Greg Von Kuster d8279f0e5c Add an altered version of Jelle Scholtalbers' enhancement code to support uploding various image data types. I've moved some of the code components around from Jelle's version, and added some fixes. The cod ein the new image_util.py file enables detections of images types without the need to create a new Image() class. ...

I've also added baseline support of the HDF5 data type in this change set, but it is currently required to be in the unsniffable_data_types list.

2011-07-27 16:14:15 -04:00

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__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

Add an altered version of Jelle Scholtalbers' enhancement code to support uploding various image data types. I've moved some of the code components around from Jelle's version, and added some fixes. The cod ein the new image_util.py file enables detections of images types without the need to create a new Image() class.

2011-07-27 16:14:15 -04:00

test_history_functions.py

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

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

No longer allow Datasets to have DatasetPermissions set such that no roles are associated with the DATASET_MANAGE_PERMISSION.

2011-06-13 10:47:51 -04:00

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

No longer allow Datasets to have DatasetPermissions set such that no roles are associated with the DATASET_MANAGE_PERMISSION.

2011-06-13 10:47:51 -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

Fix for expand grouping to allow toolbox tests to use the default parameter value.

2011-05-10 19:59:46 -04:00

test_user_info.py

Fixes in the user controller:

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