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13d61a7 John Chilton 21 November 2019, 08:39:59 UTC Version 19.9.0 of util (tag galaxy-util-19.9.0). 21 November 2019, 08:39:59 UTC
885202c John Chilton 21 November 2019, 08:38:00 UTC Packages - fix commit_version to handle multiple dev releases. 21 November 2019, 08:38:00 UTC
299a8c1 John Chilton 20 November 2019, 12:54:44 UTC Update version to 19.09 20 November 2019, 12:54:44 UTC
921178a John Chilton 20 November 2019, 12:32:45 UTC Merge pull request #9014 from nsoranzo/release_19.09_workflow_version_api_fixes [19.09] Fix name and version for export of a previous workflow version 20 November 2019, 12:32:45 UTC
512f869 Nicola Soranzo 20 November 2019, 00:01:47 UTC Fix name and version for export of a previous workflow version The API call to retrieve an old version of a workflow: ``` GET /api/workflows/<workflow_id>?version=<N> ``` was returning always the latest workflow name, while the name of a previous workflow version could have an important meaning for the user. Also, when retrieving version 0, the returned dictionary contained the latest version number instead of 0. 20 November 2019, 00:16:31 UTC
1667be8 John Chilton 19 November 2019, 19:34:12 UTC Merge pull request #8993 from martenson/whoosh-yml [19.09] make toolshed repo index understand yaml 19 November 2019, 19:34:12 UTC
fc8b832 Martin Cech 19 November 2019, 14:32:15 UTC Apply suggestions from code review @mvdbeek Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com> 19 November 2019, 14:32:15 UTC
214e9ff Björn Grüning 18 November 2019, 23:02:12 UTC Merge pull request #8999 from mvdbeek/figure_out_why_new_repo_install_not_written_to_shed_tool_conf [19.09] Fix unspecified shed_tool_config_file taking precedence over old shed_tool_conf.xml 18 November 2019, 23:02:12 UTC
8ac189a mvdbeek 18 November 2019, 20:22:17 UTC Uses fixed sam_fasta data manager from MTS and skip this test if the toolshed is down. 18 November 2019, 20:22:20 UTC
0c075f7 Martin Cech 18 November 2019, 17:05:02 UTC set logging level according to the argument also report the run summary as 'info' level 18 November 2019, 17:05:02 UTC
8668441 Martin Cech 18 November 2019, 17:01:26 UTC use configured config file when using uwsgi directly 18 November 2019, 17:01:26 UTC
5c495d6 Martin Cech 18 November 2019, 16:25:47 UTC refactor logging 18 November 2019, 16:25:47 UTC
2df309f Martin Cech 18 November 2019, 16:25:21 UTC reword, remove debug 18 November 2019, 16:25:21 UTC
19c56c7 Martin Cech 18 November 2019, 14:56:15 UTC add exec timer 18 November 2019, 14:56:15 UTC
a94017d Martin Cech 18 November 2019, 14:34:01 UTC Merge pull request #9004 from dannon/register-message-backport [19.09] Swap 'danger' to 'info' for the registration bonus message 18 November 2019, 14:34:01 UTC
f441999 Dannon Baker 15 November 2019, 19:23:43 UTC Swap 'danger' to 'info' for the registration bonus message -- 1) easy way to fix tests, and 2) it shouldn't look like an error anyway 18 November 2019, 11:11:50 UTC
945592a mvdbeek 16 November 2019, 16:24:40 UTC Fix testcase, need to use shed_tool_config_file (or get last tool_config from app) 16 November 2019, 16:24:40 UTC
0efc3bb mvdbeek 16 November 2019, 14:24:19 UTC Get toolbox then add shed_tool_config_file if unset This means we're not loading/creting this file if a valid shed_tool_conf.xml file is already in use. 16 November 2019, 15:08:55 UTC
b2f4e93 mvdbeek 16 November 2019, 10:56:00 UTC Make tearDown of integration test more robust 16 November 2019, 15:08:55 UTC
bf5d50e mvdbeek 16 November 2019, 10:44:23 UTC Raise Exception in get_shed_tool_conf_dict if invalid shed_tool_conf selected 16 November 2019, 15:08:55 UTC
1759aa5 mvdbeek 16 November 2019, 10:41:06 UTC Drop default parameter from get_shed_config_dict_by_filename, it's always None 16 November 2019, 15:08:55 UTC
a1d137a mvdbeek 15 November 2019, 18:59:34 UTC Introduce ToolBox.default_shed_tool_conf_dict and use it where appropriate This will always work unless there is a configuration error (if there are no dynamic (=shed installable) tool configs active. 16 November 2019, 14:41:08 UTC
7546c13 mvdbeek 16 November 2019, 09:45:51 UTC Fix selecting unspecified default shed_tool_config_file_set This commit fixes https://github.com/galaxyproject/galaxy/issues/8952#issuecomment-554346736 in particular. 16 November 2019, 10:46:15 UTC
62483ec mvdbeek 15 November 2019, 20:48:28 UTC Fix log message when using default shed_tool_conf file 16 November 2019, 10:46:15 UTC
610d4f0 mvdbeek 15 November 2019, 19:02:00 UTC Don't recalculate shed_conf_dict 16 November 2019, 10:46:15 UTC
c0a9414 mvdbeek 15 November 2019, 19:01:29 UTC Update shed_tool_conf if only basename of file is given 16 November 2019, 10:46:15 UTC
02f4a10 Nicola Soranzo 16 November 2019, 01:51:20 UTC Merge pull request #8976 from martenson/upload-tags [19.09] do not force library tags to be `name:` tags + backport 16 November 2019, 01:51:20 UTC
bec6a96 mvdbeek 15 November 2019, 18:58:54 UTC Use abspath whenever dealing with config_filename 15 November 2019, 18:58:54 UTC
453cad4 mvdbeek 15 November 2019, 16:32:01 UTC Log the type of tool conf that is being loaded 15 November 2019, 16:32:01 UTC
6e84af4 Martin Cech 08 November 2019, 20:05:40 UTC avoid different unicode str behavior on py2/3 15 November 2019, 15:53:53 UTC
cbeb244 Martin Cech 08 November 2019, 18:04:54 UTC prevent bootstrap to inject "!important" overflow css rule it makes library dataset page unscrollable xref https://github.com/galaxyproject/galaxy/pull/8787 15 November 2019, 15:53:48 UTC
0cf3ca9 Martin Cech 08 November 2019, 17:53:34 UTC bring some clarity to library tag handling fix tag list handling when updating ldda add test for ldda tag update add doc tests for tag parsing methods refactor 15 November 2019, 15:53:44 UTC
bbe1a8a Martin Cech 07 November 2019, 21:48:54 UTC strip the named tag prefix do not store tags like "name:name:value" 15 November 2019, 15:53:39 UTC
f3f40e5 Martin Cech 07 November 2019, 21:23:59 UTC trim the loaded value, since Galaxy tends to start with a newline 15 November 2019, 15:53:32 UTC
4725903 Martin Cech 14 November 2019, 23:17:32 UTC switch from every minute to every hour 14 November 2019, 23:17:32 UTC
dfc2075 Martin Cech 14 November 2019, 23:07:48 UTC use built-in uwsgi CRON-like feature to build shed search idnexes every hour 14 November 2019, 23:07:48 UTC
c9d9009 Martin Cech 14 November 2019, 23:07:06 UTC refactor and modernize toolshed search indexes build script mainly so it can read yml config 14 November 2019, 23:07:06 UTC
4414aef John Chilton 14 November 2019, 00:33:05 UTC Merge pull request #8985 from mvdbeek/use_path_installed_changeset_revision [19.09] Use path as source of truth for installed_changeset_revision 14 November 2019, 00:33:05 UTC
25f108f John Chilton 13 November 2019, 20:04:23 UTC Merge pull request #8959 from mvdbeek/dont_fail_if_repository_metadata_is_wrong [19.09] Make repository updates more robust 13 November 2019, 20:04:23 UTC
2f67794 mvdbeek 13 November 2019, 16:41:25 UTC Fix Tool._repository dir when tool in base of repository 13 November 2019, 16:41:25 UTC
7aa7301 Marius van den Beek 13 November 2019, 15:21:08 UTC Merge pull request #8951 from dannon/login-terms [19.09] Several registration fixes. 13 November 2019, 15:21:08 UTC
e7b64e9 Björn Grüning 13 November 2019, 14:51:22 UTC Merge pull request #8971 from mvdbeek/only_index_latest_version [19.09] Only index latest version of tools 13 November 2019, 14:51:22 UTC
1e218e0 mvdbeek 13 November 2019, 13:51:17 UTC Provide old logic as fallback Mostly for unit tests. 13 November 2019, 13:51:19 UTC
0d2cba0 mvdbeek 13 November 2019, 13:10:11 UTC Use path as source of truth for installed_changeset_revision It appears that the xml tag in shed_tool_conf.xml is frequently wrong. Fixes https://github.com/galaxyproject/galaxy/issues/8892 13 November 2019, 13:10:54 UTC
e792b55 mvdbeek 13 November 2019, 11:51:40 UTC Merge branch 'release_19.05' into release_19.09 13 November 2019, 11:51:40 UTC
f58850a Marius van den Beek 13 November 2019, 11:50:34 UTC Merge pull request #8980 from jmchilton/selenium_fixes_54 [19.05] Fix test repository self reference URL broken in dev. 13 November 2019, 11:50:34 UTC
abe6abe Marius van den Beek 13 November 2019, 09:27:13 UTC Merge pull request #8970 from bernt-matthias/topic/19.05-grouping-strip-newline [19.05] Backport #8953 grouping strip newline 13 November 2019, 09:27:13 UTC
e71257a mvdbeek 12 November 2019, 22:15:31 UTC Test repository install/uninstall and upgrade 13 November 2019, 07:49:12 UTC
34e217b John Chilton 13 November 2019, 01:27:06 UTC [19.05] Fix test repository self reference URL broken in dev. 13 November 2019, 01:27:06 UTC
1dbd284 mvdbeek 12 November 2019, 22:14:22 UTC Prefer shed_tool_conf.xml file if no shed_tool_conf file specified when intalling repositories through API 12 November 2019, 22:14:22 UTC
ee387ae Martin Cech 12 November 2019, 19:54:19 UTC do not force tags to be `name:` tags 12 November 2019, 19:54:19 UTC
711e32f Martin Cech 12 November 2019, 15:33:42 UTC Merge pull request #8969 from jmchilton/8759_backport [19.09] Backport 8759 (k8s fixes) 12 November 2019, 15:33:42 UTC
dbe440d M Bernt 11 November 2019, 08:26:06 UTC grouping: redecided for the less intrusive rstrip 12 November 2019, 14:46:34 UTC
d0dcab4 M Bernt 10 November 2019, 21:16:00 UTC grouping: strip newlines fixes https://github.com/galaxyproject/galaxy/issues/8383 more generally: if grouping is done on the last column then the newline was retained and contained in the output. 12 November 2019, 14:46:25 UTC
301d026 John Chilton 04 October 2019, 21:30:37 UTC Small fixes for k8s. 12 November 2019, 14:05:41 UTC
056b3de mvdbeek 12 November 2019, 09:51:26 UTC Only index latest version of tools 12 November 2019, 09:52:21 UTC
f304442 mvdbeek 11 November 2019, 18:20:08 UTC Fix unit test 11 November 2019, 18:20:08 UTC
0e4fb6a Nicola Soranzo 11 November 2019, 18:02:18 UTC Merge pull request #8961 from martenson/gs-deprec [19.09] add note to RN about GS 11 November 2019, 18:02:18 UTC
62706ac mvdbeek 11 November 2019, 17:25:00 UTC Attempt to update instead of clone if destinatino exists 11 November 2019, 17:25:00 UTC
3f7a0a8 Martin Cech 11 November 2019, 17:23:53 UTC Update doc/source/releases/19.09_announce.rst Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com> 11 November 2019, 17:23:53 UTC
226b7e5 Martin Cech 11 November 2019, 17:18:13 UTC add note to RN about GS 11 November 2019, 17:18:13 UTC
1afe6a1 mvdbeek 11 November 2019, 16:37:43 UTC Only skip installation if repository status is installed And update repository states throughout process. 11 November 2019, 16:57:56 UTC
fa4cb22 mvdbeek 11 November 2019, 15:39:44 UTC Try path based approach if no luck getting shed_tool_conf dict via toolbox 11 November 2019, 15:39:44 UTC
7e57146 mvdbeek 11 November 2019, 15:15:06 UTC Drop `default` argument to get_shed_config_dict/get_shed_config Their only use is to set them to `{}`. Thanks for the suggestion @nsoranzo. 11 November 2019, 15:16:30 UTC
9c5d111 mvdbeek 11 November 2019, 15:05:40 UTC Skip installation if requesting uninstallable revision and next revision is already installed 11 November 2019, 15:06:29 UTC
dd01b61 mvdbeek 11 November 2019, 13:59:29 UTC Don't error repository installation if tool appears invalid 11 November 2019, 14:30:15 UTC
fc7fd7a mvdbeek 11 November 2019, 13:51:48 UTC Clone repository if repository not on disk 11 November 2019, 14:30:15 UTC
3533668 mvdbeek 11 November 2019, 13:50:22 UTC Try harder to get shed_config_dict The path based approach might be less desirable, but works if the repository metadata isn't correct and lists a wrong shed_config_filename. And default to returning a dict instead of `None` if that doesn't succeed. 11 November 2019, 13:50:26 UTC
c3c8a17 Marius van den Beek 11 November 2019, 10:15:00 UTC Merge pull request #8950 from dannon/no-more-wobbles [19.09] Fix the running icon wobblies 11 November 2019, 10:15:00 UTC
09eedac Dannon Baker 09 November 2019, 03:07:52 UTC Fix registration warning message display (never worked?) 09 November 2019, 03:07:52 UTC
f321481 Dannon Baker 09 November 2019, 02:41:37 UTC When it's defined, add terms_url to registration interface in an iframe. 09 November 2019, 02:41:37 UTC
8a9f29c Dannon Baker 09 November 2019, 02:40:46 UTC Pass explicit props to login index component -- this fixes the bug where previously stuff nested under config wasn't unpacked. 09 November 2019, 02:40:46 UTC
fd9e61a Dannon Baker 08 November 2019, 21:58:59 UTC Fix the running wobblies 08 November 2019, 22:17:58 UTC
e3b9eb6 Martin Cech 08 November 2019, 17:11:42 UTC Merge pull request #8944 from mvdbeek/fix_library_tag_validation [19.09] Validate tag strings as well as list of tags 08 November 2019, 17:11:42 UTC
4e3a335 Björn Grüning 08 November 2019, 14:29:24 UTC Merge pull request #8942 from mvdbeek/fix_sample_reading [19.09] Fix reading loc file samples 08 November 2019, 14:29:24 UTC
3013895 mvdbeek 08 November 2019, 13:12:31 UTC Use listify to convert tag string to list tag should be a list in `_set_from_dict`. Thanks @nsoranzo. 08 November 2019, 14:19:57 UTC
3194eda Dannon 08 November 2019, 13:46:56 UTC Merge pull request #8945 from mvdbeek/fix_send_local_control_task_usage [19.09] Fix send local control task usage 08 November 2019, 13:46:56 UTC
2423a5b mvdbeek 08 November 2019, 12:18:33 UTC Fix send_local_control_task argument passing `kwargs` used to be the second argument, but it is now being interpreted as `get_response`. Since there's no response coming it'll hang until a timeout occurs. Fixes ``` galaxy.queue_worker: ERROR: Error waiting for task: '{'kwargs': {}, 'task': 'recalculate_user_disk_usage'}' sent with routing key 'control.main@613c834ba62c' Traceback (most recent call last): File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 979, in drain_events get(self._deliver, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/utils/scheduling.py", line 56, in get return self.fun(resource, callback, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 1017, in _drain_channel return channel.drain_events(callback=callback, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 761, in drain_events return self._poll(self.cycle, callback, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 402, in _poll return cycle.get(callback) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/utils/scheduling.py", line 56, in get return self.fun(resource, callback, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver message = self._get(queue) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get raise Empty() queue.Empty During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/galaxy/lib/galaxy/queue_worker.py", line 130, in send_task self.connection.drain_events(timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/connection.py", line 321, in drain_events return self.transport.drain_events(self.connection, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 982, in drain_events raise socket.timeout() socket.timeout ``` That occasionally occurs in the selenium tests. 08 November 2019, 12:29:57 UTC
97d6af0 Marius van den Beek 08 November 2019, 11:01:18 UTC Merge pull request #8939 from bgruening/its_condor_fix [19.09] check_for_entry_points() more agressively in the condor job runner 08 November 2019, 11:01:18 UTC
81532d9 mvdbeek 08 November 2019, 10:26:27 UTC Validate tag strings as well as list of tags I think it'd be better if we consistently used lists for tags, but it seems too late in 19.09 to make possibly bigger changes here. Fixes https://github.com/galaxyproject/galaxy/issues/8851 broken in https://github.com/galaxyproject/galaxy/pull/8530. 08 November 2019, 10:30:21 UTC
695d94b Bjoern Gruening 07 November 2019, 22:43:00 UTC adopt to Marius suggestion 07 November 2019, 22:43:00 UTC
ac1768c mvdbeek 07 November 2019, 19:48:36 UTC Fix reading loc file samples This must've been broken for some time. Fixes https://github.com/galaxyproject/galaxy/issues/8534 07 November 2019, 19:48:43 UTC
75402b4 Marius van den Beek 07 November 2019, 16:37:56 UTC Merge pull request #8897 from jmchilton/it_tool_interface [19.09] Structured access to Galaxy internals for (Interactive) Tools 07 November 2019, 16:37:56 UTC
af1b704 John Chilton 07 November 2019, 15:59:09 UTC Merge pull request #8901 from jmchilton/revert_ip_adjustments [19.09] Revert hacking IPs in container monitor script. 07 November 2019, 15:59:09 UTC
21cdf9b Marius van den Beek 07 November 2019, 13:55:43 UTC Merge pull request #8938 from martenson/fix-infomessage [19.09] Broaden library description/info/message 07 November 2019, 13:55:43 UTC
9aec180 John Chilton 07 November 2019, 13:35:03 UTC Merge pull request #8933 from mvdbeek/one_more_detached_instance [19.09] Fix DetachedInstanceError when tool shed packages are in play 07 November 2019, 13:35:03 UTC
657764c John Chilton 07 November 2019, 13:34:33 UTC Merge pull request #8934 from mvdbeek/dont_run_exec_after_process_if_job_failed [19.09] Don't re-determine if job failed in exec_after_process hook 07 November 2019, 13:34:33 UTC
3bd3f8f Nicola Soranzo 07 November 2019, 09:54:35 UTC Merge branch 'release_19.05' into release_19.09 07 November 2019, 09:54:35 UTC
61b9aee Bjoern Gruening 06 November 2019, 21:17:28 UTC check_for_entry_points() more agressively in the condor job runner 06 November 2019, 21:17:28 UTC
68eb3b0 Martin Cech 06 November 2019, 21:08:05 UTC if ldda message is not present but ldda info is, return it instead this is a bit of a hack but given the lack of clarity of what field does what on what object (info/message/description on ldda/ld/folder) it should help with the data presentation 06 November 2019, 21:08:05 UTC
71e2cdf John Chilton 06 November 2019, 13:54:46 UTC Merge pull request #8932 from mvdbeek/implicit_multiple_true_fix [19.05] Fix implicitly converted datasets unused when mapping over 06 November 2019, 13:54:46 UTC
bb38795 mvdbeek 06 November 2019, 13:32:47 UTC Give test data managers distinct ids and names 06 November 2019, 13:33:45 UTC
d6b69cf mvdbeek 06 November 2019, 13:21:19 UTC Use final_job_state in data manager exec_after_process This was all working correctly in my test, but removes some custom logic. It was theoretically possible for the old logic to fail if there was no output dataset for the job. 06 November 2019, 13:25:18 UTC
58f2382 John Chilton 06 November 2019, 11:44:14 UTC Allow anonymous users to use tools with injected API keys. https://github.com/galaxyproject/galaxy/pull/8897/files#r342997635 06 November 2019, 11:44:40 UTC
47872c8 mvdbeek 05 November 2019, 21:35:44 UTC Make sure tool runs fail if invalid param selected 06 November 2019, 09:00:43 UTC
4ba9591 mvdbeek 05 November 2019, 21:05:10 UTC Make select textable if dataset not converted yet 05 November 2019, 21:05:10 UTC
22b1a3c mvdbeek 05 November 2019, 19:52:43 UTC Also eagerload tool_dependency to tool shed repository relation 05 November 2019, 20:11:38 UTC
0d8311d mvdbeek 05 November 2019, 17:07:05 UTC Don't require legal values if conversion required In the UI that means you can choose any value and hit execute. Your job will still not run if that is an illegal value, but at least you can try. 05 November 2019, 17:07:08 UTC
ca080ee mvdbeek 05 November 2019, 17:03:42 UTC Start tool tag with param name 05 November 2019, 17:03:44 UTC
6931ea7 mvdbeek 05 November 2019, 09:59:13 UTC Add test for implicit conversion in multi_data inputs 05 November 2019, 13:37:07 UTC
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