Commit Graph
413 Commits
Author SHA1 Message Date
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
Nate Coraor 19236474c4 Cause lines_diff on pdf test outputs to only count the lines of a pdf which are not already ignored. 2011-03-03 12:21:22 -05:00
Daniel Blankenberg 4eb1b0a79f 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
Nate Coraor e1ea63eb9a When comparing bam files in the test framework, convert them to sam for comparison. 2011-02-23 14:53:54 -05:00
Kanwei Li 4660370320 Copy datasets feature:
- Fix functional tests
- Populate previously selected target history if attempt fails
2011-02-22 17:14:16 -05:00
Daniel Blankenberg 3854d341ad Allow toolbox tests to upload a file found located in subdirectories. Fix a bug occurring on the determination of uploaded dataset name during the handling of the removal of .gzip or .zip extension from the uploaded filenames within the toolbox test framework. 2011-02-22 16:56:11 -05:00
Guruprasad Anada ff7e8fe2e0 Fixed functional tests for the following tools: histogram, estimate indel rates, compute q-values, kernel pca. 2011-02-22 12:37:06 -05:00
Nate Coraor 7a87e6c6db Fix for 3 of the 4 failing upload tests. 2011-02-18 16:21:11 -05:00
Greg Von Kuster 023880b713 Data library fixes and improvements:
1. Fix a bug that included the option for a regular user to upload a directory of files when the config setting existed, but the user's directory did not exist.  Instead of throwing an exception, an attempt to create the directory will now be done.  If the attempt fails, the option to "Upload a directory of files" will not be included in the select list on the upload form.

2. When browsing a data library, only display the check boxes and the actions to perform on multiple selected datasets if library datasets are displayed.

3. Clean up the behavior when performing an action on multiple library datasets.  Instead of throwing an error and not allowing the action on any of the datasets if the user is not authorized to perform the action on 1 of them, all "unauthorized" datasets are now left alone and the action is performed on all datasets for which the user is authorized to perform the action.  Appropriate messages detail what occurred.

4. Allow regular users to delete multiple datasets returned from library dataset searches based on the behavior described in 3 above.

5. Do not include the "Select datasets for import into selected histories" option in the actions pop-up menu at the data library level if the library's root folder doesn't contain any accessible datasets.  Make behavior the same for folder popup menus.

6.  Add a new LibraryFolder.active_datasets mapper and eliminate the incorrect LibraryFolder.active_library_datasets property.  Callers of the incorrect property now use the mapper.

7. Eliminate the incorrect LibraryFolder.active_datasets property.

8. Fix the queries in the library_common controller's active_folders_and_lddas() and activable_folders_and_lddas() methods to return library_datasets instead of lddas, and rename the methods to be active_folders_and_library_datasets(0 and activatable_folders_and_library_datasets() respectively.

9. Fix bug where regular user could never see deleted library items when toggling show / hide deleted items.

10. Fix functional test for uploading directories of files to a library folder.  The test generally failed because not enough time would elapse before checking if the files uploaded.  The check is now performed in a later method in the test script, hopefully allowing for enough time to pass.

11. Functional test code clarifications for the browse_library() test method.
2011-02-04 16:16:00 -05:00
Greg Von Kuster e8e6753c47 Apply patch from Brad Chapman that fixes an issue when downloading a zip archive of library datasets. Also include some miscellansous imporvements and code cleanup related to changes made in change set 4964:82107691d26e. 2011-02-01 11:21:41 -05:00
Greg Von Kuster 5f9f45a068 Several data library improvements:
1. Enhance importing library dataset into the current history by now allowing the user to select from a list of existing histories or create a new named history ( similar to copying datasets ).  This feature is available for a specific library dataset, a folder ( or root folder ), when selecting multiple datasets from in a library,  and on the results page for searched library datasets.

2. Add Brad Chapman's latest patch for fixing the lucene search implementation

3. Eliminate searches on dataset state for both whoosh and lucene searches

4. Clarify the objects being searched in the regular search and advanced search boxes in the data libraries grids.

5. Add the ability to perform certain actions on 1 or more selected library datasets on the results page for searched library datasets.

6. Add a "select all" checkbox to the browse_library.mako template.

7. Fixed library functional tests accordingly.
2011-01-31 16:41:03 -05:00
Ramkrishna Chakrabarty 7e3387aabd Request type now requires at least one sample state
Added validation checks for request types with only one sample state
Bug fixes
2011-01-28 10:24:55 -05:00
Ramkrishna Chakrabarty 529098e77e Added ability to add samples after a request is submitted. 2011-01-26 11:35:52 -05:00
Greg Von Kuster af55a392fc Fix for rendering folders select field for a sample - include hte library's root folder in the select field too. Fix for setting the default name of the sample grid layout. Fix sample tracking functional test script. 2011-01-12 16:15:40 -05:00
Ramkrishna Chakrabarty 77c6f3ea06 FIxed the unwanted changes made in the previous commit 2011-01-07 16:19:59 -05:00
Ramkrishna Chakrabarty f7a35e13cb Renamed sequencer to external_service and sequencer_type to external_service_type.
Added table to associate external services to a request type.
Enhanced UI to support selection of multiple external services for a request type.
2011-01-07 16:12:36 -05:00
Ramkrishna Chakrabarty b72c2406c8 Fixed user_info and sample_tracking functional tests.
Refactored getting form values into a separate method in controller.py.
Changed request type access into a restrict permission.
Added a check when sequencer_types are not loaded.
2011-01-04 07:11:12 -05:00
Greg Von Kuster 5e2d7e83f1 Eliminate the use of the 'editing_samples' flag by adding the code needed to add new samples without calling the edit_samples method or mako template. Decoupling the different features makes them much cleaner and easier to maintain. 2011-01-03 11:11:00 -05:00
Ramkrishna Chakrabarty 7858868650 First pass of the new sequencer_type & sequencer framework
- sequencer table now populated with the unique sequencer in the request_type table
- sequencer_type is introduced which defines a sequencer
- support for sequencer (create, delete, edit)
- added support for a simple sequencer for backward compatibility
- added support for Solid sequencer
- tweaked the request_type api methods. removed the sequencer login info.
2010-12-20 10:50:50 -05:00
Greg Von Kuster 11957ed5fa Fixed as many of the issues as could be found throughout the framework due to the migration of FormValues.content from a list to a dictionary in change set 4744 b73ad3906e24. 2010-12-15 17:00:29 -05:00
Ramkrishna Chakrabarty b34ef29442 Adding a 'name' attribute in the field dict for form_definitions. In the 'form_values'
table, the 'content' column is now a JSON dict instead of a list. Made appropriate code changes.
2010-12-13 17:29:23 -05:00
Greg Von Kuster 87c645dc0e Rename the sequencer controller to be named request_type. 2010-12-09 15:59:14 -05:00
Greg Von Kuster d354a1ce35 Abstract the code supporting data library templates so templates can be used in sample tracking as well. These templates now provide support for handling information about sample runs. A RequestType can have a single association to a Run, with the run details template made available to all samples. A Sample can have many associations to Runs. 2010-12-09 14:52:27 -05:00
Ramkrishna Chakrabarty bfb5eba0fa fixed request_type permissions bug & code cleanup 2010-12-01 09:49:01 -05:00
Ramkrishna Chakrabarty 52be644eb6 sample tracking functional tests now checks if all library sub-folders show up in the selectfield when selecting a folder for a sample 2010-11-30 13:59:13 -05:00
Ramkrishna Chakrabarty 4999fc4742 Added async update of sample dataset transfer status on user dataset view page.
Fixed user info functional tests
2010-11-23 13:54:09 -05:00
Ramkrishna Chakrabarty c22691a2af Forms refactoring first pass.
sample tracking data transfer selection UI css bug fixed
2010-11-23 00:00:03 -05:00
Ramkrishna Chakrabarty d220a8c791 sample tracking functional tests
- data transfer selection, renaming initiation
- new address at request creation
- request lifecycle, rejection
Fixed ui bugs
2010-11-19 10:52:49 -05:00
Greg Von Kuster efed83a828 Move the sequencer interface ( RequestType ) components from the requests_admin controller to a new sequencer controller. 2010-11-19 10:14:08 -05:00
Greg Von Kuster c3afe4cb34 Code fixes and cleanup for adding and viewing sequencer configurations ( RequestTypes ). Move the request_type templates from the requests folder to their own request_type folder. Add the ability to edit sequencer configurations. 2010-11-18 14:16:39 -05:00
Ramkrishna Chakrabarty a244683705 Fixed naming of the library selectfield for sample operations
Fixed the broken popup menu in the data transfer grid
Fixed the missing required/optional field info in the request form
2010-11-17 16:19:11 -05:00
Ramkrishna Chakrabarty b8652ecc4e - added the change data library sample operation functional test.
- renaming dataset now checks for incorrect filename characters
- fixed bugs
2010-11-17 11:33:54 -05:00
Greg Von Kuster c3c7c89c5d More miscellaneous Sample Tracking cleanup and bug fixes, move supported form_builder field types from form_builder.BaseField to Request.model and Sample.model. 2010-11-17 10:25:12 -05:00
Ramkrishna Chakrabarty 95e9a7f5f1 Fixed functional tests and samples grid alignment bug 2010-11-16 12:20:56 -05:00
Ramkrishna Chakrabarty 80974127da Enabled the cleanup method which was disabled by mistake in the previous commit. 2010-11-15 12:24:51 -05:00
Ramkrishna Chakrabarty 394b01dfdb More tests added to sample tracking functional tests 2010-11-15 12:21:35 -05:00
Greg Von Kuster 212a7e65cf First pass at cleaning up the Galaxy Form Definition UI ( forms controller still needs a re-write ). 2010-11-15 11:46:39 -05:00
Ramkrishna Chakrabarty 34499ddbcf More changes to sample tracking functional tests
- assign target data library, editing samples, assign sample barcode
2010-11-12 16:37:36 -05:00
Greg Von Kuster 162c2b0a26 Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples. 2010-11-11 15:36:23 -05:00
Greg Von Kuster 4bbc15d6d1 Various sample tracking bug fixes: samples no longer require bar codes, change all references to 'barcode' to be 'bar_code' since that is what the model uses, and mixing the 2 is not maintainable, enhance sample popup menu options, fix broken logic that handles bulk sample library and folderr changes. 2010-11-11 14:24:02 -05:00
Ramkrishna Chakrabarty 5a452fddc3 Sample tracking functional tests refactored till add samples.
Rest of the tests are disabled.
2010-11-10 11:28:53 -05:00
Nate Coraor 1e4fba1360 Backed out changeset 081ce300b688 (some files accidentally committed). 2010-11-10 10:26:07 -05:00
Anton Nekrutenko 7c4ca2927b porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility 2010-11-10 10:17:12 -05:00
Greg Von Kuster 38eac9196f More miscellaneous bug fixes in Sample Tracking, all due to the recent UI changes. Changes the name of the test_forms_and_requests.py functional test script to be test_sample_tracking.py to more clearly reeflect what's being tested. 2010-11-02 14:49:45 -04:00
Greg Von Kuster fa8a352dcd Significant cleanup for the Sample Tracking UI. Things are more streamlined and Galaxy UI standards are now followed. 2010-11-01 18:16:50 -04:00
Ramkrishna Chakrabarty 5ee541f26d sample tracking functional tests are fixed 2010-10-15 12:49:21 -04:00
Ramkrishna Chakrabarty 4631710431 sample_tracking fixes 2010-10-14 00:24:56 -04:00
Greg Von Kuster 2942a66c90 Clean up the code in the request_admin controller. 2010-10-12 15:36:22 -04:00
Greg Von Kuster 81c76fdb96 First pass at Galaxy sample tracking re-write. Highlights: lots of code cleanup with several not-needed methods removed, many mthods and mako templates have been renamed clarify what they do, all object ids are now encoded, methods in the requests_common controller that include features requiring an admin user are now secured. More work is needed in the requests_admin controller which will be in the next commit. 2010-10-11 16:35:57 -04:00
Richard Burhans 1e6da6692a Fixed broken indentation. 2010-09-30 14:50:31 -04:00