Daniel Blankenberg
b2e2b801ea
Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is
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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
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
6aa6c5a2d8
More width hints for data source tools.
2007-07-05 19:20:33 +00:00
Daniel Blankenberg
ad8719b852
Fix ucsc test browser.
2007-03-21 19:59:58 +00:00
Daniel Blankenberg
8a207dcd87
Update UCSC direct connection to use main ucsc site. Add direct test
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connection.
2007-03-21 19:52:01 +00:00
Daniel Blankenberg