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Commit Graph
11244 Commits
Author SHA1 Message Date
Dannon Baker 814c7f926d Drop unused peek method (this used unencoded ids) 2018-09-28 11:50:18 -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
mvdbeek c524521956 Make catching XML parsing errors python2.6 compatible 2016-11-04 20:21:05 +01:00
mvdbeek f6ca913809 Log invalid xml filename 2016-11-04 17:53:12 +01:00
mvdbeek c94b2205b2 Escape section id and name when writing integrated_tool_panel.xml 
This should fix #3084.
 2016-11-04 17:42:16 +01:00
Marius van den Beek 6d27a3c4b6 Fix initial conda version at 4.0.5 
This should prevent missing `activate` in <conda_prefix>/bin when
downgrading to 3.19.3. This is what the conda people use in their CI
environment (
[see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh#L61)
and perhaps why that bug made it into the release in the first place).
 2016-10-05 18:16:24 +02:00
carlfeberhard b301fd4202 Dataset perms: correct comment 2016-09-14 13:18:46 -04:00
carlfeberhard fc3dcf3b87 Permissions, datasets: allow admin in RBAC 
- Admin are considered permitted when calling
  ** dataset_manager.permssions.access and
  ** dataset_manager.permissions.manage
- Update bad test
- Add admin test to other permission checks
 2016-09-13 13:00:58 -04:00
carlfeberhard 91a190c6eb Datasets: allow admin to serialize permissions 
And updates tests.
 2016-09-12 10:50:57 -04:00
Nicola Soranzo 33c4025fab Fix misplaced parenthesis 
Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304
 2016-08-10 14:34:08 +01:00
Eric Enns 7e389c7d54 Fixed E226 2016-07-19 14:27:26 -04:00
Eric Enns 09b9339569 Fixed to only line_count not line_count + 1 lines and added in really basic test 2016-07-19 14:27:09 -04:00
Eric Enns 5f24afb1b3 Fix off by one error, causing only first line of file to be rendered in peek. 2016-07-19 14:26:58 -04:00
Nicola Soranzo 89890d4f60 Fix move_directory_files tool dependency action when destination is not empty 
Historically this action moves the contents of the source directory to the
destination directory. Commit d38936bd8d
broke the install when e.g. the destination is $INSTALL_DIR, which is
created by Galaxy and is not empty (contains INSTALLATION.log after first
action).
 2016-06-21 17:59:17 +01:00
Nicola Soranzo 4bfa2f62fb Fix for py34-lint 2016-06-21 17:56:42 +01:00
Dannon Baker 8b2ae46467 Copy PJAs when importing a workflow. 2016-06-20 11:33:34 -04:00
Dannon Baker 75cdec9b4b Merge pull request #2479 from nsoranzo/release_16.01_fix_for_1947 
[16.01] Fix move_directory_files tool dependency action when new_file_path is on a different filesystem
 2016-06-15 10:14:32 -04:00
Nicola Soranzo 933f42619e Log all failed job status checks 2016-06-10 12:34:48 +01:00
Nicola Soranzo 7c40c85034 Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries 2016-06-10 12:31:00 +01:00
Nicola Soranzo d38936bd8d Move the whole directory instead of element by element 
Fix #1947.
 2016-06-09 18:41:10 +01:00
Nicola Soranzo d95e9b840d Refactor move_file() method 2016-06-09 17:59:39 +01:00
carlfeberhard 2a29e92ef9 API, history: fix order in most_recently_used 
- Fix ascending order used in HistoryManager.most_recent to descending
- Slightly update the docs to reflect actual value better
- Add tests
 2016-05-24 17:08:08 -04:00
Nicola Soranzo ad0647d677 Change elif to if because drmaa_state can be changed inside the if 2016-05-04 20:12:03 +01:00
Nicola Soranzo 338d254031 Use partial messages to match SLURM memory warnings 2016-05-04 19:56:48 +01:00
Lance Parsons 3005bba5e3 Remove SLURM memory limit warning from stderr if the job was successful 2016-05-04 16:20:39 +01:00
Dannon Baker 063b25f660 Merge pull request #2260 from jmchilton/fix_burst_background_workflows 
[16.01] Fix running workflows in the background when tool bursting is enabled.
 2016-05-03 18:18:00 -04:00
John Chilton 615b0b444e Fix running workflows in the background when tool bursting is enabled. 2016-04-27 15:36:45 -04:00
Dannon Baker eb15c14750 Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly. 2016-04-19 12:25:17 -04:00
Martin Cech 8e72b3095b Merge pull request #2174 from mvdbeek/reorder_job_template 
[16.01] Backport #2146 #2145
 2016-04-15 09:59:38 -04:00
Marius van den Beek 434321915a Use "$NCPUS" if defined to set GALAXY_SLOTS 
On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the
hostname of the nodes the task runs on. But we do have "$NCPUS" with the
correct number of CPUS.
 2016-04-15 10:51:11 +02:00
Marius van den Beek e193e46e30 Place $headers before integrity_check 
PBS needs the resource selection (which will be filled in using $headers) to
appear before anything else (except the shebang), so this changes the order.
 2016-04-15 10:48:10 +02:00
Dannon Baker 18c00899a3 Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 
[16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters
 2016-04-14 17:20:23 -04:00
carlfeberhard 570baa5bb6 Fix bad merge: when HTTP_GX_SECRET is None 2016-04-14 14:06:13 -04:00
carlfeberhard e26bff23ed Merge 'release_15.10' with 'release_16.01' 2016-04-14 12:59:05 -04:00
Martin Cech f85aaa4a27 port of middleware fix for TS (#2106) 2016-04-13 15:22:35 -04:00
Nicola Soranzo cde04ad52d markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. 
Fix #2135.
 2016-04-12 15:52:01 +01:00
Martin Cech f759961a29 mention planemo in the error message for disabled TS pushing 
rephrase to Norwegian
 2016-04-11 12:56:42 -04:00
Martin Cech 50268cb8ca fix missing call; add docs and refactor a bit 2016-04-07 18:22:42 -04:00
Martin Cech 0882b4d8fb use proper method for detecting admin 2016-04-06 15:32:52 -04:00
Martin Cech 9ecf99c227 make dependencies browsable again 
it would be denied previously as the dependency folder is
outside of the repository (symlink protection)
 2016-04-06 13:55:32 -04:00
Martin Cech 65a7ebee23 Merge pull request #2072 from mvdbeek/backport_1738 
[16.01] backport #1738
 2016-04-04 09:34:02 -04:00
Marius van den Beek 20f61e6a2f workaround for error message in case original toolshed had been disabled 2016-04-04 12:28:46 +02:00
John Chilton 90b95dc665 Merge pull request #2043 from martenson/update_mercurial_wheel 
[16.01] upgrade mercurial wheel to latest (fixing CVE issues)
 2016-03-31 14:26:02 -04:00
Nicola Soranzo 7d08d1b069 Specify default value when getting disable_push 2016-03-31 11:11:08 -04:00
Martin Cech dc4d4cbce7 disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#deprecation-notices 2016-03-31 11:10:58 -04:00
Martin Cech 449098d8b1 upgrade mercurial wheel to latest (fixing CVE issues) 2016-03-30 14:34:38 -04:00
John Chilton e6d3529b4c [16.01] Fix for running jobs when metadata tool is not in toolbox. 
Happens when -installed or -migrated are passed into run_tests.sh because of the way the tool shed hacks up Galaxy's tool config.
 2016-03-28 15:13:24 -04:00
Daniel Blankenberg 948a4aa55b Merge pull request #2013 from jmchilton/fix_1657_stable 
[16.01] Fix PJA creation in tool bursting threads.
 2016-03-25 15:14:29 -04:00
John Chilton 4f2661a1e9 Fix PJA creation in tool bursting threads. 
Potentially fixes #1657.
 2016-03-25 12:08:33 -04:00
Dannon Baker 7d1b525682 The response from dataproviders here can return data===null in addition to being simply undefined. This corrects the logic shortcutting and prevents errors like 'Cannot read property 'min' of null' 2016-03-25 10:37:28 -04:00