1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ef0e9bf34c0b/ changeset: ef0e9bf34c0b user: dan date: 2013-02-15 17:58:29 summary: Add missing Data Manager controller. affected #: 1 file
diff -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 -r ef0e9bf34c0b22dd355759478aa85fc2d46d49d4 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -0,0 +1,79 @@ +from galaxy import web +from galaxy.web.base.controller import BaseUIController +from galaxy.util.json import from_json_string + +import pkg_resources; +pkg_resources.require( "Paste" ) +import paste.httpexceptions + +#set up logger +import logging +log = logging.getLogger( __name__ ) + +class DataManager( BaseUIController ): + + @web.expose + def index( self, trans, **kwd ): + not_is_admin = not trans.user_is_admin() + if not_is_admin and not trans.app.config.enable_data_manager_user_view: + raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) + message = kwd.get( 'message' ) + status = kwd.get( 'status', 'info' ) + return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, view_only=not_is_admin, message=message, status=status ) + + @web.expose + def manage_data_manager( self, trans, **kwd ): + not_is_admin = not trans.user_is_admin() + if not_is_admin and not trans.app.config.enable_data_manager_user_view: + raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) + message = kwd.get( 'message' ) + status = kwd.get( 'status', 'info' ) + data_manager_id = kwd.get( 'id', None ) + data_manager = trans.app.data_managers.get_manager( data_manager_id ) + if data_manager is None: + return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data Manager (%s) was requested" % data_manager_id, status="error" ) ) + jobs = reversed( [ assoc.job for assoc in trans.sa_session.query( trans.app.model.DataManagerJobAssociation ).filter_by( data_manager_id=data_manager_id ) ] ) + return trans.fill_template( "data_manager/manage_data_manager.mako", data_manager=data_manager, jobs=jobs, view_only=not_is_admin, message=message, status=status ) + + @web.expose + def view_job( self, trans, **kwd ): + not_is_admin = not trans.user_is_admin() + if not_is_admin and not trans.app.config.enable_data_manager_user_view: + raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) + message = kwd.get( 'message' ) + status = kwd.get( 'status', 'info' ) + job_id = kwd.get( 'id', None ) + try: + job_id = trans.security.decode_id( job_id ) + job = trans.app.model.Job.get( job_id ) + except Exception, e: + job = None + log.error( "Bad job id (%s) passed to view_job: %s" % ( job_id, e ) ) + if not job: + return trans.response.send_redirect( web.url_for( controller="data_manager", action="index",message="Invalid job (%s) was requested" % job_id, status="error" ) ) + data_manager_id = job.data_manager_association.data_manager_id + data_manager = trans.app.data_managers.get_manager( data_manager_id ) + hdas = [ assoc.dataset for assoc in job.get_output_datasets() ] + data_manager_output = [] + for hda in hdas: + data_manager_json = from_json_string( open( hda.get_file_name() ).read() ) + values = [] + for key, value in data_manager_json.get( 'data_tables', {} ).iteritems(): + values.append( ( key, value ) ) + data_manager_output.append( values ) + return trans.fill_template( "data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status ) + + @web.expose + def manage_data_table( self, trans, **kwd ): + not_is_admin = not trans.user_is_admin() + if not_is_admin and not trans.app.config.enable_data_manager_user_view: + raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) + message = kwd.get( 'message' ) + status = kwd.get( 'status', 'info' ) + data_table_name = kwd.get( 'table_name', None ) + if not data_table_name: + return trans.response.send_redirect( web.url_for( controller="data_manager", action="index" ) ) + data_table = trans.app.tool_data_tables.get( data_table_name, None ) + if data_table is None: + return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data table (%s) was requested" % data_table_name, status="error" ) ) + return trans.fill_template( "data_manager/manage_data_table.mako", data_table=data_table, view_only=not_is_admin, message=message, status=status )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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