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Author SHA1 Message Date
Marius van den Beek 90eed104f0 Merge pull request #4616 from nsoranzo/fix_scripts 
Fix virtualenv activation for some scripts
 2017-09-15 08:58:25 +02:00
Dannon Baker 8b9e91310f Merge branch 'release_17.05' into dev 2017-09-14 15:17:10 -04:00
Dannon Baker 83b363d520 Merge branch 'release_17.01' into release_17.05 2017-09-14 15:10:07 -04:00
Nicola Soranzo e1be66312b Fix virtualenv activation for some scripts 
In particular add virtualenv activation to extract_dataset_parts.sh
to fix the following error when running tools which use
`<parallelism>`:
```
Fatal error:
/tmp/tmpOoQ01k/job_working_directory/000/12/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 17, in <module>
import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module>
from six import string_types
ModuleNotFoundError: No module named 'six'
```
 2017-09-14 19:58:06 +01:00
Dannon Baker a9facdc756 Merge branch 'release_16.10' into release_17.01 2017-09-14 14:54:27 -04:00
John Chilton 14ceb6d91b Merge pull request #4615 from dannon/release_16.10_backport2 
[16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview
 2017-09-14 14:10:15 -04:00
Dannon Baker 7fdce2efd9 Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. 2017-09-14 11:53:25 -04:00
Marius van den Beek 95969267c2 Merge pull request #4610 from dannon/fix_missing_histories 
Multiview missing histories fix
 2017-09-14 16:10:57 +02:00
Dannon Baker 62e73a37d3 Merge remote-tracking branch 'upstream/dev' into fix_missing_histories 2017-09-14 08:21:54 -04:00
Eric Rasche cdb95d6045 Merge pull request #4594 from martenson/fix-search-pagination 
Fix datalib search pagination
 2017-09-14 10:39:36 +02:00
Eric Rasche a9bfb04caa Merge pull request #4595 from martenson/datalib-various-fixes 
Datalibs various fixes
 2017-09-14 10:39:18 +02:00
Dannon Baker a6acf116cd Merge pull request #4607 from natefoo/py3-set-meta 
Python 3 fixes for set_metadata.py
 2017-09-13 17:22:56 -04:00
Dannon Baker 1502e00675 Some cruft fixing and configuring of Galaxy.debug output instead of commented out console.logs -- should help immensely for troubleshooting 2017-09-13 15:04:28 -04:00
Dannon Baker 4f93f88f0a Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. 2017-09-13 15:01:31 -04:00
John Chilton 52436aa4f9 Merge pull request #4600 from mvdbeek/datatypes_registroy_in_working_directory 
Write datatypes registry xml to working directory
 2017-09-13 14:57:30 -04:00
Nate Coraor b442113e76 Don't use + on iterators. 2017-09-13 13:45:29 -04:00
Martin Cech ba3ffd82d3 rebuild client 2017-09-13 13:43:08 -04:00
Martin Cech d63601eacf fix the bug with accessing length instead of the variable itself 2017-09-13 13:41:04 -04:00
Martin Cech 1f69ae5d5b refactor few functionas and rename variables 2017-09-13 13:41:04 -04:00
Martin Cech e7696027e4 remove cruft 2017-09-13 13:40:57 -04:00
Martin Cech cdca22b33e rebuild client 2017-09-13 13:38:56 -04:00
Nate Coraor 191d11c4a0 Python 3 fixes for set_metadata.py 2017-09-13 13:27:56 -04:00
Martin Cech bf89400713 remove unused requirements 
thanks @anuprulez
 2017-09-13 13:21:00 -04:00
Martin Cech 2daf4317f1 show the first page of search results 
insted of the current selected (would hide short resutls)
 2017-09-13 13:20:50 -04:00
Martin Cech 38add84971 remove unused cruft 2017-09-13 13:20:50 -04:00
Eric Rasche 11d4380d2b Merge pull request #4599 from mvdbeek/make_qsub_submissions_more_robust 
Retry job submissions in ShellJobRunner
 2017-09-13 14:39:53 +02:00
mvdbeek ecd8b90e44 Decrease log-level for resubmission msg 
and specifiy log level directly in if/else clause. Thx @erasche.
 2017-09-13 13:44:20 +02:00
Marius van den Beek e33b35def3 Merge pull request #4603 from erasche/dead-code 
Remove unreachable statements
 2017-09-13 11:31:36 +02:00
E Rasche 61e05670c2 now unused imports 2017-09-13 07:53:41 +00:00
E Rasche 60dd7306d0 Remove unreachable statements 2017-09-13 05:59:03 +00:00
mvdbeek 194b249e1d Fix import order 2017-09-12 21:08:35 +02:00
Dannon Baker 26c7abb130 Merge remote-tracking branch 'chambm/dev' into dev 2017-09-12 15:06:16 -04:00
mvdbeek 49884cdfa3 Remove references to integrated_datatypes_config 2017-09-12 19:44:02 +02:00
mvdbeek 51f2ecf857 Use a string template to write registry xml 2017-09-12 19:15:12 +02:00
mvdbeek b3b71343c1 Write out registry once per job 2017-09-12 19:15:12 +02:00
Dannon Baker 9468bef057 Merge pull request #4592 from jmchilton/workflow_click_fix 
Small improvements to workflow editor Selenium tests.
 2017-09-12 12:17:13 -04:00
Aysam Guerler 2e160935d9 Merge pull request #4578 from dannon/titles_in_views 
Delegate displaying of page titles to Layout.display()
 2017-09-12 11:49:31 -04:00
Marius van den Beek 36a3a6b3d9 Merge pull request #4569 from jvolkening/fast5 
fast5_archive datatype
 2017-09-12 15:47:55 +02:00
Nicola Soranzo c0e2db2d98 Merge pull request #4598 from mvdbeek/remove_bai_converter 
Remove bam to bai converter
 2017-09-12 14:22:07 +01:00
mvdbeek c5a08186b7 Retry job submissions in ShellJobRunner 
If I submit a large amount of jobs in a very short time I sometimes see

```
galaxy.jobs.runners.cli ERROR 2017-09-11 05:03:02,404 (17633) submission
failed (stderr): qsub: submit error (Invalid credential)
```

in my logs for a minor subset of jobs (2 out of 120 in the last instance
that this happened).
In this case waiting a little while and trying again solves the problem.
By default we will try submitting the job 3 times, and sleep 10 seconds
before trying again.
 2017-09-12 15:14:42 +02:00
mvdbeek 7e2727bc0a Remove bam to bai converter 
This converter served no real purpose (you can download bam index files
by clicking on the floppy icon, and we never had a bai datatype).
 2017-09-12 14:04:41 +02:00
Nicola Soranzo e1cdb740cb Merge pull request #4580 from jmchilton/deleted_history 
Cancel workflow invocations when histories are deleted.
 2017-09-12 01:14:42 +01:00
John Chilton 7efe561867 Rework invocation state tracking in API tests. 
At the insistence of @nsoranzo, be more explicit about waiting for workflow test in API tests. While I was in there I also setup new abstractions for waiting on state and updated various workflow cancelling tests to use test_history context for better error reporting.
 2017-09-11 16:08:29 -04:00
John Chilton 5da62ca264 Cancel workflow invocations when histories are deleted. 
With test case, rebased with spelling fixes thanks to @nsoranzo.

xref #3555 (third point)
 2017-09-11 16:07:37 -04:00
Dannon Baker c71d3035ab Merge remote-tracking branch 'upstream/dev' into titles_in_views 2017-09-11 14:56:38 -04:00
John Chilton 74a486084b Merge pull request #4579 from martenson/fix-reload-error 
datalibs: fix two bugs, refactor
 2017-09-11 14:41:53 -04:00
Dannon Baker ff5b430319 Workflow editor title fix (not new-style, to keep it simple and use the approach consistent with the .mako layout used. 2017-09-11 13:34:13 -04:00
Dannon Baker ae1c68c7db Set title on base admin page. 2017-09-11 13:09:30 -04:00
Dannon Baker ecb4e06799 We apparently always use '|' in the title, even though masthead uses '/'. It does look better. 2017-09-11 12:54:15 -04:00
Matt Chambers fd19267679 Merge pull request #2 from dannon/chambmdev 
Make client
 2017-09-11 11:04:21 -05:00