On Fri, Aug 14, 2009 at 1:14 PM, <galaxy-dev-request@bx.psu.edu> wrote: This is excellent - it seems very natural - another extremely compelling feature. Congratulations everyone!

Message: 4 Date: Fri, 14 Aug 2009 13:14:02 -0400 From: Greg Von Kuster <greg@bx.psu.edu> Subject: [galaxy-dev] [hg] galaxy 2558: Integrate 'rerun' support from        Assaf   Gordan. N... To: galaxy-dev@bx.psu.edu Message-ID:        <hg.52ad5635f01a.1250270042.-331200333@scofield.bx.psu.edu>

details:   http://www.bx.psu.edu/hg/galaxy/rev/52ad5635f01a changeset: 2558:52ad5635f01a user:      James Taylor <james@jamestaylor.org> date:      Thu Aug 13 11:27:45 2009 -0400 description: Integrate 'rerun' support from Assaf Gordan. Not supported for all tools, but checking whether the link should be displayed is expensive currently, this can be improved ghopefully.

2 file(s) affected in this change:

lib/galaxy/web/controllers/tool_runner.py templates/root/history_common.mako

diffs (118 lines):

diff -r ad5232a4dbc5 -r 52ad5635f01a lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Thu Aug 13 11:00:00 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Thu Aug 13 11:27:45 2009 -0400 @@ -5,6 +5,7 @@  from galaxy.web.base.controller import *  from galaxy.util.bunch import Bunch  from galaxy.tools import DefaultToolState +from galaxy.tools.parameters.basic import UnvalidatedValue

 import logging  log = logging.getLogger( __name__ ) @@ -52,6 +53,80 @@             add_frame.wiki_url = trans.app.config.wiki_url             add_frame.from_noframe = True         return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) + +    @web.expose +    def rerun( self, trans, id=None, from_noframe=None, **kwd ): +        """ +        Given a HistoryDatasetAssociation id, find the job and that created +        the dataset, extract the parameters, and display the appropriate tool +        form with parameters already filled in. +        """ +        if not id: +            error( "'id' parameter is required" ); +        try: +            id = int( id ) +        except: +            error( "Invalid value for 'id' parameter" ) +        # Get the dataset object +        data = trans.app.model.HistoryDatasetAssociation.get( id ) +        # Get the associated job, if any. If this hda was copied from another, +        # we need to find the job that created the origial hda +        job_hda = data +        while job_hda.copied_from_history_dataset_association: +            job_hda = job_hda.copied_from_history_dataset_association +        if not job_hda.creating_job_associations: +            error( "Could not find the job for this dataset" ) +        # Get the job object +        job = None +        for assoc in job_hda.creating_job_associations: +            job = assoc.job +            break +        if not job: +            raise Exception("Failed to get job information for dataset hid %d" % hid) +        # Get the tool object +        tool_id = job.tool_id +        try: +            # Load the tool +            toolbox = self.get_toolbox() +            tool = toolbox.tools_by_id.get( tool_id, None ) +        except: +            #this is expected, so not an exception +            error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) +        # Can't rerun upload, external data sources, et cetera. Workflow +        # compatible will proxy this for now +        if not tool.is_workflow_compatible: +            error( "The '%s' tool does not currently support rerunning." % tool.name ) +        # Get the job's parameters +        try: +            params_objects = job.get_param_values( trans.app ) +        except: +            raise Exception( "Failed to get paramemeters for dataset id %d " % hid ) +        # Unpack unvalidated values to strings, they'll be validated when the +        # form is submitted (this happens when re-running a job that was +        # initially run by a workflow) +        validated_params = {} +        for name, value in params_objects.items(): +            if isinstance( value, UnvalidatedValue ): +                validated_params [ str(name) ] = str(value) +            else: +                validated_params [ str(name) ] = value +        params_objects = validated_params +        # Create a fake tool_state for the tool, with the parameters values +        state = tool.new_state( trans ) +        state.inputs = params_objects +        tool_state_string = util.object_to_string(state.encode(tool, trans.app)) +        # Setup context for template +        history = trans.get_history() +        template = "tool_form.mako" +        vars = dict( tool_state=state, errors = {} ) +        # Is the "add frame" stuff neccesary here? +        add_frame = AddFrameData() +        add_frame.debug = trans.debug +        if from_noframe is not None: +            add_frame.wiki_url = trans.app.config.wiki_url +            add_frame.from_noframe = True +        return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) +

    @web.expose     def redirect( self, trans, redirect_url=None, **kwd ): diff -r ad5232a4dbc5 -r 52ad5635f01a templates/root/history_common.mako --- a/templates/root/history_common.mako        Thu Aug 13 11:00:00 2009 -0400 +++ b/templates/root/history_common.mako        Thu Aug 13 11:27:45 2009 -0400 @@ -51,9 +51,12 @@                 <div>${_('Job is currently running')}</div>             %elif data_state == "error":                 <div> -                    An error occurred running this job: <i>${data.display_info().strip()}</i>, -                    <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main">report this error</a> +                    An error occurred running this job: <i>${data.display_info().strip()}</i>                 </div> +               <div> +                   <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main">report this error</a> +                   | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a> +               </div>             %elif data_state == "discarded":                 <div>                     The job creating this dataset was cancelled before completion. @@ -77,6 +80,7 @@                 <div>                     %if data.has_data:                         <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> +                       | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a>                         %for display_app in data.datatype.get_display_types():                             <% display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %>                             %if len( display_links ) > 0:

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End of galaxy-dev Digest, Vol 44, Issue 22 ******************************************

-- Ross Lazarus, Associate Professor, Department of Population Medicine, Harvard Medical School; Director of Bioinformatics, Channing Laboratory, BWH 181 Longwood Ave., Boston MA 02115, USA.