diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py index 2c6ff80ce84..7d5ccc813e9 100644 --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -502,7 +502,7 @@ class Data( object ): """Returns ( target_ext, existing 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, deps=None, target_context=None): + def convert_dataset(self, trans, original_dataset, target_type, return_output=False, visible=True, deps=None, target_context=None, history=None): """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 ) @@ -525,7 +525,7 @@ class Data( object ): params[input_name] = original_dataset # Run converter, job is dispatched through Queue - converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible )[1] + converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, history=history )[1] if len(params) > 0: trans.log_event( "Converter params: %s" % (str(params)), tool_id=converter.id ) if not visible: diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 4794ce037f6..a1918759ba3 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2041,7 +2041,7 @@ class DatasetInstance( object ): depends_list = [] return dict([ (dep, self.get_converted_dataset(trans, dep)) for dep in depends_list ]) - def get_converted_dataset(self, trans, target_ext, target_context=None): + def get_converted_dataset(self, trans, target_ext, target_context=None, history=None): """ Return converted dataset(s) if they exist, along with a dict of dependencies. If not converted yet, do so and return None (the first time). If unconvertible, raise exception. @@ -2080,7 +2080,7 @@ class DatasetInstance( object ): raise NoConverterException("A dependency (%s) is missing a converter." % dependency) except KeyError: pass # No deps - new_dataset = next(iter(self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, target_context=target_context ).values())) + new_dataset = next(iter(self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, target_context=target_context, history=history ).values())) new_dataset.name = self.name self.copy_attributes( new_dataset ) assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False ) diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index e4ff04a46c2..349e94a43f9 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -41,7 +41,7 @@ class ToolAction( object ): class DefaultToolAction( object ): """Default tool action is to run an external command""" - def collect_input_datasets( self, tool, param_values, trans, current_user_roles=None ): + def _collect_input_datasets( self, tool, param_values, trans, history, current_user_roles=None ): """ Collect any dataset inputs from incoming. Returns a mapping from parameter name to Dataset instance for each tool parameter that is @@ -66,7 +66,7 @@ class DefaultToolAction( object ): if converted_dataset: data = converted_dataset else: - data = data.get_converted_dataset( trans, target_ext, target_context=parent ) + data = data.get_converted_dataset( trans, target_ext, target_context=parent, history=history ) if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): raise Exception( "User does not have permission to use a dataset (%s) provided for input." % data.id ) @@ -189,7 +189,7 @@ class DefaultToolAction( object ): # input datasets can process these normally. inp_dataset_collections = self.collect_input_dataset_collections( tool, incoming ) # Collect any input datasets from the incoming parameters - inp_data = self.collect_input_datasets( tool, incoming, trans, current_user_roles=current_user_roles ) + inp_data = self._collect_input_datasets( tool, incoming, trans, history=history, current_user_roles=current_user_roles ) return history, inp_data, inp_dataset_collections diff --git a/test/functional/tools/implicit_conversion.xml b/test/functional/tools/implicit_conversion.xml new file mode 100644 index 00000000000..8a7044cebd3 --- /dev/null +++ b/test/functional/tools/implicit_conversion.xml @@ -0,0 +1,23 @@ + + + cut -f 1 '$input1' > 'col_output' + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/sample_datatypes_conf.xml b/test/functional/tools/sample_datatypes_conf.xml index 3891cad99c4..f18a2da3a99 100644 --- a/test/functional/tools/sample_datatypes_conf.xml +++ b/test/functional/tools/sample_datatypes_conf.xml @@ -4,7 +4,9 @@ - + + + diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml index 54e6ad0fc30..71857bc8f68 100644 --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -72,6 +72,7 @@ +