Commit Graph
16 Commits
Author SHA1 Message Date
Kanwei Li 82eef1efcf Data from UCSC table browser now uses hgta_table for table name. Fixes #67 2009-11-20 15:25:13 -05:00
Daniel Blankenberg b2e2b801ea Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is
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.
2009-08-03 12:02:54 -04:00
Greg Von Kuster e55a4d84f8 More library work - requires database schema update:
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);
2009-03-09 17:02:21 -04:00
Greg Von Kuster 7e21fb74a3 Fixes for Biomart and UCSC to better ensure the data type is correctly set. A data type of "tabular" is now the default, and data will be sniffed if this is the data type. 2009-01-21 17:03:39 -05:00
Greg Von Kuster 32b4b77f74 Missed translating the primaryTable data type from UCSC in my last commit. 2008-11-13 15:17:42 -05:00
Greg Von Kuster c454370ff7 Add a new <data_type_translation> tag set to data_source tools that enable the translation of an unsupported data type to a supported one in Galaxy ( currently only used in UCSC ). Also some tweaks to the jobs reports. 2008-11-13 14:56:33 -05:00
Greg Von Kuster b74f176613 Add a new URL_method attribute to data_source tool types whose value is either "get" or "post" ( some require a get request while others require a post request ). This fixes the Biomart problem ( along with a new, well documented hack that can be eliminated when Biomart encodes the value of URL in the initial response - they'll tell us when they've fixed this ). Also added some requested info to the "send to EpiGRAPH" tool. 2008-10-27 16:03:43 -04:00
Greg Von Kuster 288912ee87 Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type. 2008-10-17 10:46:29 -04:00
Greg Von Kuster b3b6c54247 Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ). 2008-10-07 15:21:46 -04:00
Greg Von Kuster 04e0834500 Revert 2715. 2008-06-04 13:02:15 +00:00
Greg Von Kuster dedc7278a1 Requires config change, temporary files are now created in a configurable location - affects many tools. 2008-06-03 20:29:54 +00:00
Greg Von Kuster af3b0669aa Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4. 2008-03-28 15:24:50 +00:00
James Taylor 4a4c8d25dc New layouts and style.
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).
2007-07-05 18:39:36 +00:00
Daniel Blankenberg 8a207dcd87 Update UCSC direct connection to use main ucsc site. Add direct test
connection.
2007-03-21 19:52:01 +00:00
Daniel Blankenberg e013dc254e Make BED default datatype for UCSC direct connection. 2007-03-01 15:53:03 +00:00
Daniel Blankenberg 412b9a9677 Add UCSC Table Browser direct connection tool. 2007-02-28 20:46:06 +00:00