Fix UP031 errors - Part 2

lib/tool_shed/grids/admin_grids.py

@@ -401,7 +401,7 @@ def get_value(self, trans, grid, repository_metadata):
                         # We used to display the following, but grid was too cluttered.
                         # for tool_metadata_dict in metadata[ 'tools' ]:
                         #    tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] )
-                        return "%d" % len(metadata["tools"])
+                        return "{}".format(len(metadata["tools"]))
             return tools_str
 
     class DatatypesColumn(grids.TextColumn):
@@ -414,7 +414,7 @@ def get_value(self, trans, grid, repository_metadata):
                         # We used to display the following, but grid was too cluttered.
                         # for datatype_metadata_dict in metadata[ 'datatypes' ]:
                         #    datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ]
-                        return "%d" % len(metadata["datatypes"])
+                        return "{}".format(len(metadata["datatypes"]))
             return datatypes_str
 
     class WorkflowsColumn(grids.TextColumn):
@@ -432,7 +432,7 @@ def get_value(self, trans, grid, repository_metadata):
                         # workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ]
                         # for workflow_metadata_dict in workflow_metadata_dicts:
                         #    workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ]
-                        return "%d" % len(metadata["workflows"])
+                        return "{}".format(len(metadata["workflows"]))
             return workflows_str
 
     class DeletedColumn(grids.BooleanColumn):

lib/tool_shed/grids/util.py

@@ -41,7 +41,7 @@ def build_changeset_revision_select_field(
         # Display the latest revision first.
         options.insert(0, (changeset_tup[1], changeset_tup[2]))
     if add_id_to_name:
-        name = "changeset_revision_%d" % repository.id
+        name = f"changeset_revision_{repository.id}"
     else:
         name = "changeset_revision"
     select_field = SelectField(name=name, refresh_on_change=True)

lib/tool_shed/managers/repositories.py

@@ -223,7 +223,7 @@ def index_tool_ids(app: ToolShedApp, tool_ids: List[str]) -> Dict[str, Any]:
                 continue
             for tool_metadata in tools:
                 if tool_metadata["guid"] in tool_ids:
-                    repository_found.append("%d:%s" % (int(changeset), changehash))
+                    repository_found.append(f"{int(changeset)}:{changehash}")
             metadata = get_current_repository_metadata_for_changeset_revision(app, repository, changehash)
             if metadata is None:
                 continue

lib/tool_shed/metadata/repository_metadata_manager.py

@@ -943,12 +943,12 @@ def reset_metadata_on_selected_repositories(self, **kwd):
                 except Exception:
                     log.exception("Error attempting to reset metadata on repository %s", str(repository.name))
                     unsuccessful_count += 1
-            message = "Successfully reset metadata on %d %s.  " % (
+            message = "Successfully reset metadata on {} {}.  ".format(
                 successful_count,
                 inflector.cond_plural(successful_count, "repository"),
             )
             if unsuccessful_count:
-                message += "Error setting metadata on %d %s - see the paster log for details.  " % (
+                message += "Error setting metadata on {} {} - see the paster log for details.  ".format(
                     unsuccessful_count,
                     inflector.cond_plural(unsuccessful_count, "repository"),
                 )

lib/tool_shed/test/base/twilltestcase.py

@@ -669,15 +669,6 @@ def check_for_strings(self, strings_displayed=None, strings_not_displayed=None):
             for check_str in strings_not_displayed:
                 self.check_string_not_in_page(check_str)
 
-    def check_page(self, strings_displayed, strings_displayed_count, strings_not_displayed):
-        """Checks a page for strings displayed, not displayed and number of occurrences of a string"""
-        for check_str in strings_displayed:
-            self.check_page_for_string(check_str)
-        for check_str, count in strings_displayed_count:
-            self.check_string_count_in_page(check_str, count)
-        for check_str in strings_not_displayed:
-            self.check_string_not_in_page(check_str)
-
     def check_page_for_string(self, patt):
         """Looks for 'patt' in the current browser page"""
         self._browser.check_page_for_string(patt)
@@ -905,7 +896,7 @@ def browse_tools(self, strings_displayed=None, strings_not_displayed=None):
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
-    def check_count_of_metadata_revisions_associated_with_repository(self, repository: Repository, metadata_count):
+    def check_count_of_metadata_revisions_associated_with_repository(self, repository: Repository, metadata_count: int):
         self.check_repository_changelog(repository)
         self.check_string_count_in_page("Repository metadata is associated with this change set.", metadata_count)
 
@@ -1011,7 +1002,7 @@ def check_repository_invalid_tools_for_changeset_revision(
                 strings_not_displayed=strings_not_displayed,
             )
 
-    def check_string_count_in_page(self, pattern, min_count, max_count=None):
+    def check_string_count_in_page(self, pattern, min_count: int, max_count: Optional[int] = None):
         """Checks the number of 'pattern' occurrences in the current browser page"""
         page = self.last_page()
         pattern_count = page.count(pattern)
@@ -1022,14 +1013,9 @@ def check_string_count_in_page(self, pattern, min_count, max_count=None):
         # than max_count.
         if pattern_count < min_count or pattern_count > max_count:
             fname = self.write_temp_file(page)
-            errmsg = "%i occurrences of '%s' found (min. %i, max. %i).\npage content written to '%s' " % (
-                pattern_count,
-                pattern,
-                min_count,
-                max_count,
-                fname,
+            raise AssertionError(
+                f"{pattern_count} occurrences of '{pattern}' found (min. {min_count}, max. {max_count}).\npage content written to '{fname}' "
             )
-            raise AssertionError(errmsg)
 
     def check_galaxy_repository_tool_panel_section(
         self, repository: galaxy_model.ToolShedRepository, expected_tool_panel_section: str
@@ -2098,8 +2084,7 @@ def _wait_for_installation(repository: galaxy_model.ToolShedRepository, refresh)
         # This timeout currently defaults to 10 minutes.
         if timeout_counter > repository_installation_timeout:
             raise AssertionError(
-                "Repository installation timed out, %d seconds elapsed, repository state is %s."
-                % (timeout_counter, repository.status)
+                f"Repository installation timed out, {timeout_counter} seconds elapsed, repository state is {repository.status}."
             )
         time.sleep(1)
 

lib/tool_shed/test/functional/test_0000_basic_repository_features.py

@@ -362,7 +362,7 @@ def test_0130_verify_handling_of_invalid_characters(self):
         # unicode decoding error message.
         content = self._escape_page_content_if_needed("These characters should not")
         strings_displayed = [
-            "%d:%s" % (revision_number, revision_hash),
+            f"{revision_number}:{revision_hash}",
             "filtering_0000",
             "user1",
             "repos",

lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py

@@ -144,12 +144,10 @@ def test_0020_verify_dependency_metadata(self):
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, tip)
         # Make sure that the new tip is now downloadable, and that there are no other downloadable revisions.
         assert metadata_record.downloadable, "Tip is not downloadable."
+        n_downloadable_revisions = len(self._db_repository(repository).downloadable_revisions)
         assert (
-            len(self._db_repository(repository).downloadable_revisions) == 1
-        ), "Repository %s has %d downloadable revisions, expected 1." % (
-            repository.name,
-            len(self._db_repository(repository).downloadable_revisions),
-        )
+            n_downloadable_revisions == 1
+        ), f"Repository {repository.name} has {n_downloadable_revisions} downloadable revisions, expected 1."
 
     def test_0025_delete_repository_dependency(self):
         """Delete the repository_dependencies.xml from convert_chars_0440.
@@ -174,12 +172,10 @@ def test_0025_delete_repository_dependency(self):
             metadata_record.downloadable
         ), f"The revision of {repository.name} that does not contain repository_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
+        n_downloadable_revisions = len(self._db_repository(repository).downloadable_revisions)
         assert (
-            len(self._db_repository(repository).downloadable_revisions) == 2
-        ), "Repository %s has %d downloadable revisions, expected 2." % (
-            repository.name,
-            len(self._db_repository(repository).downloadable_revisions),
-        )
+            n_downloadable_revisions == 2
+        ), f"Repository {repository.name} has {n_downloadable_revisions} downloadable revisions, expected 2."
 
     def test_0030_create_bwa_package_repository(self):
         """Create and populate the bwa_package_0440 repository.
@@ -257,12 +253,10 @@ def test_0045_verify_dependency_metadata(self):
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, tip)
         # Make sure that the new tip is now downloadable, and that there are no other downloadable revisions.
         assert metadata_record.downloadable, "Tip is not downloadable."
+        n_downloadable_revisions = len(self._db_repository(repository).downloadable_revisions)
         assert (
-            len(self._db_repository(repository).downloadable_revisions) == 1
-        ), "Repository %s has %d downloadable revisions, expected 1." % (
-            repository.name,
-            len(self._db_repository(repository).downloadable_revisions),
-        )
+            n_downloadable_revisions == 1
+        ), f"Repository {repository.name} has {n_downloadable_revisions} downloadable revisions, expected 1."
 
     def test_0050_delete_complex_repository_dependency(self):
         """Delete the tool_dependencies.xml from bwa_base_0440.
@@ -287,12 +281,10 @@ def test_0050_delete_complex_repository_dependency(self):
             metadata_record.downloadable
         ), f"The revision of {repository.name} that does not contain tool_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
+        n_downloadable_revisions = len(self._db_repository(repository).downloadable_revisions)
         assert (
-            len(self._db_repository(repository).downloadable_revisions) == 2
-        ), "Repository %s has %d downloadable revisions, expected 2." % (
-            repository.name,
-            len(self._db_repository(repository).downloadable_revisions),
-        )
+            n_downloadable_revisions == 2
+        ), f"Repository {repository.name} has {n_downloadable_revisions} downloadable revisions, expected 2."
 
     def test_0055_create_bwa_tool_dependency_repository(self):
         """Create and populate the bwa_tool_dependency_0440 repository.
@@ -340,12 +332,10 @@ def test_0060_delete_bwa_tool_dependency_definition(self):
             metadata_record is None
         ), f"The tip revision of {repository.name} should not have metadata, but metadata was found."
         # Verify that the new changeset revision is not downloadable.
+        n_downloadable_revisions = len(self._db_repository(repository).downloadable_revisions)
         assert (
-            len(self._db_repository(repository).downloadable_revisions) == 1
-        ), "Repository %s has %d downloadable revisions, expected 1." % (
-            repository.name,
-            len(self._db_repository(repository).downloadable_revisions),
-        )
+            n_downloadable_revisions == 1
+        ), f"Repository {repository.name} has {n_downloadable_revisions} downloadable revisions, expected 1."
 
     def test_0065_reupload_bwa_tool_dependency_definition(self):
         """Reupload the tool_dependencies.xml file to bwa_tool_dependency_0440.
@@ -372,12 +362,10 @@ def test_0065_reupload_bwa_tool_dependency_definition(self):
             metadata_record.downloadable
         ), f"The revision of {repository.name} that contains tool_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
+        n_downloadable_revisions = len(self._db_repository(repository).downloadable_revisions)
         assert (
-            len(self._db_repository(repository).downloadable_revisions) == 1
-        ), "Repository %s has %d downloadable revisions, expected 1." % (
-            repository.name,
-            len(self._db_repository(repository).downloadable_revisions),
-        )
+            n_downloadable_revisions == 1
+        ), f"Repository {repository.name} has {n_downloadable_revisions} downloadable revisions, expected 1."
 
     def _get_repository_metadata_by_changeset_revision(self, repository: Repository, changeset: str):
         return self.get_repository_metadata_by_changeset_revision(self._db_repository(repository).id, changeset)

lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py

@@ -144,10 +144,9 @@ def test_0020_upload_updated_tool_dependency_to_package_x11(self):
         # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository.
         self.user_populator().setup_test_data_repo("libx11_proto", package_x11_repository, start=1, end=2)
         count = self._get_metadata_revision_count(package_x11_repository)
-        assert count == 1, (
-            "package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions, expected 1 but found %d"
-            % count
-        )
+        assert (
+            count == 1
+        ), f"package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions, expected 1 but found {count}"
 
     def test_0025_upload_updated_tool_dependency_to_package_emboss(self):
         """Upload a new tool_dependencies.xml to package_emboss_5_0_0_0470.
@@ -164,9 +163,9 @@ def test_0025_upload_updated_tool_dependency_to_package_emboss(self):
             "package_emboss_5_0_0_0470", package_emboss_repository, start=1, end=2
         )
         count = self._get_metadata_revision_count(package_emboss_repository)
-        assert count == 2, (
-            "package_emboss_5_0_0_0470 has incorrect number of metadata revisions, expected 2 but found %d" % count
-        )
+        assert (
+            count == 2
+        ), f"package_emboss_5_0_0_0470 has incorrect number of metadata revisions, expected 2 but found {count}"
 
     def test_0030_upload_updated_tool_dependency_to_emboss_5_repository(self):
         """Upload a new tool_dependencies.xml to emboss_5_0470.
@@ -216,11 +215,9 @@ def test_0045_reset_repository_metadata(self):
         self.reset_repository_metadata(package_emboss_repository)
         self.reset_repository_metadata(package_x11_repository)
         count = self._get_metadata_revision_count(package_emboss_repository)
-        assert count == 1, "Repository package_emboss_5_0_0 has %d installable revisions, expected 1." % count
+        assert count == 1, f"Repository package_emboss_5_0_0 has {count} installable revisions, expected 1."
         count = self._get_metadata_revision_count(package_x11_repository)
-        assert count == 1, (
-            "Repository package_x11_client_1_5_proto_7_0 has %d installable revisions, expected 1." % count
-        )
+        assert count == 1, f"Repository package_x11_client_1_5_proto_7_0 has {count} installable revisions, expected 1."
 
     def test_0050_reset_emboss_5_metadata(self):
         """Reset metadata on emboss_5.
@@ -230,4 +227,4 @@ def test_0050_reset_emboss_5_metadata(self):
         emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
         self.reset_repository_metadata(emboss_repository)
         count = self._get_metadata_revision_count(emboss_repository)
-        assert count == 1, "Repository emboss_5 has %d installable revisions, expected 1." % count
+        assert count == 1, f"Repository emboss_5 has {count} installable revisions, expected 1."