Merge pull request #3155 from nsoranzo/remove_set_output_history

Remove unnecessary set_output_history parameter

.ci/flake8_lint_include_list.txt

@@ -264,6 +264,7 @@ lib/galaxy/sample_tracking/__init__.py
 lib/galaxy/sample_tracking/sample.py
 lib/galaxy/security/validate_user_input.py
 lib/galaxy/tags/
+lib/galaxy/tools/actions/__init__.py
 lib/galaxy/tools/actions/metadata.py
 lib/galaxy/tools/cwl/
 lib/galaxy/tools/data_manager/__init__.py

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, set_output_history=True, target_context=None):
+    def convert_dataset(self, trans, original_dataset, target_type, return_output=False, visible=True, deps=None, target_context=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, set_output_history=set_output_history)[1]
+        converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible )[1]
         if len(params) > 0:
             trans.log_event( "Converter params: %s" % (str(params)), tool_id=converter.id )
         if not visible:

lib/galaxy/model/__init__.py

@@ -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, set_output_history=True, 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 ).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 )
@@ -3139,14 +3139,14 @@ class DatasetCollection( object, Dictifiable, UsesAnnotations ):
     def populated( self ):
         top_level_populated = self.populated_state == DatasetCollection.populated_states.OK
         if top_level_populated and self.has_subcollections:
-            return all(map(lambda e: e.child_collection.populated, self.elements))
+            return all(e.child_collection.populated for e in self.elements)
         return top_level_populated
 
     @property
     def waiting_for_elements( self ):
         top_level_waiting = self.populated_state == DatasetCollection.populated_states.NEW
         if not top_level_waiting and self.has_subcollections:
-            return any(map(lambda e: e.child_collection.waiting_for_elements, self.elements))
+            return any(e.child_collection.waiting_for_elements for e in self.elements)
         return top_level_waiting
 
     def mark_as_populated( self ):

lib/galaxy/tools/actions/__init__.py

@@ -1,4 +1,5 @@
 import json
+import logging
 import re
 from json import dumps
 
@@ -7,16 +8,15 @@ from six import string_types
 from galaxy import model
 from galaxy.exceptions import ObjectInvalid
 from galaxy.model import LibraryDatasetDatasetAssociation
+from galaxy.tools.parameters import update_param
 from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter, RuntimeValue
 from galaxy.tools.parameters.wrapped import WrappedParameters
-from galaxy.tools.parameters import update_param
 from galaxy.util import ExecutionTimer
 from galaxy.util.none_like import NoneDataset
 from galaxy.util.odict import odict
 from galaxy.util.template import fill_template
 from galaxy.web import url_for
 
-import logging
 log = logging.getLogger( __name__ )
 
 
@@ -193,7 +193,7 @@ class DefaultToolAction( object ):
 
         return history, inp_data, inp_dataset_collections
 
-    def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, set_output_history=True, history=None, job_params=None, rerun_remap_job_id=None, mapping_over_collection=False, execution_cache=None ):
+    def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, history=None, job_params=None, rerun_remap_job_id=None, mapping_over_collection=False, execution_cache=None ):
         """
         Executes a tool, creating job and tool outputs, associating them, and
         submitting the job to the job queue. If history is not specified, use
@@ -254,7 +254,7 @@ class DefaultToolAction( object ):
         wrapped_params = self._wrapped_params( trans, tool, incoming )
 
         out_data = odict()
-        input_collections = dict( [ (k, v[0][0]) for k, v in inp_dataset_collections.iteritems() ] )
+        input_collections = dict( (k, v[0][0]) for k, v in inp_dataset_collections.items() )
         output_collections = OutputCollections(
             trans,
             history,
@@ -345,9 +345,6 @@ class DefaultToolAction( object ):
             if not filter_output(output, incoming):
                 if output.collection:
                     collections_manager = app.dataset_collections_service
-                    # As far as I can tell - this is always true - but just verify
-                    assert set_output_history, "Cannot create dataset collection for this kind of tool."
-
                     element_identifiers = []
                     known_outputs = output.known_outputs( input_collections, collections_manager.type_registry )
                     # Just to echo TODO elsewhere - this should be restructured to allow
@@ -360,7 +357,7 @@ class DefaultToolAction( object ):
                         for parent_id in (output_part_def.parent_ids or []):
                             # TODO: replace following line with formal abstractions for doing this.
                             current_collection_type = ":".join(current_collection_type.split(":")[1:])
-                            name_to_index = dict(map(lambda (index, value): (value["name"], index), enumerate(current_element_identifiers)))
+                            name_to_index = dict((value["name"], index) for (index, value) in enumerate(current_element_identifiers))
                             if parent_id not in name_to_index:
                                 if parent_id not in current_element_identifiers:
                                     index = len(current_element_identifiers)
@@ -382,8 +379,7 @@ class DefaultToolAction( object ):
                         # Following hack causes dataset to no be added to history...
                         child_dataset_names.add( effective_output_name )
 
-                        if set_output_history:
-                            history.add_dataset( element, set_hid=set_output_hid, quota=False )
+                        history.add_dataset( element, set_hid=set_output_hid, quota=False )
                         trans.sa_session.add( element )
                         trans.sa_session.flush()
 
@@ -416,15 +412,11 @@ class DefaultToolAction( object ):
             if name not in child_dataset_names and name not in incoming:  # don't add children; or already existing datasets, i.e. async created
                 data = out_data[ name ]
                 datasets_to_persist.append( data )
-        if set_output_history:
-            # Set HID and add to history.
-            # This is brand new and certainly empty so don't worry about quota.
-            # TOOL OPTIMIZATION NOTE - from above loop to the job create below 99%+
-            # of execution time happens within in history.add_datasets.
-            history.add_datasets( trans.sa_session, datasets_to_persist, set_hid=set_output_hid, quota=False, flush=False )
-        else:
-            for data in datasets_to_persist:
-                trans.sa_session.add( data )
+        # Set HID and add to history.
+        # This is brand new and certainly empty so don't worry about quota.
+        # TOOL OPTIMIZATION NOTE - from above loop to the job create below 99%+
+        # of execution time happens within in history.add_datasets.
+        history.add_datasets( trans.sa_session, datasets_to_persist, set_hid=set_output_hid, quota=False, flush=False )
 
         # Add all the children to their parents
         for parent_name, child_name in parent_to_child_pairs:
@@ -549,7 +541,7 @@ class DefaultToolAction( object ):
         # FIXME: Don't need all of incoming here, just the defined parameters
         #        from the tool. We need to deal with tools that pass all post
         #        parameters to the command as a special case.
-        for name, dataset_collection_info_pairs in inp_dataset_collections.iteritems():
+        for name, dataset_collection_info_pairs in inp_dataset_collections.items():
             first_reduction = True
             for ( dataset_collection, reduced ) in dataset_collection_info_pairs:
                 # TODO: update incoming for list...
@@ -562,23 +554,23 @@ class DefaultToolAction( object ):
                 # datasets below?
                 # TODO: verify can have multiple with same name, don't want to loose tracability
                 job.add_input_dataset_collection( name, dataset_collection )
-        for name, value in tool.params_to_strings( incoming, trans.app ).iteritems():
+        for name, value in tool.params_to_strings( incoming, trans.app ).items():
             job.add_parameter( name, value )
         self._check_input_data_access( trans, job, inp_data, current_user_roles )
 
     def _record_outputs( self, job, out_data, output_collections ):
         out_collections = output_collections.out_collections
         out_collection_instances = output_collections.out_collection_instances
-        for name, dataset in out_data.iteritems():
+        for name, dataset in out_data.items():
             job.add_output_dataset( name, dataset )
-        for name, dataset_collection in out_collections.iteritems():
+        for name, dataset_collection in out_collections.items():
             job.add_implicit_output_dataset_collection( name, dataset_collection )
-        for name, dataset_collection_instance in out_collection_instances.iteritems():
+        for name, dataset_collection_instance in out_collection_instances.items():
             job.add_output_dataset_collection( name, dataset_collection_instance )
 
     def _check_input_data_access( self, trans, job, inp_data, current_user_roles ):
         access_timer = ExecutionTimer()
-        for name, dataset in inp_data.iteritems():
+        for name, dataset in inp_data.items():
             if dataset:
                 if not trans.app.security_agent.can_access_dataset( current_user_roles, dataset.dataset ):
                     raise Exception("User does not have permission to use a dataset (%s) provided for input." % dataset.id)