Fix mypy errors, add type

Can't reuse variable for different types: mypy complains.

lib/galaxy/model/__init__.py

@@ -1399,7 +1399,9 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     history: Mapped[Optional["History"]] = relationship(back_populates="jobs")
     library_folder: Mapped[Optional["LibraryFolder"]] = relationship()
     parameters = relationship("JobParameter")
-    input_datasets = relationship("JobToInputDatasetAssociation", back_populates="job")
+    input_datasets: Mapped[List["JobToInputDatasetAssociation"]] = relationship(
+        "JobToInputDatasetAssociation", back_populates="job"
+    )
     input_dataset_collections: Mapped[List["JobToInputDatasetCollectionAssociation"]] = relationship(
         back_populates="job"
     )

lib/galaxy/model/store/__init__.py

@@ -2076,67 +2076,73 @@ def export_jobs(
                         if include_job_data:
                             self.add_dataset(assoc.dataset)
 
-                for assoc in job.output_datasets:
+                for assoc2 in job.output_datasets:
                     # Optional data inputs will not have a dataset.
-                    if assoc.dataset:
-                        name = assoc.name
+                    if assoc2.dataset:
+                        name = assoc2.name
                         if name not in output_dataset_mapping:
                             output_dataset_mapping[name] = []
 
-                        output_dataset_mapping[name].append(self.exported_key(assoc.dataset))
+                        output_dataset_mapping[name].append(self.exported_key(assoc2.dataset))
                         if include_job_data:
-                            self.add_dataset(assoc.dataset)
+                            self.add_dataset(assoc2.dataset)
 
-                for assoc in job.input_dataset_collections:
+                for assoc3 in job.input_dataset_collections:
                     # Optional data inputs will not have a dataset.
-                    if assoc.dataset_collection:
-                        name = assoc.name
+                    if assoc3.dataset_collection:
+                        name = assoc3.name
                         if name not in input_dataset_collection_mapping:
                             input_dataset_collection_mapping[name] = []
 
-                        input_dataset_collection_mapping[name].append(self.exported_key(assoc.dataset_collection))
+                        input_dataset_collection_mapping[name].append(self.exported_key(assoc3.dataset_collection))
                         if include_job_data:
-                            self.export_collection(assoc.dataset_collection)
+                            self.export_collection(assoc3.dataset_collection)
 
-                for assoc in job.input_dataset_collection_elements:
-                    if assoc.dataset_collection_element:
-                        name = assoc.name
+                for assoc4 in job.input_dataset_collection_elements:
+                    if assoc4.dataset_collection_element:
+                        name = assoc4.name
                         if name not in input_dataset_collection_element_mapping:
                             input_dataset_collection_element_mapping[name] = []
 
                         input_dataset_collection_element_mapping[name].append(
-                            self.exported_key(assoc.dataset_collection_element)
+                            self.exported_key(assoc4.dataset_collection_element)
                         )
                         if include_job_data:
-                            if assoc.dataset_collection_element.is_collection:
-                                self.export_collection(assoc.dataset_collection_element.element_object)
+                            if assoc4.dataset_collection_element.is_collection:
+                                assert isinstance(
+                                    assoc4.dataset_collection_element.element_object, model.DatasetCollection
+                                )
+                                self.export_collection(assoc4.dataset_collection_element.element_object)
                             else:
-                                self.add_dataset(assoc.dataset_collection_element.element_object)
+                                assert isinstance(
+                                    assoc4.dataset_collection_element.element_object, model.DatasetInstance
+                                )
+                                self.add_dataset(assoc4.dataset_collection_element.element_object)
 
-                for assoc in job.output_dataset_collection_instances:
+                for assoc5 in job.output_dataset_collection_instances:
                     # Optional data outputs will not have a dataset.
                     # These are implicit outputs, we don't need to export them
-                    if assoc.dataset_collection_instance:
-                        name = assoc.name
+                    if assoc5.dataset_collection_instance:
+                        name = assoc5.name
                         if name not in output_dataset_collection_mapping:
                             output_dataset_collection_mapping[name] = []
 
                         output_dataset_collection_mapping[name].append(
-                            self.exported_key(assoc.dataset_collection_instance)
+                            self.exported_key(assoc5.dataset_collection_instance)
                         )
 
-                for assoc in job.output_dataset_collections:
-                    if assoc.dataset_collection:
-                        name = assoc.name
+                for assoc6 in job.output_dataset_collections:
+                    if assoc6.dataset_collection:
+                        name = assoc6.name
 
                         if name not in implicit_output_dataset_collection_mapping:
                             implicit_output_dataset_collection_mapping[name] = []
 
                         implicit_output_dataset_collection_mapping[name].append(
-                            self.exported_key(assoc.dataset_collection)
+                            self.exported_key(assoc6.dataset_collection)
                         )
                         if include_job_data:
-                            self.export_collection(assoc.dataset_collection)
+                            self.export_collection(assoc6.dataset_collection)
 
                 job_attrs["input_dataset_mapping"] = input_dataset_mapping
                 job_attrs["input_dataset_collection_mapping"] = input_dataset_collection_mapping

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -264,7 +264,7 @@ def common_problems(
         for job_input_assoc in job.input_datasets:
             input_dataset_instance = job_input_assoc.dataset
             if input_dataset_instance is None:
-                continue
+                continue  # type:ignore[unreachable]  # TODO if job_input_assoc.dataset is indeed never None, remove the above check
             if input_dataset_instance.get_total_size() == 0:
                 has_empty_inputs = True
             input_instance_id = input_dataset_instance.id