Commit Graph
42585 Commits
Author SHA1 Message Date
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
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
Nicola Soranzo 4b9c41503c [19.09] Fix TypeError in logging commands (#8925)
[19.09] Fix `TypeError` in logging commands
2019-11-04 09:49:41 +00:00
Sergey Golitsynskiy a855e2ca64 Fix TypeError in logging commands
Fix the following exception:

```
TypeError: not all arguments converted during string formatting
```

Also, make other log format strings more consistent: %d for numeric object IDs.
2019-11-03 21:35:07 +00:00
John Chilton fde0cd72cf Fix galaxy-data requirements.
No longer pinning sqlalchemy to 1.2.
2019-10-31 09:29:08 -04:00
Nicola Soranzo 1663c9e331 Check host_ip only once 2019-10-30 15:30:03 +00:00
John Chilton 391381d3c4 small doctest for docker port parsing 2019-10-30 11:08:27 -04:00
John Chilton ff08885c2e Only re-map container monitor host if can find IP and have 0.0.0.0. 2019-10-30 11:03:20 -04:00
John Chilton 8807a8f39f Separate new inject tests into new tool. 2019-10-30 10:09:34 -04:00
John Chilton 1240ab276b Fix id convention for test interactive tools. 2019-10-30 09:59:55 -04:00
John Chilton c9ca348c62 Update galaxy.xsd for injecting API keys. 2019-10-30 09:59:55 -04:00
John Chilton 4ccef702be Cleanup structured IT internals access commit.
- Unit test fixes and added tests.
- Change __history_id to __history_id__ per comment from @bgruening
2019-10-30 09:59:55 -04:00
John Chilton 2912094de0 Allow per-destination overrride of galaxy_url for tools.
The proper interaction between tools and jobs for determining Galaxy's URL from the destination of the tool.
2019-10-30 09:59:55 -04:00
John Chilton 2e7a0720e7 Structured access to Galaxy internals for ITs. 2019-10-30 09:59:55 -04:00
John Chilton c554118a05 Merge pull request #8896 from ic4f/sg_config40_1909
[19.09] If config_file is None, use cwd, not its parent
2019-10-29 10:35:53 -04:00
John Chilton 352e751927 Revert hacking IPs in container monitor script.
It breaks the Mac setup and seems just wrong, docker might not be on localhost. This needs to be made more specific in some way and should handle those socker commands not working on OS X.
2019-10-29 10:12:38 -04:00
Sergey Golitsynskiy bc611c1d3c If config_file is None, use cwd, not its parent
Backport #8894

Context:
https://github.com/galaxyproject/galaxy/pull/921#discussion_r304351292
2019-10-28 10:59:06 -04:00
Nicola Soranzo 7fb7862f55 Merge branch 'release_19.05' into release_19.09 2019-10-28 14:39:29 +00:00
Marius van den Beek fb1c0f8de2 Merge pull request #8895 from nsoranzo/release_19.05_followup_on_8891
[19.05] Safer fix for ``unicodify`` on exceptions with bytestring message
2019-10-28 15:18:27 +01:00
Nicola Soranzo 9c3be80a7c Safer fix for `unicodify` on exceptions with bytestring message
Follow-up on https://github.com/galaxyproject/galaxy/pull/8891 .
Should be safer for `Exception` subclasses that override `__str__()`
/ ` __unicode__()` methods.
2019-10-28 12:20:13 +00:00
Björn Grüning a7d664bb31 Merge pull request #8886 from mvdbeek/no_delete_queues
[19.09] Discard messages created before QueueWorker was started
2019-10-27 19:23:30 +01:00
John Chilton 70b2ba96b2 Merge pull request #8891 from mvdbeek/fix_unicodify_on_exceptions
[19.05] Fix unicodify on exceptions with non-utf bytestring args
2019-10-27 13:25:39 -04:00