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Author SHA1 Message Date
guerler 5dec24c21e Merge branch 'dev' of https://github.com/galaxyproject/galaxy into library_data_parameter 2015-04-19 22:59:16 -04:00
guerler 27424139a0 Add generic list value wrapper and use it for the library data tool parameter, move wrapper import into parameters 2015-04-19 22:46:45 -04:00
John Chilton 20f131efae Merge pull request #131 from bgruening/ie_docker_inject_cmd 
Add `command_inject` to Interactive Environments.
 2015-04-19 19:43:58 -05:00
Bjoern Gruening cef67fb4f1 Add command_inject to IE config files. This makes it possible to modify the executed "docker run" command from the config file. 2015-04-18 16:54:34 +02:00
Aysam Guerler 5ec0bf2962 Merge pull request #2 from jmchilton/library_data 
Add a library_data input test case and small fix.
 2015-04-17 16:24:49 -04:00
John Chilton b1d3552be4 Add a library_data input test case and small fix. 2015-04-17 14:23:38 -04:00
Martin Cech 269adc7d99 Merge pull request #129 from dannon/sqlalchemy100 
Upgrade sqlalchemy to 1.0.0 (hooray!)
 2015-04-17 14:15:43 -04:00
John Chilton 861cdf6620 Merge pull request #128 from dannon/update_kombu 
Update kombu, amqp.
 2015-04-17 11:50:00 -05:00
Dannon Baker e73d90c94e Merge pull request #121 from jmchilton/input_casting 
Improved Cheetah type casting for int/float values.
 2015-04-17 12:10:10 -04:00
Dannon Baker 5c9f783dd1 Merge pull request #126 from carlfeberhard/histories 
UI, Histories: improve highlighting of current/active content in current...
 2015-04-17 08:24:14 -04:00
guerler ebafd06fea Merge branch 'dev' of https://github.com/galaxyproject/galaxy into library_data_parameter 2015-04-16 20:02:25 -04:00
Dannon Baker d725aab54e Upgrade sqlalchemy to 1.0.0 (hooray!) 2015-04-16 17:18:08 -04:00
Dannon Baker 26b766b3bc Merge pull request #125 from jmchilton/md5 
Allow testing tool outputs based on MD5 hashes.
 2015-04-16 16:36:53 -04:00
Dannon Baker 4cd5858b61 Merge pull request #127 from jmchilton/update_test 
Small test_tools.py tweaks
 2015-04-16 16:27:52 -04:00
Carl Eberhard 9ada2f6c43 UI, Histories: improve highlighting of current/active content in current history panel 2015-04-16 16:01:23 -04:00
Dannon Baker e09761eb80 Bump amqp to 1.4.6 2015-04-16 14:53:37 -04:00
Dannon Baker 8d3c53141d Bump kombu to 3.0.24 2015-04-16 14:53:08 -04:00
John Chilton 4a56aeb7b0 test_tools.py enhancements... 2015-04-16 14:28:56 -04:00
John Chilton 7c87f6f0bf Merge pull request #124 from dannon/egg_fixing 
Slight improvement to logging in scramble code.
 2015-04-16 13:28:14 -05:00
John Chilton f7ecd1c9d2 Allow testing tool outputs based on MD5 hashes. 
This should not be considered the best practice for most text based files, but for binary files we cannot produce diffs anyway so this is probably better than storing the pointless binary blobs in repositories for instance. In particular Dan and I thought this would be useful for testing index files for data managers.

Includes test tool demonstrating this functionality, run test with

    ./run_tests.sh -framework -id md5sum
 2015-04-16 14:19:36 -04:00
Dannon Baker 1c0d694d47 Swap log string formatting to arg 2015-04-16 14:17:04 -04:00
Dannon Baker 57675eef7b Better logging in scrambler, shows more detailed error when, for example, hardlinked items in tars cause errors 2015-04-16 14:12:23 -04:00
John Chilton afc9877005 Merge pull request #123 from carlfeberhard/testing-merge 
Unit Testing Expansion
 2015-04-16 10:25:34 -05:00
Carl Eberhard f93961c497 Merge testing 2015-04-16 11:09:11 -04:00
Carl Eberhard 5ebe04cfd0 Testing: fix failing unit tests that were recently added 2015-04-16 10:45:24 -04:00
Carl Eberhard 1bc86a5fba Testing: move managers, web/base, datatypes/dataproviders, and visualization 'unit'(?) tests to using common mock objects and loading system; cleanup 2015-04-16 10:25:34 -04:00
Dannon Baker 1f90dfd86a Merge pull request #115 from guerler/revise_validation 
Revise late validation of tool parameters
 2015-04-16 09:58:14 -04:00
John Chilton 9c1550b36e Improved Cheetah type casting for int/float types. 
Based on idea by @peterjc in a discussion here - http://dev.list.galaxyproject.org/Geting-integer-value-from-InputValueWrapper-in-plugin-xml-file-td4666971.html. With simple test demonstrating new functionality. Run test with

    ./run_tests.sh -framework -id cheetah_casting
 2015-04-16 09:34:08 -04:00
John Chilton 6fe6081d2a Merge pull request #120 from carlfeberhard/testing 
Remove twill-based test_history_functions
 2015-04-15 19:24:33 -05:00
guerler 112409f4e9 Additional fix for genome builds 2015-04-15 17:50:22 -04:00
guerler 4c883d689e Fix genome build and revise drill down parameter 2015-04-15 17:33:22 -04:00
Dannon Baker 4ee3396793 Merge pull request #119 from jmchilton/toolbox_auth 
Stronger toolbox filtering.
 2015-04-15 17:28:33 -04:00
Nate Coraor a4e4e59b5a Merge pull request #117 from jmchilton/detect_errors 
Implement ``detect_errors`` attribute on tool XML.
 2015-04-15 16:43:33 -04:00
Carl Eberhard d356223135 Remove twill-based test_history_functions 2015-04-15 16:34:29 -04:00
guerler c9d5a14304 Adjust late validation test cases 2015-04-15 15:41:03 -04:00
John Chilton afcf899f13 Stronger toolbox filtering. 
- Update toolbox filtering rules to also filter on tool.allow_user_access.
 - Use toolbox filtering when listing tools not in the context of panel (so filtered tools are not returned from the API).

See also:

 - https://trello.com/c/jyl0cvFP
 - https://trello.com/c/Sg8D2PBj
 - http://dev.list.galaxyproject.org/Bug-Toolbox-filters-not-applied-in-workflows-td4662879.html

Testing:

The following command will run a superset of relevant tests:

    ./run_tests.sh -u test/unit/tools
 2015-04-15 14:40:50 -04:00
John Chilton 0fe2b601ce Implement detect_errors attribute on XML. 
If present, it can be one of

 - "default", no-op fallback to stdio tags and erroring on standard error output.
 - "exit_code", error if tool exit code is not 0. (The @jmchilton recommendation).
 - "aggressive", error if tool exit code is not 0 or either Exception: or Error: appears in standard error/output. (The @bgruening recommendation).

Refactoring and unit/functional tests to support and demonstrate this.

Run functional test with:

    ./run_tests.sh -framework -id detect_errors_aggressive

Run relevant unit tests:

    nosetests test/unit/tools/test_parsing.py

Updated from original version to reflect comments on pull request #117 - in particular the ``detect_errors`` tag was moved from ``tool`` to ``command``.
 2015-04-15 12:38:35 -04:00
Dannon Baker 6345e1b3aa Merge pull request #118 from bgruening/enhance_ruby_environment 
add option to pass arbitrary parameters to gem install
 2015-04-14 16:06:47 -04:00
Bjoern Gruening 7f0dede663 add option to pass arbitrary parameters to gem install 2015-04-14 21:10:05 +02:00
Daniel Blankenberg 29db1add02 Merge pull request #116 from martenson/ts-indexing-update 
update to toolshed indexing script
 2015-04-14 12:19:12 -04:00
Martin Cech dc736c73f2 remove another abspath; use optparse; 2015-04-14 11:31:44 -04:00
Martin Cech 66e61271b1 add comments and example; add consistency checks; remove bash script 2015-04-14 10:55:34 -04:00
guerler c40e8f618d Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_validation 2015-04-14 03:01:33 -04:00
guerler 5c8ad19ddb New library data selector for tool form 2015-04-14 02:27:38 -04:00
Dannon Baker 68bce85590 Merge pull request #114 from galaxyproject/jxtx-welcome-jhu 
Change Emory to Johns Hopkins in sample welcome.
 2015-04-13 19:28:32 -04:00
James Taylor d323fa0aad Change Emory to Johns Hopkins in sample welcome. 2015-04-13 17:21:52 -04:00
Martin Cech c12b8063e3 remove abspath 2015-04-13 14:39:31 -04:00
Martin Cech a9bc7dc5ca generate separate index for tools in repositories 2015-04-13 13:45:32 -04:00
guerler c0afb6403c Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_validation 2015-04-11 03:12:56 -04:00
John Chilton a37d6e3791 Merge pull request #112 from guerler/dev 
Disable tool sections in former workflow forms
 2015-04-10 21:33:04 -05:00