[galaxy-commits] commit/galaxy-central: 4 new changesets

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56b18b56417f/ Changeset: 56b18b56417f User: jmchilton Date: 2012-11-10 21:26:29 Summary: Refactor setting up valid extensions in DataToolParameter to eliminate code duplication, extra computation (multiple loading of same datatypes in unit tests for instance), and reduce code nesting. Affected #: 1 file diff -r 340438c62171578078323d39da398d5053b69d0a -r 56b18b56417f0c2613c79055b21170a3a92379ac lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1371,24 +1371,25 @@ # Add metadata validator if not string_as_bool( elem.get( 'no_validation', False ) ): self.validators.append( validation.MetadataValidator() ) + # Find datatypes_registry + if tool is None: + if trans: + # Must account for "Input Dataset" types, which while not a tool still need access to the real registry. + # A handle to the transaction (and thus app) will be given by the module. + datatypes_registry = trans.app.datatypes_registry + else: + #This occurs for things such as unit tests + import galaxy.datatypes.registry + datatypes_registry = galaxy.datatypes.registry.Registry() + datatypes_registry.load_datatypes() + else: + datatypes_registry = tool.app.datatypes_registry # Build tuple of classes for supported data formats formats = [] self.extensions = elem.get( 'format', 'data' ).split( "," ) for extension in self.extensions: extension = extension.strip() - if tool is None: - if trans: - # Must account for "Input Dataset" types, which while not a tool still need access to the real registry. - # A handle to the transaction (and thus app) will be given by the module. - formats.append( trans.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) - else: - #This occurs for things such as unit tests - import galaxy.datatypes.registry - datatypes_registry = galaxy.datatypes.registry.Registry() - datatypes_registry.load_datatypes() - formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) - else: - formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) + formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) self.formats = tuple( formats ) self.multiple = string_as_bool( elem.get( 'multiple', False ) ) # TODO: Enhance dynamic options for DataToolParameters. Currently, https://bitbucket.org/galaxy/galaxy-central/commits/b999689a0130/ Changeset: b999689a0130 User: jmchilton Date: 2012-11-15 15:11:02 Summary: Centeralize logic for checking if a given galaxy datatype is any of the datatypes in a given iterator (tuple, list) (used when building up tool input options and evaluating tools, checking conversions, etc...). I think this is a solid (though slight) design improvement in its own right, but it will also ease the eventually merging of composite multifiles (https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes) into galaxy-central or at least limit the divergence between galaxy-central and that fork long term. Affected #: 4 files diff -r 56b18b56417f0c2613c79055b21170a3a92379ac -r b999689a013025f2a009e313a3b6e6f65354e005 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -529,7 +529,13 @@ def has_resolution(self): return False - + def matches_any( self, target_datatypes ): + """ + Check if this datatype is of any of the target_datatypes or is + a subtype thereof. + """ + datatype_classes = tuple( [ datatype.__class__ for datatype in target_datatypes ] ) + return isinstance( self, datatype_classes ) def merge( split_files, output_file): """ diff -r 56b18b56417f0c2613c79055b21170a3a92379ac -r b999689a013025f2a009e313a3b6e6f65354e005 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -586,7 +586,7 @@ def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): """Returns ( target_ext, existing converted dataset )""" for convert_ext in self.get_converters_by_datatype( dataset.ext ): - if isinstance( self.get_datatype_by_extension( convert_ext ), accepted_formats ): + if self.get_datatype_by_extension( convert_ext ).matches_any( accepted_formats ): converted_dataset = dataset.get_converted_files_by_type( convert_ext ) if converted_dataset: ret_data = converted_dataset diff -r 56b18b56417f0c2613c79055b21170a3a92379ac -r b999689a013025f2a009e313a3b6e6f65354e005 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -36,7 +36,7 @@ def process_dataset( data, formats = None ): if formats is None: formats = input.formats - if data and not isinstance( data.datatype, formats ): + if data and not data.datatype.matches_any( formats ): # Need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion trans.sa_session.refresh( data ) target_ext, converted_dataset = data.find_conversion_destination( formats ) @@ -66,7 +66,7 @@ conversions = [] for conversion_name, conversion_extensions, conversion_datatypes in input.conversions: new_data = process_dataset( input_datasets[ prefix + input.name + str( i + 1 ) ], conversion_datatypes ) - if not new_data or isinstance( new_data.datatype, conversion_datatypes ): + if not new_data or new_data.datatype.matches_any( conversion_datatypes ): input_datasets[ prefix + conversion_name + str( i + 1 ) ] = new_data conversions.append( ( conversion_name, new_data ) ) else: @@ -86,7 +86,7 @@ conversions = [] for conversion_name, conversion_extensions, conversion_datatypes in input.conversions: new_data = process_dataset( input_datasets[ prefix + input.name ], conversion_datatypes ) - if not new_data or isinstance( new_data.datatype, conversion_datatypes ): + if not new_data or new_data.datatype.matches_any( conversion_datatypes ): input_datasets[ prefix + conversion_name ] = new_data conversions.append( ( conversion_name, new_data ) ) else: @@ -261,7 +261,9 @@ ext = input_ext if output.format_source is not None and output.format_source in inp_data: try: - ext = inp_data[output.format_source].ext + input_dataset = inp_data[output.format_source] + input_extension = input_dataset.ext + ext = input_extension except Exception, e: pass diff -r 56b18b56417f0c2613c79055b21170a3a92379ac -r b999689a013025f2a009e313a3b6e6f65354e005 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -785,7 +785,7 @@ if isinstance( dep_value, RuntimeValue ): return True #dataset not ready yet - if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): + if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not dep_value.datatype.matches_any( self.ref_input.formats ) ): return True # Dynamic, but all dependenceis are known and have values return False @@ -1037,7 +1037,7 @@ if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): + if dataset.is_pending or not dataset.datatype.matches_any( self.ref_input.formats ): return True # No late validation return False @@ -1389,8 +1389,8 @@ self.extensions = elem.get( 'format', 'data' ).split( "," ) for extension in self.extensions: extension = extension.strip() - formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) - self.formats = tuple( formats ) + formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ) ) + self.formats = formats self.multiple = string_as_bool( elem.get( 'multiple', False ) ) # TODO: Enhance dynamic options for DataToolParameters. Currently, # only the special case key='build' of type='data_meta' is @@ -1414,7 +1414,7 @@ conv_extensions = conv_elem.get( "type" ) #target datatype extension # FIXME: conv_extensions should be able to be an ordered list assert None not in [ name, type ], 'A name (%s) and type (%s) are required for explicit conversion' % ( name, type ) - conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ).__class__ + conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ) self.conversions.append( ( name, conv_extensions, conv_types ) ) def get_html_field( self, trans=None, value=None, other_values={} ): @@ -1452,7 +1452,7 @@ continue if self.options and self._options_filter_attribute( hda ) != filter_value: continue - if isinstance( hda.datatype, self.formats): + if hda.datatype.matches_any( self.formats ): selected = ( value and ( hda in value ) ) if hda.visible: hidden_text = "" @@ -1519,7 +1519,7 @@ for i, data in enumerate( datasets ): if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: is_valid = False - if isinstance( data.datatype, self.formats ): + if data.datatype.matches_any( self.formats ): is_valid = True else: target_ext, converted_dataset = data.find_conversion_destination( self.formats ) https://bitbucket.org/galaxy/galaxy-central/commits/c011bbda72b3/ Changeset: c011bbda72b3 User: jmchilton Date: 2012-11-15 15:23:15 Summary: Small refactoring of logic used to build up list of valid formats for an input data parameter. Affected #: 1 file diff -r b999689a013025f2a009e313a3b6e6f65354e005 -r c011bbda72b3e3fd974a759a53e4baef7b6121a2 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1387,9 +1387,9 @@ # Build tuple of classes for supported data formats formats = [] self.extensions = elem.get( 'format', 'data' ).split( "," ) - for extension in self.extensions: - extension = extension.strip() - formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ) ) + normalized_extensions = [extension.strip().lower() for extension in self.extensions] + for extension in normalized_extensions: + formats.append( datatypes_registry.get_datatype_by_extension( extension ) ) self.formats = formats self.multiple = string_as_bool( elem.get( 'multiple', False ) ) # TODO: Enhance dynamic options for DataToolParameters. Currently, https://bitbucket.org/galaxy/galaxy-central/commits/ada2dca97078/ Changeset: ada2dca97078 User: jmchilton Date: 2012-12-04 06:04:36 Summary: Leave process_dataset immediately if input data is `None` in collect_input_datasets of DefaultToolAction, simplifies code and eliminates some unneeded computation. Affected #: 1 file diff -r c011bbda72b3e3fd974a759a53e4baef7b6121a2 -r ada2dca97078b552d12b28e7da65d9667e28b125 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -34,9 +34,11 @@ input_datasets = dict() def visitor( prefix, input, value, parent = None ): def process_dataset( data, formats = None ): + if not data: + return data if formats is None: formats = input.formats - if data and not data.datatype.matches_any( formats ): + if not data.datatype.matches_any( formats ): # Need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion trans.sa_session.refresh( data ) target_ext, converted_dataset = data.find_conversion_destination( formats ) @@ -54,7 +56,7 @@ trans.sa_session.flush() data = new_data current_user_roles = trans.get_current_user_roles() - if data and not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): + if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): raise "User does not have permission to use a dataset (%s) provided for input." % data.id return data if isinstance( input, DataToolParameter ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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