details: http://www.bx.psu.edu/hg/galaxy/rev/3830fefb07da changeset: 1533:3830fefb07da user: Dan Blankenberg dan@bx.psu.edu date: Fri Sep 26 14:22:37 2008 -0400 description: Update to implicit converter discovery. Will now allow the use of converters that create datatypes that are a subclass of what is needed by the tool.
i.e. If tool input requires 'interval', and a datatype has a BED converter available but no interval converter, the BED converter can now be used.
5 file(s) affected in this change:
lib/galaxy/datatypes/data.py lib/galaxy/datatypes/registry.py lib/galaxy/model/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/parameters/basic.py
diffs (138 lines):
diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/datatypes/data.py Fri Sep 26 14:22:37 2008 -0400 @@ -185,6 +185,10 @@ """Returns available converters by type for this dataset""" return datatypes_registry.get_converters_by_datatype(original_dataset.ext)
+ def find_conversion_destination( self, dataset, accepted_formats, datatypes_registry, **kwd ): + """Returns ( target_ext, exisiting converted dataset )""" + return datatypes_registry.find_conversion_destination_for_dataset_by_extensions( dataset, accepted_formats, **kwd ) + def convert_dataset(self, trans, original_dataset, target_type, return_output = False, visible = True ): """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.""" converter = trans.app.datatypes_registry.get_converter_by_target_type( original_dataset.ext, target_type ) diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/datatypes/registry.py Fri Sep 26 14:22:37 2008 -0400 @@ -233,3 +233,16 @@ if target_ext in converters.keys(): return converters[target_ext] return None + def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): + """Returns ( target_ext, exisiting converted dataset )""" + for convert_ext in self.get_converters_by_datatype( dataset.ext ): + if isinstance( self.get_datatype_by_extension( convert_ext ), accepted_formats ): + datasets = dataset.get_converted_files_by_type( convert_ext ) + if datasets: + ret_data = datasets[0] + elif not converter_safe: + continue + else: + ret_data = None + return ( convert_ext, ret_data ) + return ( None, None ) \ No newline at end of file diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/model/__init__.py Fri Sep 26 14:22:37 2008 -0400 @@ -254,6 +254,10 @@
def get_converter_types(self): return self.datatype.get_converter_types( self, datatypes_registry) + + def find_conversion_destination( self, accepted_formats, **kwd ): + """Returns ( target_ext, exisiting converted dataset )""" + return self.datatype.find_conversion_destination( self, accepted_formats, datatypes_registry, **kwd )
def copy( self, copy_children = False, parent_id = None ): des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self ) diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Fri Sep 26 14:22:37 2008 -0400 @@ -29,22 +29,21 @@ def visitor( prefix, input, value, parent = None ): def process_dataset( data ): if data and not isinstance( data.datatype, input.formats ): - for target_ext in input.extensions: - if target_ext in data.get_converter_types(): - data.refresh() #need to refresh incase this conversion just took place, i.e. input above in tool performed the same conversion - datasets = data.get_converted_files_by_type( target_ext ) - if datasets: data = datasets[0] - elif input.converter_safe( param_values, trans ): - #run converter here - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) - new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] - new_data.hid = data.hid - new_data.name = data.name - new_data.flush() - assoc.dataset = new_data - assoc.flush() - data = new_data - break + data.refresh() #need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion + target_ext, converted_dataset = data.find_conversion_destination( input.formats, converter_safe = input.converter_safe( param_values, trans ) ) + if target_ext: + if converted_dataset: + data = converted_dataset + else: + #run converter here + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) + new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] + new_data.hid = data.hid + new_data.name = data.name + new_data.flush() + assoc.dataset = new_data + assoc.flush() + data = new_data return data if isinstance( input, DataToolParameter ): if isinstance( value, list ): diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Fri Sep 26 14:22:37 2008 -0400 @@ -1059,16 +1059,12 @@ selected = ( value and ( data in value ) ) field.add_option( "%s: %s" % ( hid, data.name[:30] ), data.id, selected ) else: - for target_ext in self.extensions: - if target_ext in data.get_converter_types(): - datasets = data.get_converted_files_by_type( target_ext ) - if datasets: - data = datasets[0] - elif not self.converter_safe( other_values, trans ): - continue - selected = ( value and ( data in value ) ) - field.add_option( "%s: (as %s) %s" % ( hid, target_ext, data.name[:30] ), data.id, selected ) - break #we only report the first valid converter, assume self.extensions is a priority list + target_ext, converted_dataset = data.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + if target_ext: + if converted_dataset: + data = converted_dataset + selected = ( value and ( data in value ) ) + field.add_option( "%s: (as %s) %s" % ( hid, target_ext, data.name[:30] ), data.id, selected ) # Also collect children via association object dataset_collector( data.children, hid ) dataset_collector( history.datasets, None ) @@ -1111,9 +1107,9 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - for target_ext in self.extensions: - if target_ext in data.get_converter_types(): - return True + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = True ) #need to assume converter_safe = True, since we don't know about other parameter values here + if target_ext is not None: + return True return False for i, data in enumerate( datasets ): if data.visible and not data.deleted and data.state not in [data.states.ERROR] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): @@ -1184,7 +1180,7 @@ return []
def converter_safe( self, other_values, trans ): - if trans.workflow_building_mode: + if not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: return False converter_safe = [True] def visitor( prefix, input, value, parent = None ):