1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ff17100de392/ Changeset: ff17100de392 User: dannon Date: 2013-06-18 20:04:21 Summary: Enable workflow step annotations for toolshed imported workflows. Affected #: 1 file
diff -r 81a2bb351c1a0f545a1f69b5514a29d96eb4575a -r ff17100de392abf7fba9327949308ab2594d2d07 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -12,9 +12,7 @@ from tool_shed.util import metadata_util from tool_shed.util import tool_util
-import pkg_resources - -pkg_resources.require( "SVGFig" ) +eggs.require( "SVGFig" ) import svgfig
log = logging.getLogger( __name__ ) @@ -386,6 +384,28 @@ workflow.has_errors = True # Stick this in the step temporarily. step.temp_input_connections = step_dict[ 'input_connections' ] + + # This should be considered a *temporary* hack. + # Usually we'd use the UsesAnnotation mixin, but + # that's not possible here. This entire module + # needs to die and get replaced with the regular + # galaxy/workflow methods. + from galaxy.util.sanitize_html import sanitize_html + annotation = step_dict.get( 'annotation', '') + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + new_step_annotation = trans.model.WorkflowStepAnnotationAssociation() + new_step_annotation.annotation = annotation + new_step_annotation.user = trans.user + step.annotations.append(new_step_annotation) + # Unpack and add post-job actions. + post_job_actions = step_dict.get( 'post_job_actions', {} ) + for name, pja_dict in post_job_actions.items(): + trans.model.PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], + pja_dict[ 'action_arguments' ] ) + # End temporary hack + steps.append( step ) steps_by_external_id[ step_dict[ 'id' ] ] = step # Second pass to deal with connections between steps.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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