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Fix new UP031 errors from ruff 0.4.2

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This commit is contained in:
Nicola Soranzo
2024-04-29 00:09:38 +01:00
parent 0e89124a13
commit 0629908541
127 changed files with 381 additions and 425 deletions
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scripts/api/common.py
+5 -5
View File
@@ -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
+2 -2
View File
@@ -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
+1 -1
View File
@@ -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
+4 -4
View File
@@ -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
+1 -2
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+2 -2
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+1 -1
View File
@@ -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
+2 -2
View File
@@ -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
+1 -1
View File
@@ -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 = {}