Fix new UP031 errors from ruff 0.4.2

config/plugins/webhooks/demo/tour_generator/__init__.py

@@ -59,7 +59,7 @@ class TourGenerator:
                 filename = test_datasets[input_name]
                 input_path = self._tool.test_data_path(filename)
                 if not input_path:
-                    raise ValueError('Test dataset "%s" doesn\'t exist.' % input_name)
+                    raise ValueError(f'Test dataset "{input_name}" doesn\'t exist.')
                 upload_tool = self._trans.app.toolbox.get_tool("upload1")
                 filename = os.path.basename(input_path)
                 with open(input_path, "rb") as f:
@@ -92,12 +92,12 @@ class TourGenerator:
 
     def _generate_tour(self):
         """Generate a tour."""
-        tour_name = self._tool.name + " Tour"
+        tour_name = f"{self._tool.name} Tour"
         test_inputs = self._test.inputs.keys()
         steps = [
             {
                 "title": tour_name,
-                "content": "This short tour will guide you through the <b>" + self._tool.name + "</b> tool.",
+                "content": f"This short tour will guide you through the <b>{self._tool.name}</b> tool.",
                 "orphan": True,
             }
         ]
@@ -107,26 +107,26 @@ class TourGenerator:
                 continue
             step = {
                 "title": input.label,
-                "element": "[id='form-element-%s']" % name,
+                "element": f"[id='form-element-{name}']",
                 "placement": "right",
                 "content": "",
             }
             if input.type == "text":
                 if name in test_inputs:
                     param = self._test.inputs[name]
-                    step["content"] = "Enter value(s): <b>%s</b>" % param
+                    step["content"] = f"Enter value(s): <b>{param}</b>"
                 else:
                     step["content"] = "Enter a value"
             elif input.type == "integer" or input.type == "float":
                 if name in test_inputs:
                     num_param = self._test.inputs[name][0]
-                    step["content"] = "Enter number: <b>%s</b>" % num_param
+                    step["content"] = f"Enter number: <b>{num_param}</b>"
                 else:
                     step["content"] = "Enter a number"
             elif input.type == "boolean":
                 if name in test_inputs:
                     choice = "Yes" if self._test.inputs[name][0] is True else "No"
-                    step["content"] = "Choose <b>%s</b>" % choice
+                    step["content"] = f"Choose <b>{choice}</b>"
                 else:
                     step["content"] = "Choose Yes/No"
             elif input.type == "select":
@@ -138,7 +138,7 @@ class TourGenerator:
                                 params.append(option[0])
                 if params:
                     select_param = ", ".join(params)
-                    step["content"] = "Select parameter(s): <b>%s</b>" % select_param
+                    step["content"] = f"Select parameter(s): <b>{select_param}</b>"
                 else:
                     step["content"] = "Select a parameter"
             elif input.type == "data":
@@ -151,7 +151,7 @@ class TourGenerator:
             elif input.type == "conditional":
                 param_id = f"{input.name}|{input.test_param.name}"
                 step["title"] = input.test_param.label
-                step["element"] = "[id='form-element-%s']" % param_id
+                step["element"] = f"[id='form-element-{param_id}']"
                 params = []
                 if param_id in self._test.inputs.keys():
                     for option in input.test_param.static_options:
@@ -173,24 +173,24 @@ class TourGenerator:
                                 step_msg = f"Select dataset: <b>{hid}: {dataset}</b>"
                             else:
                                 case_params = ", ".join(self._test.inputs[tour_id])
-                                step_msg = "Select parameter(s): " + "<b>%s</b>" % case_params
+                                step_msg = f"Select parameter(s): <b>{case_params}</b>"
                             cond_case_steps.append(
                                 {
                                     "title": case_title,
-                                    "element": "[id='form-element-%s']" % tour_id,
+                                    "element": f"[id='form-element-{tour_id}']",
                                     "placement": "right",
                                     "content": step_msg,
                                 }
                             )
                 if params:
                     cond_param = ", ".join(params)
-                    step["content"] = "Select parameter(s): <b>%s</b>" % cond_param
+                    step["content"] = f"Select parameter(s): <b>{cond_param}</b>"
                 else:
                     step["content"] = "Select a parameter"
             elif input.type == "data_column":
                 if name in test_inputs:
                     column_param = self._test.inputs[name][0]
-                    step["content"] = "Select <b>Column: %s</b>" % column_param
+                    step["content"] = f"Select <b>Column: {column_param}</b>"
                 else:
                     step["content"] = "Select a column"
             else:
@@ -210,7 +210,7 @@ class TourGenerator:
         self._tour = {
             "title_default": tour_name,
             "name": tour_name,
-            "description": self._tool.name + " " + self._tool.description,
+            "description": f"{self._tool.name} {self._tool.description}",
             "steps": steps,
         }
 

doc/parse_gx_xsd.py

@@ -34,7 +34,7 @@ def main():
 
 
 class Tag:
-    def __init__(self, line):
+    def __init__(self, line: str):
         assert line.startswith("$tag:")
         line_parts = line.split(" ")
         first_part = line_parts[0]
@@ -52,12 +52,12 @@ class Tag:
 
     @property
     def _pretty_title(self):
-        return " > ".join("``%s``" % p for p in self.title.split("|"))
+        return " > ".join(f"``{p}``" for p in self.title.split("|"))
 
     def build_help(self):
         tag = xmlschema_doc.find(self.xpath)
         if tag is None:
-            raise Exception("Could not find xpath for %s" % self.xpath)
+            raise Exception(f"Could not find xpath for {self.xpath}")
 
         tag_help = StringIO()
         tag_help.write("## " + self._pretty_title)
@@ -98,7 +98,7 @@ def _build_tag(tag, hide_attributes):
                     doc = _doc_or_none(element)
                     if doc is None:
                         doc = _doc_or_none(_type_el(element))
-                    assert doc is not None, "Documentation for %s is empty" % element.attrib["name"]
+                    assert doc is not None, f"Documentation for {element.attrib['name']} is empty"
                     doc = doc.strip()
 
                     element_el = _find_tag_el(element)
@@ -110,10 +110,9 @@ def _build_tag(tag, hide_attributes):
     if best_practices := _get_bp_link(annotation_el):
         tag_help.write("\n\n### Best Practices\n")
         tag_help.write(
-            """
-Find the Intergalactic Utilities Commision suggested best practices for this
-element [here](%s)."""
-            % best_practices
+            f"""
+Find the Intergalactic Utilities Commission suggested best practices for this
+element [here]({best_practices})."""
         )
     tag_help.write(_build_attributes_table(tag, attributes, hide_attributes))
 
@@ -140,7 +139,7 @@ def _get_bp_link(annotation_el):
     anchor = annotation_el.attrib.get("{http://galaxyproject.org/xml/1.0}best_practices", None)
     link = None
     if anchor:
-        link = "https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#%s" % anchor
+        link = f"https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#{anchor}"
     return link
 
 
@@ -149,7 +148,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
     attribute_table.write("\n\n")
     if attributes and not hide_attributes:
         header_prefix = "#" * header_level
-        attribute_table.write("\n%s Attributes\n\n" % header_prefix)
+        attribute_table.write(f"\n{header_prefix} Attributes\n\n")
         attribute_table.write("Attribute | Details | Required\n")
         attribute_table.write("--- | --- | ---\n")
         for attribute in attributes:
@@ -159,7 +158,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = _doc_or_none(attribute)
             if details is None:
                 type_el = _type_el(attribute)
-                assert type_el is not None, "No details or type found for %s" % name
+                assert type_el is not None, f"No details or type found for {name}"
                 details = _doc_or_none(type_el)
                 annotation_el = type_el.find("{http://www.w3.org/2001/XMLSchema}annotation")
             else:
@@ -170,10 +169,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = details.replace("|", "\\|").strip()
             best_practices = _get_bp_link(annotation_el)
             if best_practices:
-                details += (
-                    """ Find the Intergalactic Utilities Commision suggested best practices for this element [here](%s)."""
-                    % best_practices
-                )
+                details += f""" Find the Intergalactic Utilities Commission suggested best practices for this element [here]({best_practices})."""
 
             attribute_table.write(f"``{name}`` | {details} | {use}\n")
     return attribute_table.getvalue()
@@ -204,7 +200,7 @@ def _find_attributes(tag):
     for attribute_group in attribute_groups:
         attribute_group_name = attribute_group.get("ref")
         attribute_group_def = xmlschema_doc.find(
-            "//{http://www.w3.org/2001/XMLSchema}attributeGroup/[@name='%s']" % attribute_group_name
+            f"//{{http://www.w3.org/2001/XMLSchema}}attributeGroup/[@name='{attribute_group_name}']"
         )
         attributes.extend(_find_attributes(attribute_group_def))
     return attributes
@@ -219,9 +215,9 @@ def _find_tag_el(tag):
 
 def _type_el(tag):
     element_type = tag.attrib["type"]
-    type_el = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}complexType/[@name='%s']" % element_type)
+    type_el = xmlschema_doc.find(f"//{{http://www.w3.org/2001/XMLSchema}}complexType/[@name='{element_type}']")
     if type_el is None:
-        type_el = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}simpleType/[@name='%s']" % element_type)
+        type_el = xmlschema_doc.find(f"//{{http://www.w3.org/2001/XMLSchema}}simpleType/[@name='{element_type}']")
     return type_el
 
 

lib/galaxy/actions/library.py

@@ -265,7 +265,7 @@ class LibraryActions:
             if not os.path.exists(path):
                 bad_paths.append(path)
         if bad_paths:
-            message = 'Invalid paths: "%s".' % '", "'.join(bad_paths)
+            message = 'Invalid paths: "{}".'.format('", "'.join(bad_paths))
             response_code = 400
             return None, response_code, message
         return None

lib/galaxy/auth/providers/ldap_ad.py

@@ -135,8 +135,8 @@ class LDAP(AuthProvider):
         self.role_search_attribute = options.get(self.role_search_option)
         if self.auto_create_roles_or_groups and self.role_search_attribute is None:
             raise ConfigurationError(
-                "If 'auto-create-roles' or 'auto-create-groups' is True, a '%s' attribute has to"
-                " be provided." % self.role_search_option
+                f"If 'auto-create-roles' or 'auto-create-groups' is True, a '{self.role_search_option}' attribute has to"
+                " be provided."
             )
 
         return ok, failure_mode

lib/galaxy/config/__init__.py

@@ -944,7 +944,8 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
                     log.warning(
                         "The path '%s' for the 'sanitize_allowlist_file' config option is "
                         "deprecated and will be no longer checked in a future release. Please consult "
-                        "the latest version of the sample configuration file." % deprecated
+                        "the latest version of the sample configuration file.",
+                        deprecated,
                     )
                     _sanitize_allowlist_path = deprecated
                     break
@@ -965,7 +966,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         )
         # Searching data libraries
         self.ftp_upload_dir_template = kwargs.get(
-            "ftp_upload_dir_template", "${ftp_upload_dir}%s${ftp_upload_dir_identifier}" % os.path.sep
+            "ftp_upload_dir_template", f"${{ftp_upload_dir}}{os.path.sep}${{ftp_upload_dir_identifier}}"
         )
         # Support older library-specific path paste option but just default to the new
         # allow_path_paste value.

lib/galaxy/datatypes/binary.py

@@ -2089,7 +2089,7 @@ class H5MLM(H5):
         try:
             return dataset.peek
         except Exception:
-            return "HDF5 Model (%s)" % (nice_size(dataset.get_size()))
+            return f"HDF5 Model ({nice_size(dataset.get_size())})"
 
     def display_data(
         self,
@@ -4258,7 +4258,7 @@ class Pretext(Binary):
         try:
             return dataset.peek
         except Exception:
-            return "Binary pretext file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary pretext file ({nice_size(dataset.get_size())})"
 
 
 class JP2(Binary):
@@ -4302,7 +4302,7 @@ class JP2(Binary):
         try:
             return dataset.peek
         except Exception:
-            return "Binary JPEG 2000 file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary JPEG 2000 file ({nice_size(dataset.get_size())})"
 
 
 class Npz(CompressedArchive):
@@ -4356,7 +4356,7 @@ class Npz(CompressedArchive):
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class HexrdImagesNpz(Npz):
@@ -4433,7 +4433,7 @@ class HexrdImagesNpz(Npz):
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class HexrdEtaOmeNpz(Npz):
@@ -4495,7 +4495,7 @@ class HexrdEtaOmeNpz(Npz):
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class FITS(Binary):
@@ -4624,4 +4624,4 @@ class Numpy(Binary):
         try:
             return dataset.peek
         except Exception:
-            return "Binary numpy file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary numpy file ({nice_size(dataset.get_size())})"

lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py

@@ -181,7 +181,7 @@ def __main__():
                     fields = [str(item) for item in (region.chrom, region.start, region.end, name, 0, region.strand)]
                     if force_num_columns is not None and len(fields) != force_num_columns:
                         fields = force_bed_field_count(fields, count, force_num_columns)
-                    out.write("%s\n" % "\t".join(fields))
+                    out.write("{}\n".format("\t".join(fields)))
                 except Exception:
                     skipped_lines += 1
                     if first_skipped_line is None:

lib/galaxy/datatypes/converters/maf_to_fasta_converter.py

@@ -24,11 +24,12 @@ def __main__():
                 else:
                     spec_counts[spec] += 1
                 out.write(
-                    "%s\n"
-                    % maf_utilities.get_fasta_header(
-                        c,
-                        {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
-                        suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                    "{}\n".format(
+                        maf_utilities.get_fasta_header(
+                            c,
+                            {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
+                            suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                        )
                     )
                 )
                 out.write(f"{c.text}\n")

lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py

@@ -20,7 +20,7 @@ def main():
     with open(sys.argv[1]) as in_file, open(sys.argv[2], "w") as out_file:
         try:
             for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
-                out_file.write("%s\n" % "\t".join(map(str, fields)))
+                out_file.write("{}\n".format("\t".join(map(str, fields))))
         except UCSCLimitException:
             # Wiggle data was truncated, at the very least need to warn the user.
             sys.stderr.write(

lib/galaxy/datatypes/interval.py

@@ -289,18 +289,18 @@ class Interval(Tabular):
                     if t < len(elems):
                         strand = cast(str, elems[t])
                     tmp = [elems[c], elems[s], elems[e], name, "0", strand]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             elif n >= 0:  # name column (should) exists
                 for i, elems in enumerate(compression_utils.file_iter(dataset.get_file_name())):
                     name = "region_%i" % i
                     if n >= 0 and n < len(elems):
                         name = cast(str, elems[n])
                     tmp = [elems[c], elems[s], elems[e], name]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             else:
                 for elems in compression_utils.file_iter(dataset.get_file_name()):
                     tmp = [elems[c], elems[s], elems[e]]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             return compression_utils.get_fileobj(fh.name, mode="rb")
 
     def display_peek(self, dataset: DatasetProtocol) -> str:

lib/galaxy/datatypes/neo4j.py

@@ -30,9 +30,8 @@ class Neo4j(Html):
         """
         # self.regenerate_primary_file(dataset)
         rval = [
-            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
             This composite dataset is composed of the following files:<p/><ul>"
-            % (self.file_ext)
         ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""

lib/galaxy/datatypes/proteomics.py

@@ -714,7 +714,7 @@ class ProteomicsXml(GenericXml):
             if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r"<(\w*:)?%s" % self.root
+        pattern = rf"<(\w*:)?{self.root}"
         return re.search(pattern, line) is not None
 
     def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:

lib/galaxy/datatypes/qiime2.py

@@ -258,10 +258,10 @@ def _get_uuid(path):
     if len(roots) == 0:
         raise ValueError("Archive does not have a visible root directory.")
     if len(roots) > 1:
-        raise ValueError("Archive has multiple root directories: %r" % roots)
+        raise ValueError(f"Archive has multiple root directories: {roots!r}")
     uuid = roots.pop()
     if not _is_uuid4(uuid):
-        raise ValueError("Archive root directory name %r is not a valid version 4 " "UUID." % uuid)
+        raise ValueError(f"Archive root directory name {uuid!r} is not a valid version 4 UUID.")
     return uuid
 
 

lib/galaxy/datatypes/registry.py

@@ -971,9 +971,8 @@ class Registry:
         # If extension is not None and is uppercase or mixed case, we need to lowercase it
         if extension is not None and not extension.islower():
             self.log.debug(
-                "%s is not lower case, that could cause troubles in the future. \
-            Please change it to lower case"
-                % extension
+                "%s is not lower case, that could cause troubles in the future. Please change it to lower case",
+                extension,
             )
             extension = extension.lower()
         return extension

lib/galaxy/datatypes/tabular.py

@@ -1075,7 +1075,7 @@ class BaseVcf(Tabular):
     def validate(self, dataset: DatasetProtocol, **kwd) -> DatatypeValidation:
         def validate_row(row):
             if len(row) < 8:
-                raise Exception("Not enough columns in row %s" % row.join("\t"))
+                raise Exception("Not enough columns in row {}".format(row.join("\t")))
 
         validate_tabular(dataset.get_file_name(), sep="\t", validate_row=validate_row, comment_designator="#")
         return DatatypeValidation.validated()

lib/galaxy/datatypes/tracks.py

@@ -36,9 +36,8 @@ class UCSCTrackHub(Html):
         cannot rename the datasets here - they come with the default unfortunately
         """
         rval = [
-            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
             This composite dataset is composed of the following files:<p/><ul>"
-            % (self.file_ext)
         ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""

lib/galaxy/datatypes/xml.py

@@ -49,7 +49,7 @@ class GenericXml(data.Text):
             if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r"^<(\w*:)?%s" % root
+        pattern = rf"^<(\w*:)?{root}"
         return re.match(pattern, line) is not None
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:

lib/galaxy/job_execution/actions/post.py

@@ -231,11 +231,11 @@ class RenameDatasetAction(DefaultJobAction):
                     elif operation == "lower":
                         replacement = replacement.lower()
 
-                new_name = new_name.replace("#{%s}" % to_be_replaced, replacement)
+                new_name = new_name.replace(f"#{{{to_be_replaced}}}", replacement)
 
             if replacement_dict:
                 for k, v in replacement_dict.items():
-                    new_name = new_name.replace("${%s}" % k, v)
+                    new_name = new_name.replace(f"${{{k}}}", v)
 
         return new_name
 

lib/galaxy/jobs/__init__.py

@@ -2169,8 +2169,7 @@ class MinimalJobWrapper(HasResourceParameters):
                     )
                     return (
                         JobState.runner_states.OUTPUT_SIZE_LIMIT,
-                        "Job output file grew too large (greater than %s), please try different inputs or parameters"
-                        % util.nice_size(self.app.job_config.limits.output_size),
+                        f"Job output file grew too large (greater than {util.nice_size(self.app.job_config.limits.output_size)}), please try different inputs or parameters",
                     )
         if self.app.job_config.limits.walltime_delta is not None and runtime is not None:
             if runtime > self.app.job_config.limits.walltime_delta:

lib/galaxy/jobs/runners/__init__.py

@@ -169,7 +169,7 @@ class BaseJobRunner:
                 try:
                     action_str = f"galaxy.jobs.runners.{self.__class__.__name__.lower()}.{name}"
                     action_timer = self.app.execution_timer_factory.get_timer(
-                        f"internals.{action_str}", "job runner action %s for job ${job_id} executed" % (action_str)
+                        f"internals.{action_str}", f"job runner action {action_str} for job ${{job_id}} executed"
                     )
                     method(arg)
                     log.trace(action_timer.to_str(job_id=job_id))

lib/galaxy/jobs/runners/aws.py

@@ -528,7 +528,7 @@ class AWSBatchJobRunner(AsynchronousJobRunner):
             parsed_params[k] = mapper(value)  # type: ignore[operator]
         if check_required:
             raise AWSBatchRunnerException(
-                "AWSBatchJobRunner requires the following params to be provided: %s." % (", ".join(check_required))
+                "AWSBatchJobRunner requires the following params to be provided: {}.".format(", ".join(check_required))
             )
 
         # parse Platform

lib/galaxy/jobs/runners/pbs.py

@@ -13,7 +13,7 @@ except ImportError as exc:
     PBS_IMPORT_MESSAGE = (
         "The Python pbs-python package is required to use "
         "this feature, please install it or correct the "
-        "following error:\nImportError %s" % str(exc)
+        f"following error:\nImportError {exc}"
     )
 
 from galaxy import (
@@ -514,7 +514,7 @@ class PBSJobRunner(AsynchronousJobRunner):
         try:
             pbs_server_name = self.__get_pbs_server(job.destination_params)
             if pbs_server_name is None:
-                log.debug("(%s) Job queued but no destination stored in job params, cannot delete" % job_tag)
+                log.debug("(%s) Job queued but no destination stored in job params, cannot delete", job_tag)
                 return
             c = pbs.pbs_connect(util.smart_str(pbs_server_name))
             if c <= 0:

lib/galaxy/jobs/runners/state_handlers/resubmit.py

@@ -62,7 +62,7 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
         # Is destination needed here, might these be serialized to the database?
         destination = resubmit.get("environment") or resubmit.get("destination")
         log.info(
-            "%s Job will be resubmitted to '%s' because %s at " "the '%s' destination",
+            "%s Job will be resubmitted to '%s' because %s at the '%s' destination",
             job_log_prefix,
             destination,
             MESSAGES[runner_state],
@@ -106,7 +106,7 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
         if job.params is None:
             job.params = {}
         job_state.runner_state_handled = True
-        info = "This job was resubmitted to the queue because %s on its " "compute resource." % MESSAGES[runner_state]
+        info = f"This job was resubmitted to the queue because {MESSAGES[runner_state]} on its compute resource."
         job_runner.mark_as_resubmitted(job_state, info=info)
         return
 

lib/galaxy/jobs/runners/util/cli/job/lsf.py

@@ -52,7 +52,7 @@ class LSF(BaseJobExec):
         # This should be really handled outside with something like
         # parse_external. Currently CLI runner expect this to just send it in the last position
         # of the string.
-        return "bsub <%s | awk '{ print $2}' | sed 's/[<>]//g'" % script_file
+        return f"bsub <{script_file} | awk '{{ print $2}}' | sed 's/[<>]//g'"
 
     def delete(self, job_id):
         return f"bkill {job_id}"

lib/galaxy/jobs/runners/util/pykube_util.py

@@ -25,7 +25,7 @@ except ImportError as exc:
     K8S_IMPORT_MESSAGE = (
         "The Python pykube package is required to use "
         "this feature, please install it or correct the "
-        "following error:\nImportError %s" % str(exc)
+        f"following error:\nImportError {exc}"
     )
 
 log = logging.getLogger(__name__)

lib/galaxy/managers/interactivetool.py

@@ -69,7 +69,7 @@ class InteractiveToolSqlite:
                 try:
                     # Create table
                     c.execute(
-                        """CREATE TABLE %s
+                        f"""CREATE TABLE {DATABASE_TABLE_NAME}
                                  (key text,
                                   key_type text,
                                   token text,
@@ -78,7 +78,6 @@ class InteractiveToolSqlite:
                                   info text,
                                   PRIMARY KEY (key, key_type)
                                   )"""
-                        % (DATABASE_TABLE_NAME)
                     )
                 except Exception:
                     pass
@@ -90,11 +89,9 @@ class InteractiveToolSqlite:
                         key_type,
                     ),
                 )
-                insert = """INSERT INTO %s
+                insert = f"""INSERT INTO {DATABASE_TABLE_NAME}
                             (key, key_type, token, host, port, info)
-                            VALUES (?, ?, ?, ?, ?, ?)""" % (
-                    DATABASE_TABLE_NAME
-                )
+                            VALUES (?, ?, ?, ?, ?, ?)"""
                 c.execute(
                     insert,
                     (

lib/galaxy/managers/markdown_parse.py

@@ -71,10 +71,10 @@ VALID_ARGUMENTS: Dict[str, Union[List[str], DynamicArguments]] = {
     "invocation_inputs": [],
 }
 GALAXY_FLAVORED_MARKDOWN_CONTAINERS = list(VALID_ARGUMENTS.keys())
-GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>%s)" % "|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS)
+GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>{})".format("|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS))
 
 ARG_VAL_REGEX = r"""[\w_\-]+|\"[^\"]+\"|\'[^\']+\'"""
-FUNCTION_ARG = r"\s*[\w\|]+\s*=\s*(?:%s)\s*" % ARG_VAL_REGEX
+FUNCTION_ARG = rf"\s*[\w\|]+\s*=\s*(?:{ARG_VAL_REGEX})\s*"
 # embed commas between arguments
 FUNCTION_MULTIPLE_ARGS = rf"(?P<firstargcall>{FUNCTION_ARG})(?P<restargcalls>(?:,{FUNCTION_ARG})*)"
 FUNCTION_MULTIPLE_ARGS_PATTERN = re.compile(FUNCTION_MULTIPLE_ARGS)

lib/galaxy/managers/markdown_util.py

@@ -67,11 +67,11 @@ from .markdown_parse import (
 log = logging.getLogger(__name__)
 
 ARG_VAL_CAPTURED_REGEX = r"""(?:([\w_\-\|]+)|\"([^\"]+)\"|\'([^\']+)\')"""
-OUTPUT_LABEL_PATTERN = re.compile(r"output=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-INPUT_LABEL_PATTERN = re.compile(r"input=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-STEP_LABEL_PATTERN = re.compile(r"step=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-PATH_LABEL_PATTERN = re.compile(r"path=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-SIZE_PATTERN = re.compile(r"size=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
+OUTPUT_LABEL_PATTERN = re.compile(rf"output=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+INPUT_LABEL_PATTERN = re.compile(rf"input=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+STEP_LABEL_PATTERN = re.compile(rf"step=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+PATH_LABEL_PATTERN = re.compile(rf"path=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+SIZE_PATTERN = re.compile(rf"size=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
 # STEP_OUTPUT_LABEL_PATTERN = re.compile(r'step_output=([\w_\-]+)/([\w_\-]+)')
 UNENCODED_ID_PATTERN = re.compile(
     r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|implicit_collection_jobs_id|invocation_id)=([\d]+)"

lib/galaxy/managers/users.py

@@ -195,7 +195,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
                 "The configuration of this Galaxy instance does not allow admins to delete or purge users."
             )
         if not user.deleted:
-            raise exceptions.MessageException("User '%s' has not been deleted, so they cannot be purged." % user.email)
+            raise exceptions.MessageException(f"User '{user.email}' has not been deleted, so they cannot be purged.")
         private_role = self.app.security_agent.get_private_user_role(user)
         # Delete History
         for active_history in user.active_histories:

lib/galaxy/model/__init__.py

@@ -612,13 +612,10 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
     if default_usage_dataset_condition.strip():
         default_usage_dataset_condition = f"AND ( {default_usage_dataset_condition} )"
     default_usage = UNIQUE_DATASET_USER_USAGE.format(and_dataset_condition=default_usage_dataset_condition)
-    default_usage = (
-        """
-UPDATE galaxy_user SET disk_usage = (%s)
+    default_usage = f"""
+UPDATE galaxy_user SET disk_usage = ({default_usage})
 WHERE id = :id
 """
-        % default_usage
-    )
     params = {"id": user_id}
     if default_exclude_ids:
         params["exclude_object_store_ids"] = default_exclude_ids

lib/galaxy/model/deferred.py

@@ -61,9 +61,9 @@ class SimpleTransientPathMapper(TransientPathMapper):
         self._staging_directory = staging_directory
 
     def transient_paths_for(self, old_dataset: Dataset) -> TransientDatasetPaths:
-        external_filename_basename = "dataset_%s.dat" % str(old_dataset.uuid)
+        external_filename_basename = f"dataset_{old_dataset.uuid}.dat"
         external_filename = os.path.join(self._staging_directory, external_filename_basename)
-        external_extras_basename = "dataset_%s_files" % str(old_dataset.uuid)
+        external_extras_basename = f"dataset_{old_dataset.uuid}_files"
         external_extras = os.path.join(self._staging_directory, external_extras_basename)
         return TransientDatasetPaths(external_filename, external_extras, self._staging_directory)
 

lib/galaxy/model/store/__init__.py

@@ -1621,7 +1621,7 @@ class BaseDirectoryImportModelStore(ModelImportStore):
             attrs = load(open(file_name))
         else:
             if required:
-                raise Exception("Failed to find file [%s] in model store archive" % file_name)
+                raise Exception(f"Failed to find file [{file_name}] in model store archive")
             attrs = []
         return attrs
 

lib/galaxy/objectstore/__init__.py

@@ -1513,8 +1513,8 @@ def local_extra_dirs(func):
                 if c.__name__ == "DiskObjectStore":
                     return getattr(c, func.__name__)(self, *args, **kwargs)
             raise Exception(
-                "Could not call DiskObjectStore's %s method, does your "
-                "Object Store plugin inherit from DiskObjectStore?" % func.__name__
+                f"Could not call DiskObjectStore's {func.__name__} method, does your "
+                "Object Store plugin inherit from DiskObjectStore?"
             )
 
     return wraps

lib/galaxy/objectstore/rucio_extra_clients.py

@@ -35,7 +35,7 @@ class DeleteClient(UploadClient):
             if not self.rses.get(rse):
                 rse_settings = self.rses.setdefault(rse, rsemgr.get_rse_info(rse, vo=self.client.vo))
                 if not ignore_availability and rse_settings["availability_delete"] != 1:
-                    logger(logging.DEBUG, "%s is not available for deletion. No actions have been taken" % rse)
+                    logger(logging.DEBUG, "%s is not available for deletion. No actions have been taken", rse)
                     continue
 
             # protocol handling and deletion
@@ -52,8 +52,8 @@ class DeleteClient(UploadClient):
                     success = True
                 except Exception as error:
                     logger(logging.WARNING, "Delete attempt failed")
-                    logger(logging.INFO, "Exception: %s" % str(error), exc_info=True)
-            logger(logging.DEBUG, "Successfully deleted dataset %s" % pfn)
+                    logger(logging.INFO, "Exception: %s", error, exc_info=True)
+            logger(logging.DEBUG, "Successfully deleted dataset %s", pfn)
 
 
 class InPlaceIngestClient(UploadClient):
@@ -107,7 +107,7 @@ class InPlaceIngestClient(UploadClient):
             if not self.rses.get(rse):
                 rse_settings = self.rses.setdefault(rse, rsemgr.get_rse_info(rse, vo=self.client.vo))
                 if not ignore_availability and rse_settings["availability_write"] != 1:
-                    raise RSEWriteBlocked("%s is not available for writing. No actions have been taken" % rse)
+                    raise RSEWriteBlocked(f"{rse} is not available for writing. No actions have been taken")
 
             dataset_scope = file.get("dataset_scope")
             dataset_name = file.get("dataset_name")
@@ -120,7 +120,7 @@ class InPlaceIngestClient(UploadClient):
             registered_file_dids.add(f"{file['did_scope']}:{file['did_name']}")
         wrong_dids = registered_file_dids.intersection(registered_dataset_dids)
         if len(wrong_dids):
-            raise InputValidationError("DIDs used to address both files and datasets: %s" % str(wrong_dids))
+            raise InputValidationError(f"DIDs used to address both files and datasets: {wrong_dids}")
         logger(logging.DEBUG, "Input validation done.")
 
         # clear this set again to ensure that we only try to register datasets once
@@ -129,7 +129,7 @@ class InPlaceIngestClient(UploadClient):
         summary = []
         for file in files:
             basename = file["basename"]
-            logger(logging.INFO, "Preparing upload for file %s" % basename)
+            logger(logging.INFO, "Preparing upload for file %s", basename)
 
             pfn = file.get("pfn")
 
@@ -169,7 +169,7 @@ class InPlaceIngestClient(UploadClient):
             trace["transferEnd"] = time.time()
             trace["clientState"] = "DONE"
             file["state"] = "A"
-            logger(logging.INFO, "Successfully uploaded file %s" % basename)
+            logger(logging.INFO, "Successfully uploaded file %s", basename)
             self._send_trace(trace)
 
             if summary_file_path:

lib/galaxy/selenium/sizzle.py

@@ -87,22 +87,19 @@ def find_elements_by_sizzle(driver, sizzle_selector: str):
 
 
 def _inject_sizzle(driver, sizzle_url, timeout):
-    script = (
-        """
-        if(typeof(window.$) != "undefined") {
+    script = f"""
+        if(typeof(window.$) != "undefined") {{
             // Just reuse jQuery if it is available, avoids potential amd problems
             // that have cropped up with Galaxy for instance.
             window.Sizzle = window.$;
-        } else {
+        }} else {{
             var _s = document.createElement("script");
             _s.type = "text/javascript";
-            _s.src = "%s";
+            _s.src = "{sizzle_url}";
             var _h = document.getElementsByTagName("head")[0];
             _h.appendChild(_s);
-        }
+        }}
     """
-        % sizzle_url
-    )
     driver.execute_script(script)
     wait = WebDriverWait(driver, timeout)
     wait.until(lambda d: _is_sizzle_loaded(d), f"Can't inject Sizzle in {timeout} seconds")

lib/galaxy/tool_shed/tools/tool_validator.py

@@ -70,10 +70,9 @@ class ToolValidator:
                                 sample_found = True
                                 break
                         if not sample_found:
-                            correction_msg = f"This file refers to a file named <b>{str(index_file_name)}</b>.  "
-                            correction_msg += (
-                                "Upload a file named <b>%s.sample</b> to the repository to correct this error."
-                                % str(index_file_name)
+                            correction_msg = (
+                                f"This file refers to a file named <b>{index_file_name}</b>.  "
+                                f"Upload a file named <b>{index_file_name}.sample</b> to the repository to correct this error."
                             )
                             invalid_files_and_errors_tups.append((tool_config_name, correction_msg))
         return invalid_files_and_errors_tups

lib/galaxy/tool_shed/util/shed_util_common.py

@@ -163,7 +163,7 @@ def set_image_paths(app, text, encoded_repository_id=None, tool_shed_repository=
         # settings like .. images:: http_files/images/help.png
         for match in re.findall(".. image:: (?!http)/?(.+)", text):
             text = text.replace(match, match.replace("/", "%2F"))
-        text = re.sub(r"\.\. image:: (?!https?://)/?(.+)", r".. image:: %s/\1" % route_to_images, text)
+        text = re.sub(r"\.\. image:: (?!https?://)/?(.+)", rf".. image:: {route_to_images}/\1", text)
     return text
 
 

lib/galaxy/tool_util/deps/brew_exts.py

@@ -387,9 +387,9 @@ class EnvAction:
         if self.action == "set" or not environ.get(self.variable, ""):
             environ[self.variable] = self.__eval("${value}")
         elif self.action == "prepend":
-            environ[self.variable] = self.__eval("${value}:%s" % environ[self.variable])
+            environ[self.variable] = self.__eval(f"${{value}}:{environ[self.variable]}")
         else:
-            environ[self.variable] = self.__eval("%s:${value}" % environ[self.variable])
+            environ[self.variable] = self.__eval(f"{environ[self.variable]}:${{value}}")
 
     def __eval(self, template):
         return string.Template(template).safe_substitute(

lib/galaxy/tool_util/deps/mulled/mulled_build.py

@@ -307,7 +307,7 @@ def mull_targets(
         conda_bin = "mamba"
         if mamba_version is None:
             mamba_version = ""
-    involucro_args.extend(["-set", "CONDA_BIN=%s" % conda_bin])
+    involucro_args.extend(["-set", f"CONDA_BIN={conda_bin}"])
     if conda_version is not None or mamba_version is not None:
         mamba_test = "true"
         specs = []

lib/galaxy/tool_util/parser/xml.py

@@ -1133,7 +1133,8 @@ class StdioParser:
                         log.warning(
                             "Tool id %s: unable to determine if tool "
                             "stream source scanning is output, error, "
-                            "or both. Defaulting to use both." % self.id
+                            "or both. Defaulting to use both.",
+                            self.id,
                         )
                         regex.stdout_match = True
                         regex.stderr_match = True

lib/galaxy/tools/__init__.py

@@ -2103,7 +2103,7 @@ class Tool(Dictifiable):
                             )
                         parent[input.name] = value
                     except Exception:
-                        messages[prefixed_name] = "Attempt to replace invalid value for '%s' failed." % (prefixed_label)
+                        messages[prefixed_name] = f"Attempt to replace invalid value for '{prefixed_label}' failed."
                 else:
                     messages[prefixed_name] = error
 
@@ -2315,7 +2315,7 @@ class Tool(Dictifiable):
                     if os.path.exists(filesystem_path):
                         tarball_files.append((filesystem_path, tarball_path))
                         image_found = True
-                        tool_xml = tool_xml.replace("${static_path}/%s" % tarball_path, tarball_path)
+                        tool_xml = tool_xml.replace(f"${{static_path}}/{tarball_path}", tarball_path)
         # If one or more tool help images were found, add the modified tool XML to the tarball instead of the original.
         if image_found:
             with tempfile.NamedTemporaryFile(mode="w", suffix=".xml", delete=False) as fh2:
@@ -2684,7 +2684,7 @@ class Tool(Dictifiable):
             )
             if tool is None:
                 raise exceptions.MessageException(
-                    "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id
+                    f"This dataset was created by an obsolete tool ({tool_id}). Can't re-run."
                 )
             if (self.id != tool_id and self.old_id != tool_id) or self.version != tool_version:
                 if self.id == tool_id:

lib/galaxy/tools/error_reports/plugins/gitlab.py

@@ -154,7 +154,7 @@ class GitLabPlugin(BaseGitPlugin):
                         gl_emailquery = self.gitlab.users.list(search=gl_useremail)
                         log.debug(f"GitLab error reporting - User list: {gl_emailquery}")
                         if len(gl_emailquery) > 0:
-                            log.debug("GitLab error reporting - Last Committer user ID: %s" % gl_emailquery[0].get_id())
+                            log.debug("GitLab error reporting - Last Committer user ID: %s", gl_emailquery[0].get_id())
                             self.git_username_id_cache[gl_useremail] = gl_emailquery[0].get_id()
                     gl_userid = self.git_username_id_cache.get(gl_useremail, None)
 

lib/galaxy/util/markdown.py

@@ -2,7 +2,7 @@
 
 
 def literal_via_fence(content):
-    return "\n%s\n" % "\n".join(f"    {line}" for line in content.splitlines())
+    return "\n{}\n".format("\n".join(f"    {line}" for line in content.splitlines()))
 
 
 def indicate_data_truncated():

lib/galaxy/util/topsort.py

@@ -168,7 +168,7 @@ def topsort(pairlist):
             for y in successors[x]:
                 numpreds[y] = numpreds[y] - 1
                 if numpreds[y] == 0:
-                    answer.append(y)  # noqa: B038
+                    answer.append(y)
             # following "del" isn't needed; just makes
             # CycleError details easier to grasp
             del successors[x]

lib/galaxy/web/framework/middleware/profile.py

@@ -171,7 +171,7 @@ def func_std_string(func_name):
         # special case for built-in functions
         name = func_name[2]
         if name.startswith("<") and name.endswith(">"):
-            return "{%s}" % name[1:-1]
+            return f"{{{name[1:-1]}}}"
         else:
             return name
     else:

lib/galaxy/webapps/base/webapp.py

@@ -144,7 +144,7 @@ class WebApplication(base.WebApplication):
             if rule.routepath.endswith(".:(format)") or not rule.routepath.startswith("api/"):
                 continue
             # Try to replace routes various ways to encode variables with simple swagger {form}
-            swagger_path = "/%s" % RE_URL.sub(r"{\1}", rule.routepath)
+            swagger_path = "/{}".format(RE_URL.sub(r"{\1}", rule.routepath))
             controller = rule.defaults.get("controller", "")
             action = rule.defaults.get("action", "")
             # Get the list of methods for the route

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -534,7 +534,7 @@ class AdminGalaxy(controller.JSAppLauncher):
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
             return {
-                "title": "Quota '%s'" % quota.name,
+                "title": f"Quota '{quota.name}'",
                 "message": "Quota '%s' is currently associated with %d user(s) and %d group(s)."
                 % (quota.name, len(in_users), len(in_groups)),
                 "status": "info",
@@ -797,7 +797,7 @@ class AdminGalaxy(controller.JSAppLauncher):
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
             return {
-                "title": "Role '%s'" % role.name,
+                "title": f"Role '{role.name}'",
                 "message": "Role '%s' is currently associated with %d user(s) and %d group(s)."
                 % (role.name, len(in_users), len(in_groups)),
                 "status": "info",
@@ -902,7 +902,7 @@ class AdminGalaxy(controller.JSAppLauncher):
                     in_roles.append(trans.security.encode_id(role.id))
                 all_roles.append((role.name, trans.security.encode_id(role.id)))
             return {
-                "title": "Group '%s'" % group.name,
+                "title": f"Group '{group.name}'",
                 "message": "Group '%s' is currently associated with %d user(s) and %d role(s)."
                 % (group.name, len(in_users), len(in_roles)),
                 "status": "info",

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -332,7 +332,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             }
         else:
             return self.message_exception(
-                trans, "You do not have permission to edit this dataset's ( id: %s ) information." % str(dataset_id)
+                trans, f"You do not have permission to edit this dataset's ( id: {dataset_id} ) information."
             )
 
     @web.expose_api_anonymous

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -155,7 +155,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                         "value": [trans.security.encode_id(role.id) for role in in_roles],
                     }
                 )
-            return {"title": "Change default dataset permissions for history '%s'" % history.name, "inputs": inputs}
+            return {"title": f"Change default dataset permissions for history '{history.name}'", "inputs": inputs}
         else:
             self.history_manager.error_unless_mutable(history)
             permissions = {}
@@ -164,7 +164,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                 in_roles = [trans.sa_session.get(Role, trans.security.decode_id(x)) for x in in_roles]
                 permissions[trans.app.security_agent.get_action(action.action)] = in_roles
             trans.app.security_agent.history_set_default_permissions(history, permissions)
-            return {"message": "Default history '%s' dataset permissions have been changed." % history.name}
+            return {"message": f"Default history '{history.name}' dataset permissions have been changed."}
 
     @web.legacy_expose_api
     @web.require_login("make datasets private")
@@ -286,10 +286,10 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                 new_name = payload.get("name_%i" % i)
                 # validate name is empty
                 if not isinstance(new_name, str) or not new_name.strip():
-                    messages.append("You must specify a valid name for History '%s'." % cur_name)
+                    messages.append(f"You must specify a valid name for History '{cur_name}'.")
                 # skip if not the owner
                 elif h.user_id != user.id:
-                    messages.append("History '%s' does not appear to belong to you." % cur_name)
+                    messages.append(f"History '{cur_name}' does not appear to belong to you.")
                 # skip if it wouldn't be a change
                 elif new_name != cur_name:
                     h.name = new_name

lib/galaxy/webapps/galaxy/controllers/page.py

@@ -100,7 +100,7 @@ class PageController(BaseUIController, SharableMixin, UsesStoredWorkflowMixin, U
             }
         else:
             page = self.page_manager.create_page(trans, CreatePagePayload(**payload))
-            return {"message": "Page '%s' successfully created." % page.title, "status": "success"}
+            return {"message": f"Page '{page.title}' successfully created.", "status": "success"}
 
     @web.legacy_expose_api
     @web.require_login("edit pages")
@@ -159,7 +159,7 @@ class PageController(BaseUIController, SharableMixin, UsesStoredWorkflowMixin, U
                 trans.sa_session.add(p)
                 with transaction(trans.sa_session):
                     trans.sa_session.commit()
-            return {"message": "Attributes of '%s' successfully saved." % p.title, "status": "success"}
+            return {"message": f"Attributes of '{p.title}' successfully saved.", "status": "success"}
 
     @web.expose
     @web.require_login()

lib/galaxy/webapps/galaxy/controllers/tool_runner.py

@@ -46,9 +46,9 @@ class ToolRunner(BaseUIController):
     def index(self, trans, tool_id=None, from_noframe=None, **kwd):
         def __tool_404__():
             log.debug("index called with tool id '%s' but no such tool exists", tool_id)
-            trans.log_event("Tool id '%s' does not exist" % tool_id)
+            trans.log_event(f"Tool id '{tool_id}' does not exist")
             trans.response.status = 404
-            return trans.show_error_message("Tool '%s' does not exist." % (escape(tool_id)))
+            return trans.show_error_message(f"Tool '{escape(tool_id)}' does not exist.")
 
         # tool id not available, redirect to main page
         if tool_id is None:

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

@@ -225,7 +225,7 @@ class VisualizationController(
                 trans.sa_session.add(v)
                 with transaction(trans.sa_session):
                     trans.sa_session.commit()
-            return {"message": "Attributes of '%s' successfully saved." % v.title, "status": "success"}
+            return {"message": f"Attributes of '{v.title}' successfully saved.", "status": "success"}
 
     # ------------------------- registry.
     @web.expose

lib/galaxy/workflow/modules.py

@@ -138,7 +138,7 @@ def to_cwl(value, hda_references, step):
         # I think the following two checks are needed but they may
         # not be needed.
         if not value.dataset.in_ready_state():
-            why = "dataset [%s] is needed for valueFrom expression and is non-ready" % value.id
+            why = f"dataset [{value.id}] is needed for valueFrom expression and is non-ready"
             raise DelayedWorkflowEvaluation(why=why)
         if not value.is_ok:
             raise FailWorkflowEvaluation(
@@ -190,7 +190,7 @@ def from_cwl(value, hda_references, progress: "WorkflowProgress"):
             # This is going to re-file -> HDA this each iteration I think, not a good
             # implementation.
             return progress.raw_to_galaxy(value)
-        assert value["location"].startswith("step_input://"), "Invalid location %s" % value
+        assert value["location"].startswith("step_input://"), f"Invalid location {value}"
         return hda_references[int(value["location"][len("step_input://") :]) - 1]
     elif isinstance(value, dict):
         raise NotImplementedError()

lib/galaxy/workflow/refactor/execute.py

@@ -251,7 +251,7 @@ class WorkflowRefactorExecutor:
     def _apply_extract_untyped_parameter(self, action: ExtractUntypedParameter, execution: RefactorActionExecution):
         untyped_parameter_name = action.name
         new_label = action.label or untyped_parameter_name
-        target_value = "${%s}" % untyped_parameter_name
+        target_value = f"${{{untyped_parameter_name}}}"
 
         target_tool_inputs = []
         rename_pjas = []
@@ -330,7 +330,7 @@ class WorkflowRefactorExecutor:
             if untyped_parameter_name != new_label:
                 action_arguments = rename_pja.get("action_arguments")
                 old_newname = action_arguments["newname"]
-                new_newname = old_newname.replace(target_value, "${%s}" % new_label)
+                new_newname = old_newname.replace(target_value, f"${{{new_label}}}")
                 action_arguments["newname"] = new_newname
 
         optional = False

lib/galaxy_test/api/test_libraries.py

@@ -194,7 +194,7 @@ class TestLibrariesApi(ApiTestCase):
         library = self.library_populator.new_private_library(library_name)
         payload, files = self.library_populator.create_dataset_request(library, file_type="txt", contents="create_test")
         create_response = self.galaxy_interactor.post(
-            "libraries/%s/contents" % library["id"], payload, files=files, key=self.master_api_key
+            f"libraries/{library['id']}/contents", payload, files=files, key=self.master_api_key
         )
         self._assert_status_code_is(create_response, 400)
 

lib/tool_shed/dependencies/attribute_handlers.py

@@ -137,8 +137,8 @@ class RepositoryDependencyAttributeHandler:
                     elem.attrib["changeset_revision"] = lastest_installable_changeset_revision
                     altered = True
                 else:
-                    error_message = "Invalid latest installable changeset_revision %s " % str(
-                        lastest_installable_changeset_revision
+                    error_message = (
+                        f"Invalid latest installable changeset_revision {lastest_installable_changeset_revision} "
                     )
                     error_message += f"retrieved for repository {name} owned by {owner}.  "
             else:

lib/tool_shed/metadata/repository_metadata_manager.py

@@ -1036,10 +1036,10 @@ class RepositoryMetadataManager(ToolShedMetadataGenerator):
                         changeset_revisions.append(changeset_revision)
                 self._add_tool_versions(repository_id, repository_metadata, changeset_revisions)
         elif len(repo) == 1 and not self.invalid_file_tups:
-            message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % str(
-                self.repository.tip()
+            message = (
+                f"Revision <b>{self.repository.tip()}</b> includes no Galaxy utilities for which metadata can "
+                "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             )
-            message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             status = "error"
         if self.invalid_file_tups:
             message = tool_util.generate_message_for_invalid_tools(

lib/tool_shed/repository_types/util.py

@@ -43,26 +43,18 @@ def generate_message_for_repository_type_change(app, repository):
         repository_suite_definition_type_class = app.repository_types_registry.get_class_by_label(
             REPOSITORY_SUITE_DEFINITION
         )
-        message += (
-            "This repository currently contains a single file named <b>%s</b>.  If the intent of this repository is "
-            % REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
-        )
-        message += "to define relationships to a collection of repositories that contain related Galaxy utilities with "
-        message += (
-            "no plans to add additional files, consider setting its type to <b>%s</b>.<br/>"
-            % repository_suite_definition_type_class.label
+        message = (
+            f"This repository currently contains a single file named <b>{REPOSITORY_DEPENDENCY_DEFINITION_FILENAME}</b>.  If the intent of this repository is "
+            "to define relationships to a collection of repositories that contain related Galaxy utilities with "
+            f"no plans to add additional files, consider setting its type to <b>{repository_suite_definition_type_class.label}</b>.<br/>"
         )
     elif repository.can_change_type_to(app, TOOL_DEPENDENCY_DEFINITION):
         tool_dependency_definition_type_class = app.repository_types_registry.get_class_by_label(
             TOOL_DEPENDENCY_DEFINITION
         )
-        message += (
-            "This repository currently contains a single file named <b>%s</b>.  If additional files will "
-            % TOOL_DEPENDENCY_DEFINITION_FILENAME
-        )
-        message += (
-            "not be added to this repository, consider setting its type to <b>%s</b>.<br/>"
-            % tool_dependency_definition_type_class.label
+        message = (
+            f"This repository currently contains a single file named <b>{TOOL_DEPENDENCY_DEFINITION_FILENAME}</b>.  If additional files will "
+            f"not be added to this repository, consider setting its type to <b>{tool_dependency_definition_type_class.label}</b>.<br/>"
         )
     return message
 

lib/tool_shed/test/base/twilltestcase.py

@@ -2048,9 +2048,7 @@ class ShedTwillTestCase(ShedApiTestCase):
     def _assert_repo_has_tool_with_id(
         self, installed_repository: galaxy_model.ToolShedRepository, tool_id: str
     ) -> None:
-        assert "tools" in installed_repository.metadata_, (
-            "No valid tools were defined in %s." % installed_repository.name
-        )
+        assert "tools" in installed_repository.metadata_, f"No valid tools were defined in {installed_repository.name}."
         tools = installed_repository.metadata_["tools"]
         found_it = False
         for tool in tools:  # type:ignore[attr-defined]
@@ -2064,9 +2062,9 @@ class ShedTwillTestCase(ShedApiTestCase):
     def _assert_repo_has_invalid_tool_in_file(
         self, installed_repository: galaxy_model.ToolShedRepository, name: str
     ) -> None:
-        assert "invalid_tools" in installed_repository.metadata_, (
-            "No invalid tools were defined in %s." % installed_repository.name
-        )
+        assert (
+            "invalid_tools" in installed_repository.metadata_
+        ), f"No invalid tools were defined in {installed_repository.name}."
         invalid_tools = installed_repository.metadata_["invalid_tools"]
         found_it = name in invalid_tools
         assert found_it, f"Did not find invalid tool file {name} in {invalid_tools}"

lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py

@@ -165,15 +165,14 @@ class TestDeletedDependencies(ShedTwillTestCase):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains repository_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains repository_dependencies.xml is no longer downloadable."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that does not contain repository_dependencies.xml is not downloadable."
-            % repository.name
-        )
+        assert (
+            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.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 2
@@ -279,14 +278,14 @@ class TestDeletedDependencies(ShedTwillTestCase):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains tool_dependencies.xml is no longer downloadable."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that does not contain tool_dependencies.xml is not downloadable." % repository.name
-        )
+        assert (
+            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.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 2
@@ -331,9 +330,9 @@ class TestDeletedDependencies(ShedTwillTestCase):
         assert old_changeset_revision != new_changeset_revision
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains tool_dependencies.xml is no longer downloadable."
         # Check that the new tip does not have a metadata revision.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
         # If a changeset revision does not have metadata, the above method will return None.
@@ -364,15 +363,14 @@ class TestDeletedDependencies(ShedTwillTestCase):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record is None, (
-            "The revision of %s that does not contain tool_dependencies.xml should not be downloadable, but is."
-            % repository.name
-        )
+        assert (
+            metadata_record is None
+        ), f"The revision of {repository.name} that does not contain tool_dependencies.xml should not be downloadable, but is."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is not downloadable." % repository.name
-        )
+        assert (
+            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.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 1

lib/tool_shed/util/shed_util_common.py

@@ -136,20 +136,14 @@ def get_repository_file_contents(app: "ToolShedApp", file_path: str, repository_
                 safe_str = f"{safe_str}{basic_util.to_html_string(line)}"
                 # Stop reading after string is larger than MAX_CONTENT_SIZE.
                 if len(safe_str) > MAX_CONTENT_SIZE:
-                    large_str = (
-                        "<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>"
-                        % util.nice_size(MAX_CONTENT_SIZE)
-                    )
+                    large_str = f"<br/>File contents truncated because file size is larger than maximum viewing size of {util.nice_size(MAX_CONTENT_SIZE)}<br/>"
                     safe_str = f"{safe_str}{large_str}"
                     break
 
         if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
             # Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
             # This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
-            join_by_str = (
-                "<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>"
-                % util.nice_size(basic_util.MAX_DISPLAY_SIZE)
-            )
+            join_by_str = f"<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of {util.nice_size(basic_util.MAX_DISPLAY_SIZE)}...<br/><br/>"
             safe_str = util.shrink_string_by_size(
                 safe_str,
                 basic_util.MAX_DISPLAY_SIZE,

lib/tool_shed/webapp/controllers/user.py

@@ -85,8 +85,9 @@ class User(BaseUser):
         if not success and not user and trans.app.config.require_login:
             if trans.app.config.allow_user_creation:
                 create_account_str = (
-                    "  If you don't already have an account, <a href='%s'>you may create one</a>."
-                    % web.url_for(controller="user", action="create", cntrller="user")
+                    "  If you don't already have an account, <a href='{}'>you may create one</a>.".format(
+                        web.url_for(controller="user", action="create", cntrller="user")
+                    )
                 )
                 header = REQUIRE_LOGIN_TEMPLATE % ("Galaxy tool shed", create_account_str)
             else:
@@ -243,9 +244,9 @@ class User(BaseUser):
             if not message:
                 # Default to a non-userinfo-leaking response message
                 message = (
-                    "Your reset request for %s has been received.  "
+                    f"Your reset request for {escape(email)} has been received.  "
                     "Please check your email account for more instructions.  "
-                    "If you do not receive an email shortly, please contact an administrator." % (escape(email))
+                    "If you do not receive an email shortly, please contact an administrator."
                 )
                 reset_user = get_user_by_email(trans.sa_session, email, trans.app.model.User)
                 if not reset_user:
@@ -476,9 +477,7 @@ class User(BaseUser):
     @web.expose
     def logout(self, trans, logout_all=False, **kwd):
         trans.handle_user_logout(logout_all=logout_all)
-        message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % (
-            url_for("/")
-        )
+        message = f'You have been logged out.<br>To log in again <a target="_top" href="{url_for("/")}">go to the home page</a>.'
         if trans.app.config.use_remote_user and trans.app.config.remote_user_logout_href:
             trans.response.send_redirect(trans.app.config.remote_user_logout_href)
         else:

scripts/api/common.py

@@ -36,7 +36,7 @@ def get(api_key, url):
     try:
         return json.loads(urlopen(url).read())
     except ValueError as e:
-        print("URL did not return JSON data: %s" % e)
+        print(f"URL did not return JSON data: {e}")
         sys.exit(1)
 
 
@@ -87,14 +87,14 @@ def display(api_key, url, return_formatted=True):
         print("------------------")
         for n, i in enumerate(r):
             if isinstance(i, str):
-                print("  %s" % i)
+                print(f"  {i}")
             else:
                 # All collection members should have a name in the response.
                 # url is optional
                 if "url" in i:
                     print("#%d: %s" % (n + 1, i.pop("url")))
                 if "name" in i:
-                    print("  name: %s" % i.pop("name"))
+                    print(f"  name: {i.pop('name')}")
                 try:
                     for k, v in i.items():
                         print(f"  {k}: {v}")
@@ -112,7 +112,7 @@ def display(api_key, url, return_formatted=True):
     elif isinstance(r, str):
         print(r)
     else:
-        print("response is unknown type: %s" % type(r))
+        print(f"response is unknown type: {type(r)}")
 
 
 def submit(api_key, url, data, return_formatted=True):
@@ -143,7 +143,7 @@ def submit(api_key, url, data, return_formatted=True):
                 else:
                     print("----")
                 if "name" in i:
-                    print("  name: %s" % i.pop("name"))
+                    print(f"  name: {i.pop('name')}")
                 for k, v in i.items():
                     print(f"  {k}: {v}")
             else:

scripts/api/data_manager_example_execute.py

@@ -47,7 +47,7 @@ def run_tool(tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_
 
 
 def get_dataset_state(hda_id, api_key, galaxy_url):
-    datasets_url = urljoin(galaxy_url, "api/datasets/%s" % hda_id)
+    datasets_url = urljoin(galaxy_url, f"api/datasets/{hda_id}")
     dataset_info = get(api_key, datasets_url)
     return dataset_info["state"]
 
@@ -117,7 +117,7 @@ if __name__ == "__main__":
                 wait=False,
             )
         else:
-            "dbkey (%s) was specified more than once, skipping additional specification." % (dbkey)
+            f"dbkey ({dbkey}) was specified more than once, skipping additional specification."
 
     print("Genomes Queued for downloading.")
 

scripts/api/display.py

@@ -9,7 +9,7 @@ from common import display  # noqa: I100,I202
 try:
     display(*sys.argv[1:3])
 except TypeError as e:
-    print("usage: %s key url" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url")
     print(e)
     sys.exit(1)
 except URLError as e:

scripts/api/example_watch_folder.py

@@ -33,11 +33,11 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
         lib_create_data = {"name": data_library}
         library = submit(api_key, api_url + "libraries", lib_create_data, return_formatted=False)
         library_id = library[0]["id"]
-    folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted=False)
+    folders = display(api_key, api_url + f"libraries/{library_id}/contents", return_formatted=False)
     for f in folders:
         if f["name"] == "/":
             library_folder_id = f["id"]
-    workflow = display(api_key, api_url + "workflows/%s" % workflow, return_formatted=False)
+    workflow = display(api_key, api_url + f"workflows/{workflow}", return_formatted=False)
     if not workflow:
         print("Workflow %s not found, terminating.")
         sys.exit(1)
@@ -57,7 +57,7 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
                 data["upload_option"] = "upload_paths"
                 data["filesystem_paths"] = fullpath
                 data["create_type"] = "file"
-                libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted=False)
+                libset = submit(api_key, api_url + f"libraries/{library_id}/contents", data, return_formatted=False)
                 # TODO Handle this better, but the datatype isn't always
                 # set for the followup workflow execution without this
                 # pause.
@@ -88,6 +88,6 @@ if __name__ == "__main__":
         data_library = sys.argv[5]
         workflow = sys.argv[6]
     except IndexError:
-        print("usage: %s key url in_folder out_folder data_library workflow" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url in_folder out_folder data_library workflow")
         sys.exit(1)
     main(api_key, api_url, in_folder, out_folder, data_library, workflow)

scripts/api/filter_failed_datasets_from_collection.py

@@ -16,8 +16,7 @@ from bioblend.galaxy import (
 
 if len(sys.argv) < 5:
     print(
-        "Usage: %s <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>"
-        % sys.argv[0]
+        f"Usage: {sys.argv[0]} <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>"
     )
     exit(0)
 

scripts/api/history_create_history.py

@@ -8,7 +8,7 @@ from common import submit
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [name] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [name] ")
     sys.exit(1)
 try:
     data = {}

scripts/api/history_delete_history.py

@@ -8,7 +8,7 @@ from common import delete
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [purge (true/false)] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [purge (true/false)] ")
     sys.exit(1)
 try:
     data = {}

scripts/api/import_library_dataset_to_history.py

@@ -10,7 +10,7 @@ try:
     data = {}
     data["from_ld_id"] = sys.argv[3]
 except IndexError:
-    print("usage: %s key url library_file_id" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url library_file_id")
     print("    library_file_id is from /api/libraries/<library_id>/contents/<library_file_id>")
     sys.exit(1)
 

scripts/api/library_create_folder.py

@@ -11,7 +11,7 @@ try:
     data["name"] = sys.argv[4]
     data["create_type"] = "folder"
 except IndexError:
-    print("usage: %s key url folder_id name [description]" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url folder_id name [description]")
     sys.exit(1)
 try:
     data["description"] = sys.argv[5]

scripts/api/library_create_library.py

@@ -9,7 +9,7 @@ try:
     data = {}
     data["name"] = sys.argv[3]
 except IndexError:
-    print("usage: %s key url name [description] [synopsys]" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url name [description] [synopsys]")
     sys.exit(1)
 try:
     data["description"] = sys.argv[4]

scripts/api/library_upload_from_import_dir.py

@@ -18,7 +18,7 @@ try:
     data["upload_option"] = "upload_directory"
     data["create_type"] = "file"
 except IndexError:
-    print("usage: %s key url folder_id file_type server_dir dbkey" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url folder_id file_type server_dir dbkey")
     sys.exit(1)
 
 submit(sys.argv[1], sys.argv[2], data)

scripts/api/load_data_with_metadata.py

@@ -39,7 +39,7 @@ def load_file(fullpath, api_key, api_url, library_id, library_folder_id, uuid_fi
     if uuid_field is not None and uuid_field in ext_meta:
         data["uuid"] = ext_meta[uuid_field]
 
-    libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted=True)
+    libset = submit(api_key, api_url + f"libraries/{library_id}/contents", data, return_formatted=True)
     print(libset)
 
 
@@ -54,7 +54,7 @@ def main(api_key, api_url, in_folder, data_library, uuid_field=None):
         lib_create_data = {"name": data_library}
         library = submit(api_key, api_url + "libraries", lib_create_data, return_formatted=False)
         library_id = library["id"]
-    folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted=False)
+    folders = display(api_key, api_url + f"libraries/{library_id}/contents", return_formatted=False)
     for f in folders:
         if f["name"] == "/":
             library_folder_id = f["id"]

scripts/api/reset_metadata_on_installed_repositories.py

@@ -15,7 +15,7 @@ from common import submit
 
 def main(options):
     base_galaxy_url = options.galaxy_url.rstrip("/")
-    url = "%s/api/tool_shed_repositories/reset_metadata_on_installed_repositories" % base_galaxy_url
+    url = f"{base_galaxy_url}/api/tool_shed_repositories/reset_metadata_on_installed_repositories"
     submit(options.api, url, {})
 
 

scripts/api/workflow_delete.py

@@ -17,7 +17,7 @@ from common import delete
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [purge (true/false)] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [purge (true/false)] ")
     sys.exit(1)
 try:
     data = {}

scripts/api/workflow_execute.py

@@ -24,7 +24,7 @@ def main():
             step, src, ds_id = v.split("=")
             data["ds_map"][step] = {"src": src, "id": ds_id}
     except IndexError:
-        print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url workflow_id history step=src=dataset_id")
         sys.exit(1)
     submit(sys.argv[1], sys.argv[2], data)
 

scripts/api/workflow_execute_parameters.py

@@ -46,7 +46,7 @@ def main():
                     print("TOOL ID ERROR:")
 
     except IndexError:
-        print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url workflow_id history step=src=dataset_id")
         sys.exit(1)
     submit(sys.argv[1], sys.argv[2], data)
 

scripts/api/workflow_import.py

@@ -14,14 +14,14 @@ from common import submit
 def main():
     api_key = sys.argv[1]
     api_base_url = sys.argv[2]
-    api_url = "%s/api/workflows" % api_base_url
+    api_url = f"{api_base_url}/api/workflows"
     try:
         data = {}
         data["installed_repository_file"] = sys.argv[3]
         if len(sys.argv) > 4 and sys.argv[4] == "--add_to_menu":
             data["add_to_menu"] = True
     except IndexError:
-        print("usage: %s key galaxy_url workflow_file" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key galaxy_url workflow_file")
         sys.exit(1)
     submit(api_key, api_url, data, return_formatted=False)
 

scripts/api/workflow_import_from_file_rpark.py

@@ -20,7 +20,7 @@ def openWorkflow(in_file):
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [name] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [name] ")
     sys.exit(1)
 try:
     data = {}

scripts/apply_tags.py

@@ -29,12 +29,12 @@ class ApplyTagsHistory:
             try:
                 update_history = history.show_history(self.history_id)
             except Exception as exception:
-                print("Some problem occurred with history: %s" % self.history_id)
+                print(f"Some problem occurred with history: {self.history_id}")
                 print(exception)
                 return
         update_history_id = update_history["id"]
-        print("History name: %s" % update_history["name"])
-        print("History id: %s" % update_history_id)
+        print(f"History name: {update_history['name']}")
+        print(f"History id: {update_history_id}")
         self.find_dataset_parents_update_tags(history, job, update_history_id)
 
     def find_dataset_parents_update_tags(self, history, job, history_id):

scripts/build_toolbox.py

@@ -141,7 +141,7 @@ def scanfiles(filenamelist):
             newtoolelement = ET.Element("tool", attrib)
             toolboxpositionelements = toolelement.findall("toolboxposition")
             if not toolboxpositionelements:
-                print("DBG> %s has no toolboxposition" % fn)
+                print(f"DBG> {fn} has no toolboxposition")
             else:
                 for toolboxpositionelement in toolboxpositionelements:
                     toolbox.add(newtoolelement, toolboxpositionelement)

scripts/check_python.py

@@ -3,6 +3,8 @@ If the current installed Python version is not supported, prints an error
 message to stderr and returns 1
 """
 
+from __future__ import print_function  # noqa: UP010
+
 import sys
 
 
@@ -13,13 +15,12 @@ def check_python():
     else:
         version_string = ".".join(str(_) for _ in sys.version_info[:3])
         msg = (
-            """\
-ERROR: Your Python version is: %s
+            """ERROR: Your Python version is: %s
 Galaxy is currently supported on Python >=3.8 .
 To run Galaxy, please install a supported Python version.
 If a supported version is already installed but is not your default,
 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
-on how to force Galaxy to use a different version."""
+on how to force Galaxy to use a different version."""  # noqa: UP031
             % version_string
         )
         print(msg, file=sys.stderr)

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -151,7 +151,7 @@ def main():
     template_file = args.template
     if template_file is None:
         default_template = os.path.join(scriptdir, "admin_cleanup_deletion_template.txt")
-        sample_template_file = "%s.sample" % default_template
+        sample_template_file = f"{default_template}.sample"
         if os.path.exists(default_template):
             template_file = default_template
         elif os.path.exists(sample_template_file):
@@ -164,7 +164,7 @@ def main():
                 "found, please specify template as an option (--template)."
             )
     elif not os.path.exists(template_file):
-        parser.error("Specified template file (%s) not found." % template_file)
+        parser.error(f"Specified template file ({template_file}) not found.")
 
     config = galaxy.config.Configuration(**app_properties)
 
@@ -273,9 +273,9 @@ def administrative_delete_datasets(
         subject = "Galaxy Server Cleanup " "- %d datasets DELETED" % len(dataset_list)
         fromaddr = config.email_from
         print()
-        print("From: %s" % fromaddr)
-        print("To: %s" % email)
-        print("Subject: %s" % subject)
+        print(f"From: {fromaddr}")
+        print(f"To: {email}")
+        print(f"Subject: {subject}")
         print("----------")
         print(msgtext)
         if not info_only:

scripts/cleanup_datasets/pgcleanup.py

@@ -143,22 +143,22 @@ class Action:
         else:
             logf = os.path.join(self._log_dir, self.name + ".log")
         if self._dry_run:
-            log.info("--dry-run specified, logging changes to stderr instead of log file: %s" % logf)
+            log.info("--dry-run specified, logging changes to stderr instead of log file: %s", logf)
             h = set_log_handler()
         else:
-            log.info("Opening log file: %s" % logf)
+            log.info("Opening log file: %s", logf)
             h = set_log_handler(filename=logf)
         h.setLevel(logging.DEBUG if self._debug else logging.INFO)
         h.setFormatter(LevelFormatter())
         self.__log = logging.getLogger(self.name)
         self.__log.addHandler(h)
         self.__log.propagate = False
-        m = ("==== Log opened: %s " % datetime.datetime.now().isoformat()).ljust(72, "=")
+        m = (f"==== Log opened: {datetime.datetime.now().isoformat()} ").ljust(72, "=")
         self.__log.info(m)
-        self.__log.info(f"Epoch time for this action: {self._epoch_time}")
+        self.__log.info("Epoch time for this action: %s", self._epoch_time)
 
     def __close_log(self):
-        m = ("==== Log closed: %s " % datetime.datetime.now().isoformat()).ljust(72, "=")
+        m = (f"==== Log closed: {datetime.datetime.now().isoformat()} ").ljust(72, "=")
         self.log.info(m)
         self.__log = None
 
@@ -1221,7 +1221,7 @@ class Cleanup:
             self.__conn = psycopg2.connect(cursor_factory=NamedTupleCursor, **args)
             # TODO: is this per session or cursor?
             if self.args.work_mem is not None:
-                log.info("Setting work_mem to %s" % self.args.work_mem)
+                log.info("Setting work_mem to %s", self.args.work_mem)
                 self.__conn.cursor().execute("SET work_mem TO %s", (self.args.work_mem,))
         return self.__conn
 
@@ -1271,7 +1271,7 @@ class Cleanup:
             nargs="*",
             metavar="ACTION",
             default=[],
-            help="Action(s) to perform, chosen from: %s" % ", ".join(sorted(self.actions.keys())),
+            help="Action(s) to perform, chosen from: {}".format(", ".join(sorted(self.actions.keys()))),
         )
         self.args = parser.parse_args()
 
@@ -1292,7 +1292,7 @@ class Cleanup:
         ok = True
         for name in self.args.actions:
             if name not in self.actions.keys():
-                log.error("Unknown action in sequence: %s" % name)
+                log.error("Unknown action in sequence: %s", name)
                 ok = False
         if not ok:
             log.critical("Exiting due to previous error(s)")
@@ -1381,7 +1381,7 @@ class Cleanup:
             self.__current_action = name
             with cls(self) as action:
                 self._run_action(action)
-            log.info("Finished %s" % name)
+            log.info("Finished %s", name)
 
 
 if __name__ == "__main__":

scripts/config_sample_to_kwalify.py

@@ -55,14 +55,14 @@ def _dump_option(option, current_section_desc):
             type = "str"
     if default == "None":
         default = None
-    print_line("%s:" % key)
-    print_line("  type: %s" % type)
+    print_line(f"{key}:")
+    print_line(f"  type: {type}")
     if default is not None:
-        print_line("  default: %s" % default)
+        print_line(f"  default: {default}")
     # print_line("  required: false")
     print_line("  desc: |")
     for line in current_section_desc:
-        print_line("    %s" % line)
+        print_line(f"    {line}")
     print_line("")
 
 

scripts/db_shell.py

@@ -85,7 +85,7 @@ def printquery(statement, bind=None):
             """
             if isinstance(value, str):
                 value = value.replace("'", "''")
-                return "'%s'" % value
+                return f"'{value}'"
             elif value is None:
                 return "NULL"
             elif isinstance(value, (float, int)):
@@ -93,10 +93,10 @@ def printquery(statement, bind=None):
             elif isinstance(value, decimal.Decimal):
                 return str(value)
             elif isinstance(value, datetime.datetime):
-                return "TO_DATE('%s','YYYY-MM-DD HH24:MI:SS')" % value.strftime("%Y-%m-%d %H:%M:%S")
+                return f"TO_DATE('{value.strftime('%Y-%m-%d %H:%M:%S')}','YYYY-MM-DD HH24:MI:SS')"
 
             else:
-                raise NotImplementedError("Don't know how to literal-quote value %r" % value)
+                raise NotImplementedError(f"Don't know how to literal-quote value {value!r}")
 
     compiler = LiteralCompiler(dialect, statement)
     print(compiler.process(statement))

scripts/drmaa_external_killer.py

@@ -14,7 +14,7 @@ import drmaa
 
 def validate_paramters():
     if len(sys.argv) < 3:
-        sys.stderr.write("usage: %s [job ID] [user uid]\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} [job ID] [user uid]\n")
         exit(1)
 
     jobID = sys.argv[1]

scripts/drmaa_external_runner.py

@@ -50,14 +50,14 @@ def get_user_id_by_name(username):
     try:
         pw = pwd.getpwnam(username)
     except KeyError:
-        sys.stderr.write("error: User name (%s) is not valid.\n" % username)
+        sys.stderr.write(f"error: User name ({username}) is not valid.\n")
         exit(1)
     return pw.pw_uid
 
 
 def json_file_exists(json_filename):
     if not os.path.exists(json_filename):
-        sys.stderr.write("error: JobTemplate file (%s) doesn't exist\n" % (json_filename))
+        sys.stderr.write(f"error: JobTemplate file ({json_filename}) doesn't exist\n")
         exit(1)
 
     return True
@@ -70,7 +70,7 @@ def validate_paramters():
         sys.argv.remove("--assign_all_groups")
 
     if len(sys.argv) < 3:
-        sys.stderr.write("usage: %s [USER-ID] [JSON-JOB-TEMPLATE-FILE]\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} [USER-ID] [JSON-JOB-TEMPLATE-FILE]\n")
         exit(1)
 
     userid = sys.argv[1]

scripts/dump_library_paths.py

@@ -138,11 +138,11 @@ def _get_library_dataset_paths(args, kwargs):
         filename = object_store.get_filename(dataset)
         files_dir = dataset.get_extra_files_path()
         if (args.exists and object_store.exists(dataset)) or not args.exists:
-            output.write("%s\n" % _path(filename, args))
+            output.write(f"{_path(filename, args)}\n")
         elif args.exists:
             log.warning("Missing %s", filename)
         if files_dir and os.path.exists(files_dir):
-            output.write("%s\n" % _path(files_dir, args))
+            output.write(f"{_path(files_dir, args)}\n")
         last_library = library
     output.close()
 

scripts/external_chown_script.py

@@ -15,7 +15,7 @@ ALLOWED_PATHS = None
 
 def validate_parameters():
     if len(sys.argv) < 4:
-        sys.stderr.write("usage: %s path user_name gid\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} path user_name gid\n")
         exit(1)
 
     path = os.path.abspath(sys.argv[1])
@@ -28,7 +28,7 @@ def validate_parameters():
                 allowed = True
                 break
     if not allowed:
-        sys.stderr.write("owner and group modifications in %s are not allowed\n" % path)
+        sys.stderr.write(f"owner and group modifications in {path} are not allowed\n")
         sys.exit(1)
 
     galaxy_user_name = sys.argv[2]
@@ -44,7 +44,7 @@ def main():
         (stdoutdata, stderrdata) = p.communicate()
         exitcode = p.returncode
         if exitcode != 0:
-            sys.exit("external_chown_script: could not chown\ncmd was %s\n" % " ".join(cmd))
+            sys.exit("external_chown_script: could not chown\ncmd was {}\n".format(" ".join(cmd)))
 
 
 if __name__ == "__main__":

scripts/grt/export.py

@@ -56,7 +56,7 @@ def kw_metrics(job):
 
 def round_to_2sd(number):
     if number:
-        return str(int(float("%.2g" % number)))
+        return str(int(float(f"{number:.2g}")))
     else:
         return "-1"
 

scripts/loc_files/create_all_fasta_loc.py

@@ -272,16 +272,16 @@ def __main__():
         paths_to_look_in = [os.path.join(options.genome_dir, "%s")]
 
     # say what we're looking in
-    print("\nLooking in:\n\t%s" % "\n\t".join(p % "<build_name>" for p in paths_to_look_in))
-    poss_names = ["<build_name>%s" % _ for _ in variants]
-    print("for files that are named %s" % ", ".join(poss_names[:-1]), end=" ")
+    print("\nLooking in:\n\t{}".format("\n\t".join(p % "<build_name>" for p in paths_to_look_in)))
+    poss_names = [f"<build_name>{_}" for _ in variants]
+    print("for files that are named {}".format(", ".join(poss_names[:-1])), end=" ")
     if len(poss_names) > 1:
-        print("or %s" % poss_names[-1], end=" ")
+        print(f"or {poss_names[-1]}", end=" ")
     if len(options.fasta_exts) == 1:
-        print("with the extension %s." % ", ".join(fasta_exts[:-1]))
+        print("with the extension {}.".format(", ".join(fasta_exts[:-1])))
     else:
         print("with the extension {} or {}.".format(", ".join(fasta_exts[:-1]), fasta_exts[-1]))
-    print("\nSkipping the following:\n\t%s" % "\n\t".join(exemptions))
+    print("\nSkipping the following:\n\t{}".format("\n\t".join(exemptions)))
 
     # get column names
     col_values = []
@@ -350,40 +350,33 @@ def __main__():
 
     # output results
     print(
-        "\nThere were %s fasta files found that were not included because they did not have the expected file names."
-        % len(unmatching_fasta_paths)
+        f"\nThere were {len(unmatching_fasta_paths)} fasta files found that were not included because they did not have the expected file names."
     )
-    print("%s fasta files were found and listed.\n" % len(fasta_locs.keys()))
+    print(f"{len(fasta_locs.keys())} fasta files were found and listed.\n")
 
     # output unmatching fasta files
     if options.unmatching_fasta and unmatching_fasta_paths:
-        open(options.unmatching_fasta, "wb").write("%s\n" % "\n".join(unmatching_fasta_paths))
+        open(options.unmatching_fasta, "wb").write("{}\n".format("\n".join(unmatching_fasta_paths)))
 
     # output loc file
-    if options.append:
-        all_fasta_loc = open(loc_path, "ab")
-    else:
-        all_fasta_loc = open(loc_path, "wb")
-    # put sample loc file text at top of file if appropriate
-    if sample_text:
-        if options.loc_sample_name:
-            all_fasta_loc.write("%s\n" % open(options.loc_sample_name, "rb").read().strip())
-        else:
-            all_fasta_loc.write("%s\n" % open("%s.sample" % loc_path, "rb").read().strip())
-    # output list of fasta files in alphabetical order
-    fasta_bases = list(fasta_locs.keys())
-    fasta_bases.sort(key=str.upper)
-    for fb in fasta_bases:
-        out_line = []
-        for col in col_values:
-            try:
-                out_line.append(fasta_locs[fb][col])
-            except KeyError:
-                raise Exception("Unexpected column (%s) encountered" % col)
-        if out_line:
-            all_fasta_loc.write("%s\n" % "\t".join(out_line))
-    # close up output loc file
-    all_fasta_loc.close()
+    with open(loc_path, "ab" if options.append else "wb") as all_fasta_loc:
+        # put sample loc file text at top of file if appropriate
+        if sample_text:
+            loc_sample_name = options.loc_sample_name if options.loc_sample_name else f"{loc_path}.sample"
+            with open(loc_sample_name, "rb") as loc_sample_name_fh:
+                all_fasta_loc.write(f"{loc_sample_name_fh.read().strip()}\n")
+        # output list of fasta files in alphabetical order
+        fasta_bases = list(fasta_locs.keys())
+        fasta_bases.sort(key=str.upper)
+        for fb in fasta_bases:
+            out_line = []
+            for col in col_values:
+                try:
+                    out_line.append(fasta_locs[fb][col])
+                except KeyError:
+                    raise Exception(f"Unexpected column ({col}) encountered")
+            if out_line:
+                all_fasta_loc.write("{}\n".format("\t".join(out_line)))
 
 
 if __name__ == "__main__":

scripts/microbes/create_bacteria_loc_file.py

@@ -95,11 +95,11 @@ def __main__():
                     chr["chromosome"],
                     "sequence",
                     "fasta",
-                    os.path.join(org["base_dir"], "%s.fna" % chr["chromosome"]),
+                    os.path.join(org["base_dir"], f"{chr['chromosome']}.fna"),
                 )
             )
             # GeneMark
-            if os.path.exists(os.path.join(org["base_dir"], "%s.GeneMark.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMark.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -109,11 +109,11 @@ def __main__():
                         chr["chromosome"],
                         "GeneMark",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.GeneMark.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMark.bed"),
                     )
                 )
             # GenMarkHMM
-            if os.path.exists(os.path.join(org["base_dir"], "%s.GeneMarkHMM.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMarkHMM.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -123,11 +123,11 @@ def __main__():
                         chr["chromosome"],
                         "GeneMarkHMM",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.GeneMarkHMM.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMarkHMM.bed"),
                     )
                 )
             # Glimmer3
-            if os.path.exists(os.path.join(org["base_dir"], "%s.Glimmer3.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.Glimmer3.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -137,7 +137,7 @@ def __main__():
                         chr["chromosome"],
                         "Glimmer3",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.Glimmer3.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.Glimmer3.bed"),
                     )
                 )
 

scripts/microbes/create_nib_seq_loc_file.py

@@ -74,8 +74,8 @@ def __main__():
         for chr in org["chrs"]:
             chr = org["chrs"][chr]
 
-            fasta_file = os.path.join(org["base_dir"], "%s.fna" % chr["chromosome"])
-            nib_out_file = os.path.join(seq_path, "%s.nib " % chr["chromosome"])
+            fasta_file = os.path.join(org["base_dir"], f"{chr['chromosome']}.fna")
+            nib_out_file = os.path.join(seq_path, f"{chr['chromosome']}.nib ")
             # create nibs using faToNib binary
             # TODO: when bx supports writing nib, use it here instead
             command = f"faToNib {fasta_file} {nib_out_file}"

scripts/microbes/harvest_bacteria.py

@@ -158,18 +158,18 @@ def process_FASTA(filename, org_num, refseq):
     fasta = "".join(fasta)
 
     # Create Chrom Info File:
-    chrom_info_file = open(os.path.join(os.path.split(filename)[0], "%s.info" % refseq), "wb+")
+    chrom_info_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.info"), "wb+")
     chrom_info_file.write(f"chromosome={refseq}\nname={chr_name}\nlength={len(fasta)}\norganism={org_num}\n")
     try:
-        chrom_info_file.write("gi=%s\n" % accesions["gi"])
+        chrom_info_file.write(f"gi={accesions['gi']}\n")
     except Exception:
         chrom_info_file.write("gi=None\n")
     try:
-        chrom_info_file.write("gb=%s\n" % accesions["gb"])
+        chrom_info_file.write(f"gb={accesions['gb']}\n")
     except Exception:
         chrom_info_file.write("gb=None\n")
     try:
-        chrom_info_file.write("refseq=%s\n" % refseq)
+        chrom_info_file.write(f"refseq={refseq}\n")
     except Exception:
         chrom_info_file.write("refseq=None\n")
     chrom_info_file.close()
@@ -191,7 +191,7 @@ def process_Glimmer3(filename, org_num, refseq):
     except Exception as e:
         print("Converting Glimmer3 to bed FAILED! For chrom:", refseq, "file:", filename, e)
         glimmer3_bed = []
-    glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.Glimmer3.bed" % refseq), "wb+")
+    glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.Glimmer3.bed"), "wb+")
     glimmer3_bed_file.write("\n".join(glimmer3_bed))
     glimmer3_bed_file.close()
 
@@ -202,7 +202,7 @@ def process_GeneMarkHMM(filename, org_num, refseq):
     except Exception as e:
         print("Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMarkHMM_bed = []
-    geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMarkHMM.bed" % refseq), "wb+")
+    geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.GeneMarkHMM.bed"), "wb+")
     geneMarkHMM_bed_bed_file.write("\n".join(geneMarkHMM_bed))
     geneMarkHMM_bed_bed_file.close()
 
@@ -213,7 +213,7 @@ def process_GeneMark(filename, org_num, refseq):
     except Exception as e:
         print("Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMark_bed = []
-    geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMark.bed" % refseq), "wb+")
+    geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.GeneMark.bed"), "wb+")
     geneMark_bed_bed_file.write("\n".join(geneMark_bed))
     geneMark_bed_bed_file.close()
 
@@ -228,9 +228,9 @@ def __main__():
 
     try:
         os.mkdir(base_dir)
-        print("path '%s' has been created" % base_dir)
+        print(f"path '{base_dir}' has been created")
     except Exception:
-        print("path '%s' seems to already exist" % base_dir)
+        print(f"path '{base_dir}' seems to already exist")
 
     for org_num, name, chroms, kingdom, group, _, _, info_url, ftp_url in iter_genome_projects():
         if chroms is None:
@@ -240,7 +240,7 @@ def __main__():
             org_dir = os.path.join(base_dir, org_num)
             os.mkdir(org_dir)
         except Exception:
-            print("Organism %s already exists on disk, skipping" % org_num)
+            print(f"Organism {org_num} already exists on disk, skipping")
             continue
 
         # get ftp contents
@@ -254,14 +254,14 @@ def __main__():
                 print("Org:", org_num, "chrom:", refseq, "[", time.time() - start_time, "seconds elapsed. ]")
 
         # Create org info file
-        info_file = open(os.path.join(org_dir, "%s.info" % org_num), "wb+")
-        info_file.write("genome project id=%s\n" % org_num)
-        info_file.write("name=%s\n" % name)
-        info_file.write("kingdom=%s\n" % kingdom)
-        info_file.write("group=%s\n" % group)
-        info_file.write("chromosomes=%s\n" % ",".join(chroms))
-        info_file.write("info url=%s\n" % info_url)
-        info_file.write("ftp url=%s\n" % ftp_url)
+        info_file = open(os.path.join(org_dir, f"{org_num}.info"), "wb+")
+        info_file.write(f"genome project id={org_num}\n")
+        info_file.write(f"name={name}\n")
+        info_file.write(f"kingdom={kingdom}\n")
+        info_file.write(f"group={group}\n")
+        info_file.write("chromosomes={}\n".format(",".join(chroms)))
+        info_file.write(f"info url={info_url}\n")
+        info_file.write(f"ftp url={ftp_url}\n")
         info_file.close()
 
     print("Finished Harvesting", "[", time.time() - start_time, "seconds elapsed. ]")

scripts/pages_identifier_conversion.py

@@ -58,11 +58,11 @@ def main(argv):
                     with transaction(session):
                         session.commit()
                 else:
-                    print("Modifying revision %s." % p.id)
+                    print(f"Modifying revision {p.id}.")
                     print(difflib.unified_diff(p.content, newcontent))
         except Exception:
             logging.exception(
-                "Error parsing page, rolling changes back and skipping revision %s.  Please report this error." % p.id
+                "Error parsing page, rolling changes back and skipping revision %s.  Please report this error.", p.id
             )
             session.rollback()
 

scripts/runtime_stats.py

@@ -90,7 +90,7 @@ def parse_arguments():
     parser.add_argument("-M", "--max", type=int, default=-1, help="Ignore runtimes greater than MAX seconds")
     parser.add_argument("-u", "--user", help="Return stats for only this user (id, email, " "or username)")
     parser.add_argument(
-        "-s", "--source", default="metrics", help="Runtime data source (SOURCES: %s)" % ", ".join(DATA_SOURCES)
+        "-s", "--source", default="metrics", help="Runtime data source (SOURCES: {})".format(", ".join(DATA_SOURCES))
     )
     args = parser.parse_args()
 
@@ -144,13 +144,13 @@ def query(
             if row:
                 user_id = row[0]
             else:
-                print("Invalid user: %s" % user)
+                print(f"Invalid user: {user}")
                 sys.exit(1)
 
     if like:
-        query_tool_id = "%%/%s/%%" % tool_id
+        query_tool_id = f"%/{tool_id}/%"
     elif "/" in tool_id and not re.match(r"\d+\.\d+", tool_id.split("/")[-1]):
-        query_tool_id = "%s%%" % tool_id
+        query_tool_id = f"{tool_id}%"
         like = True
     else:
         query_tool_id = tool_id
@@ -187,14 +187,14 @@ def query(
         if min > 0 and max > 0:
             time_clause = """WHERE ctimes[1] - ctimes[2] > interval %s
           AND ctimes[1] - ctimes[2] < interval %s"""
-            sql_args.append("%s seconds" % min)
-            sql_args.append("%s seconds" % max)
+            sql_args.append(f"{min} seconds")
+            sql_args.append(f"{max} seconds")
         elif min > 0:
             time_clause = "WHERE ctimes[1] - ctimes[2] > interval %s"
-            sql_args.append("%s seconds" % min)
+            sql_args.append(f"{min} seconds")
         elif max > 0:
             time_clause = "WHERE ctimes[1] - ctimes[2] < interval %s"
-            sql_args.append("%s seconds" % max)
+            sql_args.append(f"{max} seconds")
         else:
             time_clause = ""
         sql = HISTORY_SQL
@@ -218,7 +218,7 @@ def query(
         return
 
     if user:
-        print("Displaying statistics for user %s" % user)
+        print(f"Displaying statistics for user {user}")
 
     stats = (
         ("Mean runtime", numpy.mean(times)),
@@ -229,11 +229,11 @@ def query(
 
     for name, seconds in stats:
         hours, minutes = nice_times(seconds)
-        msg = name + " is %0.0f seconds" % seconds
+        msg = name + f" is {seconds:0.0f} seconds"
         if minutes:
-            msg += " (=%0.2f minutes)" % minutes
+            msg += f" (={minutes:0.2f} minutes)"
         if hours:
-            msg += " (=%0.2f hours)" % hours
+            msg += f" (={hours:0.2f} hours)"
         print(msg)
 
 

scripts/set_user_disk_usage.py

@@ -62,9 +62,9 @@ def quotacheck(sa_session, users, engine, object_store):
         print("none")
     else:
         if new > current:
-            print("+%s" % (nice_size(new - current)))
+            print(f"+{nice_size(new - current)}")
         else:
-            print("-%s" % (nice_size(current - new)))
+            print(f"-{nice_size(current - new)}")
 
 
 if __name__ == "__main__":

scripts/tests_markdown.py

@@ -244,10 +244,10 @@ def __inject_api_timing_summary_test(test):
             continue
 
         endpoint_summary = {"total_time": summarize_times(timings), "label": endpoint[len("api.") :]}
-        sql_times = "sql.%s" % endpoint
+        sql_times = f"sql.{endpoint}"
         if sql_times in timing:
             endpoint_summary["sql_time"] = summarize_times(timing[sql_times])
-        sql_queries = "sqlqueries.%s" % endpoint
+        sql_queries = f"sqlqueries.{endpoint}"
         if sql_queries in counter:
             endpoint_summary["sql_queries"] = summarize_counter(counter[sql_queries])
         api_endpoints[endpoint] = endpoint_summary