Normal [Workbench] Hide file preview buttons when preview isn't possible with current keep-web config 07/07/2021 06:27 PM

2223 Arvados Bug Resolved Normal Repository owner_uuid and Arvados admins should get RW permission in gitolite Ward Vandewege 05/05/2014 09:05 PM

7232 Arvados Bug New Normal [Keep] keepstore should notify sysadmin about error conditions (trying harder than just log.Print()) 07/07/2021 06:28 PM

13763 Arvados Bug New Normal [API] groups#contents response should obey caller-provided order (not sort on type first) 07/06/2021 09:10 PM

4836 Arvados Bug Resolved Normal [Workbench] Ensure first tab content loads when shown, even if location hash indicated a different tab during initial page render Brett Smith 01/06/2015 07:23 PM

12107 Arvados Bug Resolved Normal [API] jobs.create should not do slow git operations Tom Clegg 09/25/2017 01:16 AM

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

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

12991 Arvados Bug Resolved Normal [crunch2] Propagate memory limit from runtime constraints to docker container Tom Clegg 07/23/2018 07:22 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

17202 Arvados Bug Resolved Normal [keep-web] Don't use 303-with-cookie when serving inline preview content as a third-party site Tom Clegg 05/25/2021 05:05 PM

15910 Arvados Bug Resolved Normal [crunch-run] Crash while writing output files Tom Clegg 01/22/2020 02:55 PM

19095 Arvados Bug Resolved Normal Update singularity dependency to get loopback device fix Tom Clegg 05/26/2022 06:29 PM

3023 Arvados Bug Resolved Normal Fix infinite-scroll on collections and pipeline templates chooser 06/16/2014 09:50 AM

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