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71df810ddb293faffc4c2c8711bef600e698cfd9
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14534 Commits
Author SHA1 Message Date
Nicola Soranzo 71df810ddb Document <hook> sub-element of <code> 
This is deprecated and used only by:
- https://toolshed.g2.bx.psu.edu/view/devteam/cluster/
- https://toolshed.g2.bx.psu.edu/view/devteam/merge/

Fix https://github.com/galaxyproject/galaxy/issues/3516 .
 2017-06-02 15:09:44 +01:00
Nicola Soranzo 92952882d2 Fix some links and syntax errors in tool XML doc 2017-06-02 15:09:44 +01:00
Nicola Soranzo d807ed0f75 Merge branch 'release_17.05' into dev 
Conflicts:
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/bundled/login.bundled.js.map
 2017-06-02 15:05:14 +01:00
Aysam Guerler 0272e188a8 Merge pull request #4139 from dannon/tag_sorting 
[17.05] Tag fixes
 2017-06-02 02:05:44 -04:00
Dannon Baker 20d2303d34 Merge remote-tracking branch 'upstream/release_17.05' into dev 2017-06-01 13:39:36 -04:00
E Rasche 2f992d90ae Rebase 2017-06-01 16:43:21 +00:00
Daniel Blankenberg c2348340cf Fix for Data Tables loaded from a URL. 2017-06-01 12:36:37 -04:00
Dannon Baker 0954290e5d Combine list comprehensions, slightly tweak logic. 2017-06-01 10:38:18 -04:00
Dannon Baker 12905321ca Allow hashtag usage in workflow PJA tag addition mechanism 2017-06-01 10:38:18 -04:00
Dannon Baker 0c43954e8d Slight tweak of logic in tag filtering PJA 2017-06-01 10:38:18 -04:00
Dannon Baker 967c363786 Filter tags for empties (fixes #4127) 2017-06-01 10:38:18 -04:00
Daniel Blankenberg a9d0d3671a Fix for returning a fileobject in compression_utils.py when handling a zipfile. 
Will return the first named object in the archive. zipfile.os_zipfile does not exist...
 2017-05-31 16:55:32 -04:00
Dannon Baker b6597d43f3 Merge remote-tracking branch 'upstream/release_17.05' into dev 2017-05-31 15:06:35 -04:00
Dannon Baker 9896fc0e9f Merge pull request #4092 from bgruening/workflowexport_mako 
New Configure Workflow Menu UI
 2017-05-30 13:36:12 -04:00
Martin Cech 42e274d334 Merge pull request #4122 from galaxyproject/release_17.01 
[17.05] merge Release 17.01
 2017-05-30 10:11:51 -04:00
peterjc 54d6a54367 Avoid locale specific string.letters for job_name 
The job_name sanitation can fail if the locale specific
string.letters contains unexpected characters. e.g.
Saravanaraj Ayyampalayam reported getting the following
under locale en_US.iso885915

Traceback (most recent call last):
  File /.../galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 397, in <genexpr>
    job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name )
UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position 52: ordinal not in range(128)

See http://dev.list.galaxyproject.org/Issue-with-job-name-UnicodeDecodeError-in-drmaa-td4670784.html
or https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-May/025687.html

The downside of this proposed change would be to mask
reasonable non ASCII letters from the job name on a
well defined system with consistent locale settings
for both Galaxy and the Cluster. But ASCII only seems
safer.
 2017-05-29 17:40:37 +01:00
John Chilton 55336d2c31 Fix legacy Python path for genome diversity tools from miller lab. 
Fixes #4108.
 2017-05-28 19:34:20 -04:00
Dannon Baker dd06a01746 Handle *both* paths for tag appending using the now-dict correctly. 2017-05-26 10:22:13 +01:00
Dannon Baker b6e8d3e8ac Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though. 2017-05-26 10:14:48 +01:00
Dannon Baker 68433b1eff Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one) 2017-05-25 15:33:09 +01:00
guerler 6f5e76eecc Fix bad merge for populate model 2017-05-24 12:59:30 -04:00
Martin Cech 18ef6a6ab0 Update version to 17.05 2017-05-24 10:47:27 -04:00
Martin Cech e50c787aa7 Merge branch 'release_17.05' into dev 2017-05-24 10:47:20 -04:00
Nicola Soranzo 31015a83af Remove residual comment 
Follow-up on https://github.com/galaxyproject/galaxy/pull/4089
 2017-05-24 11:18:47 +01:00
Nicola Soranzo e0c0111524 Merge branch 'release_17.05' into dev 2017-05-23 23:32:33 +01:00
Martin Cech 0268f5078c Merge pull request #4107 from guerler/fix_repeats_in_workflows 
[17.05] Fixes repeat handling in workflow editor, store values as passed from ui
 2017-05-23 13:50:26 -04:00
Martin Cech 3d1da8e11d Merge pull request #4089 from mvdbeek/no_global_changes 
[17.05] Do not modify self.app.config.tool_data_path
 2017-05-23 13:19:41 -04:00
Martin Cech aa8aafb109 Merge pull request #4104 from dannon/tags_continued 
[17.05] Change to only inheriting 'name' tags
 2017-05-23 13:01:19 -04:00
guerler 4dcc145dbf Remove composite api function and duplicate resource connector 2017-05-23 12:19:03 -04:00
guerler 6f8472e525 Fixes repeat handling in workflow editor, store values as passed from ui 2017-05-23 08:08:28 -04:00
Nicola Soranzo e4de203c7d Raise an exception if name or action are not defined 
instead of silently skipping the <environment_variable> tool dependency
 2017-05-23 10:38:06 +01:00
Nicola Soranzo a033a5821a Allow empty <environment_variable> 
Presently trying to install a ToolShed tool dependency defined as

<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="MYVAR" action="set_to"></environment_variable>
    </set_environment>
</tool_dependency>

results in EnvManager.create_env_var_dict() returning None, which in turn
causes the dependency silently not being installed with this error in the
logs:

tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler DEBUG 2017-05-23 10:08:23,798 Error setting environment for tool dependency: local variable 'tool_dependency' referenced before assignment
 2017-05-23 10:35:25 +01:00
anuprulez 53037f6006 Updating url in the comments of workflow api 2017-05-23 11:24:15 +02:00
anuprulez 852aa51225 Making one api url for getting and setting workflows menu 2017-05-23 11:12:57 +02:00
anuprulez 56fcd293b5 Fixing PR review comments 2017-05-22 19:26:44 +02:00
anuprulez 8975327cfd Adjusting indentation 2017-05-22 15:35:14 +02:00
anuprulez 60cb6b4d31 Fixing PR review comment to split api calls into two 2017-05-22 15:28:53 +02:00
anuprulez 358ce8013f Merging with dev 2017-05-22 14:44:56 +02:00
Nicola Soranzo 47339bf1f3 Catch specific exception type 
Also remove unused variable
 2017-05-22 09:40:31 +01:00
Bjoern Gruening 9ec6c13fa9 update openbabel to version 2.4.1 2017-05-21 14:12:58 +02:00
anuprulez 35ec338d5d Fixing build failure comments and removing commented out lines 2017-05-20 11:37:03 +02:00
mvdbeek a1c14ee8fa Do not modify self.app.config.tool_data_path 
and self.app.config.tool_data_table_config_path during metadata setting.

xref https://github.com/galaxyproject/tools-iuc/issues/1315.

I suspect multiple threads installing tool simultaneously may have led
to self.app.config.tool_data_path and/or
self.app.config.tool_data_table_config_path being set to a temporary
directory. Initial testing looks like this is not necessary.
 2017-05-19 20:04:17 +02:00
Dannon Baker 69219e2228 Merge pull request #4087 from galaxyproject/release_17.05 
merge release 17.05
 2017-05-19 12:13:38 -04:00
anuprulez f0d28992a4 Merging with dev 2017-05-19 13:50:51 +02:00
Martin Cech 238e2a7e5f remove the content alert from TS response 2017-05-18 13:29:21 -04:00
John Chilton 7028ca04c7 Merge pull request #3946 from theosotr/feature-chronos 
Add job runner for Chronos
 2017-05-18 09:24:57 -04:00
Björn Grüning 4125f79161 Merge pull request #4034 from jmchilton/k8_name_fixed 
[17.05] Sanitize container names sending to Kubernetes.
 2017-05-17 22:36:51 +02:00
Martin Cech b9fb2de42b Merge pull request #3626 from davebx/ts_api_backbone 
API installation of toolshed repositories.
 2017-05-17 13:22:48 -04:00
Martin Cech 272fbd2235 enable TS beta isntallation interface by default 2017-05-17 13:21:33 -04:00
Martin Cech 5eadd4842d Merge branch 'release_17.05' into dev 2017-05-16 15:55:16 -04:00