Commit Graph
11 Commits
Author SHA1 Message Date
Daniel Blankenberg 3f78f9a449 Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0. 2014-06-27 14:44:55 -04:00
Nate Coraor 9c64fc123e Remove broken and/or obsolete tools. 2014-01-27 13:58:31 -05:00
Daniel Blankenberg 694300ce97 Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters. 2011-04-21 13:12:10 -04:00
Daniel Blankenberg 58963cc97d Remove link target from intermine datasource tools. 2011-03-22 20:29:32 -04:00
Daniel Blankenberg f92b25d2f5 Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.
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.
2009-12-07 10:19:41 -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 051a78bc39 Add new tool config for flymine production server. 2009-01-13 10:55:08 -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 b4890c1bbb Integrate with intermine ( data source ) and epigraph ( data destination ). Receiving data from epigraph coming soon. Data is sent to epigraph using a combination of DATA_URL and REDIRECT_URL tool params. This tool creates jobs, but does not queue them for execution. 2008-09-22 10:36:34 -04:00