Evgeny Anatskiy
29622bba69
add history rename test
2017-09-05 23:12:38 +02:00
John Chilton
580811d740
Potential fix for transiently failing Selenium published histories test.
...
The the [latest Selenium test execution](https://jenkins.galaxyproject.org/job/selenium/212/testReport/ ) most of the published histories tests failed. It looks like this is because of the three histories that were supposed to be published, only 2 were actually published. My best guess for what happeend was that the click of the button to publish the history occurred but the next Selenium command happened so quickly that the page had not gotten a chance to respond to the click. This tweaked approach to publishing histories ensures we stay on the page until the "unpublish" link appears - this will either fix the problem or rule this theory out as the explanation.
2017-09-05 14:48:30 -04:00
Martin Cech
f78eca8912
remove unused import
2017-09-05 14:28:21 -04:00
mvdbeek
8c4716e71d
Use environment markers to select bz2file when python is < 3.3
2017-09-05 19:32:37 +02:00
Dannon Baker
7db47e7e3c
Merge pull request #4557 from jmchilton/shared_histories_unbound
...
Prevent unbound variable error history controller.
2017-09-05 13:27:51 -04:00
John Chilton
b734581495
Merge pull request #4561 from mvdbeek/reintroduce_missing_tool_test
...
Revert "Remove Selenium test that is broken because Galaxy is broken."
2017-09-05 13:19:43 -04:00
mvdbeek
2541928855
Revert "Remove Selenium test that is broken because Galaxy is broken."
...
This reverts commit a91c03d440
2017-09-05 18:46:13 +02:00
Björn Grüning
3962ba94d7
Merge pull request #4549 from jmchilton/selenium_fixes_18
...
Assorted Selenium test fixes
2017-09-05 18:42:16 +02:00
mvdbeek
cccf79ac5f
Make bz2file dependency conditional on python being below version 3.3
2017-09-05 18:30:25 +02:00
Nicola Soranzo
235bdca1eb
Merge pull request #4556 from jmchilton/conditional_chronos
...
Make chronos dependency conditional.
2017-09-05 17:26:05 +01:00
jvolkening
87b798d40a
FAST5 archive support
2017-09-05 11:08:54 -05:00
mvdbeek
4de0ec59f3
Add bz2file to list of requirements
2017-09-05 17:54:24 +02:00
Martin Cech
b12d29d14b
improve docs and access checks
...
thanks @nsoranzo
2017-09-05 11:50:33 -04:00
John Chilton
65b86e3eb0
Merge pull request #4553 from mvdbeek/allow_exporting_workflow_with_uninstalled_tools
...
Allow exporting workflows when tool is uninstalled
2017-09-05 11:04:59 -04:00
mvdbeek
46c85ffa98
Allow working with pbzip2 compressed files
...
This adds supprt for uploading and uncompressing pbzip2 compressed
files by exchanging the bz2 module with bz2file (recommended as workaround in
https://docs.python.org/2/library/bz2.html ). The problem was reported by
@alpapan in #4538 and this commit should fix #4538 .
Depends on https://github.com/galaxyproject/starforge/pull/147 for the
bz2file wheel.
2017-09-05 16:54:34 +02:00
John Chilton
338b0c994c
Merge pull request #4511 from FredericBGA/import_history_and_symlink
...
import of history works even if we use symlink in database directory
2017-09-05 10:53:44 -04:00
John Chilton
c671581900
Prevent unbound variable error history controller.
...
Fixes #4423 I suppose - thanks @erasche.
2017-09-05 10:39:42 -04:00
John Chilton
932a3aa3be
Make chronos dependency conditional.
...
Fixes #4085 .
2017-09-05 10:28:16 -04:00
Martin Cech
a13bd06f48
Merge pull request #4555 from jmchilton/lower_matching_threshold
...
Lower threshold for auto-matching dataset pairs in the collection builder
2017-09-05 10:15:31 -04:00
Martin Cech
63392a6107
fix copypasta
2017-09-05 10:07:05 -04:00
John Chilton
1e3bd2d4e8
Merge pull request #4489 from arbernard/LMOD_Dependency_resolver
...
New Dependency resolver for the LMOD environment modules system
2017-09-05 09:29:07 -04:00
John Chilton
96cf1b94f1
Lower threshold for auto-matching dataset pairs in the collection builder.
...
Thanks to @mvdbeek for originally testing this and verifying it works.
Fixes #4349 .
2017-09-05 09:21:47 -04:00
Dannon Baker
6e6845b498
Merge pull request #4534 from jmchilton/collection_import_export_test_case
...
Refactor history import/export tests to allow collection testing.
2017-09-05 08:59:04 -04:00
mvdbeek
bff6b58a1b
Allow exporting workflows when tool is uninstalled
2017-09-05 14:24:06 +02:00
John Chilton
af9173d7cf
Merge pull request #4552 from mvdbeek/fix_missing_tools_wf_editor_alternative
...
Fix missing tools wf editor alternative
2017-09-05 08:03:14 -04:00
mvdbeek
40c9ca5ee9
Log warning for missing tools when building workflow modules
2017-09-05 13:34:50 +02:00
mvdbeek
09c96dace2
Fix extra-space (thx @nsoranzo)
2017-09-05 12:46:28 +02:00
mvdbeek
33defd1307
Revert "Properly raise Exception if tool not found"
...
This reverts commit 1015b510f8
2017-09-05 12:32:08 +02:00
mvdbeek
686cb48c71
Alternative fix for workflow editor hang with missing tools
2017-09-05 12:20:42 +02:00
John Chilton
a91c03d440
Remove Selenium test that is broken because Galaxy is broken.
...
See (https://github.com/galaxyproject/galaxy/issues/4548 ) for more information on the underlying issue.
2017-09-04 21:30:00 -04:00
John Chilton
ebcb4aa623
Possible fix for a transient failure in the published histories grid tests.
...
See failure here (https://jenkins.galaxyproject.org/job/selenium/210/testReport/selenium_tests.test_published_histories_grid/HistoryGridTestCase/test_history_grid_sort_by_owner/ ).
Uses technique to retry atomic assertions that may not be immediately true but will settle as the DOM is updated in response to changes to be true (added in https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af78aab2deaaaa ).
2017-09-04 21:21:20 -04:00
John Chilton
4d3452c09e
Update the default testing Selenium Chrome Docker target.
...
Some recent changes was incompatible with some bug in the older version (possibly this bug https://bugs.chromium.org/p/chromedriver/issues/detail?id=1552 ), the result is a huge number of failures in Jenkins as some persistent session error occurs. For example the older (https://jenkins.galaxyproject.org/job/selenium/209/testReport/ ) but with me hacking the Jenkins job to make this change only two tests fail (https://jenkins.galaxyproject.org/job/selenium/210/testReport/ ).
2017-09-04 21:13:13 -04:00
Martin Cech
9b4cd096e1
Merge pull request #4505 from jmchilton/composite_upload_refine
...
Tests and clarifications for composite uploads.
2017-09-04 21:02:40 -04:00
Nicola Soranzo
003344ac2f
Merge pull request #4546 from mvdbeek/tool_form_followup
...
Check user roles only once if user has no roles
2017-09-04 17:05:43 +01:00
mvdbeek
9556c467e3
Check user roles only once if user has no roles
...
The previous implementation in #4541 would check user roles multiple
times if a user has no roles.
Noticed by @nsoranzo, many thanks!
2017-09-04 17:08:59 +02:00
John Chilton
3d9809a50d
Merge pull request #4512 from martenson/improving-datalibraries
...
A round of data libraries improvements.
2017-09-04 00:21:51 -04:00
John Chilton
8f1303217e
Merge pull request #4495 from erasche/parse-once
...
41% reduction in freiburg galaxy startup time
2017-09-03 20:17:56 -04:00
John Chilton
f6fa7c39f1
Merge pull request #4542 from mvdbeek/build_module_speedup
...
Add a small howto on profiling galaxy code
2017-09-03 20:13:10 -04:00
Björn Grüning
b2ceef5b6c
Merge pull request #4536 from jmchilton/test_refactoring
...
Refactor test modules toward cleaner dependencies
2017-09-03 21:41:32 +02:00
mvdbeek
2e5bbad353
Clarify the last section
2017-09-03 19:47:29 +02:00
mvdbeek
634f7dcd39
Add a small howto on profiling galaxy code
2017-09-03 19:38:56 +02:00
Evgeny Anatskiy
a1e79b13e1
add the first test
2017-09-03 19:04:33 +02:00
Aysam Guerler
ae7e1f97f0
Merge pull request #4541 from mvdbeek/build_module_speedup
...
Speedup toolform building
2017-09-03 12:32:43 -04:00
mvdbeek
2d8b242e69
Fix caching of get_converters_by_datatype result
2017-09-03 17:17:49 +02:00
mvdbeek
d1a2007275
Cache user roles during WorkRequestContext lifetime
...
This speeds up building the tool module by a factor of 5.
2017-09-03 16:27:05 +02:00
Björn Grüning
ea9f5f7eb2
Merge pull request #4524 from jmchilton/selenium_fixes_16
...
Fix workflow run Selenium test and make it more robust.
2017-09-03 16:25:35 +02:00
mvdbeek
471707bd7d
Build converters_by_datatype only once per registry lifetime
2017-09-03 13:19:06 +02:00
mvdbeek
06db29413e
Move instead of copying converted datasets when possible
...
shutil.move tries to move files by renaming them. If that fails with
OSError (due to permission or cross-filesystem rename) it falls back to
copying files followed by removing them
(https://github.com/python/cpython/blob/2.7/Lib/shutil.py#L279 ). By
using shutil.move and catching permission problems we avoid an
unnecessary copy if source and destination are on the same filesystem.
Also avoids shutil.move if the upload tool is run as real-user which
should fix https://github.com/galaxyproject/galaxy/issues/4300 .
2017-09-03 12:03:36 +02:00
mvdbeek
62ef8b52ae
Fix sniffing for non-binary files
2017-09-03 10:49:23 +02:00
mvdbeek
14497719ba
Prevent in-place editing if purge_source is false
...
When importing files from the FTP folder the admin can choose to prevent
purging of imported files. In this case the source file should not be
modified in-place by galaxy.
This also modifies relevant bare `except:` statements and modifies
the meaning of `in_place` in upload.py from no external chown script to
do not edit files in place if we keep the source file.
This fixes https://github.com/galaxyproject/galaxy/issues/4527 .
2017-09-03 09:48:39 +02:00
Evgeny Anatskiy