From aea241c97e6a4b6872e1a6a81164cae7e40b0e29 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 27 Nov 2024 23:48:24 +0000 Subject: [PATCH] Fix UP031 errors - Part 3 Also: - Small code refactorings. - Add type annotations. --- lib/galaxy/util/__init__.py | 12 ++++------ lib/galaxy/util/heartbeat.py | 22 ++++++------------- lib/galaxy/util/permutations.py | 3 +-- lib/galaxy/util/rules_dsl.py | 2 +- .../visualization/data_providers/basic.py | 7 +++--- .../visualization/data_providers/cigar.py | 14 ++++++------ .../visualization/data_providers/genome.py | 12 +++++----- lib/galaxy/web/framework/base.py | 2 +- .../web/framework/middleware/profile.py | 5 ++--- .../web/framework/middleware/translogger.py | 6 +---- lib/galaxy/web/proxy/__init__.py | 10 +++------ lib/galaxy/webapps/base/controller.py | 2 +- .../webapps/galaxy/controllers/admin.py | 17 +++++--------- .../webapps/galaxy/controllers/async.py | 6 ++--- .../webapps/galaxy/controllers/dataset.py | 12 ++++------ .../webapps/galaxy/controllers/forms.py | 8 +++---- .../webapps/galaxy/controllers/history.py | 8 +++---- lib/galaxy/webapps/galaxy/controllers/root.py | 2 +- .../webapps/galaxy/controllers/tool_runner.py | 2 +- .../webapps/reports/controllers/history.py | 2 +- .../webapps/reports/controllers/system.py | 13 +++++------ .../webapps/reports/controllers/tools.py | 8 +++---- lib/galaxy/workflow/extract.py | 2 +- lib/galaxy/workflow/modules.py | 2 +- lib/galaxy/workflow/refactor/execute.py | 2 +- 25 files changed, 70 insertions(+), 111 deletions(-) diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py index d2c8617c08bd..ed39a98f9e54 100644 --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -525,9 +525,7 @@ def shrink_stream_by_size( rval = value.read(size) value.seek(start) return rval - raise ValueError( - "With the provided join_by value (%s), the minimum size value is %i." % (join_by, min_size) - ) + raise ValueError(f"With the provided join_by value ({join_by}), the minimum size value is {min_size}.") left_index = right_index = int((size - len_join_by) / 2) if left_index + right_index + len_join_by < size: if left_larger: @@ -566,9 +564,7 @@ def shrink_string_by_size( return value[:size] elif end_on_size_error: return value[-size:] - raise ValueError( - "With the provided join_by value (%s), the minimum size value is %i." % (join_by, min_size) - ) + raise ValueError(f"With the provided join_by value ({join_by}), the minimum size value is {min_size}.") left_index = right_index = int((size - len_join_by) / 2) if left_index + right_index + len_join_by < size: if left_larger: @@ -1540,7 +1536,7 @@ def nice_size(size: Union[float, int, str, Decimal]) -> str: return "??? bytes" size, prefix = metric_prefix(size, 1024) if prefix == "": - return "%d bytes" % size + return f"{int(size)} bytes" else: return f"{size:.1f} {prefix}B" @@ -1841,7 +1837,7 @@ def build_url(base_url, port=80, scheme="http", pathspec=None, params=None, dose parsed_url.scheme = scheme assert parsed_url.scheme in ("http", "https", "ftp"), f"Invalid URL scheme: {parsed_url.scheme}" if port != 80: - url = "%s://%s:%d/%s" % (parsed_url.scheme, parsed_url.netloc.rstrip("/"), int(port), parsed_url.path) + url = "{}://{}:{}/{}".format(parsed_url.scheme, parsed_url.netloc.rstrip("/"), int(port), parsed_url.path) else: url = f"{parsed_url.scheme}://{parsed_url.netloc.rstrip('/')}/{parsed_url.path.lstrip('/')}" if len(pathspec) > 0: diff --git a/lib/galaxy/util/heartbeat.py b/lib/galaxy/util/heartbeat.py index 901f87291e8b..520ddde12348 100644 --- a/lib/galaxy/util/heartbeat.py +++ b/lib/galaxy/util/heartbeat.py @@ -3,6 +3,7 @@ import threading import time import traceback +from typing import Dict def get_current_thread_object_dict(): @@ -42,7 +43,7 @@ def __init__(self, config, name="Heartbeat Thread", period=20, fname="heartbeat. self.fname_nonsleeping = None self.file_nonsleeping = None self.pid = None - self.nonsleeping_heartbeats = {} + self.nonsleeping_heartbeats: Dict[int, int] = {} # Event to wait on when sleeping, allows us to interrupt for shutdown self.wait_event = threading.Event() @@ -63,16 +64,16 @@ def open_logs(self): if self.file is None or self.file.closed: self.file = open(self.fname, "a") self.file_nonsleeping = open(self.fname_nonsleeping, "a") - self.file.write("Heartbeat for pid %d thread started at %s\n\n" % (self.pid, time.asctime())) + self.file.write(f"Heartbeat for pid {self.pid} thread started at {time.asctime()}\n\n") self.file_nonsleeping.write( - "Non-Sleeping-threads for pid %d thread started at %s\n\n" % (self.pid, time.asctime()) + f"Non-Sleeping-threads for pid {self.pid} thread started at {time.asctime()}\n\n" ) def close_logs(self): if self.file is not None and not self.file.closed: - self.file.write("Heartbeat for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime())) + self.file.write(f"Heartbeat for pid {self.pid} thread stopped at {time.asctime()}\n\n") self.file_nonsleeping.write( - "Non-Sleeping-threads for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime()) + f"Non-Sleeping-threads for pid {self.pid} thread stopped at {time.asctime()}\n\n" ) self.file.close() self.file_nonsleeping.close() @@ -183,16 +184,7 @@ def print_nonsleeping(self, threads_object_dict): good_frame = self.get_interesting_stack_frame(tb) self.file_nonsleeping.write( - 'Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n File %s:%d\n Function "%s"\n %s\n' - % ( - thread_id, - object, - self.nonsleeping_heartbeats[thread_id], - good_frame[0], - good_frame[1], - good_frame[2], - good_frame[3], - ) + f'Thread {thread_id}\t{object}\tnon-sleeping for {self.nonsleeping_heartbeats[thread_id]} heartbeat(s)\n File {good_frame[0]}:{good_frame[1]}\n Function "{good_frame[2]}"\n {good_frame[3]}\n' ) all_threads_are_sleeping = False diff --git a/lib/galaxy/util/permutations.py b/lib/galaxy/util/permutations.py index 92573d8c6dbc..023778ce9332 100644 --- a/lib/galaxy/util/permutations.py +++ b/lib/galaxy/util/permutations.py @@ -60,8 +60,7 @@ def __extend_with_matched_combos(single_inputs, multi_inputs, nested): continue if len(multi_input_values) != len(first_multi_value): raise InputMatchedException( - "Received %d inputs for '%s' and %d inputs for '%s', these should be of equal length" - % (len(multi_input_values), multi_input_key, len(first_multi_value), first_multi_input_key) + f"Received {len(multi_input_values)} inputs for '{multi_input_key}' and {len(first_multi_value)} inputs for '{first_multi_input_key}', these should be of equal length" ) for index, value in enumerate(multi_input_values): diff --git a/lib/galaxy/util/rules_dsl.py b/lib/galaxy/util/rules_dsl.py index 3ce75495e7a3..ebea78be82a1 100644 --- a/lib/galaxy/util/rules_dsl.py +++ b/lib/galaxy/util/rules_dsl.py @@ -187,7 +187,7 @@ def apply(self, rule, data, sources): new_rows = [] for index, row in enumerate(data): - new_rows.append(row + ["%d" % (index + start)]) + new_rows.append(row + [f"{index + start}"]) return new_rows, sources diff --git a/lib/galaxy/visualization/data_providers/basic.py b/lib/galaxy/visualization/data_providers/basic.py index 686b5e870c24..8629f30d14de 100644 --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -77,10 +77,9 @@ def get_data(self, columns=None, start_val=0, max_vals=None, skip_comments=True, # columns is an array of ints for now (should handle column names later) columns = loads(columns) for column in columns: - assert (column < self.original_dataset.metadata.columns) and ( - column >= 0 - ), "column index (%d) must be positive and less" % (column) + " than the number of columns: %d" % ( - self.original_dataset.metadata.columns + assert column < self.original_dataset.metadata.columns and column >= 0, ( + f"column index ({column}) must be positive and less" + f" than the number of columns: {self.original_dataset.metadata.columns}" ) # set up the response, column lists diff --git a/lib/galaxy/visualization/data_providers/cigar.py b/lib/galaxy/visualization/data_providers/cigar.py index 41d5e9435960..5a2fd934688d 100644 --- a/lib/galaxy/visualization/data_providers/cigar.py +++ b/lib/galaxy/visualization/data_providers/cigar.py @@ -43,34 +43,34 @@ def get_ref_based_read_seq_and_cigar(read_seq, read_start, ref_seq, ref_seq_star new_op = "X" # Include mismatched bases in new read sequence. new_read_seq += read_seq[read_pos : read_pos + count] - new_cigar += "%i%s" % (count, new_op) + new_cigar += f"{count}{new_op}" total_count += count read_pos += count ref_seq_pos += count # If end of read falls outside of ref_seq data, leave as M. if total_count < op_len: - new_cigar += "%iM" % (op_len - total_count) + new_cigar += "%sM" % (op_len - total_count) elif op == 1: # Insertion - new_cigar += "%i%s" % (op_len, cigar_ops[op]) + new_cigar += f"{op_len}{cigar_ops[op]}" # Include insertion bases in new read sequence. new_read_seq += read_seq[read_pos : read_pos + op_len] read_pos += op_len elif op in [2, 3, 6]: # Deletion, Skip, or Padding ref_seq_pos += op_len - new_cigar += "%i%s" % (op_len, cigar_ops[op]) + new_cigar += f"{op_len}{cigar_ops[op]}" elif op == 4: # Soft clipping read_pos += op_len - new_cigar += "%i%s" % (op_len, cigar_ops[op]) + new_cigar += f"{op_len}{cigar_ops[op]}" elif op == 5: # Hard clipping - new_cigar += "%i%s" % (op_len, cigar_ops[op]) + new_cigar += f"{op_len}{cigar_ops[op]}" elif op in [7, 8]: # Match or mismatch if op == 8: # Include mismatched bases in new read sequence. new_read_seq += read_seq[read_pos : read_pos + op_len] read_pos += op_len ref_seq_pos += op_len - new_cigar += "%i%s" % (op_len, cigar_ops[op]) + new_cigar += f"{op_len}{cigar_ops[op]}" return (new_read_seq, new_cigar) diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index f241ceebf286..907615712f10 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -251,7 +251,7 @@ def get_genome_data(self, chroms_info, **kwargs): # create a dummy dict if necessary. if not chrom_data: chrom_data = {"data": None} - chrom_data["region"] = "%s:%i-%i" % (chrom, 0, chrom_len) + chrom_data["region"] = f"{chrom}:{0}-{chrom_len}" genome_data.append(chrom_data) return {"data": genome_data, "dataset_type": self.dataset_type} @@ -970,7 +970,7 @@ def _nth_read_iterator(read_iterator, threshold): pair = paired_pending[qname] results.append( [ - hash("%i_%s" % (pair["start"], qname)), + hash("{}_{}".format(pair["start"], qname)), pair["start"], read.pos + read_len, qname, @@ -997,7 +997,7 @@ def _nth_read_iterator(read_iterator, threshold): else: results.append( [ - hash("%i_%s" % (read.pos, qname)), + hash(f"{read.pos}_{qname}"), read.pos, read.pos + read_len, qname, @@ -1028,9 +1028,7 @@ def _nth_read_iterator(read_iterator, threshold): r1 = [read["start"], read["end"], read["cigar"], read["strand"], read["seq"]] r2 = [read["mate_start"], read["mate_start"]] - results.append( - [hash("%i_%s" % (read_start, qname)), read_start, read_end, qname, r1, r2, [read["mapq"], 125]] - ) + results.append([hash(f"{read_start}_{qname}"), read_start, read_end, qname, r1, r2, [read["mapq"], 125]]) # Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data. # bamfile.close() @@ -1052,7 +1050,7 @@ def convert_cigar(read, start_field, cigar_field, seq_field): cigar_ops = "MIDNSHP=X" read_cigar = "" for op_tuple in read[cigar_field]: - read_cigar += "%i%s" % (op_tuple[1], cigar_ops[op_tuple[0]]) + read_cigar += f"{op_tuple[1]}{cigar_ops[op_tuple[0]]}" read[cigar_field] = read_cigar # Choose method for processing reads. Use reference-based compression diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py index b0c72256d411..875494d3a378 100644 --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -530,7 +530,7 @@ def wsgi_status(self): """ if isinstance(self.status, int): exception = webob.exc.status_map.get(self.status) - return "%d %s" % (exception.code, exception.title) + return f"{exception.code} {exception.title}" else: return self.status diff --git a/lib/galaxy/web/framework/middleware/profile.py b/lib/galaxy/web/framework/middleware/profile.py index 649ec2933596..672c90d4154e 100644 --- a/lib/galaxy/web/framework/middleware/profile.py +++ b/lib/galaxy/web/framework/middleware/profile.py @@ -88,8 +88,7 @@ def pstats_as_html(stats, *sel_list): rval = [] # Number of function calls, primitive calls, total time rval.append( - "
%d function calls (%d primitive) in %0.3f CPU seconds
" - % (stats.total_calls, stats.prim_calls, stats.total_tt) + f"
{stats.total_calls} function calls ({stats.prim_calls} primitive) in {stats.total_tt:0.3f} CPU seconds
" ) # Extract functions that match 'sel_list' funcs, order_message, select_message = get_func_list(stats, sel_list) @@ -175,4 +174,4 @@ def func_std_string(func_name): else: return name else: - return "%s:%d(%s)" % func_name + return "{}:{}({})".format(*func_name) diff --git a/lib/galaxy/web/framework/middleware/translogger.py b/lib/galaxy/web/framework/middleware/translogger.py index aedfb83c6227..cd988621dfac 100644 --- a/lib/galaxy/web/framework/middleware/translogger.py +++ b/lib/galaxy/web/framework/middleware/translogger.py @@ -80,17 +80,13 @@ def write_log(self, environ, method, req_uri, start, status, bytes): offset = time.altzone / 60 / 60 * -100 else: offset = time.timezone / 60 / 60 * -100 - if offset >= 0: - offset = "+%0.4d" % (offset) - elif offset < 0: - offset = "%0.4d" % (offset) d = { "REMOTE_ADDR": environ.get("REMOTE_ADDR") or "-", "REMOTE_USER": environ.get("REMOTE_USER") or "-", "REQUEST_METHOD": method, "REQUEST_URI": req_uri, "HTTP_VERSION": environ.get("SERVER_PROTOCOL"), - "time": time.strftime("%d/%b/%Y:%H:%M:%S ", start) + offset, + "time": time.strftime("%d/%b/%Y:%H:%M:%S ", start) + f"{int(offset):+05}", "status": status.split(None, 1)[0], "bytes": bytes, "HTTP_REFERER": environ.get("HTTP_REFERER", "-"), diff --git a/lib/galaxy/web/proxy/__init__.py b/lib/galaxy/web/proxy/__init__.py index d0212756fa4f..68ef06046513 100644 --- a/lib/galaxy/web/proxy/__init__.py +++ b/lib/galaxy/web/proxy/__init__.py @@ -96,7 +96,7 @@ def setup_proxy( host = host[0 : host.index(":")] scheme = trans.request.scheme if not self.dynamic_proxy_external_proxy: - proxy_url = "%s://%s:%d" % (scheme, host, self.dynamic_proxy_bind_port) + proxy_url = f"{scheme}://{host}:{self.dynamic_proxy_bind_port}" else: proxy_url = f"{scheme}://{host}{proxy_prefix}" return { @@ -160,11 +160,7 @@ def launch_proxy_command(self, config): args = [ "gxproxy", # Must be on path. TODO: wheel? "--listenAddr", - "%s:%d" - % ( - config.dynamic_proxy_bind_ip, - config.dynamic_proxy_bind_port, - ), + f"{config.dynamic_proxy_bind_ip}:{config.dynamic_proxy_bind_port}", "--listenPath", "/".join(((config.cookie_path or url_for("/")), config.dynamic_proxy_prefix)), "--cookieName", @@ -197,7 +193,7 @@ def __init__(self, host=None, port=None): host = DEFAULT_PROXY_TO_HOST if port is None: port = sockets.unused_port() - log.info("Obtained unused port %d" % port) + log.info(f"Obtained unused port {port}") self.host = host self.port = port diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py index 9ee829bfae28..b74eae017646 100644 --- a/lib/galaxy/webapps/base/controller.py +++ b/lib/galaxy/webapps/base/controller.py @@ -1297,7 +1297,7 @@ def _scan_json_block(self, meta, prefix=""): yield from self._scan_json_block(meta[a], f"{prefix}/{a}") elif isinstance(meta, list): for i, a in enumerate(meta): - yield from self._scan_json_block(a, prefix + "[%d]" % (i)) + yield from self._scan_json_block(a, prefix + f"[{i}]") else: # BUG: Everything is cast to string, which can lead to false positives # for cross type comparisions, ie "True" == True diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index 634c668b1f01..2ea9e1a339c1 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -539,8 +539,7 @@ def manage_users_and_groups_for_quota(self, trans, payload=None, **kwd): all_groups.append((group.name, trans.security.encode_id(group.id))) return { "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)), + "message": f"Quota '{quota.name}' is currently associated with {len(in_users)} user(s) and {len(in_groups)} group(s).", "status": "info", "inputs": [ build_select_input("in_groups", "Groups", all_groups, in_groups), @@ -802,8 +801,7 @@ def manage_users_and_groups_for_role(self, trans, payload=None, **kwd): all_groups.append((group.name, trans.security.encode_id(group.id))) return { "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)), + "message": f"Role '{role.name}' is currently associated with {len(in_users)} user(s) and {len(in_groups)} group(s).", "status": "info", "inputs": [ build_select_input("in_groups", "Groups", all_groups, in_groups), @@ -889,8 +887,7 @@ def manage_users_and_roles_for_group(self, trans, payload=None, **kwd): all_roles.append((role.name, trans.security.encode_id(role.id))) return { "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)), + "message": f"Group '{group.name}' is currently associated with {len(in_users)} user(s) and {len(in_roles)} role(s).", "status": "info", "inputs": [ build_select_input("in_roles", "Roles", all_roles, in_roles), @@ -993,11 +990,7 @@ def create_group(self, trans, payload=None, **kwd): num_in_roles = len(in_roles) with transaction(trans.sa_session): trans.sa_session.commit() - message = "Group '%s' has been created with %d associated users and %d associated roles." % ( - group.name, - len(in_users), - num_in_roles, - ) + message = f"Group '{group.name}' has been created with {len(in_users)} associated users and {num_in_roles} associated roles." if auto_create_checked: message += ( "One of the roles associated with this group is the newly created role with the same name." @@ -1034,7 +1027,7 @@ def reset_user_password(self, trans, payload=None, **kwd): trans.sa_session.add(user) with transaction(trans.sa_session): trans.sa_session.commit() - return {"message": "Passwords reset for %d user(s)." % len(users)} + return {"message": f"Passwords reset for {len(users)} user(s)."} else: return self.message_exception(trans, "Please specify user ids.") diff --git a/lib/galaxy/webapps/galaxy/controllers/async.py b/lib/galaxy/webapps/galaxy/controllers/async.py index 7a8c45a7badf..8ed26bf95603 100644 --- a/lib/galaxy/webapps/galaxy/controllers/async.py +++ b/lib/galaxy/webapps/galaxy/controllers/async.py @@ -95,7 +95,7 @@ def index(self, trans, tool_id=None, data_secret=None, **kwd): STATUS = params.get("STATUS") if STATUS == "OK": - key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) + key = hmac_new(trans.app.config.tool_secret, f"{data.id}:{data.history_id}") if key != data_secret: return f"You do not have permission to alter data {data_id}." if not params.get("GALAXY_URL"): @@ -203,10 +203,10 @@ def index(self, trans, tool_id=None, data_secret=None, **kwd): trans.sa_session.commit() # Need to explicitly create the file data.dataset.object_store.create(data.dataset) - trans.log_event("Added dataset %d to history %d" % (data.id, trans.history.id), tool_id=tool_id) + trans.log_event(f"Added dataset {data.id} to history {trans.history.id}", tool_id=tool_id) try: - key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) + key = hmac_new(trans.app.config.tool_secret, f"{data.id}:{data.history_id}") galaxy_url = f"{trans.request.url_path}/async/{tool_id}/{data.id}/{key}" params.update({"GALAXY_URL": galaxy_url}) params.update({"data_id": data.id}) diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py index 6d98060692da..4be64e58b4e0 100644 --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -724,11 +724,7 @@ def copy_datasets( else: target_histories = [history] if len(target_histories) != len(target_history_ids): - error_msg = ( - error_msg - + "You do not have permission to add datasets to %i requested histories. " - % (len(target_history_ids) - len(target_histories)) - ) + error_msg += f"You do not have permission to add datasets to {len(target_history_ids) - len(target_histories)} requested histories. " source_contents = list( map(trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get, decoded_dataset_ids) ) @@ -741,10 +737,10 @@ def copy_datasets( source_contents.sort(key=lambda content: content.hid) for content in source_contents: if content is None: - error_msg = f"{error_msg}You tried to copy a dataset that does not exist. " + error_msg += "You tried to copy a dataset that does not exist. " invalid_contents += 1 elif content.history != history: - error_msg = f"{error_msg}You tried to copy a dataset which is not in your current history. " + error_msg += "You tried to copy a dataset which is not in your current history. " invalid_contents += 1 else: for hist in target_histories: @@ -772,7 +768,7 @@ def copy_datasets( ) num_source = len(source_content_ids) - invalid_contents num_target = len(target_histories) - done_msg = "%i %s copied to %i %s: %s." % ( + done_msg = "{} {} copied to {} {}: {}.".format( num_source, inflector.cond_plural(num_source, "dataset"), num_target, diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py index 112f8fa998cc..251b8efee5a4 100644 --- a/lib/galaxy/webapps/galaxy/controllers/forms.py +++ b/lib/galaxy/webapps/galaxy/controllers/forms.py @@ -140,8 +140,8 @@ def create_form(self, trans, payload=None, **kwd): if len(row) >= 6: for column in range(len(row)): row[column] = str(row[column]).strip('"') - prefix = "fields_%i|" % index - payload[f"{prefix}name"] = "%i_imported_field" % (index + 1) + prefix = f"fields_{index}|" + payload[f"{prefix}name"] = f"{index + 1}_imported_field" payload[f"{prefix}label"] = row[0] payload[f"{prefix}helptext"] = row[1] payload[f"{prefix}type"] = row[2] @@ -152,7 +152,7 @@ def create_form(self, trans, payload=None, **kwd): new_form, message = self.save_form_definition(trans, None, payload) if new_form is None: return self.message_exception(trans, message) - imported = (" with %i imported fields" % index) if index > 0 else "" + imported = (f" with {index} imported fields") if index > 0 else "" message = f"The form '{payload.get('name')}' has been created{imported}." return {"message": message} @@ -235,7 +235,7 @@ def get_current_form(self, trans, payload=None, **kwd): fields = [] index = 0 while True: - prefix = "fields_%i|" % index + prefix = f"fields_{index}|" if f"{prefix}label" in payload: field_attributes = ["name", "label", "helptext", "required", "type", "selectlist", "default"] field_dict = {attr: payload.get(f"{prefix}{attr}") for attr in field_attributes} diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py index 03739a9e4016..56afb50cda4e 100644 --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -231,9 +231,7 @@ def purge_deleted_datasets(self, trans): except Exception: log.exception(f"Unable to purge dataset ({hda.dataset.id}) on purge of hda ({hda.id}):") count += 1 - return trans.show_ok_message( - "%d datasets have been deleted permanently" % count, refresh_frames=["history"] - ) + return trans.show_ok_message(f"{count} datasets have been deleted permanently", refresh_frames=["history"]) return trans.show_error_message("Cannot purge deleted datasets from this session.") @web.expose_api_anonymous @@ -267,7 +265,7 @@ def rename(self, trans, payload=None, **kwd): return { "title": "Change history name(s)", "inputs": [ - {"name": "name_%i" % i, "label": f"Current: {h.name}", "value": h.name} + {"name": f"name_{i}", "label": f"Current: {h.name}", "value": h.name} for i, h in enumerate(histories) ], } @@ -275,7 +273,7 @@ def rename(self, trans, payload=None, **kwd): messages = [] for i, h in enumerate(histories): cur_name = h.get_display_name() - new_name = payload.get("name_%i" % i) + new_name = payload.get(f"name_{i}") # validate name is empty if not isinstance(new_name, str) or not new_name.strip(): messages.append(f"You must specify a valid name for History '{cur_name}'.") diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py index 1d03e3b37647..b08ba4431d8d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -122,7 +122,7 @@ def display_as(self, trans: GalaxyWebTransaction, id=None, display_app=None, **k return data.as_display_type(display_app, **kwd) else: trans.response.status = "400" - return "No data with id=%d" % id + return f"No data with id={id}" @web.expose def welcome(self, trans: GalaxyWebTransaction, **kwargs): diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py index d3337bb8e602..e6bf157400b1 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -145,7 +145,7 @@ def rerun(self, trans, id=None, job_id=None, **kwd): if job: job_id = trans.security.encode_id(job.id) else: - raise Exception("Failed to get job information for dataset hid %d" % data.hid) + raise Exception(f"Failed to get job information for dataset hid {data.hid}") return trans.response.send_redirect(url_for(controller="root", job_id=job_id)) @web.expose diff --git a/lib/galaxy/webapps/reports/controllers/history.py b/lib/galaxy/webapps/reports/controllers/history.py index cb6f184b55ab..f27debf3aba6 100644 --- a/lib/galaxy/webapps/reports/controllers/history.py +++ b/lib/galaxy/webapps/reports/controllers/history.py @@ -137,7 +137,7 @@ def history_and_dataset_per_user(self, trans, **kwd): for user in users: dataset = datasets.get(user, [0, 0]) history = histories.get(user, 0) - data[user] = ("%d (%s)" % (history, int_to_octet(dataset[1])), dataset[0]) + data[user] = (f"{history} ({int_to_octet(dataset[1])})", dataset[0]) return trans.fill_template( "/webapps/reports/history_and_dataset_per_user.mako", diff --git a/lib/galaxy/webapps/reports/controllers/system.py b/lib/galaxy/webapps/reports/controllers/system.py index 0b18f18f2d5d..589d44e79dab 100644 --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -87,10 +87,7 @@ def userless_histories(self, trans, **kwd): if not dataset.deleted: dataset_count += 1 history_count += 1 - message = ( - "%d userless histories ( including a total of %d datasets ) have not been updated for at least %d days." - % (history_count, dataset_count, userless_histories_days) - ) + message = f"{history_count} userless histories ( including a total of {dataset_count} datasets ) have not been updated for at least {userless_histories_days} days." else: message = "Enter the number of days." return str(userless_histories_days), message @@ -133,8 +130,8 @@ def deleted_histories(self, trans, **kwd): pass history_count += 1 message = ( - "%d histories ( including a total of %d datasets ) were deleted more than %d days ago, but have not yet been purged, " - "disk space: %s." % (history_count, dataset_count, deleted_histories_days, nice_size(disk_space, True)) + f"{history_count} histories ( including a total of {dataset_count} datasets ) were deleted more than {deleted_histories_days} days ago, but have not yet been purged, " + f"disk space: {nice_size(disk_space, True)}." ) else: message = "Enter the number of days." @@ -163,8 +160,8 @@ def deleted_datasets(self, trans, **kwd): except Exception: pass message = ( - "%d datasets were deleted more than %d days ago, but have not yet been purged," - " disk space: %s." % (dataset_count, deleted_datasets_days, nice_size(disk_space, True)) + f"{dataset_count} datasets were deleted more than {deleted_datasets_days} days ago, but have not yet been purged," + f" disk space: {nice_size(disk_space, True)}." ) else: message = "Enter the number of days." diff --git a/lib/galaxy/webapps/reports/controllers/tools.py b/lib/galaxy/webapps/reports/controllers/tools.py index 0979f522b3e7..570d67beeba0 100644 --- a/lib/galaxy/webapps/reports/controllers/tools.py +++ b/lib/galaxy/webapps/reports/controllers/tools.py @@ -49,19 +49,19 @@ class Tools(BaseUIController): def formatted(self, date, colored=False): splited = str(date).split(",") if len(splited) == 2: - returned = "%s %dH" % (splited[0], int(splited[1].split(":")[0])) + returned = "{} {}H".format(splited[0], int(splited[1].split(":")[0])) if colored: return f'{returned}' return returned else: splited = tuple(float(_) for _ in str(date).split(":")) if splited[0]: - returned = "%d h. %d min." % splited[:2] + returned = f"{int(splited[0])} h. {int(splited[1])} min." if colored: return f'{returned}' return returned if splited[1]: - return "%d min. %d sec." % splited[1:3] + return f"{int(splited[1])} min. {int(splited[2])} sec." return f"{splited[2]:.1f} sec." @web.expose @@ -365,7 +365,7 @@ def tool_error_messages(self, trans, **kwd): sentence += f"
{word}" count += 1 if sentence in new_key: - new_key = new_key.replace(sentence, f"
{word}{' [this line in %d times]' % count}") + new_key = new_key.replace(sentence, f"
{word} [this line in {count} times]") data[new_key] = counter[key] return trans.fill_template( diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py index d96be13b35cc..76b5c6212c86 100644 --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -442,7 +442,7 @@ def cleanup(prefix, inputs, values): group_values = values[key] for i, rep_values in enumerate(group_values): rep_index = rep_values["__index__"] - cleanup("%s%s_%d|" % (prefix, key, rep_index), input.inputs, group_values[i]) + cleanup(f"{prefix}{key}_{rep_index}|", input.inputs, group_values[i]) elif isinstance(input, Conditional): # Scrub dynamic resource related parameters from workflows, # they cause problems and the workflow probably should include diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py index bf7fffae9d90..abb72160652a 100644 --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -168,7 +168,7 @@ def to_cwl(value, hda_references, step): hda_references.append(value) properties = { "class": "File", - "location": "step_input://%d" % len(hda_references), + "location": f"step_input://{len(hda_references)}", } set_basename_and_derived_properties( properties, value.dataset.created_from_basename or element_identifier or value.name diff --git a/lib/galaxy/workflow/refactor/execute.py b/lib/galaxy/workflow/refactor/execute.py index 264fa843d830..7f050e67eb0a 100644 --- a/lib/galaxy/workflow/refactor/execute.py +++ b/lib/galaxy/workflow/refactor/execute.py @@ -116,7 +116,7 @@ def _apply_add_step(self, action: AddStepAction, execution: RefactorActionExecut order_index = len(steps) step_dict = { "order_index": order_index, - "id": "new_%d" % order_index, + "id": f"new_{order_index}", "type": action.type, } if action.tool_state: