| 02746a6 | Chris Miller | 26 July 2021, 18:57:01 UTC | updating cwltool path path changed in more recent docker versions | 26 July 2021, 18:57:01 UTC |
| df99eae | Thomas B. Mooney | 21 July 2021, 17:27:18 UTC | Merge pull request #2027 from tmooney/list_build_queue_knows_about_anps Add a per-AnP limit for scheduled builds. | 21 July 2021, 17:27:18 UTC |
| 6e25052 | Thomas B. Mooney | 21 July 2021, 15:31:39 UTC | Add a per-AnP limit for scheduled builds. This way a single project won't monopolize the queues when it has a job group configured that causes its builds to PEND even when slots are available for other builds to run. | 21 July 2021, 16:10:22 UTC |
| 40d32f1 | Thomas B. Mooney | 19 July 2021, 19:39:26 UTC | Merge pull request #2026 from tmooney/only_assign_when_data_to_assign Only try to assign existing data when there is some. | 19 July 2021, 19:39:26 UTC |
| 72ce27d | Thomas B. Mooney | 19 July 2021, 15:32:42 UTC | Only try to assign existing data when there is some! | 19 July 2021, 15:32:42 UTC |
| ae5b070 | Thomas B. Mooney | 19 July 2021, 15:08:36 UTC | Merge pull request #2021 from tmooney/silence_errors_in_disk_create Avoid warnings about numeric comparisons. | 19 July 2021, 15:08:36 UTC |
| b2b4b20 | Thomas B. Mooney | 19 July 2021, 15:08:16 UTC | Merge pull request #2019 from tmooney/cleanup_succeeded_for_compute1 Handle not having automatic mounts in Cleanup Succeeded | 19 July 2021, 15:08:16 UTC |
| 7911616 | Thomas B. Mooney | 19 July 2021, 15:06:57 UTC | Merge pull request #2022 from tmooney/import_data_for_work_order_lives_up_to_its_promises The help text claims it assigns all data, so let's do it. | 19 July 2021, 15:06:57 UTC |
| 076e0ae | Thomas B. Mooney | 15 July 2021, 20:26:55 UTC | Merge pull request #2024 from tmooney/logger_monkeypatch Monkeypatch to get around longstanding bug in Logger. | 15 July 2021, 20:26:55 UTC |
| 46e8087 | Thomas B. Mooney | 15 July 2021, 20:26:31 UTC | Merge pull request #2025 from tmooney/model_metric_column_names Address errors with metric ghost class [to fix CWL requeueing]. | 15 July 2021, 20:26:31 UTC |
| c1ab162 | Thomas B. Mooney | 12 July 2021, 18:54:58 UTC | Address errors with metric ghost class. When deleting metrics (to replace them), UR was complaining about the column names not matching the database. The capitalized names were held over from before we switched to PostgreSQL, so let's just lowercase them now. | 12 July 2021, 18:54:58 UTC |
| 4dded1f | Thomas B. Mooney | 24 June 2021, 14:38:40 UTC | Fix logic. | 24 June 2021, 14:38:40 UTC |
| a59436e | Thomas B. Mooney | 23 June 2021, 20:29:16 UTC | Monkeypatch to get around longstanding bug in Logger. I think we should switch users of this to use the UR logging methods instead, but this is a quick fix for now. | 23 June 2021, 20:29:16 UTC |
| e498f3c | Thomas B. Mooney | 23 June 2021, 20:06:57 UTC | Merge pull request #2023 from tmooney/confg_file_for_instrument_data Optionally check instrument data against a supplied config file. | 23 June 2021, 20:06:57 UTC |
| df51a53 | Thomas B. Mooney | 23 June 2021, 19:44:09 UTC | Optionally check instrument data against a supplied config file. | 23 June 2021, 19:44:09 UTC |
| d6d5975 | Thomas B. Mooney | 17 June 2021, 20:58:04 UTC | The help text claims it assigns all data, so let's do it. | 17 June 2021, 20:58:04 UTC |
| 7d6f740 | Thomas B. Mooney | 17 June 2021, 20:04:40 UTC | Avoid warnings about numeric comparisons. These UUIDs sure look like numbers to me, anyway :) | 17 June 2021, 20:04:40 UTC |
| 5c05536 | Thomas B. Mooney | 15 June 2021, 22:45:08 UTC | Command to purge allocations for abandoned builds for current user. | 17 June 2021, 16:45:10 UTC |
| 516f985 | Thomas B. Mooney | 16 June 2021, 19:59:29 UTC | Merge pull request #2020 from tmooney/remove_dot Remove accidental double-concatenation. | 16 June 2021, 19:59:29 UTC |
| e9c7f40 | Thomas B. Mooney | 16 June 2021, 19:52:37 UTC | Remove accidental double-concatenation. | 16 June 2021, 19:52:37 UTC |
| 185e790 | Thomas B. Mooney | 15 June 2021, 20:37:49 UTC | Allow for cleaning up via subjob so that mounts can be specified. This is necessary for our new cluster volumes that aren't mounted automatically. | 15 June 2021, 20:37:49 UTC |
| 87ae31b | Thomas B. Mooney | 15 June 2021, 20:34:57 UTC | Add an interactive option to Genome::Sys::LSF::bsub. The main feature of this would be to allow stdout/stderr to be passed through from the job. It does allow for interactivity within the nested job if necessary, too. | 15 June 2021, 20:34:57 UTC |
| 6c32c75 | Thomas B. Mooney | 15 June 2021, 15:09:22 UTC | Pull up possible-volumes logic into AnP class itself. Better testing, too! | 15 June 2021, 15:09:22 UTC |
| 05b88ab | Thomas B. Mooney | 10 June 2021, 16:54:00 UTC | Merge pull request #2018 from tmooney/import_move_option Add option to trusted-data importer to delete the source files. | 10 June 2021, 16:54:00 UTC |
| 11ea45f | Thomas B. Mooney | 09 June 2021, 17:58:57 UTC | Add option to trusted-data importer to delete the source files. | 09 June 2021, 17:58:57 UTC |
| 20f75e9 | Thomas B. Mooney | 02 June 2021, 20:56:24 UTC | Merge pull request #2017 from tmooney/lims_config_is_cake Use a hardcoded lims docker image. | 02 June 2021, 20:56:24 UTC |
| 2b80e56 | Thomas B. Mooney | 01 June 2021, 20:36:31 UTC | Use a hardcoded lims docker image. This purports to look it up in config, but the config is a lie. The latest version of the config is itself stored inside the docker image, so it's not possible to look it up from the outside. Rather than rely on an old version of the config, just put in the current latest value. | 01 June 2021, 20:36:31 UTC |
| da03b55 | Thomas B. Mooney | 01 June 2021, 16:52:18 UTC | Merge pull request #2016 from tmooney/tolerate_disk_volumes_where_groups_belong_in_lims_importer Tolerate the user specifying an explicit volume instead of a group. | 01 June 2021, 16:52:18 UTC |
| 60b9a6c | Thomas B. Mooney | 01 June 2021, 16:51:52 UTC | Merge pull request #2015 from tmooney/synonym_file_converter Add a "synonym file" converter algorithm. | 01 June 2021, 16:51:52 UTC |
| 1e9effd | Thomas B. Mooney | 01 June 2021, 16:50:54 UTC | Merge pull request #2014 from tmooney/refseq_build_uses_anp_config Use AnP config for build creation/running in refseqs. | 01 June 2021, 16:50:54 UTC |
| ad0e800 | Thomas B. Mooney | 27 May 2021, 14:49:37 UTC | Tolerate the user specifying an explicit volume instead of a group. The remote volume support regressed the tolerance added in #1866 in this particular case. It could still be avoided by using the right type of data being requested, though! | 27 May 2021, 14:49:37 UTC |
| 8617aa0 | Thomas B. Mooney | 25 May 2021, 20:14:26 UTC | Add a "synonym file" converter algorithm. The file is a two-column format with the first column being the target chromosome in the destination reference and the second column being the chromosome in the source reference. (This should match the format of synonym files for VEP.) | 25 May 2021, 20:14:26 UTC |
| ab08d16 | Thomas B. Mooney | 25 May 2021, 18:31:38 UTC | Set a basic environment file for the mock "system" AnP. Tests building reference sequences now need an environment file like those building other build types already do. | 25 May 2021, 18:48:23 UTC |
| 0e3c8a3 | Thomas B. Mooney | 25 May 2021, 17:59:34 UTC | Use AnP config for build creation/running in refseqs. | 25 May 2021, 17:59:34 UTC |
| 0f58a00 | Thomas B. Mooney | 25 May 2021, 17:40:14 UTC | Merge pull request #2013 from tmooney/delete_tag_bridges_on_delete Support deleting a config profile item with linked tags. | 25 May 2021, 17:40:14 UTC |
| 5a4abc9 | Thomas B. Mooney | 20 May 2021, 22:12:46 UTC | Support deleting a config profile item with linked tags. This will still fail if the config was ever used for models (which prevents crazy cascading deletes!), but an unused config that happened to have a tag can now be cleaned up. | 20 May 2021, 22:12:46 UTC |
| ae02a8e | John Garza | 13 May 2021, 21:50:51 UTC | Merge pull request #2012 from johnegarza/skip_disk_querying Skip disk querying | 13 May 2021, 21:50:51 UTC |
| 352477d | johnegarza | 13 May 2021, 20:51:55 UTC | More relevant var name | 13 May 2021, 20:51:55 UTC |
| 7b5d91c | johnegarza | 13 May 2021, 20:38:08 UTC | Skip direct disk space queries when allocation path creation is skipped | 13 May 2021, 20:38:08 UTC |
| c2e9669 | John Garza | 11 May 2021, 23:14:19 UTC | Merge pull request #2011 from johnegarza/python3_gsutil_focal Call gsutil with python3 in Ubuntu 20.04 focal based images | 11 May 2021, 23:14:19 UTC |
| 2e4d2db | johnegarza | 11 May 2021, 22:55:56 UTC | Call gsutil with python3 in Ubuntu 20.04 focal based images | 11 May 2021, 22:55:56 UTC |
| 7c49c6d | John Garza | 10 May 2021, 21:45:19 UTC | Merge pull request #2010 from johnegarza/gcp_config_bucket_var Use env variables instead of hardcoding gcp bucket | 10 May 2021, 21:45:19 UTC |
| 47b3277 | johnegarza | 10 May 2021, 21:25:10 UTC | Use env variables instead of hardcoding gcp bucket | 10 May 2021, 21:25:10 UTC |
| 7ace67e | John Garza | 10 May 2021, 20:55:57 UTC | Merge pull request #2009 from johnegarza/update_commands Add an update env file command | 10 May 2021, 20:55:57 UTC |
| 4c04df1 | John Garza | 10 May 2021, 20:55:13 UTC | Merge pull request #2007 from johnegarza/config_skip_allocation_creation Skip allocation path creation for config files | 10 May 2021, 20:55:13 UTC |
| ba32611 | johnegarza | 06 May 2021, 21:39:09 UTC | fix number of tests | 06 May 2021, 21:39:09 UTC |
| 2a6b9b5 | johnegarza | 06 May 2021, 21:33:20 UTC | Add a basic test case | 06 May 2021, 21:33:20 UTC |
| 5361726 | johnegarza | 06 May 2021, 20:01:35 UTC | Keep language consistent | 06 May 2021, 20:01:35 UTC |
| e9b1dde | johnegarza | 05 May 2021, 22:11:20 UTC | Initial work to allow updating AnP environment files | 05 May 2021, 22:11:20 UTC |
| 0ee82ef | johnegarza | 05 May 2021, 21:38:59 UTC | Handle no-commit further upstream | 05 May 2021, 21:38:59 UTC |
| 141c293 | johnegarza | 05 May 2021, 21:14:58 UTC | Use spaces not tabs | 05 May 2021, 21:14:58 UTC |
| 167159c | johnegarza | 04 May 2021, 22:31:53 UTC | Make sure tests can create allocations | 04 May 2021, 22:31:53 UTC |
| 596c145 | johnegarza | 04 May 2021, 21:13:44 UTC | Retain CQID ability to directly write to filesystem | 04 May 2021, 21:13:44 UTC |
| bfe3dc4 | johnegarza | 04 May 2021, 20:50:30 UTC | Better var name and skip path creation for config items too | 04 May 2021, 20:50:30 UTC |
| 0ff0a89 | johnegarza | 03 May 2021, 23:20:34 UTC | Skip creating allocation dirs for env config | 03 May 2021, 23:20:34 UTC |
| 3c5eb40 | John Garza | 03 May 2021, 21:10:59 UTC | Merge pull request #2006 from johnegarza/fix_uploaded_config_name Fix uploaded file name | 03 May 2021, 21:10:59 UTC |
| 00c39e7 | John Garza | 03 May 2021, 20:49:03 UTC | Fix variables Co-authored-by: Thomas B. Mooney <mooney@wustl.edu> | 03 May 2021, 20:49:03 UTC |
| 8e1ce00 | John Garza | 03 May 2021, 20:48:03 UTC | Use join to construct uploaded file name Co-authored-by: Thomas B. Mooney <mooney@wustl.edu> | 03 May 2021, 20:48:03 UTC |
| 6a2f4a3 | johnegarza | 03 May 2021, 20:32:32 UTC | Fix uploaded file name | 03 May 2021, 20:32:32 UTC |
| 13cde6b | John Garza | 30 April 2021, 21:20:36 UTC | Merge pull request #2005 from johnegarza/basic_config_file_changes Basic config file changes | 30 April 2021, 21:20:36 UTC |
| 5b8093e | johnegarza | 29 April 2021, 22:39:08 UTC | Keep terminology consistent | 29 April 2021, 22:39:08 UTC |
| 8b24aea | johnegarza | 29 April 2021, 22:01:25 UTC | Inform the user that the file will not be immediately available | 29 April 2021, 22:01:25 UTC |
| 41dea8b | johnegarza | 29 April 2021, 20:31:30 UTC | Pass original name so update script can use it | 29 April 2021, 20:31:30 UTC |
| 3e2cf8b | Thomas B. Mooney | 28 April 2021, 20:51:31 UTC | Merge pull request #2002 from tmooney/anp_create_wanna_create AnP Create: Now with More Interactivity! | 28 April 2021, 20:51:31 UTC |
| 9dcc085 | Thomas B. Mooney | 28 April 2021, 17:00:57 UTC | Make the interactive menu item adding more interactive. The --no-config option or the --analysis-menu-item options bypass this prompt as per usual, so automated use of this command is still possible. | 28 April 2021, 20:45:52 UTC |
| 14ee58c | Thomas B. Mooney | 28 April 2021, 20:44:01 UTC | Merge pull request #2004 from tmooney/allocation_cleanup_knows_about_certificates Check for certificates for the production database connection. | 28 April 2021, 20:44:01 UTC |
| c35c81f | Thomas B. Mooney | 28 April 2021, 19:46:05 UTC | Check for certificates for the production database connection. | 28 April 2021, 20:14:24 UTC |
| 5a1a89a | Thomas B. Mooney | 28 April 2021, 19:19:51 UTC | Merge pull request #2003 from tmooney/testtracker_certs_in_conf Include certs in test-tracker server config. | 28 April 2021, 19:19:51 UTC |
| 21043d9 | Thomas B. Mooney | 28 April 2021, 18:53:46 UTC | Include certs in test-tracker server config. Once again not a useful file for the world at large, but helpful for us! | 28 April 2021, 18:53:46 UTC |
| 3b0215d | Thomas B. Mooney | 28 April 2021, 17:00:01 UTC | Print IDs instead of object hashes in list. Sure it's still inscrutable, but at least it's an inscrutable list of values someone might possibly be able to use. | 28 April 2021, 17:00:01 UTC |
| 4873a90 | johnegarza | 27 April 2021, 23:26:22 UTC | Basic change for the add-config-file cmd | 27 April 2021, 23:26:22 UTC |
| e9434f4 | johnegarza | 27 April 2021, 21:51:55 UTC | Restore old functionality for test cases | 27 April 2021, 21:51:55 UTC |
| 93757dc | Thomas B. Mooney | 23 April 2021, 18:22:15 UTC | Merge pull request #1999 from tmooney/usage_log_dsn Update connection string for usage log. | 23 April 2021, 18:22:15 UTC |
| 6d70e33 | Thomas B. Mooney | 22 April 2021, 22:30:57 UTC | Update connection string for usage log. It makes me sad this string is hardcoded here, but I guess updating it once every several years isn't so bad :) | 22 April 2021, 22:30:57 UTC |
| a82decc | johnegarza | 22 April 2021, 20:48:43 UTC | Minimum change to add env cmd that uploads to gcp instead of copying locally | 22 April 2021, 20:48:43 UTC |
| 44d575e | Thomas B. Mooney | 14 April 2021, 18:26:30 UTC | Merge pull request #1998 from tmooney/monitor_jobs_when_call_caching When call-caching is enabled, check the health of jobs. | 14 April 2021, 18:26:30 UTC |
| f4035f5 | Thomas B. Mooney | 14 April 2021, 15:16:23 UTC | When call-caching is enabled, check the health of jobs. Before we were letting jobs fail and manually running `script.submit` for replacement jobs in the event of LSF failure due to the high cost of starting a workflow from the beginning over such a trivial failure. With call-caching that cost is reduced, so it's better to have quicker notification of issues. | 14 April 2021, 15:16:23 UTC |
| f19d9c1 | Thomas B. Mooney | 12 April 2021, 20:00:27 UTC | Merge pull request #1997 from tmooney/use_filetest_access Enable ACL support for filetests. | 12 April 2021, 20:00:27 UTC |
| f2e6974 | Thomas B. Mooney | 24 March 2021, 18:42:19 UTC | Enable ACL support for filetests. Less performant, sure, but actually works with a lovely non-posix-compliant filesystem, too! See also: https://perldoc.perl.org/filetest | 24 March 2021, 18:42:19 UTC |
| 96de3cf | Thomas B. Mooney | 22 March 2021, 20:59:53 UTC | Merge pull request #1996 from tmooney/du_apparent_size Use the apparent size for allocations. | 22 March 2021, 20:59:53 UTC |
| 29930af | Thomas B. Mooney | 22 March 2021, 20:59:45 UTC | Merge pull request #1995 from tmooney/requeue_for_build_retry Add ability to queue rebuilds for CwlPipeline builds. | 22 March 2021, 20:59:45 UTC |
| 288c115 | Thomas B. Mooney | 17 March 2021, 19:57:21 UTC | Use the apparent size for allocations. With the fancy fancy cache layer we're using these days, the actual size of files that haven't been pulled into the cache is not detemrined correctly by `du`. But the apparent size is good enough! | 17 March 2021, 19:57:21 UTC |
| 7487982 | Thomas B. Mooney | 15 March 2021, 20:43:03 UTC | Add ability to queue rebuilds for CwlPipeline builds. This functions like `genome model build queue` but for restarting builds rather than creating new ones. Since we're moving away from supporting the queue for arbitrary users, this is set up to only allowing the queue of failed "production" builds. | 15 March 2021, 20:43:03 UTC |
| fc62358 | Thomas B. Mooney | 09 February 2021, 16:03:09 UTC | Merge pull request #1992 from tmooney/merge_with_liftover Need to liftOver each track individually. | 09 February 2021, 16:03:09 UTC |
| 9186b05 | Thomas B. Mooney | 09 February 2021, 16:02:00 UTC | Merge pull request #1994 from tmooney/volume_and_group_create Create commands for disk groups and volumes | 09 February 2021, 16:02:00 UTC |
| 617f61d | Thomas B. Mooney | 26 January 2021, 18:28:18 UTC | Add help/doc sections to new volume/group create commands. | 26 January 2021, 18:28:18 UTC |
| c87f212 | Thomas B. Mooney | 26 January 2021, 16:24:46 UTC | New command to help create volumes. | 26 January 2021, 16:24:46 UTC |
| 1f88462 | Thomas B. Mooney | 25 January 2021, 23:20:33 UTC | New command to facilitate creating disk groups. | 25 January 2021, 23:20:33 UTC |
| cb71a24 | Thomas B. Mooney | 01 December 2020, 19:59:37 UTC | Merge pull request #1990 from tmooney/possible_volumes Add true value to end of module. | 01 December 2020, 19:59:37 UTC |
| deb9ee3 | Thomas B. Mooney | 12 November 2020, 16:44:01 UTC | Merge pull request #1991 from tmooney/bqm_remote Make the "prod-builder" run_as configurable. | 12 November 2020, 16:44:01 UTC |
| 6e282f4 | Thomas B. Mooney | 12 November 2020, 16:43:39 UTC | Merge pull request #1993 from tmooney/move_cwlpipelines Use more UR-centric approach to test for owner class existence. | 12 November 2020, 16:43:39 UTC |
| 751dbc9 | Thomas B. Mooney | 09 November 2020, 19:20:02 UTC | Use more UR-centric approach to test for owner class existence. UR classes don't necessarily have defined perl module files, and we don't support auto-updating any non-UR classes, so this should be good enough! | 09 November 2020, 19:20:02 UTC |
| 2d3cf39 | Thomas B. Mooney | 27 October 2020, 20:23:23 UTC | Need to liftOver each track individually. This assumes that the two existing track names are the ones that exist for multi-tracked files. "Weird" tracks will not work right. | 27 October 2020, 20:23:23 UTC |
| ee980b3 | Thomas B. Mooney | 19 October 2020, 17:30:48 UTC | Merge pull request #1988 from tmooney/auto_remote_sync_admin Auto-connect production imports to remote volumes. | 19 October 2020, 17:30:48 UTC |
| 0d73a55 | Thomas B. Mooney | 15 October 2020, 19:02:13 UTC | Make the "prod-builder" run_as configurable. Now that we're operating on multiple clusters we've run into a situation where it'd be nice to distinguish between then with different "run_as" indications. This will let us change it when run on the new cluster while leaving it the same on the old. (Or someone enterprising could set the appropriate environment variable to setup for the "other" cluster for the one they're on!) | 15 October 2020, 19:02:13 UTC |
| 1584b35 | Thomas B. Mooney | 14 October 2020, 19:16:50 UTC | Add true value to end of module. | 14 October 2020, 19:16:50 UTC |
| f9d5142 | Thomas B. Mooney | 14 October 2020, 17:28:09 UTC | Merge pull request #1989 from tmooney/possible_volumes New command to help identify which volumes to mount. | 14 October 2020, 17:28:09 UTC |
| 072763f | Thomas B. Mooney | 14 October 2020, 14:48:54 UTC | Merge pull request #1983 from tmooney/prod-builder_for_wo_projects Stop hardcoding "apipe-builder" when determining applicable models | 14 October 2020, 14:48:54 UTC |
| 2a0beb1 | Thomas B. Mooney | 13 October 2020, 21:41:39 UTC | New command to help identify which volumes to mount. This command lists the possible volumes configured for an AnP. This could be used for a safe list of volumes to mount when launching a container to work with the AnP. | 13 October 2020, 21:41:39 UTC |
| 91121e8 | Thomas B. Mooney | 12 October 2020, 15:43:04 UTC | Keep dbh connection open on short-lived shellcmd runs. The one in the cleanup guard is especially important, since on a successful run it'll be running as the system shuts down. In that circumstance calling the disconnect process may fail. | 12 October 2020, 15:43:04 UTC |
