Fix new E721 errors from ruff 0.0.290

lib/galaxy/config/__init__.py

@@ -517,7 +517,7 @@ def resolve(key):
         for key in self.schema.paths_to_resolve:
             value = getattr(self, key)
             # Check if value is a list or should be listified; if so, listify and resolve each item separately.
-            if type(value) is list or (self.listify_options and key in self.listify_options):
+            if isinstance(value, list) or (self.listify_options and key in self.listify_options):
                 saved_values = listify(getattr(self, key), do_strip=True)  # listify and save original value
                 setattr(self, key, "_")  # replace value with temporary placeholder
                 resolve(key)  # resolve temporary value (`_` becomes `parent-path/_`)
@@ -546,7 +546,7 @@ def get_path(current_path, initial_path):
             return current_path
 
         current_value = getattr(self, key)  # resolved path or list of resolved paths
-        if type(current_value) is list:
+        if isinstance(current_value, list):
             initial_paths = listify(self._raw_config[key], do_strip=True)  # initial unresolved paths
             updated_paths = []
             # check and, if needed, update each path in the list

lib/galaxy/jobs/__init__.py

@@ -903,24 +903,24 @@ def get_job_runner_plugins(self, handler_id):
         return rval
 
     def is_id(self, collection):
-        """Given a collection of handlers or destinations, indicate whether the collection represents a tag or a real ID
+        """Given a collection of handlers or destinations, indicate whether the collection represents a real ID
 
         :param collection: A representation of a destination or handler
         :type collection: tuple or list
 
         :returns: bool
         """
-        return type(collection) == tuple
+        return isinstance(collection, tuple)
 
     def is_tag(self, collection):
-        """Given a collection of handlers or destinations, indicate whether the collection represents a tag or a real ID
+        """Given a collection of handlers or destinations, indicate whether the collection represents a tag
 
         :param collection: A representation of a destination or handler
         :type collection: tuple or list
 
         :returns: bool
         """
-        return type(collection) == list
+        return isinstance(collection, list)
 
     def convert_legacy_destinations(self, job_runners):
         """Converts legacy (from a URL) destinations to contain the appropriate runner params defined in the URL.

lib/galaxy/selenium/navigates_galaxy.py

@@ -2028,7 +2028,7 @@ def assert_success_message(self, contains=None):
 
     def assert_message(self, element, contains=None):
         if contains is not None:
-            if type(element) == list:
+            if isinstance(element, list):
                 assert any(
                     contains in el.text for el in element
                 ), f"{contains} was not found in {[el.text for el in element]}"

lib/galaxy/tools/actions/upload_common.py

@@ -55,7 +55,7 @@ def persist_uploads(params, trans):
                 local_filename = util.mkstemp_ln(f.file.name, "upload_file_data_")
                 f.file.close()
                 upload_dataset["file_data"] = dict(filename=f.filename, local_filename=local_filename)
-            elif type(f) == dict and "local_filename" not in f:
+            elif isinstance(f, dict) and "local_filename" not in f:
                 raise Exception("Uploaded file was encoded in a way not understood by Galaxy.")
             if (
                 "url_paste" in upload_dataset

lib/galaxy/tools/parameters/basic.py

@@ -659,7 +659,7 @@ def from_json(self, value, trans=None, other_values=None):
         if isinstance(value, FilesPayload):
             # multi-part upload handled and persisted in service layer
             return value.dict()
-        if type(value) == dict:
+        elif isinstance(value, dict):
             if "session_id" in value:
                 # handle api upload
                 session_id = value["session_id"]

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -150,7 +150,7 @@ def set_workflow_menu(self, trans: GalaxyWebTransaction, payload=None, **kwd):
         workflow_ids = payload.get("workflow_ids")
         if workflow_ids is None:
             workflow_ids = []
-        elif type(workflow_ids) != list:
+        elif not isinstance(workflow_ids, list):
             workflow_ids = [workflow_ids]
         workflow_ids_decoded = []
         # Decode the encoded workflow ids

lib/galaxy/workflow/resources/__init__.py

@@ -70,7 +70,7 @@ def _resource_parameters_by_group(trans, **kwds):
         for group_name, group_def in by_group.get("groups", {}).items():
             if group_name == default_group or group_name in user_groups:
                 for tag in group_def:
-                    if type(tag) is dict:
+                    if isinstance(tag, dict):
                         if tag.get("name") not in user_permissions:
                             user_permissions[tag.get("name")] = {}
                         for option in tag.get("options"):
@@ -131,7 +131,7 @@ def validate_by_group_workflow_parameters_mapper(by_group, workflow_resource_par
             )
         for group in by_group["groups"]:
             for attrib in by_group["groups"][group]:
-                if type(attrib) is dict:
+                if isinstance(attrib, dict):
                     if "name" not in attrib:
                         raise Exception(
                             "'workflow_resource_params_mapper' YAML file is malformed, "

lib/tool_shed/webapp/api/repositories.py

@@ -1041,7 +1041,7 @@ def create_changeset_revision(self, trans, id, payload, **kwd):
             local_filename = util.mkstemp_ln(file_data.file.name, "upload_file_data_")
             file_data.file.close()
             file_data = dict(filename=file_data.filename, local_filename=local_filename)
-        elif type(file_data) == dict and "local_filename" not in file_data:
+        elif isinstance(file_data, dict) and "local_filename" not in file_data:
             raise Exception("Uploaded file was encoded in a way not understood.")
 
         commit_message = kwd.get("commit_message", "Uploaded")

scripts/api/common.py

@@ -81,7 +81,7 @@ def display(api_key, url, return_formatted=True):
         sys.exit(1)
     if not return_formatted:
         return r
-    elif type(r) == list:
+    elif isinstance(r, list):
         # Response is a collection as defined in the REST style.
         print("Collection Members")
         print("------------------")
@@ -103,7 +103,7 @@ def display(api_key, url, return_formatted=True):
                         print(item)
         print("")
         print("%d element(s) in collection" % len(r))
-    elif type(r) == dict:
+    elif isinstance(r, dict):
         # Response is an element as defined in the REST style.
         print("Member Information")
         print("------------------")
@@ -133,11 +133,11 @@ def submit(api_key, url, data, return_formatted=True):
         return r
     print("Response")
     print("--------")
-    if type(r) == list:
+    if isinstance(r, list):
         # Currently the only implemented responses are lists of dicts, because
         # submission creates some number of collection elements.
         for i in r:
-            if type(i) == dict:
+            if isinstance(i, dict):
                 if "url" in i:
                     print(i.pop("url"))
                 else:

tools/data_source/upload.py

@@ -283,7 +283,7 @@ def __read_paramfile(path):
     with open(path) as fh:
         obj = load(fh)
     # If there's a single dataset in an old-style paramfile it'll still parse, but it'll be a dict
-    assert type(obj) == list
+    assert isinstance(obj, list)
     return obj
 
 

tools/stats/gsummary.py

@@ -176,7 +176,7 @@ def main():
             stop_err("Computation resulted in the following error: %s" % str(s))
         summary = summary.as_py(BASIC_CONVERSION)
         outfile.write("#%s\n" % headings_str)
-        if type(summary) is dict:
+        if isinstance(summary, dict):
             # using rpy
             outfile.write("%s\n" % "\t".join("%g" % summary[k] for k in headings))
         else: