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

..

__init__.py

New functional test harness. Update to recent nose. No longer rely on nose to manage the embedded web server (this is not done in functional_tests.py). Log page contents to a temporary file on check_page_for_string error.

2009-10-20 13:08:29 -04:00

test_admin_features.py

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.

2011-03-10 15:48:00 -05:00

test_data_security.py

Move the upload_option (ie., file, directory, filesystem paths, import from history) into a select list on the data library upload form. Selecting an upload_option now performs a refresh_on_change on the upload form so that any form contents entered before selecting the option are now retained. Improvements and bug fixes were made throughout the pieces of the framework that support this.

2010-09-17 15:23:58 -04:00

test_DNAse_flanked_genes.py

Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.

2009-11-11 15:59:41 -05:00

test_get_data.py

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

test_history_functions.py

Disable functional test for not being able to import your own history which was enabled in 5248:dc9efb540f61.

2011-03-23 08:42:01 -04:00

test_library_features.py

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

test_library_security.py

Data library fixes and improvements:

2011-02-04 16:16:00 -05:00

test_library_templates.py

Data library fixes and improvements:

2011-02-04 16:16:00 -05:00

test_metadata_editing.py

De-couple the user controller from the model, adding a webapp param to some method signatures to allow for different webapps to use the controller. Clean up the methods in the controller, eliminating all that are no longer used. Fix the verification mehtod for resetting user names to use rules for setting user names. Add new mako templates for the login and reset password methods instead of the inline form building. Fix a bug where the user's private roles was not correctly updated when the user's email address was changed. Overhaul the test_user_info functional test script, cleaning up the mehtod code and to provide coverage for all of the above fixed bugs.

2010-03-31 09:42:50 -04:00

test_sample_tracking.py

Fixes in the user controller:

2011-03-22 10:33:42 -04:00

test_tags.py

Decouple the TagHandler from the model by allowing sub-classes to point to a specified model. Add a baseline functional tests script to provide coverage for tagging histories and history items ( more coverage is needed, of course, and can easily be added to this script ).

2010-04-13 15:35:32 -04:00

test_toolbox.py

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -05:00

test_user_info.py

Fixes in the user controller:

2011-03-22 10:33:42 -04:00