Merge pull request galaxyproject#18067 from nsoranzo/flake8-implicit-…

…str-concat

Enable flake8-implicit-str-concat ruff rules

client/src/api/schema/schema.ts

@@ -19398,7 +19398,7 @@ export interface operations {
          * @description Allows remote job running mechanisms to get a fresh OIDC token that can be used on remote side to authorize user. It is not meant to represent part of Galaxy's stable, user facing API
          */
         parameters: {
-            /** @description A key used to authenticate this request as acting onbehalf or a job runner for the specified job */
+            /** @description A key used to authenticate this request as acting on behalf or a job runner for the specified job */
             /** @description OIDC provider name */
             query: {
                 job_key: string;

lib/galaxy/authnz/managers.py

@@ -95,8 +95,9 @@ def _parse_oidc_config(self, config_file):
                         func = getattr(builtins, child.get("Type"))
                 except AttributeError:
                     log.error(
-                        "The value of attribute `Type`, `{}`, is not a valid built-in type;" " skipping this node"
-                    ).format(child.get("Type"))
+                        "The value of attribute `Type`, `%s`, is not a valid built-in type; skipping this node",
+                        child.get("Type"),
+                    )
                     continue
                 self.oidc_config[child.get("Property")] = func(child.get("Value"))
         except ImportError:

lib/galaxy/celery/base_task.py

@@ -87,7 +87,7 @@ def calculate_task_start_time(  # type: ignore
             update_stmt = (
                 update(CeleryUserRateLimit)
                 .where(CeleryUserRateLimit.user_id == user_id)
-                .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', " ":now) "))
+                .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', :now)"))
                 .returning(CeleryUserRateLimit.last_scheduled_time)
             )
             result = sa_session.execute(update_stmt, {"interval": task_interval_secs, "now": now}).all()

lib/galaxy/datatypes/molecules.py

@@ -877,15 +877,15 @@ def get_matcher(self) -> re.Pattern:
         """
         pat = (
             r"(ATOM|HETATM)\s+"
-            + r"(\d+)\s+"
-            + r"([A-Z0-9]+)\s+"
-            + r"([A-Z0-9]+)\s+"
-            + r"(([A-Z]?)\s+)?"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
+            r"(\d+)\s+"
+            r"([A-Z0-9]+)\s+"
+            r"([A-Z0-9]+)\s+"
+            r"(([A-Z]?)\s+)?"
+            r"([-+]?\d*\.\d+|\d+)\s+"
+            r"([-+]?\d*\.\d+|\d+)\s+"
+            r"([-+]?\d*\.\d+|\d+)\s+"
+            r"([-+]?\d*\.\d+|\d+)\s+"
+            r"([-+]?\d*\.\d+|\d+)\s+"
         )
         return re.compile(pat)
 

lib/galaxy/datatypes/qiime2.py

@@ -275,7 +275,7 @@ def _get_versions(path, uuid):
         framework_version = framework_version_line.split(":")[1].strip()
         return version, framework_version
     except Exception:
-        raise ValueError("Archive does not contain a correctly formatted" " VERSION file.")
+        raise ValueError("Archive does not contain a correctly formatted VERSION file.")
 
 
 def _open_file_in_archive(zip_path, path, uuid):

lib/galaxy/datatypes/tabular.py

@@ -1223,7 +1223,8 @@ def __init__(self, **kwd):
             "DESC",
             "SRAS",
             "PRAS",
-            "PART_CHROM" "PART_CONTIG",
+            "PART_CHROM",
+            "PART_CONTIG",
             "PART_OFFSET",
             "PART_STRAND",
             "FILT",

lib/galaxy/jobs/__init__.py

@@ -1331,7 +1331,7 @@ def clear_working_directory(self):
         job = self.get_job()
         if not os.path.exists(self.working_directory):
             log.warning(
-                "(%s): Working directory clear requested but %s does " "not exist", self.job_id, self.working_directory
+                "(%s): Working directory clear requested but %s does not exist", self.job_id, self.working_directory
             )
             return
 
@@ -1535,7 +1535,7 @@ def change_state(self, state, info=False, flush=True, job=None):
 
         if job.state in model.Job.terminal_states:
             log.warning(
-                "(%s) Ignoring state change from '%s' to '%s' for job " "that is already terminal",
+                "(%s) Ignoring state change from '%s' to '%s' for job that is already terminal",
                 job.id,
                 job.state,
                 state,

lib/galaxy/jobs/dynamic_tool_destination.py

@@ -1773,11 +1773,13 @@ def get_typo_correction(typo_str, word_set, max_dist):
         "--check-config",
         dest="check_config",
         nargs="?",
-        help="Use this option to validate tool_destinations.yml."
-        + " Optionally, provide the path to the tool_destinations.yml"
-        + " that you would like to check, and/or the path to the related"
-        + " job_conf.xml. Default: galaxy/config/tool_destinations.yml"
-        + "and galaxy/config/job_conf.xml",
+        help=(
+            "Use this option to validate tool_destinations.yml."
+            " Optionally, provide the path to the tool_destinations.yml"
+            " that you would like to check, and/or the path to the related"
+            " job_conf.xml. Default: galaxy/config/tool_destinations.yml"
+            "and galaxy/config/job_conf.xml"
+        ),
     )
 
     parser.add_argument("-j", "--job-config", dest="job_config")

lib/galaxy/jobs/runners/aws.py

@@ -399,7 +399,7 @@ def stop_job(self, job_wrapper):
         log.debug(msg.format(name=job_name))
 
     def recover(self, job, job_wrapper):
-        msg = "(name!r/runner!r) is still in {state!s} state, adding to" " the runner monitor queue"
+        msg = "(name!r/runner!r) is still in {state!s} state, adding to the runner monitor queue"
         job_id = job.get_job_runner_external_id()
         job_name = self.JOB_NAME_PREFIX + job_wrapper.get_id_tag()
         ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper)

lib/galaxy/jobs/runners/chronos.py

@@ -178,7 +178,7 @@ def stop_job(self, job_wrapper):
             LOGGER.error(msg.format(name=job_name))
 
     def recover(self, job, job_wrapper):
-        msg = "(name!r/runner!r) is still in {state!s} state, adding to" " the runner monitor queue"
+        msg = "(name!r/runner!r) is still in {state!s} state, adding to the runner monitor queue"
         job_id = job.get_job_runner_external_id()
         ajs = AsynchronousJobState(
             files_dir=job_wrapper.working_directory,

lib/galaxy/model/__init__.py

@@ -3252,7 +3252,7 @@ def add_dataset(self, dataset, parent_id=None, genome_build=None, set_hid=True,
         elif not isinstance(dataset, (HistoryDatasetAssociation, HistoryDatasetCollectionAssociation)):
             raise TypeError(
                 "You can only add Dataset and HistoryDatasetAssociation instances to a history"
-                + f" ( you tried to add {str(dataset)} )."
+                f" ( you tried to add {str(dataset)} )."
             )
         is_dataset = is_hda(dataset)
         if parent_id:

lib/galaxy/objectstore/pithos.py

@@ -83,7 +83,7 @@ def parse_config_xml(config_xml):
             log.error(msg)
             raise Exception(msg)
     except Exception:
-        log.exception("Malformed PithosObjectStore Configuration XML -- " "unable to continue")
+        log.exception("Malformed PithosObjectStore Configuration XML, unable to continue")
         raise
     return r
 
@@ -325,7 +325,7 @@ def _size(self, obj, **kwargs) -> int:
             try:
                 return os.path.getsize(self._get_cache_path(path))
             except OSError as ex:
-                log.warning(f"Could not get size of file {path} in local cache," f"will try Pithos. Error: {ex}")
+                log.warning("Could not get size of file %s in local cache, will try Pithos. Error: %s", path, ex)
         try:
             file = self.pithos.get_object_info(path)
         except ClientError as ce:
@@ -408,7 +408,7 @@ def _update_from_file(self, obj, **kwargs):
         if kwargs.get("create"):
             self._create(obj, **kwargs)
         if not self._exists(obj, **kwargs):
-            raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, " f"kwargs: {kwargs}")
+            raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, kwargs: {kwargs}")
 
         path = self._construct_path(obj, **kwargs)
         cache_path = self._get_cache_path(path)

lib/galaxy/objectstore/rucio.py

@@ -594,7 +594,7 @@ def _register_file(self, rel_path, file_name):
             file_name = self._get_cache_path(rel_path)
             if not os.path.islink(file_name):
                 raise ObjectInvalid(
-                    "rucio objectstore._register_file, rucio_register_only " "is set, but file in cache is not a link "
+                    "rucio objectstore._register_file, rucio_register_only is set, but file in cache is not a link "
                 )
         if os.path.islink(file_name):
             file_name = os.readlink(file_name)

lib/galaxy/schema/schema.py

@@ -1563,14 +1563,14 @@ class CreateHistoryPayload(Model):
         default=None,
         title="History ID",
         description=(
-            "The encoded ID of the history to copy. " "Provide this value only if you want to copy an existing history."
+            "The encoded ID of the history to copy. Provide this value only if you want to copy an existing history."
         ),
     )
     all_datasets: Optional[bool] = Field(
         default=True,
         title="All Datasets",
         description=(
-            "Whether to copy also deleted HDAs/HDCAs. Only applies when " "providing a `history_id` to copy from."
+            "Whether to copy also deleted HDAs/HDCAs. Only applies when providing a `history_id` to copy from."
         ),
     )
     archive_source: Optional[str] = Field(
@@ -3411,7 +3411,7 @@ class ShareWithPayload(Model):
         ...,
         title="User Identifiers",
         description=(
-            "A collection of encoded IDs (or email addresses) of users " "that this resource will be shared with."
+            "A collection of encoded IDs (or email addresses) of users that this resource will be shared with."
         ),
     )
     share_option: Optional[SharingOptions] = Field(

lib/galaxy/tool_util/verify/test_data.py

@@ -11,11 +11,11 @@
 )
 
 UPDATE_TEMPLATE = Template(
-    "git --work-tree $dir --git-dir $dir/.git fetch && " "git --work-tree $dir --git-dir $dir/.git merge origin/master"
+    "git --work-tree $dir --git-dir $dir/.git fetch && git --work-tree $dir --git-dir $dir/.git merge origin/master"
 )
 
 UPDATE_FAILED_TEMPLATE = Template(
-    "Warning failed to update test repository $dir - " "update stdout was [$stdout] and stderr was [$stderr]."
+    "Warning failed to update test repository $dir - update stdout was [$stdout] and stderr was [$stderr]."
 )
 
 

lib/galaxy/tools/data_fetch.py

@@ -305,7 +305,7 @@ def _resolve_item_with_primary(item):
                 if datatype.dataset_content_needs_grooming(path):
                     err_msg = (
                         "The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be "
-                        + "<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed."
+                        "<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed."
                     )
                     raise UploadProblemException(err_msg)
 

lib/galaxy/tools/search/__init__.py

@@ -233,7 +233,7 @@ def build_index(self, tool_cache, toolbox, index_help: bool = True) -> None:
                 # Add tool document to index (or overwrite if existing)
                 writer.update_document(**add_doc_kwds)
 
-        log.debug(f"Toolbox index of panel {self.panel_view_id}" f" finished {execution_timer}")
+        log.debug("Toolbox index of panel %s finished %s", self.panel_view_id, execution_timer)
 
     def _get_tools_to_remove(self, tool_cache) -> list:
         """Return list of tool IDs to be removed from index."""

lib/galaxy/util/custom_logging/fluent_log.py

@@ -12,7 +12,7 @@
     FluentSender = None
 
 
-FLUENT_IMPORT_MESSAGE = "The Python fluent package is required to use this " "feature, please install it"
+FLUENT_IMPORT_MESSAGE = "The Python fluent package is required to use this feature, please install it"
 
 
 class FluentTraceLogger:

lib/galaxy/webapps/galaxy/api/cloudauthz.py

@@ -122,9 +122,9 @@ def create(self, trans, payload, **kwargs):
         description = payload.get("description", "")
 
         if not isinstance(config, dict):
-            log.debug(msg_template.format(f"invalid config type `{type(config)}`, expect `dict`"))
+            log.debug(msg_template.format(f"invalid config type `{type(config)}`, expected `dict`"))
             raise RequestParameterInvalidException(
-                "Invalid type for the required `config` variable; expect `dict` " f"but received `{type(config)}`."
+                f"Invalid type for the required `config` variable; expected `dict` but received `{type(config)}`."
             )
         if authn_id:
             try:

lib/galaxy/webapps/galaxy/api/job_tokens.py

@@ -39,7 +39,7 @@ def get_token(
         job_id: EncodedDatabaseIdField,
         job_key: str = Query(
             description=(
-                "A key used to authenticate this request as acting on" "behalf or a job runner for the specified job"
+                "A key used to authenticate this request as acting on behalf or a job runner for the specified job"
             ),
         ),
         provider: str = Query(

lib/galaxy/webapps/galaxy/api/remote_files.py

@@ -37,7 +37,7 @@
 TargetQueryParam: str = Query(
     default=RemoteFilesTarget.ftpdir,
     title="Target source",
-    description=("The source to load datasets from." " Possible values: ftpdir, userdir, importdir"),
+    description=("The source to load datasets from. Possible values: ftpdir, userdir, importdir"),
 )
 
 FormatQueryParam: Optional[RemoteFilesFormat] = Query(
@@ -54,7 +54,7 @@
     default=None,
     title="Recursive",
     description=(
-        "Whether to recursively lists all sub-directories." " This will be `True` by default depending on the `target`."
+        "Whether to recursively lists all sub-directories. This will be `True` by default depending on the `target`."
     ),
 )
 

lib/galaxy/webapps/galaxy/controllers/visualization.py

@@ -19,7 +19,6 @@
     UsesItemRatings,
 )
 from galaxy.structured_app import StructuredApp
-from galaxy.util import unicodify
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.visualization.genomes import GenomeRegion
 from galaxy.webapps.base.controller import (
@@ -263,9 +262,8 @@ def _handle_plugin_error(self, trans, visualization_name, exception):
             raise exception
         return trans.show_error_message(
             "There was an error rendering the visualization. "
-            + "Contact your Galaxy administrator if the problem persists."
-            + "<br/>Details: "
-            + unicodify(exception),
+            "Contact your Galaxy administrator if the problem persists."
+            f"<br/>Details: {exception}",
             use_panels=False,
         )
 

lib/galaxy/webapps/galaxy/services/library_folders.py

@@ -218,7 +218,7 @@ def set_permissions(
             trans.app.security_agent.set_all_library_permissions(trans, folder, permissions)
         else:
             raise RequestParameterInvalidException(
-                'The mandatory parameter "action" has an invalid value.' 'Allowed values are: "set_permissions"'
+                'The mandatory parameter "action" has an invalid value. Allowed values are: "set_permissions"'
             )
         current_permissions = self.folder_manager.get_current_roles(trans, folder)
         return LibraryFolderCurrentPermissions(**current_permissions)

pyproject.toml

@@ -191,8 +191,9 @@ exclude = [
 
 [tool.ruff.lint]
 # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
-# flake8-comprehensions (C4), flake8-logging-format (G) and pyupgrade (UP)
-select = ["E", "F", "B", "C4", "G", "UP"]
+# flake8-comprehensions (C4), flake8-logging-format (G),
+# flake8-implicit-str-concat (ISC) and pyupgrade (UP)
+select = ["E", "F", "B", "C4", "G", "ISC", "UP"]
 # Exceptions:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # B9 flake8-bugbear opinionated warnings

scripts/api/upload_to_history.py

@@ -12,7 +12,7 @@
 except ImportError:
     print(
         "Could not import the requests module. See http://docs.python-requests.org/en/latest/"
-        + " or install with 'pip install requests'"
+        " or install with 'pip install requests'"
     )
     raise
 
@@ -46,7 +46,7 @@ def upload_file(base_url, api_key, history_id, filepath, **kwargs):
     if len(sys.argv) < 5:
         print(
             "history_upload.py <api key> <galaxy base url> <history id> <filepath to upload>\n"
-            + "  (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')"
+            "  (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')"
         )
         sys.exit(1)
 

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -93,7 +93,7 @@ def main():
         help="config file (legacy, use --config instead)",
     )
     parser.add_argument("-d", "--days", dest="days", action="store", type=int, help="number of days (60)", default=60)
-    parser.add_argument("--tool_id", default=None, help="Text to match against tool_id" "Default: match all")
+    parser.add_argument("--tool_id", default=None, help="Text to match against tool_id. Default: match all")
     parser.add_argument(
         "--template",
         default=None,
@@ -121,10 +121,10 @@ def main():
         default=False,
     )
     parser.add_argument(
-        "--smtp", default=None, help="SMTP Server to use to send email. " "Default: [read from galaxy config file]"
+        "--smtp", default=None, help="SMTP Server to use to send email. Default: [read from galaxy config file]"
     )
     parser.add_argument(
-        "--fromaddr", default=None, help="From address to use to send email. " "Default: [read from galaxy config file]"
+        "--fromaddr", default=None, help="From address to use to send email. Default: [read from galaxy config file]"
     )
     populate_config_args(parser)
 
@@ -138,14 +138,12 @@ def main():
     if args.smtp is not None:
         app_properties["smtp_server"] = args.smtp
     if app_properties.get("smtp_server") is None:
-        parser.error("SMTP Server must be specified as an option (--smtp) " "or in the config file (smtp_server)")
+        parser.error("SMTP Server must be specified as an option (--smtp) or in the config file (smtp_server)")
 
     if args.fromaddr is not None:
         app_properties["email_from"] = args.fromaddr
     if app_properties.get("email_from") is None:
-        parser.error(
-            "From address must be specified as an option " "(--fromaddr) or in the config file " "(email_from)"
-        )
+        parser.error("From address must be specified as an option (--fromaddr) or in the config file (email_from)")
 
     scriptdir = os.path.dirname(os.path.abspath(__file__))
     template_file = args.template
@@ -262,15 +260,15 @@ def administrative_delete_datasets(
                     # Mark the HistoryDatasetAssociation as deleted
                     hda.deleted = True
                     app.sa_session.add(hda)
-                    print("Marked HistoryDatasetAssociation id %d as " "deleted" % hda.id)
+                    print("Marked HistoryDatasetAssociation id %d as deleted" % hda.id)
                 session = app.sa_session()
                 with transaction(session):
                     session.commit()
 
     emailtemplate = Template(filename=template_file)
     for email, dataset_list in user_notifications.items():
         msgtext = emailtemplate.render(email=email, datasets=dataset_list, cutoff=cutoff_days)
-        subject = "Galaxy Server Cleanup " "- %d datasets DELETED" % len(dataset_list)
+        subject = "Galaxy Server Cleanup - %d datasets DELETED" % len(dataset_list)
         fromaddr = config.email_from
         print()
         print(f"From: {fromaddr}")