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11216 Commits
Author SHA1 Message Date
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
John Chilton dc49a9cbc1 Fix unbound error that is possible if using tool bursting. 2016-03-24 14:35:51 +00:00
Martin Cech 21e71a9b46 Merge pull request #1905 from dannon/library_errors 
[16.01] Encoding in libraries
 2016-03-23 12:04:27 -04:00
Nicola Soranzo 9eb1db82ca Do not convert spaces to tabs when importing datasets into a library. 
Reported (with fix provided) by Fabien Mareuil in
http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-header-td4669160.html
 2016-03-22 20:03:32 +00:00
Björn Grüning 30750c32e4 Merge pull request #1880 from dannon/fix_migration_0131_mysql 
[16.01] Fixes to subworkflow migration 0131
 2016-03-22 14:14:43 +01:00
Dannon Baker 566f556b07 Merge pull request #1952 from guerler/fix_tool_access_000 
[16.01] Fix tool access rights and forwarding
 2016-03-21 19:29:31 -04:00
Dannon Baker 377ccbe23b Merge pull request #1967 from jmchilton/fix_optional_numeric_params 
[16.01] Fix #1721.
 2016-03-21 16:18:27 -04:00
John Chilton 2efd9c2687 Fix #1721. 
TODO: write test...
 2016-03-21 13:51:26 +00:00
John Chilton 9e9dfdfd55 Fix workflow scheduler log message. 2016-03-21 00:51:18 +00:00
guerler 054fdf76f0 Parse user when filtering tools 2016-03-18 20:48:24 -04:00
guerler bd0439d9b7 Fix tool access rights and forwarding 2016-03-18 20:12:21 -04:00
Dannon Baker e3e49a477d extreme casting to 1) make this code actually work with python 2, and 3) work should the web framework ever be functional in python3 2016-03-17 15:49:23 -04:00
Dannon Baker 4ef186812f Encode user_login as utf8 prior to directory manipulation. 2016-03-17 14:45:46 -04:00
Dannon Baker 98c65dcee0 Swap back to the first fix, update metrics api to use new signature. 2016-03-17 13:13:19 -04:00
Dannon Baker 87bcb5f5a1 Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names. 2016-03-17 12:09:02 -04:00
Dannon Baker f277f99aed Fix handling of time in fluent logger. 2016-03-17 11:43:52 -04:00
Dannon Baker 9a343efe8b Merge pull request #1930 from mvdbeek/more_bytestring_for_pysam 
[16.01] Ensure chrom, start, end as bytestring in BamDataProvider
 2016-03-15 16:16:22 -04:00
Marius van den Beek 18473a187e Ensure chrom, start, end as bytestring in BamDataProvider 2016-03-15 19:41:09 +01:00
Nicola Soranzo 5a50a4691c Merge pull request #1909 from mvdbeek/backport_repository_for_dependency_relationship 
[16.01] Backport  PR #1868
 2016-03-11 14:49:06 +00:00
Marius van den Beek d6e38c7d48 remove unused import 2016-03-11 13:10:08 +01:00
Marius van den Beek b3e9398c3a Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship 2016-03-11 13:10:02 +01:00
Martin Cech 3abd2c213a Merge pull request #1898 from dannon/quota_api_fix_fabien 
[16.01] Quota API issue with serialization to JSON of Decimal
 2016-03-10 20:23:00 -05:00
Dannon Baker 62b5f20756 Remove unnecessary encoding in remote_files. This allows paths and 
filenames like Ăfile.txt
 2016-03-10 20:09:37 -05:00
Dannon Baker a351c75687 Extra documentation for @mvdbeek 2016-03-09 11:31:18 -05:00
Dannon Baker f0b7a34dd3 Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html 2016-03-09 11:07:12 -05:00
Dannon Baker c6f3e9b5b2 Slight cleanup, remove outdated comment regarding tabixfile.close() 2016-03-09 10:52:31 -05:00
Dannon Baker 50f1089c72 Slight tweaks to our tabix usage. This fixes trackster without more divergence in our version of pysam. 2016-03-09 10:40:19 -05:00
Dannon Baker 0f97b50e9c Different logic for mysql (just don't worry about keys, due to the agony -- access to the database is entirely procedural and due to this we'd likely see any issues breaking these fk constraints in postgres before mysql (if ever) anyway. 2016-03-07 18:14:04 -05:00
Dannon Baker ad6273307d We can't flip storedworkflow back to non-nullable in a downgrade step here, so don't try. Just leave it alone. 2016-03-07 11:57:51 -05:00