opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-29 17:42:12 +08:00
Code Issues Packages Projects Releases Wiki Activity
29,590 Commits 63 Branches 246 Tags
e8ee2741f9093496aa68c2afe435aa9fc7dd8fcc
Commit Graph
29590 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Dannon Baker e8ee2741f9 Merge pull request #4567 from martenson/index-refresh-logging 
add logging to ts index building
 2017-09-06 15:27:25 -04:00
Martin Cech 095c1045b6 add logging to ts index building 2017-09-06 14:05:05 -04:00
Nicola Soranzo eb799267ee Merge branch 'release_17.05' into dev 2017-09-06 18:27:56 +01:00
Nicola Soranzo 41fe55129a Merge branch 'release_17.01' into release_17.05 
Conflicts:
	lib/galaxy/datatypes/data.py
 2017-09-06 18:26:49 +01:00
Dannon Baker a95566b36c Merge pull request #4562 from jmchilton/selenium_fixes_19 
Potential fix for transiently failing Selenium published histories test.
 2017-09-06 13:20:39 -04:00
Nicola Soranzo 759780b72c Merge branch 'release_16.10' into release_17.01 2017-09-06 18:19:50 +01:00
Nicola Soranzo 140c570517 Merge branch 'release_16.07' into release_16.10 2017-09-06 18:18:51 +01:00
Nicola Soranzo 4345d8e7d7 Merge branch 'release_16.04' into release_16.07 
Conflicts:
	lib/galaxy/config.py
 2017-09-06 18:12:53 +01:00
Nicola Soranzo dad5563cac Merge branch 'release_16.01' into release_16.04 2017-09-06 18:06:07 +01:00
Dannon Baker 2207e7f8aa Merge pull request #4565 from jmchilton/backport_uwsgi_fix 
[16.01] Backport uwsgi fix from #2836.
 2017-09-06 12:35:30 -04:00
John Chilton 02c7792985 [16.01] Backport uwsgi fix from #2836. 
Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy.

https://github.com/galaxyproject/galaxy/pull/2836
 2017-09-06 09:34:11 -04:00
Nicola Soranzo 37802abee2 Merge pull request #4560 from martenson/improving-datalibraries 
improve docs and access checks in datalibs manager/api
 2017-09-06 09:11:15 +01:00
Nicola Soranzo 486f436e76 Merge pull request #4559 from mvdbeek/use_bzip2file 
Allow working with pbzip2 compressed files
 2017-09-06 01:32:26 +01:00
Dannon Baker 3aacbdffd6 Merge pull request #4547 from martenson/library-import-conversions 
allow linking, posix and spaces conversions in datalib imports
 2017-09-05 17:54:33 -04:00
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
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