Dave Bouvier
13793b39cc
Add missing hda name length check to submit_form.
2013-05-09 13:49:13 -04:00
Dave Bouvier
1a338323d4
Update login methods in twilltestcase to be more robust.
2013-05-08 16:50:00 -04:00
Dave Bouvier
663b390536
Fix failing functional test for dataset features.
2013-04-28 11:03:41 -04:00
Dave Bouvier
ad329a1d37
Fix for failing upload tool functional tests.
2013-04-25 15:16:23 -04:00
Dave Bouvier
86a4ab8ad3
Fix functional test issue with forms having refresh_on_change.
2013-04-24 09:52:40 -04:00
Dave Bouvier
b84b45e7d0
Added even more information to the tool_test_errors dict. Separated failed and passed tests in the metadata record. Added documentation.
2013-03-08 14:25:06 -05:00
Dave Bouvier
fb0eea6c80
Added more information to the tool test environment dict. Restrict when do_not_test flag is set. Made test logging format more structured. Moved some utility code to the util module.
2013-03-06 16:07:32 -05:00
Dave Bouvier
4dc0ae6cc8
Script to check repositories and determine whether functional tests are defined for all tools, and set the do_not_test flag accordingly. Cleaned up the install and test framework and functional test common methods.
2013-03-05 10:23:21 -05:00
Dave Bouvier
8d2655503b
Improved documentation for automated repository installation and testing. Handle cases where a repository is missing test data. Limit the list of repositories to test to those that have tools. Update the parse_tool_panel_config method to return a flag specifying whether test data was found for the specified tool panel entry.
2013-03-01 15:13:20 -05:00
Dave Bouvier
36ea9db697
Extension of framework to automate the installation of a list of tool shed repositories to also run any functional tests in the tools contained within each repository.
2013-02-20 14:27:36 -05:00
Dave Bouvier
41852b5bbc
Functional tests for dataset parameters and error report form.
2013-02-08 10:40:37 -05:00
Jeremy Goecks
6d323f2e3b
Update history functional tests for changes in f93113b
2013-01-15 17:17:32 -05:00
Carl Eberhard
c9605d19ec
functional tests, tags: fix test_005_add_tag_to_history to check for tag using get_tagging_elt_async; twilltestcase: add get_tags (get_tagging_elt_async)
2012-12-20 15:20:42 -05:00
Carl Eberhard
d777d8a4e9
Fixes to upload functional tests (test_get_data.py); TwillTestCase: add is_history_empty which checks the length of HDA JSON instead of relying on html, add check_hda_json_key_value which checks a specific HDA's JSON for a specific value
2012-12-11 17:29:35 -05:00
Carl Eberhard
b6d4e00bc2
Fixes to history functional tests; Twilltestcase: added function to parse and check json, exact string matcher
2012-12-10 17:44:11 -05:00
Dave Bouvier
68c75523ae
Fix for TwillTestCase.wait() with the new client-side histories.
2012-11-16 15:39:50 -05:00
Daniel Blankenberg
ce3737e33b
Tweak for functional tests of BAM outputs on Macs.
2012-10-23 12:28:22 -04:00
Dannon Baker
13356dff74
Remove unused imports, fix exception log str(e) (which was actually e imported from another package, not the exception...)
2012-10-16 16:47:31 -04:00
Dannon Baker
fe5fb9a666
Fix test cases failing due to non-reflected password change. This resolves failures of:
...
functional.test_user_info.TestUserInfo.test_010_user_reqistration_multiple_user_info_forms
functional.test_user_info.TestUserInfo.test_015_user_reqistration_single_user_info_forms
functional.test_user_info.TestUserInfo.test_020_edit_user_info
functional.test_user_info.TestUserInfo.test_999_reset_data_for_later_test_runs
2012-10-16 16:43:58 -04:00
James Taylor
eefd9af8f7
test framework: no longer pass webapp argument to requests
2012-10-01 15:24:36 -04:00
Carl Eberhard
7ee4bce898
small fix to twilltestcase when GALAXY_TEST_SAVE fails
2012-08-15 11:13:13 -04:00
Carl Eberhard
b2a5996a6c
tool-data change to fix bwa_wrapper.test_tool_000001; backbone history.js start
2012-08-14 13:15:48 -04:00
Nate Coraor
23919dfbc6
Fix job manager/handler shutdown, functional tests due to referer -> redirect rename, and check_galaxy script for dataset display -> html table change.
2012-04-16 14:56:24 -04:00
Greg Von Kuster
816a43c2f9
Enhance the functional test framework to support testing tools contained in installed repositories that were not migrated from the Galaxy distribution. To test these tools, use: sh run_functional_tests.sh --installed
2012-03-29 15:02:36 -04:00
Greg Von Kuster
60c0bdf17b
Enhance the functional test framework to support tools migrated from the distribution and installed from the tool shed. To test these tools, use: sh run_functional_tests.sh --migrated
2012-03-29 12:03:14 -04:00
Greg Von Kuster
6a82d13692
Fixes for transferring sample datasets and viewing . managing transferred sample datasets.
2012-03-29 10:17:51 -04:00
Jeremy Goecks
2490f2e9c1
Update functional tests to be compatible with 0d1d62b8be2e
2012-01-17 09:05:11 -05:00
Nate Coraor
3c5c6ce091
Fix for some output changes I made to functional tests.
2011-12-08 10:14:29 -05:00
Nate Coraor
44344fe2e0
Fix the dataset controller's stderr method and add one for stdout. Link to
...
both from the dataset info page. The functional tests will now provide output
of these on tool test failure. The functional tests can now use
tool_dependency_dir as well.
2011-12-06 11:29:02 -05:00
Greg Von Kuster
39d74e80b3
Fix some broken functional tests and fixes for deleting multiple data libraries and resetting the password for multiple users. Fixes issue # 678.
2011-12-05 09:58:36 -05:00
Nate Coraor
cbb7111ea9
Bugfix for tool tests without attributes.
2011-09-02 10:16:07 -04:00
John Chilton
9ac9830a49
Small whitespace fix for bug introduced by last merge.
2011-08-31 11:31:23 -05:00
John Chilton
eaeb4d7c20
Merged latest galaxy-central.
2011-08-31 11:08:30 -05:00
Ross Lazarus
5b2e7947ea
Fixed sam_merge.xml to call Picard MergeSamFiles.jar so metadata can be propagated through to the new merged bam from all the individual files - the samtools version of merge would require this to be done separately and passed in with the -h option whereas Picard does it automatically. Added one more test. Interesting that the test for that tool has been failing to correctly pass metadata but passing the buildbot anyway. Thanks to Camille Stephan for pointing out the bug.
...
Changes to rgManQQ so the user can obtain a decent pdf image. When millions of points are plotted, these are humongous so GS is called to compress the resulting pdf and they are now of reasonable size. PDF's are now linked from the thumbnails. Some minor fiddling with point size on the Manhatten plots so the intersting ones are a little more obvious.
Minor tweak to twilltestcase.py so composite file components are copied correctly to the directory specified by GALAXY_TEST_SAVE. This makes updating test artefacts much simpler because running tests with GALAXY_TEST_SAVE pointing somewhere will now save every tested output file.
2011-08-04 12:43:30 +10:00
Nate Coraor
0756941512
Move a number of dataset-related methods from the root controller to the dataset controller and encode their ids. Also add user disk usage accounting.
2011-07-26 13:30:07 -04:00
John Chilton
10129b8a17
Merged latest galaxy-central changes.
2011-07-25 13:13:17 -05:00
Kanwei Li
1abb36734a
Escaping in tests should be more specific
2011-06-17 16:45:25 -04:00
John Chilton
ce6aeb31c3
Enhancements to Galaxy's functional testing framework as outlined in issue 490. https://bitbucket.org/galaxy/galaxy-central/issue/490/enabling-iterative-test-driven-development
2011-05-17 15:29:02 -05:00
Daniel Blankenberg
3cbead3137
Add a "contains" compare type to functional tests. Enables simple checking for substrings in a test output file, on a line-by-line basis. TODO: Enhance to enforce order.
2011-05-10 20:11:52 -04:00
Kelly Vincent
d6deb67bf2
Added -h flag to samtools view command in functional test's bam to sam conversion so that it keeps the header
2011-04-22 14:58:44 -04:00
Ross Lazarus
ee6bd2cf46
Changes to allow all test outputs generated by twill to be saved to a folder pointed to by
...
an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests
If the environment variable is empty, all tests procede as usual and test outputs are deleted
without saving
2011-04-14 08:09:48 -04:00
Greg Von Kuster
8ba7de4c8b
Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
2011-03-23 12:18:57 -04:00
Greg Von Kuster
e83efed183
Fixes in the user controller:
...
1. Eliminate some long-standing security issues
2. Encode all object ids - many were not being encoded
3. Eliminate all unnecessary methods
4. Rewite several poorly written methods
5. Fix several bugs related to USER_INFO form definitions
2011-03-22 10:33:42 -04:00
Daniel Blankenberg
c52ba62119
When using re_match comparison method in functional tests and line counts do not match, print out first 40 lines of the history file.
2011-03-16 22:27:15 -04:00
Greg Von Kuster
7640af8e06
Don't alter the contents of a file while uploading to a data library if using the filesystem_paths option. This partially resolves the issue where a supposedly sorted BAM file was being resorted upon upload to a data library when using this option. A better imlementation of determining whether a BAM file has been sorted (so that it does not get resorted) remains to be done.
2011-03-15 09:38:29 -04:00
Greg Von Kuster
df6f94b1d0
Per request from Peter Cock, turn the "Copy data into Galaxy?" check box into a select list that clarifies the behavior. The default is to copy files into Galaxy.
2011-03-11 14:56:11 -05:00
Greg Von Kuster
c650958915
Apply a corrected version of the patch from Peter Cock that flips the  "Preserve directory structure?" setting when uploading library datasets from filesystem paths.
2011-03-11 10:01:54 -05:00
Greg Von Kuster
0e79bf2632
Add a checkbox to the Create Group page that if checked will create a new Role with the same name. This provides a similar feature the the existing checkbox on the Create Role page.
...
However, the behavior is now changed such that new associations are created when the checkbox is checked whereas before, only the Group or Role objects with the same name were created, but not associated with anything.
This code was very old, so I did some cleanup / improvements as well. Functional tests enhanced to reflect changes.
2011-03-10 15:48:00 -05:00
Greg Von Kuster
a5ea34e29a
Add functional tests to cover some recent new library features, and a couple of miscellaneous UI improvements.
2011-03-09 14:50:54 -05:00
Nate Coraor
a221548e8f
An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix.
2011-03-08 11:17:57 -05:00
Dave Bouvier