Changeset 125:3fcd0890c2ac

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Timestamp:
03/08/07 19:12:11 (2 years ago)
Author:
James Taylor <james@bx.psu.edu>
branch:
default
convert_revision:
svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@1411
Message:

Support for viewing the full stderr/stdout text associated with "error"
datasets and for sending email reports.

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  • lib/galaxy/app.py

    r80 r125  
    33from galaxy import config, db, jobs, util, tools, web 
    44import galaxy.model.mapping 
    5 from galaxy.interfaces import root, tool_runner, proxy, async, admin, user, error 
     5from galaxy.interfaces import root, tool_runner, proxy, async, admin, user, error, dataset 
    66from galaxy.web import middleware 
    77 
    …… 
    6060    webapp.add_controller( 'user', user.User( app ) ) 
    6161    webapp.add_controller( 'error', error.Error( app ) ) 
     62    webapp.add_controller( 'dataset', dataset.DatasetInterface( app ) ) 
    6263    # These two routes handle our simple needs at the moment 
    6364    webapp.add_route( '/async/:tool_id/:data_id', controller='async', action='index', tool_id=None, data_id=None ) 
    64     webapp.add_route( '/:controller/:action', action='index' ) 
     65    webapp.add_route( '/:controller/:action/:id', action='index', id=None ) 
    6566    webapp.add_route( '/:action', controller='root', action='index' ) 
    6667    webapp.finalize_config() 

  • lib/galaxy/config.py

    r113 r125  
    3434        self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") 
    3535        self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu") 
     36        self.error_email_to = kwargs.get( 'error_email_to', None ) 
     37        self.smtp_server = kwargs.get( 'smtp_server', None ) 
    3638        self.use_pbs = kwargs.get('use_pbs', False ) 
    3739        self.pbs_server = kwargs.get('pbs_server', "" ) 

  • lib/galaxy/model/__init__.py

    r115 r125  
    287287        self.galaxy_session = galaxy_session 
    288288        self.history = history 
    289          
    290  

  • lib/galaxy/model/mapping.py

    r117 r125  
    137137 
    138138assign_mapper( context, Dataset, Dataset.table, 
    139     properties=dict( children=relation( DatasetChildAssociation, primaryjoin=( DatasetChildAssociation.table.c.parent_dataset_id == Dataset.table.c.id ), 
    140                                         lazy=False ) ) ) 
     139    properties=dict( children=relation( DatasetChildAssociation, primaryjoin=( DatasetChildAssociation.table.c.parent_dataset_id == Dataset.table.c.id ), lazy=False ) ) ) 
    141140                                         
    142141assign_mapper( context, DatasetChildAssociation, DatasetChildAssociation.table, 
    …… 
    182181    properties=dict( galaxy_session=relation( GalaxySession ),  
    183182                     history=relation( History ) ) ) 
     183                      
     184Dataset.mapper.add_property( "creating_job_associations", relation( JobToOutputDatasetAssociation ) ) 
    184185     
    185186def db_next_hid( self ): 

  • templates/history.tmpl

    r115 r125  
    180180                        <div>Job is waiting to run</div> 
    181181                        #* THIS SHOULD SAY CANCEL, DELETING QUEUED/RUNNING JOBS SHOULD REMOVE THEM FROM THE QUEUE *# 
    182                         <a href="delete?id=$data.id">delete</a>  
     182                        #* <a href="delete?id=$data.id">delete</a> *# 
    183183                    #elif $data_state == "running" 
    184184                        <div>Job is currently running</div> 
    185                         <a href="delete?id=$data.id">delete</a>  
     185                        #*<a href="delete?id=$data.id">delete</a> *# 
    186186                    #elif $data_state == "error" 
    187                         <div>An error occurred running this job: <i>$data.display_info</i></div> 
    188                         <a href="delete?id=$data.id">delete</a>  
     187                        <div>An error occurred running this job: <i>$data.display_info</i>, <a href="${h.url_for( controller='dataset', action='errors', id=$data.id )}" target="galaxy_main">more info</a></div> 
     188                        #*<a href="delete?id=$data.id">delete</a> *# 
    189189                    #else 
    190190                    <div> 

  • universe_wsgi.ini.sample

    r79 r125  
    7171# path to sendmail 
    7272sendmail_path = /usr/sbin/sendmail 
     73# SMTP server 
     74## smtp_server = ... 
     75# Address to email error reports to 
     76## error_email_to = ... 
    7377# Address to join mailing list 
    7478mailing_join_addr = galaxy-user-join@bx.psu.edu