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Commit Graph
9546 Commits
Author SHA1 Message Date
Renato Alves aa857fcdbd Remove bad HTML tags from login template 2015-05-28 16:16:14 +01:00
dpryan79 6cc83bf0b9 Ensure that asbool is imported 2015-05-27 13:16:29 +02:00
dpryan79 3536ff923c Allow the condor job runner to respect the embed_metadata_in_job parameter 2015-05-27 13:02:23 +02:00
John Chilton 3946ff50bb Merge pull request #80 from erasche/jbrowse-ie 
Add EDAM IDs to datatypes
 2015-05-22 09:42:59 -05:00
John Chilton 887ebcd4a0 More tweaks to edam mappings. 2015-05-22 10:34:13 -04:00
Daniel Blankenberg 5e97f5a1ae Allow external display applications optional access to files within a datasets extra_files_path by setting allow_extra_files_access="True" within the parameter. 2015-05-21 14:07:29 -04:00
John Chilton 1a39b6aa79 Merge remote-tracking branch 'jmchilton/release_15.05' into dev 2015-05-20 15:48:25 -04:00
Daniel Blankenberg 9e67ba6de2 Merge pull request #278 from natefoo/load_speedup_cherrypick 
[15.05] Significant speedup of tool panel/homepage loading
 2015-05-20 12:49:18 -04:00
Nate Coraor 27476764e9 Merge pull request #273 from jmchilton/test_bool_fixes 
[15.05] Fixes for boolean & select handling in test data elements.
 2015-05-20 12:29:44 -04:00
abretaud c567530723 handle adding/removing tools from toolshed 
(cherry picked from commit 911acd7a6e)
 2015-05-20 12:21:21 -04:00
abretaud 0d3c849d4f perf optimization: store tools' section in a dict instead of looping through the whole list of sections/tools for each tool 
(cherry picked from commit b8261db255)
 2015-05-20 12:21:15 -04:00
John Chilton 7f12d33b67 Add endpoint /api/datatypes/edam_formats... 
... which maps Galaxy extensions to EDAM formats.
 2015-05-20 09:40:24 -04:00
John Chilton 4228d32d35 Add edam_format(s) to input and output descriptions in the API. 2015-05-20 09:16:14 -04:00
John Chilton e1c4a51274 Fix edam format on BAM. 2015-05-20 09:16:13 -04:00
Nicola Soranzo 09b900d873 Fix typos in comment. 2015-05-20 11:30:12 +01:00
Dannon Baker fc423a9bf4 Merge pull request #268 from guerler/api_build_history_id 
Accept history id in tool model building api
 2015-05-19 16:17:47 -04:00
John Chilton 18c708981d Merge pull request #270 from erasche/xmfa 
Mauve XMFA datatype
 2015-05-19 15:08:14 -05:00
John Chilton f469db3d7e Fixes for boolean & select handling in test data elements. 
- Allow boolean "truevalue"/"falsevalue" to be used in plain (non-conditional test element) parameters (see https://trello.com/c/iGk3f1pE).
 - Fix conditionals to use processed values - so this fix and 5b6c092aa0 are applid to these elements as well. (http://osdir.com/ml/general/2015-05/msg24402.html).

This also adds tests to verify these behaviors.

Run most relevant tests with commands:

    ./run_tests.sh -framework -id simple_constructs
    ./run_tests.sh -framework -id multi_select
    ./run_tests.sh -framework -id boolean_conditional
 2015-05-19 12:43:32 -04:00
Nate Coraor b8289d20bb Merge remote-tracking branch 'upstream/release_15.05' into dev 2015-05-19 11:01:25 -04:00
guerler 15480dc4f1 Disable automated history creation in data tool parameters 2015-05-18 18:39:47 -04:00
Eric Rasche e54e3f2d01 Remove debugging 2015-05-18 13:02:32 -05:00
Eric Rasche 5853ecc2be Switch to egrep for searching 2015-05-18 12:59:04 -05:00
Eric Rasche 21368266ce Implement XMFA Datatype 
This is used with Mauve/ProgressiveMauve.

Additionally a bug is fixed in the Stockholm datatype which
would have prevented proper sequence count autodetection.
 2015-05-18 12:58:42 -05:00
guerler 609739b703 Update error message 2015-05-18 09:24:27 -04:00
guerler 25d8aea20e Provide proper validation messages for missing or unavailable histories 2015-05-18 09:21:19 -04:00
guerler d5103412ab Replace current history by parsed history in sub functions 2015-05-18 08:44:05 -04:00
guerler 7a53663c34 Parse history id through tool model building api 2015-05-17 01:52:26 -04:00
John Chilton 08e2c351d9 Add edam formats to most Galaxy datatypes and a script for producing a mapping. 
See notes in scripts/edam_mapping.py for more information on mapping.

This is based on mapping of terms done by Eric Rasche (@erasche) (in galaxyproject/galaxy#80) and by the team at Pasteur including @hmenager, @fmareuil, and @odoppelt (in https://docs.google.com/spreadsheets/d/1vptTpJvQfb5FOtRJOajjftUkL9aZ0eeVdhUPvd9h5wY/edit#gid=0).

Current mapping at time of commit is https://gist.github.com/jmchilton/73cd540d7a08488843d7.
 2015-05-16 16:47:39 -04:00
John Chilton 308a8e3737 Merge remote-tracking branch 'galaxyproject-careful/release_15.05' into dev 
Conflicts:
	config/plugins/interactive_environments/ipython/config/ipython.ini.sample
 2015-05-15 13:41:29 -04:00
John Chilton 2cac7e817b Fix implicit output collection names when mapping over collections. 2015-05-15 11:06:19 -04:00
Björn Grüning 62772bc86e Fix bug in history sharing. 2015-05-14 23:16:55 +02:00
John Chilton 4ad4688fde Fix label's on output collections. 
Thanks to @kellrott for reporting the issue.

https://trello.com/c/Qc2A4rsw
 2015-05-14 16:33:39 -04:00
John Chilton fbaba4b463 Fix auto-hiding collections when mapping over tools. 
Broken by that moron @jmchilton in 44f7317fa5.
 2015-05-14 16:33:39 -04:00
John Chilton 2a977039cc Merge pull request #230 from erasche/rstudio 
RStudio IE
 2015-05-14 13:38:29 -05:00
John Chilton ed8112b422 Fix problems introduced in IE refactorings. 2015-05-14 14:32:49 -04:00
Nate Coraor 656d9bef50 Merge remote-tracking branch 'upstream/release_15.05' into dev 
Conflicts:
	lib/galaxy/version.py
 2015-05-14 11:11:46 -04:00
John Chilton 998d0e8a8c IE: Move IPython-specific password hashing out of framework into plugin. 
See dicussion here - https://github.com/erasche/galaxy/commit/23459f318507255a2bb1d1fb647e1581bd2090e1.
 2015-05-14 10:15:49 -04:00
John Chilton 851186dc7f Have trans.user_ftp_dir return None instead of error if ftp_upload_dir unset. 
This is now called on each upload job eb538e00bd and if ftp_upload_dir is None and this was throwing the following exception - https://gist.github.com/jmchilton/fdfb808e13998fbe17bd.
 2015-05-14 09:42:03 -04:00
John Chilton 624d540c04 IEs: Move temp dir handling into ie_request to simplify interface. 2015-05-13 23:08:21 -04:00
John Chilton 55e523ea63 Introduce new IE launch abstraction. 
In addition to reducing duplication between IPython and RStudio - it also shields them from low-level details and creates an interface we could more reasonably generalize to something like qsubing the docker commands or using Docker Swarm.
 2015-05-13 23:08:20 -04:00
John Chilton 23459f3185 Expose and cache raw IE password to simplify RStudio plugin. 2015-05-13 23:08:20 -04:00
John Chilton 687a8947e2 Merge pull request #229 from erasche/ie-updates2 
IE Updates
 2015-05-13 19:42:21 -05:00
Nate Coraor 0090d9a8cd Bump verison to 15.05 2015-05-13 17:09:38 -04:00
Dannon Baker cfea0386f4 Missed one. 2015-05-13 15:47:56 -04:00
Dannon Baker 0a7f50dbaa Change sanitization of workflow pja's for display in workflow/run to happen in get_short_str, trusting that output. This is probably still overzealous, and we should check if there's a way to exploit tool.output_names (and if not, pull back on that sanitization). 2015-05-13 15:45:01 -04:00
guerler 32e027d431 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into library_data_parameter 
Conflicts:
	static/maps/mvc/form/form-section.js.map
	static/scripts/mvc/form/form-section.js
 2015-05-13 04:19:08 -04:00
Carl Eberhard d1c14bd1a1 Histories, API: do not consider deleted datasets when calculating history state; test 2015-05-12 16:57:17 -04:00
Eric Rasche 88456ca5d5 Merge branch 'ie-updates2' of github.com:erasche/galaxy into ie-updates2 2015-05-11 17:16:17 -05:00
Eric Rasche 13afcbd478 Remove unused extra 
This moved to env_override in the run command builder
 2015-05-11 17:15:56 -05:00
Nate Coraor 32edb07930 Merge pull request #247 from blankenberg/baseurl-fix 
[15.05] Fixes for BaseURLToolParameter. Data source tools will now work again…
 2015-05-11 16:14:35 -04:00