Commit Graph
9 Commits
Author SHA1 Message Date
Helena Rasche 646b133bb3 Add EDAM topics to unannotated tools 2020-10-30 17:59:45 +01:00
Nicola Soranzo ef4f5ccda4 Remove deprecated `interpreter attribute from tools <command>` 2020-03-05 12:53:09 +01:00
peterjc fce2184e5b Make tool version explicit (Job runner would assume 1.0.0) 2015-03-09 15:21:48 +00:00
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 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