Add/fix type annotations

lib/galaxy/job_metrics/__init__.py

@@ -20,10 +20,12 @@
 )
 from typing import (
     Any,
+    cast,
     Dict,
     List,
     NamedTuple,
     Optional,
+    TYPE_CHECKING,
 )
 
 from galaxy import util
@@ -34,6 +36,9 @@
     Safety,
 )
 
+if TYPE_CHECKING:
+    from galaxy.job_metrics.instrumenters import InstrumentPlugin
+
 log = logging.getLogger(__name__)
 
 
@@ -72,7 +77,7 @@ class JobMetrics:
 
     def __init__(self, conf_file=None, conf_dict=None, **kwargs):
         """Load :class:`JobInstrumenter` objects from specified configuration file."""
-        self.plugin_classes = self.__plugins_dict()
+        self.plugin_classes = cast(Dict[str, "InstrumentPlugin"], self.__plugins_dict())
         if conf_file and os.path.exists(conf_file):
             self.default_job_instrumenter = JobInstrumenter.from_file(self.plugin_classes, conf_file, **kwargs)
         elif conf_dict or conf_dict is None:

lib/galaxy/job_metrics/formatting.py

@@ -14,7 +14,7 @@ class FormattedMetric(NamedTuple):
 class JobMetricFormatter:
     """Format job metric key-value pairs for human consumption in Web UI."""
 
-    def format(self, key: Any, value: Any) -> FormattedMetric:
+    def format(self, key: str, value: Any) -> FormattedMetric:
         return FormattedMetric(str(key), str(value))
 
 

lib/galaxy/tool_util/cwl/util.py

@@ -146,8 +146,8 @@ def galactic_job_json(
     for Galaxy.
     """
 
-    datasets = []
-    dataset_collections = []
+    datasets: List[Dict[str, Any]] = []
+    dataset_collections: List[Dict[str, Any]] = []
 
     def response_to_hda(target: UploadTarget, upload_response: Dict[str, Any]) -> Dict[str, str]:
         assert isinstance(upload_response, dict), upload_response
@@ -277,7 +277,7 @@ def replacement_file(value):
 
         return upload_file(file_path, secondary_files_tar_path, filetype=filetype, **kwd)
 
-    def replacement_directory(value):
+    def replacement_directory(value: Dict[str, Any]) -> Dict[str, Any]:
         file_path = value.get("location", None) or value.get("path", None)
         if file_path is None:
             return value

lib/galaxy/tools/wrappers.py

@@ -642,9 +642,9 @@ def __init__(
         self.collection = collection
 
         elements = collection.elements
-        element_instances = {}
+        element_instances: Dict[str, Union[DatasetCollectionWrapper, DatasetFilenameWrapper]] = {}
 
-        element_instance_list = []
+        element_instance_list: List[Union[DatasetCollectionWrapper, DatasetFilenameWrapper]] = []
         for dataset_collection_element in elements:
             element_object = dataset_collection_element.element_object
             element_identifier = dataset_collection_element.element_identifier

lib/galaxy/workflow/modules.py

@@ -463,7 +463,9 @@ def decode_runtime_state(self, step, runtime_state):
         state.decode(runtime_state, Bunch(inputs=self.get_runtime_inputs(step)), self.trans.app)
         return state
 
-    def execute(self, trans, progress, invocation_step, use_cached_job=False):
+    def execute(
+        self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
+    ) -> Optional[bool]:
         """Execute the given workflow invocation step.
 
         Use the supplied workflow progress object to track outputs, find
@@ -508,7 +510,7 @@ def get_informal_replacement_parameters(self, step) -> List[str]:
 
         return []
 
-    def compute_collection_info(self, progress, step, all_inputs):
+    def compute_collection_info(self, progress: "WorkflowProgress", step, all_inputs):
         """
         Use get_all_inputs (if implemented) to determine collection mapping for execution.
         """
@@ -526,7 +528,7 @@ def compute_collection_info(self, progress, step, all_inputs):
                 collection_info.when_values = progress.when_values
         return collection_info or progress.subworkflow_collection_info
 
-    def _find_collections_to_match(self, progress, step, all_inputs):
+    def _find_collections_to_match(self, progress: "WorkflowProgress", step, all_inputs) -> matching.CollectionsToMatch:
         collections_to_match = matching.CollectionsToMatch()
         dataset_collection_type_descriptions = self.trans.app.dataset_collection_manager.collection_type_descriptions
 
@@ -756,7 +758,9 @@ def get_post_job_actions(self, incoming):
     def get_content_id(self):
         return self.trans.security.encode_id(self.subworkflow.id)
 
-    def execute(self, trans, progress, invocation_step, use_cached_job=False):
+    def execute(
+        self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
+    ) -> Optional[bool]:
         """Execute the given workflow step in the given workflow invocation.
         Use the supplied workflow progress object to track outputs, find
         inputs, etc...
@@ -929,7 +933,9 @@ def get_runtime_state(self):
     def get_all_inputs(self, data_only=False, connectable_only=False):
         return []
 
-    def execute(self, trans, progress, invocation_step, use_cached_job=False):
+    def execute(
+        self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
+    ) -> Optional[bool]:
         invocation = invocation_step.workflow_invocation
         step = invocation_step.workflow_step
         input_value = step.state.inputs["input"]
@@ -963,6 +969,7 @@ def execute(self, trans, progress, invocation_step, use_cached_job=False):
             if content:
                 invocation.add_input(content, step.id)
         progress.set_outputs_for_input(invocation_step, step_outputs)
+        return None
 
     def recover_mapping(self, invocation_step, progress):
         progress.set_outputs_for_input(invocation_step, already_persisted=True)
@@ -1522,7 +1529,9 @@ def get_all_outputs(self, data_only=False):
             )
         ]
 
-    def execute(self, trans, progress, invocation_step, use_cached_job=False):
+    def execute(
+        self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
+    ) -> Optional[bool]:
         step = invocation_step.workflow_step
         input_value = step.state.inputs["input"]
         if input_value is None:
@@ -1535,6 +1544,7 @@ def execute(self, trans, progress, invocation_step, use_cached_job=False):
             input_value = default_value.get("value", NO_REPLACEMENT)
         step_outputs = dict(output=input_value)
         progress.set_outputs_for_input(invocation_step, step_outputs)
+        return None
 
     def step_state_to_tool_state(self, state):
         state = safe_loads(state)
@@ -1666,9 +1676,12 @@ def get_runtime_state(self):
         state.inputs = dict()
         return state
 
-    def execute(self, trans, progress, invocation_step, use_cached_job=False):
+    def execute(
+        self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
+    ) -> Optional[bool]:
         step = invocation_step.workflow_step
         progress.mark_step_outputs_delayed(step, why="executing pause step")
+        return None
 
     def recover_mapping(self, invocation_step, progress):
         if invocation_step:
@@ -2131,7 +2144,9 @@ def decode_runtime_state(self, step, runtime_state):
                 f"Tool {self.tool_id} missing. Cannot recover runtime state.", tool_id=self.tool_id
             )
 
-    def execute(self, trans, progress, invocation_step, use_cached_job=False):
+    def execute(
+        self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
+    ) -> Optional[bool]:
         invocation = invocation_step.workflow_invocation
         step = invocation_step.workflow_step
         tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version, tool_uuid=step.tool_uuid)
@@ -2171,7 +2186,7 @@ def execute(self, trans, progress, invocation_step, use_cached_job=False):
             found_replacement_keys = set()
 
             # Connect up
-            def callback(input, prefixed_name, **kwargs):
+            def callback(input, prefixed_name: str, **kwargs):
                 input_dict = all_inputs_by_name[prefixed_name]
 
                 replacement: Union[model.Dataset, NoReplacement] = NO_REPLACEMENT

lib/galaxy/workflow/run.py

@@ -144,6 +144,8 @@ def queue_invoke(
 
 
 class WorkflowInvoker:
+    progress: "WorkflowProgress"
+
     def __init__(
         self,
         trans: "WorkRequestContext",
@@ -348,7 +350,7 @@ class WorkflowProgress:
     def __init__(
         self,
         workflow_invocation: WorkflowInvocation,
-        inputs_by_step_id: Any,
+        inputs_by_step_id: Dict[int, Any],
         module_injector: ModuleInjector,
         param_map: Dict[int, Dict[str, Any]],
         jobs_per_scheduling_iteration: int = -1,
@@ -415,7 +417,7 @@ def remaining_steps(
                 remaining_steps.append((step, invocation_step))
         return remaining_steps
 
-    def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[str, Any]) -> Any:
+    def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[str, Any]):
         replacement: Union[
             modules.NoReplacement,
             model.DatasetCollectionInstance,
@@ -447,7 +449,7 @@ def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[st
                         replacement = raw_to_galaxy(trans, step_input.default_value)
         return replacement
 
-    def replacement_for_connection(self, connection: "WorkflowStepConnection", is_data: bool = True) -> Any:
+    def replacement_for_connection(self, connection: "WorkflowStepConnection", is_data: bool = True):
         output_step_id = connection.output_step.id
         output_name = connection.output_name
         if output_step_id not in self.outputs:
@@ -530,7 +532,7 @@ def replacement_for_connection(self, connection: "WorkflowStepConnection", is_da
 
         return replacement
 
-    def get_replacement_workflow_output(self, workflow_output: "WorkflowOutput") -> Any:
+    def get_replacement_workflow_output(self, workflow_output: "WorkflowOutput"):
         step = workflow_output.workflow_step
         output_name = workflow_output.output_name
         step_outputs = self.outputs[step.id]
@@ -541,7 +543,10 @@ def get_replacement_workflow_output(self, workflow_output: "WorkflowOutput") ->
             return step_outputs[output_name]
 
     def set_outputs_for_input(
-        self, invocation_step: WorkflowInvocationStep, outputs: Any = None, already_persisted: bool = False
+        self,
+        invocation_step: WorkflowInvocationStep,
+        outputs: Optional[Dict[str, Any]] = None,
+        already_persisted: bool = False,
     ) -> None:
         step = invocation_step.workflow_step