7 Commits

Include renames

Author	SHA1	Message	Date
Greg Von Kuster	08e0d5e532	Fixes for Bam data type's set_meta() and sam_to_bam tool, indexes will now be properly created for bam datasets. Fixes also for uploading Bam files, they will no longer be uncompressed on upload.	2009-12-04 19:51:46 -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	a9cd544be9	Add a defaulttimeout setting of 10 minutes to the urlopen() call for requests to remote data sources.	2009-05-28 11:10:44 -04:00
Greg Von Kuster	2647f72e4a	Add ability for data_source tools to append parameters passed in the initial response to the value of URL prior to Galaxy's post to the URL. This is a cleaner method for Biomart and also gets GBrowse to wrok.	2008-12-13 23:35:29 -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
Daniel Blankenberg	b9e242e4eb	Add a new metadata type of Metadata Files. ... These are now used to store the list of chromosomes for species as well as the index for MAF files. MAF tools have been enhanced to make use of index files when available. TODO: When datasets are purged from disk, these files should also be purged.	2008-10-22 13:49:22 -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