opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
17,434 Commits 69 Branches 243 Tags
5dec24c21e519d03dfdcd0928fa8401ee7cfcb8e
Commit Graph
1540 Commits
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
John Chilton b1d3552be4 Add a library_data input test case and small fix. 2015-04-17 14:23:38 -04:00
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 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
John Chilton 4a56aeb7b0 test_tools.py enhancements... 2015-04-16 14:28:56 -04:00
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
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
Dannon Baker 4ee3396793 Merge pull request #119 from jmchilton/toolbox_auth 
Stronger toolbox filtering.
 2015-04-15 17:28:33 -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
Daniel Blankenberg 4716d30b69 Minor typos fixed in test/functional/tools/README.txt 2015-04-10 16:38:34 -04:00
Daniel Blankenberg 53258816a7 Add test for BAM metadata reference name selector in tool to test/functional/tools. 2015-04-10 15:46:52 -04:00
John Chilton 38b06a704b Merge pull request #35 from guerler/tool_form_section_tag 
Tool form section tag
 2015-04-10 07:52:37 -05:00
John Chilton c983f029cc Merge pull request #8 from jmchilton/argument_name 
Add argument to tool parameters.
 2015-04-09 15:03:05 -05:00
Nicola Soranzo 8254caba54 Update many links which redirect to https. 2015-04-09 20:37:03 +01:00
Dannon Baker 30f0670ade Merge pull request #76 from carlfeberhard/managers 
Managers
 2015-04-09 12:44:19 -04:00
Dannon Baker 799ace9a4f Merge pull request #100 from jmchilton/test 
Small test tool updates
 2015-04-09 09:58:52 -04:00
John Chilton fe461599d6 Add test tool demonstrating/testing type inheritance. 2015-04-09 09:41:43 -04:00
John Chilton e84d3225ec Add more simple constructs to simple_constructs.xml test tool. 
These demonstrate different kinds of simple selectors - using them for testing workflow runtime parameter problems.
 2015-04-09 09:33:26 -04:00
Dannon Baker af7cfadfc4 Merge pull request #99 from jmchilton/travis_enhance_1 
TraivsCI: More comprehensive checks for *very* broken stuff.
 2015-04-09 07:35:08 -04:00
John Chilton 7c9413c13d Fix undefined name in recently refactored yaml_to_workflow.py. 2015-04-08 23:22:28 -04:00
guerler 388587de1c Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_section_tag 
Conflicts:
	lib/galaxy/tools/__init__.py
 2015-04-06 12:30:17 -04:00
John Chilton 7c319a1bcd More functional tests of output actions. 
- Add example tool demonstrating/testing specifing format via conditional output actions.
 - Add API test testing mapping collections over tools without output action formatting.
 - Add API test testing more complex actions using the Cut1 tool.
 2015-04-06 09:08:01 -04:00
Carl Eberhard 179d11db85 Merge managers.datasets with dev and remove conflicts 2015-04-02 14:39:45 -04:00
Carl Eberhard ceeff0a03c Fix to c1f7210: remove print statements and minor fixes 2015-04-02 14:22:26 -04:00
Carl Eberhard c1f721086f Managers: attempt to extract trans from de/serializers 2015-04-02 13:49:03 -04:00
Carl Eberhard fafea361ac Managers: remove trans param as much as possible (this results in some clunky use of current_history kwarg) 2015-04-01 15:21:25 -04:00
Carl Eberhard f8c6725c42 Managers, filters: allow remapping of attribute keys; expand tests 2015-03-31 15:35:17 -04:00
Carl Eberhard 9f1be65937 Managers: re-add dataset assoc job methods, move primary id serialization into base serializer, minor fixes and refactoring, expand tests 2015-03-31 11:15:49 -04:00
Carl Eberhard 188ff0076f Managers, Users: corrections and refactoring, expansion of tests 2015-03-30 18:00:13 -04:00
Carl Eberhard c3f30fbdc5 Managers: refactor hda manager into dataset/dataset assoc/etc., begin to expand rbac security for datasets, expand tests 2015-03-29 19:58:12 -04:00
guerler 5aa73d0e05 Merge branch 'dev' into tool_form_section_tag 
Conflicts:
	lib/galaxy/tools/test.py
 2015-03-26 17:04:29 -04:00
Carl Eberhard 9b1cc1dfdf Browser testing: add test for passing null/None to misc_info during an update 2015-03-25 18:42:03 -04:00
John Chilton a357e2b613 Workflow scaling test infrastructure. 
- Add script to hit the API with workflows requests.
 - Update testing Dockerfile to allow just booting up with a fixed master API key for this test to leverage.
 - WIP: on updating test Dockerfile to work with slurm, multiple handlers, uwsgi, etc...
 2015-03-25 14:54:48 -04:00
John Chilton ed7a45324b Refactor API testing helpers to allow use with bioblend. 
Going to use bioblend for performance testing instead of galaxy_interactor. This refactoring allows all of those helpers to be reused with bioblend backing the helpers instead of galaxy_interactor.
 2015-03-25 14:45:12 -04:00
John Chilton 1f6ee2fa8f Refactor collection test def objects out of galaxy.tools. 
Part of ongoing effort to isolate the galaxy.tools.parser and not have it depend on things in galaxy.tools outside that module.
 2015-03-25 14:43:53 -04:00
John Chilton 3813429f7e Refactor tool status check objects into parse module. 
Part of ongoing effort to isolate the galaxy.tools.parser and not have it depend on things in galaxy.tools outside that module.
 2015-03-25 14:43:53 -04:00
John Chilton 3b263a8df4 Tool testing sections. 
- Add example tool for testing (section.xml).
 - Implement popular flat group style test cases for section elements (first example in section.xml).
 - Implement nested groupping style test cases for section elements (section example in section.xml).
 2015-03-23 20:04:49 -04:00
John Chilton 8cb06d7fc2 More informative error message for bam conversion errors. 
Hopefully this will help debug this issue (https://trello.com/c/TL0IdLlG) reported by @peterjc.
 2015-03-23 09:35:21 -04:00
Carl Eberhard de78429ceb Managers: fallback to string validation for genome_build validation; Browser tests: update tests to reflect looser validation of genome_build 2015-03-17 15:45:39 -04:00
John Chilton 65def71495 Add github citation example. 
Based (very loosely) on reponse from:

http://tex.stackexchange.com/questions/35977/how-to-add-a-url-to-a-latex-bibtex-file
 2015-03-16 11:14:01 -04:00
John Chilton 3d7e5230d4 Test tool fixes. 
- Fix filename spelling to top_level_data parameter test tool.
 - Fix for composite test tool (toolbox won't load it without a name).
 2015-03-15 09:53:05 -04:00