details: http://www.bx.psu.edu/hg/galaxy/rev/94df4d059b19 changeset: 1695:94df4d059b19 user: Nate Coraor nate@bx.psu.edu date: Fri Jan 09 15:59:29 2009 -0500 description: Add an option to override the output dataset(s) path, so they may be written to the working directory. This allows administrators to mount datasets read-only on cluster nodes.

3 file(s) affected in this change:

lib/galaxy/config.py lib/galaxy/jobs/__init__.py lib/galaxy/tools/__init__.py

diffs (100 lines):

diff -r 58744d4bda7b -r 94df4d059b19 lib/galaxy/config.py --- a/lib/galaxy/config.py Fri Jan 09 14:07:16 2009 -0500 +++ b/lib/galaxy/config.py Fri Jan 09 15:59:29 2009 -0500 @@ -45,6 +45,7 @@ self.job_scheduler_policy = kwargs.get("job_scheduler_policy", "FIFO") self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") ) self.job_working_directory = resolve_path( kwargs.get( "job_working_directory", "database/job_working_directory" ), self.root ) + self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) ) self.admin_pass = kwargs.get('admin_pass',"galaxy") self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu") diff -r 58744d4bda7b -r 94df4d059b19 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Jan 09 14:07:16 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Fri Jan 09 15:59:29 2009 -0500 @@ -350,7 +350,7 @@ incoming['userId'] = userId incoming['userEmail'] = userEmail # Build params, done before hook so hook can use - param_dict = self.tool.build_param_dict( incoming, inp_data, out_data ) + param_dict = self.tool.build_param_dict( incoming, inp_data, out_data, self.working_directory ) # Certain tools require tasks to be completed prior to job execution # ( this used to be performed in the "exec_before_job" hook, but hooks are deprecated ). if self.tool.tool_type is not None: @@ -471,6 +471,13 @@ else: job.state = 'ok' for dataset_assoc in job.output_datasets: + if self.app.config.outputs_to_working_directory: + false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % dataset_assoc.dataset.id ) ) + if os.path.exists( false_path ): + os.rename( false_path, dataset_assoc.dataset.file_name ) + log.debug( "Moved %s to %s" % ( false_path, dataset_assoc.dataset.file_name ) ) + else: + log.warning( "Missing output file in working directory: %s" % false_path ) for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running dataset.blurb = 'done' dataset.peek = 'no peek' diff -r 58744d4bda7b -r 94df4d059b19 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Jan 09 14:07:16 2009 -0500 +++ b/lib/galaxy/tools/__init__.py Fri Jan 09 15:59:29 2009 -0500 @@ -1045,7 +1045,7 @@ input.validate( value, None ) input_values[ input.name ] = value

- def build_param_dict( self, incoming, input_datasets, output_datasets ): + def build_param_dict( self, incoming, input_datasets, output_datasets, working_directory = None ): """ Build the dictionary of parameters for substituting into the command line. Each value is wrapped in a `InputValueWrapper`, which allows @@ -1090,7 +1090,13 @@ for child in data.children: param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) for name, data in output_datasets.items(): - param_dict[name] = DatasetFilenameWrapper( data ) + # Write outputs to the working directory (for security purposes) if desired. + if self.app.config.outputs_to_working_directory and working_directory is not None: + false_path = os.path.abspath( os.path.join( working_directory, "galaxy_dataset_%d.dat" % data.id ) ) + param_dict[name] = DatasetFilenameWrapper( data, false_path = false_path ) + open( false_path, 'w' ).close() + else: + param_dict[name] = DatasetFilenameWrapper( data ) # Provide access to a path to store additional files # TODO: path munging for cluster/dataset server relocatability param_dict[name].files_path = os.path.abspath(os.path.join(self.app.config.new_file_path, "dataset_%s_files" % (data.id) )) @@ -1433,7 +1439,7 @@ def items( self ): return iter( [ ( k, self.get( k ) ) for k, v in self.metadata.items() ] )

- def __init__( self, dataset, datatypes_registry = None, tool = None, name = None ): + def __init__( self, dataset, datatypes_registry = None, tool = None, name = None, false_path = None ): if not dataset: try: #TODO: allow this to work when working with grouping @@ -1444,10 +1450,17 @@ else: self.dataset = dataset self.metadata = self.MetadataWrapper( dataset.metadata ) + self.false_path = false_path def __str__( self ): - return self.dataset.file_name + if self.false_path is not None: + return self.false_path + else: + return self.dataset.file_name def __getattr__( self, key ): - return getattr( self.dataset, key ) + if self.false_path is not None and key == 'file_name': + return self.false_path + else: + return getattr( self.dataset, key )

def json_fix( val ): if isinstance( val, list ): @@ -1467,4 +1480,4 @@ value[composite_key] = incoming[key + "_" + composite_key] return value else: - return incoming.get( key, default ) \ No newline at end of file + return incoming.get( key, default )