Fix new ruff 0.11.0 errors

Also:
- Add and fix type annotations
- Fix call of `object_store_allows_id_selection()` method

cron/build_chrom_db.py

@@ -17,7 +17,7 @@ import os
 import sys
 from urllib.parse import urlencode
 
-import parse_builds  # noqa: I100,I202
+import parse_builds
 
 from galaxy.util import requests
 

lib/galaxy/jobs/__init__.py

@@ -17,6 +17,7 @@ import traceback
 from json import loads
 from typing import (
     Any,
+    Callable,
     Dict,
     Iterable,
     List,
@@ -1629,19 +1630,19 @@ class MinimalJobWrapper(HasResourceParameters):
     def set_job_destination(self, job_destination, external_id=None, flush=True, job=None):
         """Subclasses should implement this to persist a destination, if necessary."""
 
-    def _set_object_store_ids(self, job):
+    def _set_object_store_ids(self, job: Job):
         if job.object_store_id:
             # We aren't setting this during job creation anymore, but some existing
             # jobs may have this set. Skip this following code if that is the case.
             return
 
         object_store = self.app.object_store
-        if not object_store.object_store_allows_id_selection:
+        if not object_store.object_store_allows_id_selection():
             self._set_object_store_ids_basic(job)
         else:
             self._set_object_store_ids_full(job)
 
-    def _set_object_store_ids_basic(self, job):
+    def _set_object_store_ids_basic(self, job: Job):
         object_store_id = self.get_destination_configuration("object_store_id", None)
         object_store_populator = ObjectStorePopulator(self.app, job.user)
         require_shareable = job.requires_shareable_storage(self.app.security_agent)
@@ -1662,11 +1663,11 @@ class MinimalJobWrapper(HasResourceParameters):
         job.object_store_id = object_store_populator.object_store_id
         self._setup_working_directory(job=job)
 
-    def _set_object_store_ids_full(self, job):
+    def _set_object_store_ids_full(self, job: Job):
         user = job.user
         object_store_id = self.get_destination_configuration("object_store_id", None)
-        split_object_stores = None
-        object_store_id_overrides = None
+        split_object_stores: Optional[Callable[[str], ObjectStorePopulator]] = None
+        object_store_id_overrides: Optional[Dict[str, Optional[str]]] = None
 
         if object_store_id is None:
             object_store_id = job.preferred_object_store_id
@@ -1687,7 +1688,11 @@ class MinimalJobWrapper(HasResourceParameters):
                 # directory?
                 object_store_id = invocation_object_stores.preferred_outputs_object_store_id
                 object_store_populator = intermediate_object_store_populator
-                output_names = [o.output_name for o in workflow_invocation_step.workflow_step.unique_workflow_outputs]
+                output_names = [
+                    o.output_name
+                    for o in workflow_invocation_step.workflow_step.unique_workflow_outputs
+                    if o.output_name
+                ]
                 if invocation_object_stores.step_effective_outputs is not None:
                     output_names = [
                         o for o in output_names if invocation_object_stores.is_output_name_an_effective_output(o)
@@ -1696,9 +1701,9 @@ class MinimalJobWrapper(HasResourceParameters):
                 # we resolve the precreated datasets here with object store populators
                 # but for dynamically created datasets after the job we need to record
                 # the outputs and set them accordingly
-                object_store_id_overrides = {o: preferred_outputs_object_store_id for o in output_names}
+                object_store_id_overrides = dict.fromkeys(output_names, preferred_outputs_object_store_id)
 
-                def split_object_stores(output_name):  # noqa: F811 https://github.com/PyCQA/pyflakes/issues/783
+                def split_object_stores(output_name: str):  # noqa: F811 https://github.com/PyCQA/pyflakes/issues/783
                     if "|__part__|" in output_name:
                         output_name = output_name.split("|__part__|", 1)[0]
                     if output_name in output_names:
@@ -1718,7 +1723,7 @@ class MinimalJobWrapper(HasResourceParameters):
                 object_store_id = user.preferred_object_store_id
 
         require_shareable = job.requires_shareable_storage(self.app.security_agent)
-        if not split_object_stores:
+        if split_object_stores is None:
             object_store_populator = ObjectStorePopulator(self.app, user)
 
             if object_store_id:

lib/galaxy/managers/datatypes.py

@@ -54,7 +54,7 @@ def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
         n = f"{c.__module__}.{c.__name__}"
         types = {n}
         visit_bases(types, c)
-        class_to_classes[n] = {t: True for t in types}
+        class_to_classes[n] = dict.fromkeys(types, True)
     return DatatypesMap(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)
 
 

lib/galaxy/model/__init__.py

@@ -1504,7 +1504,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     params: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     handler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     preferred_object_store_id: Mapped[Optional[str]] = mapped_column(String(255))
-    object_store_id_overrides: Mapped[Optional[STR_TO_STR_DICT]] = mapped_column(JSONType)
+    object_store_id_overrides: Mapped[Optional[Dict[str, Optional[str]]]] = mapped_column(JSONType)
     tool_request_id: Mapped[Optional[int]] = mapped_column(ForeignKey("tool_request.id"), index=True)
 
     dynamic_tool: Mapped[Optional["DynamicTool"]] = relationship()
@@ -8284,7 +8284,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
         # Older Galaxy workflows may have multiple WorkflowOutputs
         # per "output_name", when serving these back to the editor
         # feed only a "best" output per "output_name.""
-        outputs = {}
+        outputs: Dict[str, WorkflowOutput] = {}
         for workflow_output in self.workflow_outputs:
             output_name = workflow_output.output_name
 

lib/galaxy/model/store/discover.py

@@ -498,7 +498,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
         default_object_store_id = job.object_store_id
         if not output_name:
             return default_object_store_id
-        object_store_id_overrides: Dict[str, str] = job.object_store_id_overrides or {}
+        object_store_id_overrides = job.object_store_id_overrides or {}
         return object_store_id_overrides.get(output_name, default_object_store_id)
 
     @property

lib/galaxy/web_stack/__init__.py

@@ -268,7 +268,7 @@ class WeblessApplicationStack(ApplicationStack):
 
     @property
     def configured_pools(self):
-        return {p: self.config.server_name for p in self.config.attach_to_pools}
+        return dict.fromkeys(self.config.attach_to_pools, self.config.server_name)
 
     def in_pool(self, pool_name):
         return pool_name in self.config.attach_to_pools

scripts/api/data_manager_example_execute.py

@@ -8,7 +8,7 @@ import optparse
 import time
 from urllib.parse import urljoin
 
-from common import (  # noqa: I100,I202
+from common import (
     get,
     post,
 )

scripts/api/display.py

@@ -4,7 +4,7 @@ import os
 import sys
 from urllib.error import URLError
 
-from common import display  # noqa: I100,I202
+from common import display
 
 try:
     display(*sys.argv[1:3])

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -59,7 +59,7 @@ from sqlalchemy import (
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
 
-from cleanup_datasets import CleanupDatasetsApplication  # noqa: I100
+from cleanup_datasets import CleanupDatasetsApplication
 
 import galaxy.config
 import galaxy.util

scripts/microbes/harvest_bacteria.py

@@ -18,7 +18,7 @@ try:
 except ImportError:
     raise Exception("BeautifulSoup4 library not found, please install it, e.g. with 'pip install BeautifulSoup4'")
 
-from util import (  # noqa: I202
+from util import (
     get_bed_from_genbank,
     get_bed_from_GeneMark,
     get_bed_from_GeneMarkHMM,