Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles.
Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes.
Future Enhancement:
Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
greater than config.output_size_limit, no data will be retrieved and an error message will be provided to the user.
Tools using this script have been updated to provide the max file size on the command line.
Resolves ticket #93.
1) include templates in the upload form for library datasets
2) Add user_id column to library_dataset_dataset_association table
3) Add message column to library_dataset_dataset_association table
4) Several miscellaneous bug fixes related to uploading library datasets
SQL commands required:
ALTER TABLE library_dataset_dataset_association ADD COLUMN user_id INTEGER;
ALTER TABLE library_dataset_dataset_association ADD CONSTRAINT library_dataset_dataset_association_user_id_id_fkey FOREIGN KEY (user_id) REFERENCES galaxy_user(id);
ALTER TABLE library_dataset_dataset_association ADD COLUMN message VARCHAR(255);
They are somewhat independent (you can use the new layout with the old style
and vice versa) but they belong together.
Tested in Firefox, Safari, IE5.5, IE6, but there are still some features
to be implemented before this is ready for 'main'.
To use, first add "new_style_june_2007=true" to the app:universe section of
universe_wsgi.ini (this gives you the new layout). Second change document_root
to "%(here)s/static/june_2007_style/blue" in the app:static_style section.
Style Features: simplifications, fewer 'hatched' images, space savings in some
places, small changes to the color scheme (same general feel, but the colors
are better matched). Main changes are to history, the new style support nested
datasets much better.
Layout features: no framesets (just iframes, some of which can be replaced with divs and ajax down the road). Frames are resizable and hideable. Tools can provide width hints and history will automatically hide (try UCSC main to see this).
Daniel Blankenberg