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Fix UP031 errors

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reported by ruff 0.8.0 .
This commit is contained in:
Nicola Soranzo
2024-11-24 21:35:20 +00:00
parent 1d99e6ddff
commit 26a4e146e0
28 changed files with 85 additions and 82 deletions
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cron/build_chrom_db.py
+1 -1
View File
@@ -47,7 +47,7 @@ def getchrominfo(url, db):
if len(fields) > 1 and len(fields[0]) > 0 and int(fields[1]) > 0:
yield [fields[0], fields[1]]
else:
raise Exception("Problem parsing line %d '%s' in page '%s'" % (i, line, page))
raise Exception(f"Problem parsing line {i} '{line}' in page '{page}'")
if __name__ == "__main__":
lib/galaxy/app.py
+1 -1
View File
@@ -551,7 +551,7 @@ class MinimalGalaxyApplication(BasicSharedApp, HaltableContainer, SentryClientMi
database_exists(url)
break
except Exception:
log.info("Waiting for database: attempt %d of %d" % (i, attempts))
log.info("Waiting for database: attempt %d of %d", i, attempts)
time.sleep(pause)
@property
lib/galaxy_test/api/test_jobs.py
+3 -4
View File
@@ -1129,10 +1129,9 @@ steps:
if search_count == expected_search_count:
break
time.sleep(1)
assert search_count == expected_search_count, "expected to find %d jobs, got %d jobs" % (
expected_search_count,
search_count,
)
assert (
search_count == expected_search_count
), f"expected to find {expected_search_count} jobs, got {search_count} jobs"
return search_count
def _search_count(self, search_payload):
lib/galaxy_test/api/test_workflow_extraction.py
+7 -6
View File
@@ -5,6 +5,7 @@ from json import (
dumps,
loads,
)
from typing import Optional
from galaxy_test.base.populators import (
skip_without_tool,
@@ -611,11 +612,11 @@ test_data:
downloaded_workflow = download_response.json()
return downloaded_workflow
def _get_steps_of_type(self, downloaded_workflow, type, expected_len=None):
def _get_steps_of_type(self, downloaded_workflow, type: str, expected_len: Optional[int] = None):
steps = [s for s in downloaded_workflow["steps"].values() if s["type"] == type]
if expected_len is not None:
n = len(steps)
assert n == expected_len, "Expected %d steps of type %s, found %d" % (expected_len, type, n)
assert n == expected_len, f"Expected {expected_len} steps of type {type}, found {n}"
return sorted(steps, key=operator.itemgetter("id"))
def __job_id(self, history_id, dataset_id):
@@ -645,10 +646,10 @@ test_data:
def __check_workflow(
self,
workflow,
step_count=None,
verify_connected=False,
data_input_count=None,
data_collection_input_count=None,
step_count: Optional[int] = None,
verify_connected: bool = False,
data_input_count: Optional[int] = None,
data_collection_input_count: Optional[int] = None,
tool_ids=None,
):
steps = workflow["steps"]
lib/galaxy_test/selenium/framework.py
+4 -4
View File
@@ -233,7 +233,7 @@ retry_assertion_during_transitions = partial(
class TestSnapshot:
__test__ = False # Prevent pytest from discovering this class (issue #12071)
def __init__(self, driver, index, description):
def __init__(self, driver, index: int, description: str):
self.screenshot_binary = driver.get_screenshot_as_png()
self.description = description
self.index = index
@@ -241,7 +241,7 @@ class TestSnapshot:
self.stack = traceback.format_stack()
def write_to_error_directory(self, write_file_func):
prefix = "%d-%s" % (self.index, self.description)
prefix = f"{self.index}-{self.description}"
write_file_func(f"{prefix}-screenshot.png", self.screenshot_binary, raw=True)
write_file_func(f"{prefix}-traceback.txt", self.exc)
write_file_func(f"{prefix}-stack.txt", str(self.stack))
@@ -331,7 +331,7 @@ class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin, Use
def tear_down_selenium(self):
self.tear_down_driver()
def snapshot(self, description):
def snapshot(self, description: str):
"""Create a debug snapshot (DOM, screenshot, etc...) that is written out on tool failure.
This information will be automatically written to a per-test directory created for all
@@ -371,7 +371,7 @@ class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin, Use
copy = 1
while os.path.exists(target):
# Maybe previously a test re-run - keep the original.
target = os.path.join(GALAXY_TEST_SCREENSHOTS_DIRECTORY, "%s-%d%s" % (label, copy, extension))
target = os.path.join(GALAXY_TEST_SCREENSHOTS_DIRECTORY, f"{label}-{copy}{extension}")
copy += 1
return target
lib/galaxy_test/selenium/test_uploads.py
+5 -5
View File
@@ -16,7 +16,7 @@ class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions):
self.history_panel_wait_for_hid_ok(1)
history_count = len(self.history_contents())
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
self.history_panel_click_item_title(hid=1, wait=True)
self.assert_item_summary_includes(1, "28 lines")
@@ -28,7 +28,7 @@ class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions):
self.history_panel_wait_for_hid_ok(1)
history_count = len(self.history_contents())
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
@selenium_test
def test_upload_pasted_url_content(self):
@@ -37,7 +37,7 @@ class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions):
self.history_panel_wait_for_hid_ok(1)
history_count = len(self.history_contents())
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
@selenium_test
def test_upload_composite_dataset_pasted_data(self):
@@ -46,7 +46,7 @@ class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions):
self.history_panel_wait_for_hid_ok(1)
history_count = len(self.history_contents())
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
self.history_panel_click_item_title(hid=1, wait=True)
self.history_panel_item_view_dataset_details(1)
@@ -62,7 +62,7 @@ class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions):
self.history_panel_wait_for_hid_ok(1)
history_contents = self.history_contents()
history_count = len(history_contents)
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
hda = history_contents[0]
assert hda["name"] == "1.sam", hda
scripts/api/common.py
+2 -2
View File
@@ -92,7 +92,7 @@ def display(api_key, url, return_formatted=True):
# 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")))
print("#{}: {}".format(n + 1, i.pop("url")))
if "name" in i:
print(f" name: {i.pop('name')}")
try:
@@ -102,7 +102,7 @@ def display(api_key, url, return_formatted=True):
for item in i:
print(item)
print("")
print("%d element(s) in collection" % len(r))
print(f"{len(r)} element(s) in collection")
elif isinstance(r, dict):
# Response is an element as defined in the REST style.
print("Member Information")
scripts/apply_tags.py
+3 -3
View File
@@ -48,7 +48,7 @@ class ApplyTagsHistory:
count_datasets_updated = 0
# get all datasets belonging to a history
all_datasets = history.show_history(history_id, contents=True)
print("Total datasets: %d. Updating their tags may take a while..." % len(all_datasets))
print(f"Total datasets: {len(all_datasets)}. Updating their tags may take a while...")
for dataset in all_datasets:
try:
if not dataset["deleted"] and dataset["state"] == "ok":
@@ -91,7 +91,7 @@ class ApplyTagsHistory:
)
if is_updated:
count_datasets_updated += 1
print("Tags of %d datasets updated" % count_datasets_updated)
print(f"Tags of {count_datasets_updated} datasets updated")
def collect_parent_ids(self, datasets_inheritance_chain):
"""
@@ -158,4 +158,4 @@ if __name__ == "__main__":
history_tags = ApplyTagsHistory(sys.argv[1], sys.argv[2], history_id)
history_tags.read_galaxy_history()
end_time = time.time()
print("Program finished in %d seconds" % int(end_time - start_time))
print(f"Program finished in {int(end_time - start_time)} seconds")
scripts/build_toolbox.py
+3 -3
View File
@@ -55,7 +55,7 @@ class ToolBox:
sectionorder = self.sectionorders[section]
# Sortorder: add intelligent mix to the front
self.tools[("%05d-%s" % (sectionorder, section), label, order, section)].append(toolelement)
self.tools[(f"{sectionorder:05d}-{section}", label, order, section)].append(toolelement)
def addElementsTo(self, rootelement):
toolkeys = list(self.tools.keys())
@@ -77,7 +77,7 @@ class ToolBox:
currentlabel = ""
if section:
sectionnumber += 1
attrib = {"name": section, "id": "section%d" % sectionnumber}
attrib = {"name": section, "id": f"section{sectionnumber}"}
sectionelement = ET.Element("section", attrib)
rootelement.append(sectionelement)
currentelement = sectionelement
@@ -90,7 +90,7 @@ class ToolBox:
currentlabel = label
if label:
labelnumber += 1
attrib = {"text": label, "id": "label%d" % labelnumber}
attrib = {"text": label, "id": f"label{labelnumber}"}
labelelement = ET.Element("label", attrib)
currentelement.append(labelelement)
scripts/cleanup_datasets/admin_cleanup_datasets.py
+4 -4
View File
@@ -171,7 +171,7 @@ def main():
now = strftime("%Y-%m-%d %H:%M:%S")
print("##########################################")
print("\n# %s - Handling stuff older than %i days" % (now, args.days))
print(f"\n# {now} - Handling stuff older than {args.days} days")
if args.info_only:
print("# Displaying info only ( --info_only )\n")
@@ -260,7 +260,7 @@ def administrative_delete_datasets(
# Mark the HistoryDatasetAssociation as deleted
hda.deleted = True
app.sa_session.add(hda)
print("Marked HistoryDatasetAssociation id %d as deleted" % hda.id)
print(f"Marked HistoryDatasetAssociation id {hda.id} as deleted")
session = app.sa_session()
with transaction(session):
session.commit()
@@ -268,7 +268,7 @@ def administrative_delete_datasets(
emailtemplate = Template(filename=template_file)
for email, dataset_list in user_notifications.items():
msgtext = emailtemplate.render(email=email, datasets=dataset_list, cutoff=cutoff_days)
subject = "Galaxy Server Cleanup - %d datasets DELETED" % len(dataset_list)
subject = f"Galaxy Server Cleanup - {len(dataset_list)} datasets DELETED"
fromaddr = config.email_from
print()
print(f"From: {fromaddr}")
@@ -281,7 +281,7 @@ def administrative_delete_datasets(
stop = time.time()
print()
print("Marked %d dataset instances as deleted" % deleted_instance_count)
print(f"Marked {deleted_instance_count} dataset instances as deleted")
print("Total elapsed time: ", stop - start)
print("##########################################")
scripts/cleanup_datasets/pgcleanup.py
+3 -2
View File
@@ -409,7 +409,7 @@ class RequiresDiskUsageRecalculation:
new_args[key] = val
self._update(sql, new_args, add_event=False)
self.log.info("recalculate_disk_usage user_id %i" % user_id)
self.log.info("recalculate_disk_usage user_id %i", user_id)
class RemovesMetadataFiles(RemovesObjects):
@@ -1317,7 +1317,8 @@ class Cleanup:
else:
log.info(
"Not executing event creation (increments sequence even when rolling back), using an old "
"event ID (%i) for dry run" % max_id
"event ID (%i) for dry run",
max_id,
)
return max_id
scripts/drmaa_external_killer.py
+4 -4
View File
@@ -12,7 +12,7 @@ import sys
import drmaa
def validate_paramters():
def validate_parameters():
if len(sys.argv) < 3:
sys.stderr.write(f"usage: {sys.argv[0]} [job ID] [user uid]\n")
exit(1)
@@ -22,7 +22,7 @@ def validate_paramters():
return jobID, uid
def set_user(uid):
def set_user(uid: int):
try:
gid = pwd.getpwuid(uid).pw_gid
os.setgid(gid)
@@ -30,7 +30,7 @@ def set_user(uid):
except OSError as e:
if e.errno == errno.EPERM:
sys.stderr.write(
"error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid
f"error: setuid({uid}) failed: permission denied. Did you setup 'sudo' correctly for this script?\n"
)
exit(1)
else:
@@ -48,7 +48,7 @@ def set_user(uid):
def main():
jobID, uid = validate_paramters()
jobID, uid = validate_parameters()
set_user(uid)
s = drmaa.Session()
s.initialize()
scripts/drmaa_external_runner.py
+5 -5
View File
@@ -41,7 +41,7 @@ def valid_numeric_userid(userid):
try:
pwd.getpwuid(uid)
except KeyError:
sys.stderr.write("error: User-ID (%d) is not valid.\n" % uid)
sys.stderr.write(f"error: User-ID ({uid}) is not valid.\n")
exit(1)
return True
@@ -63,7 +63,7 @@ def json_file_exists(json_filename):
return True
def validate_paramters():
def validate_parameters():
assign_all_groups = False
if "--assign_all_groups" in sys.argv:
assign_all_groups = True
@@ -88,7 +88,7 @@ def validate_paramters():
return uid, json_filename, assign_all_groups
def set_user(uid, assign_all_groups):
def set_user(uid: int, assign_all_groups: bool):
try:
# Get user's default group and set it to current process to make sure
# file permissions are inherited correctly
@@ -108,7 +108,7 @@ def set_user(uid, assign_all_groups):
except OSError as e:
if e.errno == errno.EPERM:
sys.stderr.write(
"error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid
f"error: setuid({uid}) failed: permission denied. Did you setup 'sudo' correctly for this script?\n"
)
exit(1)
else:
@@ -128,7 +128,7 @@ def set_user(uid, assign_all_groups):
def main():
userid, json_filename, assign_all_groups = validate_paramters()
userid, json_filename, assign_all_groups = validate_parameters()
# load JSON job template data
json_file_exists(json_filename)
with open(json_filename) as f:
scripts/metagenomics/convert_title.py
+3 -3
View File
@@ -18,7 +18,7 @@ if __name__ == "__main__":
if len_seq > 0:
if gi is None:
raise Exception("The first sequence does not have an header.")
print(">%s_%d" % (gi, len_seq))
print(f">{gi}_{len_seq}")
print("\n".join(seq))
title = line
fields = title.split("|")
@@ -33,10 +33,10 @@ if __name__ == "__main__":
seq.append(line)
len_seq += len(line)
if len_seq > 0:
print(">%s_%d" % (gi, len_seq))
print(f">{gi}_{len_seq}")
print("\n".join(seq))
print(
"Unable to find gi number for %d sequences, the title is replaced as giunknown" % (invalid_lines),
f"Unable to find gi number for {invalid_lines} sequences, the title is replaced as giunknown",
file=sys.stderr,
)
scripts/runtime_stats.py
+2 -2
View File
@@ -205,14 +205,14 @@ def query(
if debug:
print("Executed:")
print(cur.query)
print("Query returned %d rows" % cur.rowcount)
print(f"Query returned {cur.rowcount} rows")
if source == "metrics":
times = numpy.array([r[0] for r in cur if r[0]])
elif source == "history":
times = numpy.array([r[0].total_seconds() for r in cur if r[0]])
print("Collected %d times" % times.size)
print(f"Collected {times.size} times")
if times.size == 0:
return
scripts/set_dataset_sizes.py
+3 -3
View File
@@ -37,9 +37,9 @@ if __name__ == "__main__":
set = 0
dataset_count = sa_session.query(model.Dataset).count()
print("Processing %i datasets..." % dataset_count)
print(f"Processing {dataset_count} datasets...")
percent = 0
print("Completed %i%%" % percent, end=" ")
print(f"Completed {percent}%", end=" ")
sys.stdout.flush()
for i, dataset in enumerate(sa_session.query(model.Dataset).enable_eagerloads(False).yield_per(1000)):
if dataset.total_size is None:
@@ -51,7 +51,7 @@ if __name__ == "__main__":
new_percent = int(float(i) / dataset_count * 100)
if new_percent != percent:
percent = new_percent
print("\rCompleted %i%%" % percent, end=" ")
print(f"\rCompleted {percent}%", end=" ")
sys.stdout.flush()
with transaction(session):
session.commit()
scripts/set_user_disk_usage.py
+2 -2
View File
@@ -74,9 +74,9 @@ if __name__ == "__main__":
if not args.username and not args.email:
user_count = sa_session.query(model.User).count()
print("Processing %i users..." % user_count)
print(f"Processing {user_count} users...")
for i, user in enumerate(sa_session.query(model.User).enable_eagerloads(False).yield_per(1000)):
print("%3i%%" % int(float(i) / user_count * 100), end=" ")
print(f"{int(float(i) / user_count * 100):3d}%", end=" ")
quotacheck(sa_session, user, engine, object_store)
print("100% complete")
object_store.shutdown()
scripts/tool_shed/api/common.py
+2 -2
View File
@@ -33,13 +33,13 @@ def display(url, api_key=None, return_formatted=True):
# 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")))
print("#{}: {}".format(n + 1, i.pop("url")))
if "name" in i:
print(f" name: {i.pop('name')}")
for k, v in i.items():
print(f" {k}: {v}")
print()
print("%d element(s) in collection" % len(r))
print(f"{len(r)} element(s) in collection")
elif isinstance(r, dict):
# Response is an element as defined in the REST style.
print("Member Information")
scripts/tool_shed/deprecate_repositories_without_metadata.py
+2 -2
View File
@@ -80,7 +80,7 @@ def main():
cutoff_time = datetime.utcnow() - timedelta(days=options.days)
now = strftime("%Y-%m-%d %H:%M:%S")
print("\n####################################################################################")
print("# %s - Handling stuff older than %i days" % (now, options.days))
print(f"# {now} - Handling stuff older than {options.days} days")
if options.info_only:
print("# Displaying info only ( --info_only )")
@@ -183,7 +183,7 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
app, owner.username, owner.email, repositories_by_owner[repository_owner]["repositories"], days
)
stop = time.time()
print("# Deprecated %d repositories." % len(repositories))
print(f"# Deprecated {len(repositories)} repositories.")
print("# Elapsed time: ", stop - start)
print("####################################################################################")
scripts/tools/maf/check_loc_file.py
+5 -5
View File
@@ -40,19 +40,19 @@ def __main__():
# indexed species
for spec in indexed_for_species:
if spec not in species_indexed_in_maf:
print("Line %i, %s claims to be indexed for %s, but indexes do not exist." % (i, uid, spec))
print(f"Line {i}, {uid} claims to be indexed for {spec}, but indexes do not exist.")
for spec in species_indexed_in_maf:
if spec not in indexed_for_species:
print("Line %i, %s is indexed for %s, but is not listed in loc file." % (i, uid, spec))
print(f"Line {i}, {uid} is indexed for {spec}, but is not listed in loc file.")
# existing species
for spec in species_exist:
if spec not in species_found_in_maf:
print("Line %i, %s claims to have blocks for %s, but was not found in MAF files." % (i, uid, spec))
print(f"Line {i}, {uid} claims to have blocks for {spec}, but was not found in MAF files.")
for spec in species_found_in_maf:
if spec not in species_exist:
print("Line %i, %s contains %s, but is not listed in loc file." % (i, uid, spec))
print(f"Line {i}, {uid} contains {spec}, but is not listed in loc file.")
except Exception as e:
print("Line %i is invalid: %s" % (i, e))
print(f"Line {i} is invalid: {e}")
if __name__ == "__main__":
test/functional/test_toolbox.py
+2 -2
View File
@@ -105,9 +105,9 @@ def build_tests(
for tool_version, version_summary in tool_summary.items():
count = version_summary["count"]
for i in range(count):
test_function_name = "test_tool_%06d" % all_versions_test_count
test_function_name = f"test_tool_{all_versions_test_count:06d}"
test_method = make_test_method(tool_version, i, test_function_name)
test_method.__doc__ = "( %s ) > Test-%d" % (tool_id, all_versions_test_count + 1)
test_method.__doc__ = f"( {tool_id} ) > Test-{all_versions_test_count + 1}"
namespace[test_function_name] = test_method
namespace["tool_id"] = tool_id
namespace["galaxy_interactor"] = galaxy_interactor
test/functional/webhooks/phdcomics/__init__.py
+1 -1
View File
@@ -29,7 +29,7 @@ def main(trans, webhook, params):
)
random_id = random.randint(1, webhook.config["latest_id"])
url = "http://www.phdcomics.com/comics/archive.php?comicid=%d" % random_id
url = f"http://www.phdcomics.com/comics/archive.php?comicid={random_id}"
content = urlopen(url).read()
soup = BeautifulSoup(content, "html.parser")
comic_img = soup.find_all("img", id="comic2")
test/integration_selenium/test_upload_ftp.py
+1 -1
View File
@@ -27,7 +27,7 @@ class TestUploadFtpSeleniumIntegration(SeleniumIntegrationTestCase):
self.components.upload.file_dialog.wait_for_and_click()
self.components.upload.file_source_selector(path="gxftp://").wait_for_and_click()
for i in range(n):
self.components.upload.file_source_selector(path="gxftp://%i.txt" % i).wait_for_and_click()
self.components.upload.file_source_selector(path=f"gxftp://{i}.txt").wait_for_and_click()
self.components.upload.file_dialog_ok.wait_for_and_click()
for i in range(n):
self.components.upload.row(n=i).wait_for_visible()
test/manual/gen_history_export_test_artifacts.py
+1 -1
View File
@@ -47,7 +47,7 @@ def _run(args, gi):
def _gi(args):
gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
name = "histexport-user-%d" % random.randint(0, 1000000)
name = f"histexport-user-{random.randint(0, 1000000)}"
user = gi.users.create_local_user(name, f"{name}@galaxytesting.dev", "pass123")
user_id = user["id"]
test/manual/workflows_scaling.py
+2 -2
View File
@@ -81,7 +81,7 @@ def _run(args, gi, workflow_id, uuid):
if uuid is not None:
contents = []
for i in range(args.collection_size):
contents.append("random dataset number #%d" % i)
contents.append(f"random dataset number #{i}")
hdca = dataset_collection_populator.create_list_in_history(history_id, contents=contents).json()
label_map = {
uuid: {"src": "hdca", "id": hdca["id"]},
@@ -172,7 +172,7 @@ def _link(link, output_name=None):
def _gi(args):
gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
name = "wftest-user-%d" % random.randint(0, 1000000)
name = f"wftest-user-{random.randint(0, 1000000)}"
user = gi.users.create_local_user(name, f"{name}@galaxytesting.dev", "pass123")
user_id = user["id"]
test/unit/app/test_markdown_validate.py
+4 -2
View File
@@ -1,3 +1,5 @@
from typing import Optional
from galaxy.managers.markdown_parse import validate_galaxy_markdown
@@ -5,14 +7,14 @@ def assert_markdown_valid(markdown):
validate_galaxy_markdown(markdown)
def assert_markdown_invalid(markdown, at_line=None):
def assert_markdown_invalid(markdown, at_line: Optional[int] = None):
failed = False
try:
validate_galaxy_markdown(markdown)
except ValueError as e:
failed = True
if at_line is not None:
assert "Invalid line %d" % (at_line + 1) in str(e)
assert f"Invalid line {at_line + 1}" in str(e)
assert failed, f"Expected markdown [{markdown}] to fail validation but it did not."
test/unit/data/dataset_collections/test_matching.py
+1 -1
View File
@@ -78,7 +78,7 @@ def build_collections_to_match(*items):
collection_instance, subcollection_type = item
else:
collection_instance, subcollection_type = item, None
to_match.add("input_%d" % i, collection_instance, subcollection_type)
to_match.add(f"input_{i}", collection_instance, subcollection_type)
return to_match
test/unit/data/test_model_copy.py
+9 -9
View File
@@ -36,7 +36,7 @@ THREAD_LOCAL_LOG = threading.local()
def test_history_dataset_copy(num_datasets=NUM_DATASETS, include_metadata_file=INCLUDE_METADATA_FILE):
with _setup_mapping_and_user() as (test_config, object_store, model, old_history):
for i in range(num_datasets):
hda_path = test_config.write("moo", "test_metadata_original_%d" % i)
hda_path = test_config.write("moo", f"test_metadata_original_{i}")
_create_hda(model, object_store, old_history, hda_path, include_metadata_file=include_metadata_file)
session = model.context
@@ -62,7 +62,7 @@ def test_history_dataset_copy(num_datasets=NUM_DATASETS, include_metadata_file=I
if include_metadata_file:
_check_metadata_file(hda)
annotation_str = hda.get_item_annotation_str(model.context, old_history.user, hda)
assert annotation_str == "annotation #%d" % hda.hid, annotation_str
assert annotation_str == f"annotation #{hda.hid}", annotation_str
def test_history_collection_copy(list_size=NUM_DATASETS):
@@ -70,7 +70,7 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
for i in range(NUM_COLLECTIONS):
hdas = []
for i in range(list_size * 2):
hda_path = test_config.write("moo", "test_metadata_original_%d" % i)
hda_path = test_config.write("moo", f"test_metadata_original_{i}")
hda = _create_hda(
model, object_store, old_history, hda_path, visible=False, include_metadata_file=False
)
@@ -100,7 +100,7 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
model.context,
old_history.user,
history_dataset_collection,
"annotation #%d" % history_dataset_collection.hid,
f"annotation #{history_dataset_collection.hid}",
)
session = model.context
@@ -118,7 +118,7 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
# if not instances:
# print("FULL FLUSH...")
# else:
# print("Flushing just %s" % instances)
# print(f"Flushing just {instances}")
history_copy_timer = ExecutionTimer()
new_history = old_history.copy(target_user=old_history.user)
@@ -127,12 +127,12 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
for hda in new_history.active_datasets:
assert hda.get_size() == 3
annotation_str = hda.get_item_annotation_str(model.context, old_history.user, hda)
assert annotation_str == "annotation #%d" % hda.hid, annotation_str
assert annotation_str == f"annotation #{hda.hid}", annotation_str
assert len(new_history.active_dataset_collections) == NUM_COLLECTIONS
for hdca in new_history.active_dataset_collections:
annotation_str = hdca.get_item_annotation_str(model.context, old_history.user, hdca)
assert annotation_str == "annotation #%d" % hdca.hid, annotation_str
assert annotation_str == f"annotation #{hdca.hid}", annotation_str
@contextlib.contextmanager
@@ -180,7 +180,7 @@ def _create_hda(
_check_metadata_file(hda)
hda.set_size()
history.add_dataset(hda)
hda.add_item_annotation(sa_session, history.user, hda, "annotation #%d" % hda.hid)
hda.add_item_annotation(sa_session, history.user, hda, f"annotation #{hda.hid}")
return hda
@@ -190,4 +190,4 @@ def _check_metadata_file(hda):
assert os.path.exists(copied_index)
with open(copied_index) as f:
assert f.read() == "moo"
assert copied_index.endswith("metadata_%d.dat" % hda.id)
assert copied_index.endswith(f"metadata_{hda.id}.dat")