Commit Graph
42605 Commits
Author SHA1 Message Date
Martin Cech dfc20759a7 use built-in uwsgi CRON-like feature to build shed search idnexes every hour 2019-11-14 18:07:48 -05:00
Martin Cech c9d9009299 refactor and modernize toolshed search indexes build script
mainly so it can read yml config
2019-11-14 18:07:06 -05:00
Marius van den Beek 7aa73016fe Merge pull request #8951 from dannon/login-terms
[19.09] Several registration fixes.
2019-11-13 16:21:08 +01:00
Björn Grüning e7b64e9697 Merge pull request #8971 from mvdbeek/only_index_latest_version
[19.09] Only index latest version of tools
2019-11-13 15:51:22 +01:00
mvdbeek e792b551c7 Merge branch 'release_19.05' into release_19.09 2019-11-13 12:51:40 +01:00
Marius van den Beek f58850a4b9 Merge pull request #8980 from jmchilton/selenium_fixes_54
[19.05] Fix test repository self reference URL broken in dev.
2019-11-13 12:50:34 +01:00
Marius van den Beek abe6abef40 Merge pull request #8970 from bernt-matthias/topic/19.05-grouping-strip-newline
[19.05] Backport #8953 grouping strip newline
2019-11-13 10:27:13 +01:00
John Chilton 34e217b328 [19.05] Fix test repository self reference URL broken in dev. 2019-11-12 20:27:06 -05:00
Martin Cech 711e32f3c2 Merge pull request #8969 from jmchilton/8759_backport
[19.09] Backport 8759 (k8s fixes)
2019-11-12 10:33:42 -05:00
M Bernt dbe440df3e grouping: redecided for the less intrusive rstrip 2019-11-12 15:46:34 +01:00
M Bernt d0dcab4628 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.
2019-11-12 15:46:25 +01:00
John Chilton 301d026bfb Small fixes for k8s. 2019-11-12 09:05:41 -05:00
mvdbeek 056b3ded2b Only index latest version of tools 2019-11-12 10:52:21 +01:00
Nicola Soranzo 0e4fb6a22a Merge pull request #8961 from martenson/gs-deprec
[19.09] add note to RN about GS
2019-11-11 18:02:18 +00:00
Martin CechandNicola Soranzo 3f7a0a8441 Update doc/source/releases/19.09_announce.rst
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
2019-11-11 12:23:53 -05:00
Martin Cech 226b7e5bf0 add note to RN about GS 2019-11-11 12:18:13 -05:00
Marius van den Beek c3c8a1728a Merge pull request #8950 from dannon/no-more-wobbles
[19.09] Fix the running icon wobblies
2019-11-11 11:15:00 +01:00
Dannon Baker 09eedace59 Fix registration warning message display (never worked?) 2019-11-08 22:07:52 -05:00
Dannon Baker f32148168d When it's defined, add terms_url to registration interface in an iframe. 2019-11-08 21:41:37 -05:00
Dannon Baker 8a9f29cbf9 Pass explicit props to login index component -- this fixes the bug where previously stuff nested under config wasn't unpacked. 2019-11-08 21:40:46 -05:00
Dannon Baker fd9e61a0d6 Fix the running wobblies 2019-11-08 17:17:58 -05:00
Martin Cech e3b9eb62f6 Merge pull request #8944 from mvdbeek/fix_library_tag_validation
[19.09] Validate tag strings as well as list of tags
2019-11-08 12:11:42 -05:00
Björn Grüning 4e3a3350b5 Merge pull request #8942 from mvdbeek/fix_sample_reading
[19.09] Fix reading loc file samples
2019-11-08 15:29:24 +01:00
mvdbeek 3013895f78 Use listify to convert tag string to list
tag should be a list in `_set_from_dict`.

Thanks @nsoranzo.
2019-11-08 15:19:57 +01:00
Dannon 3194eda08b Merge pull request #8945 from mvdbeek/fix_send_local_control_task_usage
[19.09] Fix send local control task usage
2019-11-08 08:46:56 -05:00
mvdbeek 2423a5b2dc 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.
2019-11-08 13:29:57 +01:00
Marius van den Beek 97d6af0b6e Merge pull request #8939 from bgruening/its_condor_fix
[19.09] check_for_entry_points() more agressively in the condor job runner
2019-11-08 12:01:18 +01:00
mvdbeek 81532d9c64 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.
2019-11-08 11:30:21 +01:00
Bjoern Gruening 695d94bf8c adopt to Marius suggestion 2019-11-07 23:43:00 +01:00
mvdbeek ac1768c8d8 Fix reading loc file samples
This must've been broken for some time.
Fixes https://github.com/galaxyproject/galaxy/issues/8534
2019-11-07 20:48:43 +01:00
Marius van den Beek 75402b4bab Merge pull request #8897 from jmchilton/it_tool_interface
[19.09] Structured access to Galaxy internals for (Interactive) Tools
2019-11-07 17:37:56 +01:00
John Chilton af1b704bad Merge pull request #8901 from jmchilton/revert_ip_adjustments
[19.09] Revert hacking IPs in container monitor script.
2019-11-07 10:59:09 -05:00
Marius van den Beek 21cdf9bcbc Merge pull request #8938 from martenson/fix-infomessage
[19.09] Broaden library description/info/message
2019-11-07 14:55:43 +01:00
John Chilton 9aec180341 Merge pull request #8933 from mvdbeek/one_more_detached_instance
[19.09] Fix DetachedInstanceError when tool shed packages are in play
2019-11-07 08:35:03 -05:00
John Chilton 657764cfb4 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
2019-11-07 08:34:33 -05:00
Nicola Soranzo 3bd3f8f41c Merge branch 'release_19.05' into release_19.09 2019-11-07 09:54:35 +00:00
Bjoern Gruening 61b9aee3ff check_for_entry_points() more agressively in the condor job runner 2019-11-06 22:17:28 +01:00
Martin Cech 68eb3b000f 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
2019-11-06 16:08:05 -05:00
John Chilton 71e2cdf981 Merge pull request #8932 from mvdbeek/implicit_multiple_true_fix
[19.05] Fix implicitly converted datasets unused when mapping over
2019-11-06 08:54:46 -05:00
mvdbeek bb38795e75 Give test data managers distinct ids and names 2019-11-06 14:33:45 +01:00
mvdbeek d6b69cf6d5 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.
2019-11-06 14:25:18 +01:00
John Chilton 58f2382ad0 Allow anonymous users to use tools with injected API keys.
https://github.com/galaxyproject/galaxy/pull/8897/files#r342997635
2019-11-06 06:44:40 -05:00
mvdbeek 47872c82fd Make sure tool runs fail if invalid param selected 2019-11-06 10:00:43 +01:00
mvdbeek 4ba9591cb9 Make select textable if dataset not converted yet 2019-11-05 22:05:10 +01:00
mvdbeek 22b1a3c723 Also eagerload tool_dependency to tool shed repository relation 2019-11-05 21:11:38 +01:00
mvdbeek 0d8311d385 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.
2019-11-05 18:07:08 +01:00
mvdbeek ca080eeef1 Start tool tag with param name 2019-11-05 18:03:44 +01:00
mvdbeek 6931ea733b Add test for implicit conversion in multi_data inputs 2019-11-05 14:37:07 +01:00
mvdbeek dc0f68ba68 Fix implicitly converted datasets unused when mapping over 2019-11-05 10:20:15 +01:00
Marius van den Beek 1b776b5b0b Merge pull request #8916 from jmchilton/data_req_fix
[19.09] Fix galaxy-data package requirements.
2019-11-04 11:45:58 +01:00