improve typing of lib/galaxy/tools/actions/__init__.py

lib/galaxy/tools/actions/__init__.py

@@ -3,7 +3,7 @@
 import os
 import re
 from json import dumps
-
+from typing import Any, cast, Dict, List, Set, Union
 
 from galaxy import model
 from galaxy.exceptions import ItemAccessibilityException
@@ -69,7 +69,7 @@ def _collect_input_datasets(self, tool, param_values, trans, history, current_us
         if current_user_roles is None:
             current_user_roles = trans.get_current_user_roles()
         input_datasets = {}
-        all_permissions = {}
+        all_permissions: Dict[str, Set[str]] = {}
 
         def record_permission(action, role_id):
             if action not in all_permissions:
@@ -211,7 +211,7 @@ def append_to_key(the_dict, key, value):
                 the_dict[key] = []
             the_dict[key].append(value)
 
-        input_dataset_collections = dict()
+        input_dataset_collections: Dict[str, str] = {}
 
         def visitor(input, value, prefix, parent=None, prefixed_name=None, **kwargs):
             if isinstance(input, DataToolParameter):
@@ -228,7 +228,7 @@ def visitor(input, value, prefix, parent=None, prefixed_name=None, **kwargs):
                         # collection with individual datasets. Database will still
                         # record collection which should be enought for workflow
                         # extraction and tool rerun.
-                        if hasattr(value, 'child_collection'):
+                        if isinstance(value, model.DatasetCollectionElement):
                             # if we are mapping a collection over a tool, we only require the child_collection
                             dataset_instances = value.child_collection.dataset_instances
                         else:
@@ -473,7 +473,10 @@ def handle_output(name, output, hidden=None):
                         # Output collection is mapped over and has already been copied from original job
                         continue
                     collections_manager = app.dataset_collection_manager
-                    element_identifiers = []
+                    element_identifiers: List[
+                        Dict[str, Union[str, List[Dict[str, Union[str, List[Any]]]]]]
+                    ] = []
+                    # mypy doesn't yet support recursive type definitions
                     known_outputs = output.known_outputs(input_collections, collections_manager.type_registry)
                     # Just to echo TODO elsewhere - this should be restructured to allow
                     # nested collections.
@@ -497,7 +500,19 @@ def handle_output(name, output, hidden=None):
                                     ))
                                 else:
                                     index = name_to_index[parent_id]
-                            current_element_identifiers = current_element_identifiers[index]["element_identifiers"]
+                            current_element_identifiers = cast(
+                                List[
+                                    Dict[
+                                        str,
+                                        Union[
+                                            str, List[Dict[str, Union[str, List[Any]]]]
+                                        ],
+                                    ]
+                                ],
+                                current_element_identifiers[index][
+                                    "element_identifiers"
+                                ],
+                            )
 
                         effective_output_name = output_part_def.effective_output_name
                         element = handle_output(effective_output_name, output_part_def.output_def, hidden=True)
@@ -722,7 +737,7 @@ def _record_inputs(self, trans, tool, job, incoming, inp_data, inp_dataset_colle
         # 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.
-        reductions = {}
+        reductions: Dict[str, List[str]] = {}
         for name, dataset_collection_info_pairs in inp_dataset_collections.items():
             for (dataset_collection, reduced) in dataset_collection_info_pairs:
                 if reduced:

setup.cfg

@@ -553,8 +553,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.tools.cache]
 check_untyped_defs = False
-[mypy-galaxy.tools.actions]
-check_untyped_defs = False
 [mypy-galaxy.tool_util.deps.containers]
 check_untyped_defs = False
 [mypy-galaxy.managers.users]