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Merge pull request #17653 from galaxybot/dev_auto_update_dependencies

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Update Python dependencies
This commit is contained in:
Dannon
2024-03-12 14:32:25 -05:00
committed by GitHub
parent 0a3e222e62 437b39ce36
commit a62177e525
38 changed files with 159 additions and 233 deletions
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lib/galaxy/authnz/managers.py
+28 -28
View File
@@ -75,8 +75,8 @@ class AuthnzManager:
for child in root:
if child.tag != "Setter":
log.error(
"Expect a node with `Setter` tag, found a node with `{}` tag instead; "
"skipping this node.".format(child.tag)
"Expect a node with `Setter` tag, found a node with `%s` tag instead; skipping this node.",
child.tag,
)
continue
if "Property" not in child.attrib or "Value" not in child.attrib or "Type" not in child.attrib:
@@ -118,8 +118,8 @@ class AuthnzManager:
for child in root:
if child.tag != "provider":
log.error(
"Expect a node with `provider` tag, found a node with `{}` tag instead; "
"skipping the node.".format(child.tag)
"Expect a node with `provider` tag, found a node with `%s` tag instead; skipping the node.",
child.tag,
)
continue
if "name" not in child.attrib:
@@ -268,18 +268,22 @@ class AuthnzManager:
config["id_token"] = cloudauthz.authn.get_id_token(strategy)
except requests.exceptions.HTTPError as e:
msg = (
"Sign-out from Galaxy and remove its access from `{}`, then log back in using `{}` "
"account.".format(self._unify_provider_name(cloudauthz.authn.provider), cloudauthz.authn.uid)
f"Sign-out from Galaxy and remove its access from `{self._unify_provider_name(cloudauthz.authn.provider)}`, "
"then log back in using `{cloudauthz.authn.uid}` account."
)
log.debug(
"Failed to get/refresh ID token for user with ID `{}` for assuming authz_id `{}`. "
"Failed to get/refresh ID token for user with ID `%s` for assuming authz_id `%s`. "
"User may not have a refresh token. If the problem persists, set the `prompt` key to "
"`consent` in `oidc_backends_config.xml`, then restart Galaxy and ask user to: {}"
"Error Message: `{}`".format(user_id, cloudauthz.id, msg, e.response.text)
"`consent` in `oidc_backends_config.xml`, then restart Galaxy and ask user to: %s"
"Error Message: `%s`",
user_id,
cloudauthz.id,
msg,
e.response.text,
)
raise exceptions.AuthenticationFailed(
err_msg="An error occurred getting your ID token. {}. If the problem persists, please "
"contact Galaxy admin.".format(msg)
err_msg=f"An error occurred getting your ID token. {msg}. If the problem persists, please "
"contact Galaxy admin."
)
return config
@@ -287,14 +291,13 @@ class AuthnzManager:
def can_user_assume_authn(trans, authn_id):
qres = trans.sa_session.query(model.UserAuthnzToken).get(authn_id)
if qres is None:
msg = "Authentication record with the given `authn_id` (`{}`) not found.".format(
trans.security.encode_id(authn_id)
)
msg = f"Authentication record with the given `authn_id` (`{trans.security.encode_id(authn_id)}`) not found."
log.debug(msg)
raise exceptions.ObjectNotFound(msg)
if qres.user_id != trans.user.id:
msg = "The request authentication with ID `{}` is not accessible to user with ID " "`{}`.".format(
trans.security.encode_id(authn_id), trans.security.encode_id(trans.user.id)
msg = (
f"The request authentication with ID `{trans.security.encode_id(authn_id)}` is not accessible to user with ID "
f"`{trans.security.encode_id(trans.user.id)}`."
)
log.warning(msg)
raise exceptions.ItemAccessibilityException(msg)
@@ -322,8 +325,8 @@ class AuthnzManager:
raise exceptions.ObjectNotFound("An authorization configuration with given ID not found.")
if user_id != qres.user_id:
msg = (
"The request authorization configuration (with ID:`{}`) is not accessible for user with "
"ID:`{}`.".format(qres.id, user_id)
f"The request authorization configuration (with ID:`{qres.id}`) is not accessible for user with "
f"ID:`{user_id}`."
)
log.warning(msg)
raise exceptions.ItemAccessibilityException(msg)
@@ -499,11 +502,7 @@ class AuthnzManager:
return backend.disconnect(provider, trans, email, disconnect_redirect_url)
return backend.disconnect(provider, trans, disconnect_redirect_url)
except Exception:
msg = (
"An error occurred when disconnecting authentication with `{}` identity provider for user `{}`".format(
provider, trans.user.username
)
)
msg = f"An error occurred when disconnecting authentication with `{provider}` identity provider for user `{trans.user.username}`"
log.exception(msg)
return False, msg, None
@@ -543,9 +542,9 @@ class AuthnzManager:
try:
ca = CloudAuthz()
log.info(
"Requesting credentials using CloudAuthz with config id `{}` on be half of user `{}`.".format(
cloudauthz.id, user_id
)
"Requesting credentials using CloudAuthz with config id `%s` on be half of user `%s`.",
cloudauthz.id,
user_id,
)
credentials = ca.authorize(cloudauthz.provider, config)
return credentials
@@ -594,8 +593,9 @@ class AuthnzManager:
)
credentials = self.get_cloud_access_credentials(cloudauthz, sa_session, user_id, request)
log.info(
"Writing credentials generated using CloudAuthz with config id `{}` to the following file: `{}`"
"".format(cloudauthz.id, filename)
"Writing credentials generated using CloudAuthz with config id `%s` to the following file: `%s`",
cloudauthz.id,
filename,
)
with open(filename, "w") as f:
f.write(json.dumps(credentials))
lib/galaxy/config/__init__.py
+6 -2
View File
@@ -539,8 +539,12 @@ class BaseAppConfiguration(HasDynamicProperties):
if self._path_exists(new_path): # That's a bingo!
resolves_to = self.schema.paths_to_resolve.get(key)
log.warning(
"Paths for the '{0}' option should be relative to '{1}'. To suppress this warning, "
"move '{0}' into '{1}', or set it's value to an absolute path.".format(key, resolves_to)
"Paths for the '%s' option should be relative to '%s'. To suppress this warning, "
"move '%s' into '%s', or set its value to an absolute path.",
key,
resolves_to,
key,
resolves_to,
)
return new_path
return current_path
lib/galaxy/config/schema.py
+2 -2
View File
@@ -92,8 +92,8 @@ class AppSchema(Schema):
def check_exists(option, key):
if not option:
message = (
"Invalid schema: property '{}' listed as path resolution target "
"for '{}' does not exist".format(resolves_to, key)
f"Invalid schema: property '{resolves_to}' listed as path resolution target "
f"for '{key}' does not exist"
)
raise_error(message)
lib/galaxy/datatypes/sequence.py
+1 -8
View File
@@ -277,14 +277,7 @@ class Sequence(data.Text):
start_chunk = -1
# extract, unzip, trim, recompress
result.append(
"(dd bs=1 skip={} count={} if={} 2> /dev/null )| zcat | ( tail -n +{} 2> /dev/null) | head -{} | gzip -c >> {}".format(
start_copy,
end_copy - start_copy,
input_name,
skip_sequences * 4 + 1,
sequences_to_extract * 4,
output_name,
)
f"(dd bs=1 skip={start_copy} count={end_copy - start_copy} if={input_name} 2> /dev/null )| zcat | ( tail -n +{skip_sequences * 4 + 1} 2> /dev/null) | head -{sequences_to_extract * 4} | gzip -c >> {output_name}"
)
else: # whole section - add it to the start_chunk/end_chunk accumulator
if start_chunk == -1:
lib/galaxy/datatypes/sniff.py
+1 -4
View File
@@ -24,7 +24,6 @@ from typing import (
from typing_extensions import Protocol
from galaxy import util
from galaxy.files.uris import stream_url_to_file as files_stream_url_to_file
from galaxy.util import (
compression_utils,
@@ -837,9 +836,7 @@ def handle_compressed_file(
except OSError as e:
os.remove(uncompressed.name)
raise OSError(
"Problem uncompressing {} data, please try retrieving the data uncompressed: {}".format(
compressed_type, util.unicodify(e)
)
f"Problem uncompressing {compressed_type} data, please try retrieving the data uncompressed: {e}"
)
finally:
is_compressed = False
lib/galaxy/datatypes/upload_util.py
+2 -2
View File
@@ -101,8 +101,8 @@ def handle_upload(
if registry.is_extension_unsniffable_binary(upload_ext):
stdout = (
"Warning: The file's datatype cannot be determined from its contents and was guessed based on"
" its extension, to avoid this warning, manually set the file 'Type' to '{ext}' when uploading"
" this type of file".format(ext=upload_ext)
f" its extension, to avoid this warning, manually set the file 'Type' to '{upload_ext}' when uploading"
" this type of file"
)
ext = upload_ext
else:
lib/galaxy/dependencies/dev-requirements.txt
+8 -8
View File
@@ -45,8 +45,8 @@ httpcore==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.2 ; python_version >= "3.8" and python_version < "3.10"
importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.3 ; python_version >= "3.8" and python_version < "3.10"
iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -76,13 +76,13 @@ nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.13"
numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
packaging==23.2 ; python_version >= "3.8" and python_version < "3.13"
packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.41.2 ; python_version >= "3.8" and python_version < "3.13"
playwright==1.42.0 ; python_version >= "3.8" and python_version < "3.13"
pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -95,10 +95,10 @@ pygithub==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13"
pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.5 ; python_version >= "3.8" and python_version < "3.13"
pytest-asyncio==0.23.5.post1 ; python_version >= "3.8" and python_version < "3.13"
pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-cov==4.1.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -108,7 +108,7 @@ pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-mock==3.12.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
pytest-postgresql==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
@@ -155,7 +155,7 @@ tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
trio==0.24.0 ; python_version >= "3.8" and python_version < "3.13"
tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
twill==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.10.0 ; python_version >= "3.8" and python_version < "3.13"
tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
lib/galaxy/dependencies/pinned-lint-requirements.txt
+1 -1
View File
@@ -4,4 +4,4 @@ flake8-bugbear==24.2.6
mccabe==0.7.0
pycodestyle==2.11.1
pyflakes==3.2.0
ruff==0.3.0
ruff==0.3.2
lib/galaxy/dependencies/pinned-requirements.txt
+8 -8
View File
@@ -2,7 +2,7 @@
a2wsgi==1.10.2 ; python_version >= "3.8" and python_version < "3.13"
adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.12.0 ; python_version >= "3.8" and python_version < "3.13"
aiobotocore==2.12.1 ; python_version >= "3.8" and python_version < "3.13"
aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -16,7 +16,7 @@ anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
apispec==6.5.0 ; python_version >= "3.8" and python_version < "3.13"
appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
argcomplete==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
argcomplete==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13"
attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -87,8 +87,8 @@ h5grove==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.2 ; python_version >= "3.8" and python_version < "3.9"
importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13"
importlib-resources==6.1.3 ; python_version >= "3.8" and python_version < "3.9"
isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
isal==1.6.0 ; python_version >= "3.8" and python_version < "3.13"
isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -119,7 +119,7 @@ numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
orjson==3.9.15 ; python_version >= "3.8" and python_version < "3.13"
oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
packaging==23.2 ; python_version >= "3.8" and python_version < "3.13"
packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
paste==3.7.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -147,7 +147,7 @@ pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13"
pysam==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
@@ -179,10 +179,10 @@ setuptools==69.1.1 ; python_version >= "3.8" and python_version < "3.13"
shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
social-auth-core[openidconnect]==4.5.3 ; python_version >= "3.8" and python_version < "3.13"
social-auth-core==4.5.3 ; python_version >= "3.8" and python_version < "3.13"
sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
sqlalchemy==1.4.51 ; python_version >= "3.8" and python_version < "3.13"
sqlalchemy==1.4.52 ; python_version >= "3.8" and python_version < "3.13"
sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+3 -3
View File
@@ -3,7 +3,7 @@ cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_
cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
mypy==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
mypy==1.9.0 ; python_version >= "3.8" and python_version < "3.13"
pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13"
pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -12,7 +12,7 @@ types-bleach==6.1.0.20240222 ; python_version >= "3.8" and python_version < "3.1
types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.20.0.20240304 ; python_version >= "3.8" and python_version < "3.13"
types-docutils==0.20.0.20240310 ; python_version >= "3.8" and python_version < "3.13"
types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13"
types-markdown==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13"
types-paramiko==3.4.0.20240205 ; python_version >= "3.8" and python_version < "3.13"
@@ -20,6 +20,6 @@ types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.13"
types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.13"
types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
types-six==1.16.21.20240301 ; python_version >= "3.8" and python_version < "3.13"
types-six==1.16.21.20240310 ; python_version >= "3.8" and python_version < "3.13"
types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
typing-extensions==4.10.0 ; python_version >= "3.8" and python_version < "3.13"
lib/galaxy/job_metrics/instrumenters/cgroup.py
+7 -4
View File
@@ -1,8 +1,6 @@
"""The module describes the ``cgroup`` job metrics plugin."""
import decimal
import logging
import numbers
from collections import namedtuple
from typing import (
Any,
@@ -123,8 +121,13 @@ class CgroupPluginFormatter(formatting.JobMetricFormatter):
return formatting.FormattedMetric(title, nice_size(value))
except ValueError:
pass
elif isinstance(value, (decimal.Decimal, numbers.Integral, numbers.Real)) and value == int(value):
value = int(value)
else:
try:
int_value = int(value)
if value == int_value:
value = int_value
except TypeError:
pass
return formatting.FormattedMetric(title, str(value))
lib/galaxy/jobs/__init__.py
+3 -6
View File
@@ -640,10 +640,9 @@ class JobConfiguration(ConfiguresHandlers):
fields = []
for field_name in fields_names:
if field_name not in self.resource_parameters:
message = "Failed to find field for resource {} in resource parameters {}".format(
field_name, self.resource_parameters
raise KeyError(
f"Failed to find field for resource {field_name} in resource parameters {self.resource_parameters}"
)
raise KeyError(message)
fields.append(parse_xml_string(self.resource_parameters[field_name]))
if fields:
@@ -2209,9 +2208,7 @@ class MinimalJobWrapper(HasResourceParameters):
try:
if not tmp_dir or util.asbool(tmp_dir):
working_directory = self.working_directory
return """$([ ! -e '{0}/tmp' ] || mv '{0}/tmp' '{0}'/tmp.$(date +%Y%m%d-%H%M%S) ; mkdir '{0}/tmp'; echo '{0}/tmp')""".format(
working_directory
)
return f"""$([ ! -e '{working_directory}/tmp' ] || mv '{working_directory}/tmp' '{working_directory}'/tmp.$(date +%Y%m%d-%H%M%S) ; mkdir '{working_directory}/tmp'; echo '{working_directory}/tmp')"""
else:
return tmp_dir
except ValueError:
lib/galaxy/jobs/command_factory.py
+1 -7
View File
@@ -181,13 +181,7 @@ def __externalize_commands(
source_command = ""
if container:
source_command = container.source_environment
script_contents = "#!{}\n{}{}{}{}".format(
shell,
integrity_injection,
set_e,
source_command,
tool_commands,
)
script_contents = f"#!{shell}\n{integrity_injection}{set_e}{source_command}{tool_commands}"
write_script(
local_container_script,
script_contents,
lib/galaxy/jobs/runners/kubernetes.py
+11 -9
View File
@@ -1002,9 +1002,10 @@ class KubernetesJobRunner(AsynchronousJobRunner):
except Exception as e:
log.exception(
"({}/{}) User killed running job, but error encountered during termination: {}".format(
job.id, job.get_job_runner_external_id(), e
)
"(%s/%s) User killed running job, but error encountered during termination: %s",
job.id,
job.get_job_runner_external_id(),
e,
)
def recover(self, job, job_wrapper):
@@ -1023,18 +1024,19 @@ class KubernetesJobRunner(AsynchronousJobRunner):
ajs.command_line = job.command_line
if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
log.debug(
"({}/{}) is still in {} state, adding to the runner monitor queue".format(
job.id, job.job_runner_external_id, job.state
)
"(%s/%s) is still in %s state, adding to the runner monitor queue",
job.id,
job.job_runner_external_id,
job.state,
)
ajs.old_state = model.Job.states.RUNNING
ajs.running = True
self.monitor_queue.put(ajs)
elif job.state == model.Job.states.QUEUED:
log.debug(
"({}/{}) is still in queued state, adding to the runner monitor queue".format(
job.id, job.job_runner_external_id
)
"(%s/%s) is still in queued state, adding to the runner monitor queue",
job.id,
job.job_runner_external_id,
)
ajs.old_state = model.Job.states.QUEUED
ajs.running = False
lib/galaxy/managers/cloud.py
+11 -10
View File
@@ -281,12 +281,14 @@ class CloudManager(sharable.SharableModelManager):
)
if key is None:
log.exception(
"Could not get object `{}` for user `{}`. Object may not exist, or the provided credentials are "
"invalid or not authorized to read the bucket/object.".format(obj, trans.user.id)
"Could not get object `%s` for user `%s`. Object may not exist, or the provided credentials are "
"invalid or not authorized to read the bucket/object.",
obj,
trans.user.id,
)
raise ObjectNotFound(
"Could not get the object `{}`. Please check if the object exists, and credentials are valid and "
"authorized to read the bucket and object. ".format(obj)
f"Could not get the object `{obj}`. Please check if the object exists, and credentials are valid and "
"authorized to read the bucket and object. "
)
params = Params(self._get_inputs(obj, key, input_args), sanitize=False)
@@ -299,9 +301,7 @@ class CloudManager(sharable.SharableModelManager):
job_errors = output.get("job_errors", [])
if job_errors:
raise ValueError(
"Following error occurred while getting the given object(s) from {}: {}".format(
cloudauthz.provider, job_errors
)
f"Following error occurred while getting the given object(s) from {cloudauthz.provider}: {job_errors}"
)
else:
for d in output["out_data"]:
@@ -391,9 +391,10 @@ class CloudManager(sharable.SharableModelManager):
except Exception as e:
err_msg = f"maybe invalid or unauthorized credentials. {util.unicodify(e)}"
log.debug(
"Failed to send the dataset `{}` per user `{}` request to cloud, {}".format(
object_label, trans.user.id, err_msg
)
"Failed to send the dataset `%s` per user `%s` request to cloud, %s",
object_label,
trans.user.id,
err_msg,
)
failed.append(json.dumps({"object": object_label, "error": err_msg}))
return sent, failed
lib/galaxy/managers/markdown_util.py
+12 -20
View File
@@ -849,42 +849,34 @@ def resolve_invocation_markdown(trans, invocation, workflow_markdown):
continue
if output_assoc.history_content_type == "dataset":
section_markdown += """#### Output Dataset: {}
section_markdown += f"""#### Output Dataset: {output_assoc.workflow_output.label}
```galaxy
history_dataset_display(output="{}")
history_dataset_display(output="{output_assoc.workflow_output.label}")
```
""".format(
output_assoc.workflow_output.label, output_assoc.workflow_output.label
)
"""
else:
section_markdown += """#### Output Dataset Collection: {}
section_markdown += f"""#### Output Dataset Collection: {output_assoc.workflow_output.label}
```galaxy
history_dataset_collection_display(output="{}")
history_dataset_collection_display(output="{output_assoc.workflow_output.label}")
```
""".format(
output_assoc.workflow_output.label, output_assoc.workflow_output.label
)
"""
elif container == "invocation_inputs":
for input_assoc in invocation.input_associations:
if not input_assoc.workflow_step.label:
continue
if input_assoc.history_content_type == "dataset":
section_markdown += """#### Input Dataset: {}
section_markdown += f"""#### Input Dataset: {input_assoc.workflow_step.label}
```galaxy
history_dataset_display(input="{}")
history_dataset_display(input="{input_assoc.workflow_step.label}")
```
""".format(
input_assoc.workflow_step.label, input_assoc.workflow_step.label
)
"""
else:
section_markdown += """#### Input Dataset Collection: {}
section_markdown += f"""#### Input Dataset Collection: {input_assoc.workflow_step.label}
```galaxy
history_dataset_collection_display(input={})
history_dataset_collection_display(input={input_assoc.workflow_step.label})
```
""".format(
input_assoc.workflow_step.label, input_assoc.workflow_step.label
)
"""
else:
return line, False
return section_markdown, True
lib/galaxy/objectstore/cloud.py
+3 -2
View File
@@ -229,8 +229,9 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
raise Exception(msg)
if len(missing_config) > 0:
msg = "The following configuration required for {} cloud backend " "are missing: {}".format(
provider, missing_config
msg = (
f"The following configuration required for {provider} cloud backend "
f"are missing: {missing_config}"
)
log.error(msg)
raise Exception(msg)
lib/galaxy/objectstore/irods.py
+3 -3
View File
@@ -302,9 +302,9 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
# seconds ago, release the connection (as its stale)
if (curr_time - conn.create_time).total_seconds() > refresh_time:
log.debug(
"Idle connection with id {} was created more than {} seconds ago. Releasing the connection.".format(
id(conn), refresh_time
)
"Idle connection with id %s was created more than %s seconds ago. Releasing the connection.",
id(conn),
refresh_time,
)
self.session.pool.release_connection(conn, True)
stop_connection_pool_monitor_event.wait(connection_pool_monitor_interval)
lib/galaxy/objectstore/pithos.py
+1 -4
View File
@@ -420,10 +420,7 @@ class PithosObjectStore(ConcreteObjectStore):
shutil.copy2(source_path, cache_path)
self._fix_permissions(cache_path)
except OSError:
log.exception(
'Trouble copying source file "{source}" to cache "{cache}"'
"".format(source=source_path, cache=cache_path)
)
log.exception('Trouble copying source file "%s" to cache "%s"', source_path, cache_path)
else:
with open(cache_path) as f:
self.pithos.upload_object(obj, f)
lib/galaxy/tool_shed/util/container_util.py
+1 -13
View File
@@ -25,19 +25,7 @@ def generate_repository_dependencies_key_for_repository(
# of the Galaxy database for an installed repository. This value does not include the protocol, but does include
# the port if there is one.
tool_shed = remove_protocol_from_tool_shed_url(toolshed_base_url)
return "{}{}{}{}{}{}{}{}{}{}{}".format(
tool_shed,
STRSEP,
repository_name,
STRSEP,
repository_owner,
STRSEP,
changeset_revision,
STRSEP,
str(prior_installation_required),
STRSEP,
str(only_if_compiling_contained_td),
)
return f"{tool_shed}{STRSEP}{repository_name}{STRSEP}{repository_owner}{STRSEP}{changeset_revision}{STRSEP}{prior_installation_required}{STRSEP}{only_if_compiling_contained_td}"
def get_components_from_key(key: str) -> tuple:
lib/galaxy/tool_shed/util/shed_util_common.py
+3 -9
View File
@@ -115,8 +115,8 @@ def get_tool_panel_config_tool_path_install_dir(app, repository):
defined in a single shed-related tool panel config.
"""
tool_shed = common_util.remove_port_from_tool_shed_url(str(repository.tool_shed))
relative_install_dir = "{}/repos/{}/{}/{}".format(
tool_shed, str(repository.owner), str(repository.name), str(repository.installed_changeset_revision)
relative_install_dir = (
f"{tool_shed}/repos/{repository.owner}/{repository.name}/{repository.installed_changeset_revision}"
)
# Get the relative tool installation paths from each of the shed tool configs.
shed_config_dict = repository.get_shed_config_dict(app)
@@ -149,13 +149,7 @@ def set_image_paths(app, text, encoded_repository_id=None, tool_shed_repository=
# We're in the tool shed.
route_to_images = f"/repository/static/images/{encoded_repository_id}"
elif tool_shed_repository and tool_id and tool_version:
route_to_images = "shed_tool_static/{shed}/{owner}/{repo}/{tool}/{version}".format(
shed=tool_shed_repository.tool_shed,
owner=tool_shed_repository.owner,
repo=tool_shed_repository.name,
tool=tool_id,
version=tool_version,
)
route_to_images = f"shed_tool_static/{tool_shed_repository.tool_shed}/{tool_shed_repository.owner}/{tool_shed_repository.name}/{tool_id}/{tool_version}"
else:
raise Exception(
"encoded_repository_id or tool_shed_repository and tool_id and tool_version must be provided"
lib/galaxy/tool_util/cwl/representation.py
+2 -6
View File
@@ -369,9 +369,7 @@ def to_galaxy_parameters(tool, as_dict):
type_representation_name = "null"
elif as_dict_value is NOT_PRESENT or as_dict_value is None:
raise RequestParameterInvalidException(
"Cannot translate CWL datatype - value [{}] of type [{}] with case_strings [{}]. Non-null property must be set.".format(
as_dict_value, type(as_dict_value), case_strings
)
f"Cannot translate CWL datatype - value [{as_dict_value}] of type [{type(as_dict_value)}] with case_strings [{case_strings}]. Non-null property must be set."
)
elif isinstance(as_dict_value, bool) and "boolean" in case_strings:
type_representation_name = "boolean"
@@ -406,9 +404,7 @@ def to_galaxy_parameters(tool, as_dict):
type_representation_name = "json"
else:
raise RequestParameterInvalidException(
"Cannot translate CWL datatype - value [{}] of type [{}] with case_strings [{}].".format(
as_dict_value, type(as_dict_value), case_strings
)
f"Cannot translate CWL datatype - value [{as_dict_value}] of type [{type(as_dict_value)}] with case_strings [{case_strings}]."
)
galaxy_request[f"{input_name}|_cwl__type_"] = type_representation_name
if type_representation_name != "null":
lib/galaxy/tool_util/deps/resolvers/modules.py
+1 -3
View File
@@ -227,9 +227,7 @@ class ModuleDependency(Dependency):
module_to_load = self.module_name
if self.module_version:
module_to_load = f"{self.module_name}/{self.module_version}"
command = "MODULEPATH={}; export MODULEPATH; eval `{} sh load {}`".format(
self.module_dependency_resolver.modulepath, self.module_dependency_resolver.modulecmd, module_to_load
)
command = f"MODULEPATH={self.module_dependency_resolver.modulepath}; export MODULEPATH; eval `{self.module_dependency_resolver.modulecmd} sh load {module_to_load}`"
return command
lib/galaxy/tools/error_reports/plugins/github.py
+1 -6
View File
@@ -99,12 +99,7 @@ class GithubPlugin(BaseGitPlugin):
else:
self._append_issue(issue_cache_key, error_title, error_message)
return (
"Submitted error report to GitHub. Your issue number is [#{}]({}/{}/issues/{})".format(
self.issue_cache[issue_cache_key][error_title].number,
self.github_base_url,
github_projecturl,
self.issue_cache[issue_cache_key][error_title].number,
),
f"Submitted error report to GitHub. Your issue number is [#{self.issue_cache[issue_cache_key][error_title].number}]({self.github_base_url}/{github_projecturl}/issues/{self.issue_cache[issue_cache_key][error_title].number})",
"success",
)
lib/galaxy/tools/error_reports/plugins/gitlab.py
+1 -6
View File
@@ -185,12 +185,7 @@ class GitLabPlugin(BaseGitPlugin):
)
return (
"Submitted error report to GitLab. Your Issue number is [#{}]({}/{}/issues/{})".format(
self.issue_cache[issue_cache_key][error_title],
self.gitlab_base_url,
gitlab_projecturl,
self.issue_cache[issue_cache_key][error_title],
),
f"Submitted error report to GitLab. Your Issue number is [#{self.issue_cache[issue_cache_key][error_title]}]({self.gitlab_base_url}/{gitlab_projecturl}/issues/{self.issue_cache[issue_cache_key][error_title]})",
"success",
)
lib/galaxy/tools/errors.py
+1 -3
View File
@@ -248,9 +248,7 @@ class EmailErrorReporter(ErrorReporter):
to += f", {email.strip()}"
subject = f"Galaxy tool error report from {email}"
try:
subject = "{} ({})".format(
subject, self.app.toolbox.get_tool(self.job.tool_id, self.job.tool_version).old_id
)
subject = f"{subject} ({self.app.toolbox.get_tool(self.job.tool_id, self.job.tool_version).old_id})"
except Exception:
pass
lib/galaxy/util/__init__.py
+11 -6
View File
@@ -1412,9 +1412,12 @@ def umask_fix_perms(path, umask, unmasked_perms, gid=None):
os.chmod(path, perms)
except Exception as e:
log.warning(
"Unable to honor umask ({}) for {}, tried to set: {} but mode remains {}, error was: {}".format(
oct(umask), path, oct(perms), oct(stat.S_IMODE(st.st_mode)), unicodify(e)
)
"Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s",
oct(umask),
path,
oct(perms),
oct(stat.S_IMODE(st.st_mode)),
e,
)
# fix group
if gid is not None and st.st_gid != gid:
@@ -1428,9 +1431,11 @@ def umask_fix_perms(path, umask, unmasked_perms, gid=None):
desired_group = gid
current_group = st.st_gid
log.warning(
"Unable to honor primary group ({}) for {}, group remains {}, error was: {}".format(
desired_group, path, current_group, unicodify(e)
)
"Unable to honor primary group (%s) for %s, group remains %s, error was: %s",
desired_group,
path,
current_group,
e,
)
lib/galaxy/web/framework/middleware/error.py
+4 -6
View File
@@ -450,13 +450,11 @@ def send_report(rep, exc_data, html=True):
output = StringIO()
traceback.print_exc(file=output)
if html:
return """
<p>Additionally an error occurred while sending the {} report:
return f"""
<p>Additionally an error occurred while sending the {markupsafe.escape(str(rep))} report:
<pre>{}</pre>
</p>""".format(
markupsafe.escape(str(rep)), output.getvalue()
)
<pre>{output.getvalue()}</pre>
</p>"""
else:
return f"Additionally an error occurred while sending the {rep} report:\n{output.getvalue()}"
else:
lib/galaxy/web_stack/message.py
+3 -3
View File
@@ -149,9 +149,9 @@ class TaskMessage(ParamMessage):
def default_handler(self, msg):
"""Can be bound to an instance of any class that has message handling methods named like `_handle_{task}_method`"""
name = f"_handle_{msg.task}_msg"
assert name in dir(self), "{cls} has no method _handle_{task}_msg, cannot handle message: {msg}".format(
cls=self.__class__.__name__, task=msg.task, msg=msg
)
assert name in dir(
self
), f"{self.__class__.__name__} has no method _handle_{msg.task}_msg, cannot handle message: {msg}"
getattr(self, f"_handle_{msg.task}_msg")(**msg.params)
@property
lib/galaxy/webapps/galaxy/api/cloudauthz.py
+3 -2
View File
@@ -143,8 +143,9 @@ class CloudAuthzController(BaseGalaxyAPIController):
for ca in trans.user.cloudauthz:
if ca.equals(trans.user.id, provider, authn_id, config):
log.debug(
"Rejected user `{}`'s request to create cloud authorization because a similar config "
"already exists.".format(trans.user.id)
"Rejected user `%s`'s request to create cloud authorization because a similar config "
"already exists.",
trans.user.id,
)
raise ActionInputError("A similar cloud authorization configuration is already defined.")
lib/galaxy/webapps/galaxy/api/library_datasets.py
+1 -3
View File
@@ -501,9 +501,7 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
path, allowlist=[full_dir] + trans.app.config.user_library_import_symlink_allowlist, username=username
):
# the path is a dir and contains files that symlink outside the user dir
error = "User attempted to import a path that resolves to a path outside of their import dir: {} -> {}".format(
path, os.path.realpath(path)
)
error = f"User attempted to import a path that resolves to a path outside of their import dir: {path} -> {os.path.realpath(path)}"
if trans.app.config.user_library_import_check_permissions:
error += " or is not readable for them."
log.error(error)
lib/galaxy/webapps/galaxy/controllers/authnz.py
+6 -6
View File
@@ -89,10 +89,10 @@ class OIDC(JSAppLauncher):
if not bool(kwargs):
log.error(f"OIDC callback received no data for provider `{provider}` and user `{user}`")
return trans.show_error_message(
"Did not receive any information from the `{}` identity provider to complete user `{}` authentication "
f"Did not receive any information from the `{provider}` identity provider to complete user `{user}` authentication "
"flow. Please try again, and if the problem persists, contact the Galaxy instance admin. Also note "
"that this endpoint is to receive authentication callbacks only, and should not be called/reached by "
"a user.".format(provider, user)
"a user."
)
if "error" in kwargs:
log.error(
@@ -127,9 +127,9 @@ class OIDC(JSAppLauncher):
user = user if user is not None else trans.user
if user is None:
return trans.show_error_message(
"An unknown error occurred when handling the callback from `{}` "
f"An unknown error occurred when handling the callback from `{provider}` "
"identity provider. Please try again, and if the problem persists, "
"contact the Galaxy instance admin.".format(provider)
"contact the Galaxy instance admin."
)
trans.handle_user_login(user)
# Record which idp provider was logged into, so we can logout of it later
@@ -152,9 +152,9 @@ class OIDC(JSAppLauncher):
user = user if user is not None else trans.user
if user is None:
return trans.show_error_message(
"An unknown error occurred when handling the callback from `{}` "
f"An unknown error occurred when handling the callback from `{provider}` "
"identity provider. Please try again, and if the problem persists, "
"contact the Galaxy instance admin.".format(provider)
"contact the Galaxy instance admin."
)
trans.handle_user_login(user)
# Record which idp provider was logged into, so we can logout of it later
lib/tool_shed/grids/repository_grids.py
+1 -6
View File
@@ -857,12 +857,7 @@ class RepositoriesWithInvalidToolsGrid(RepositoryGrid):
metadata = repository_metadata.metadata
if invalid_tools := metadata.get("invalid_tools", []):
for invalid_tool_config in invalid_tools:
href_str = '<a href="load_invalid_tool?repository_id={}&tool_config={}&changeset_revision={}">{}</a>'.format(
trans.security.encode_id(repository.id),
invalid_tool_config,
repository_metadata.changeset_revision,
invalid_tool_config,
)
href_str = f'<a href="load_invalid_tool?repository_id={trans.security.encode_id(repository.id)}&tool_config={invalid_tool_config}&changeset_revision={repository_metadata.changeset_revision}">{invalid_tool_config}</a>'
val += href_str
val += "<br/>"
val = val.rstrip("<br/>")
lib/tool_shed/webapp/controllers/repository.py
+1 -6
View File
@@ -976,12 +976,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
return self.install_matched_repository_grid(trans, **kwd)
else:
kwd["message"] = (
"tool id: <b>{}</b><br/>tool name: <b>{}</b><br/>tool version: <b>{}</b><br/>exact matches only: <b>{}</b>".format(
basic_util.stringify(tool_ids),
escape(basic_util.stringify(tool_names)),
escape(basic_util.stringify(tool_versions)),
exact_matches_checked,
)
f"tool id: <b>{basic_util.stringify(tool_ids)}</b><br/>tool name: <b>{escape(basic_util.stringify(tool_names))}</b><br/>tool version: <b>{escape(basic_util.stringify(tool_versions))}</b><br/>exact matches only: <b>{exact_matches_checked}</b>"
)
self.matched_repository_grid.title = "Repositories with matching tools"
return self.matched_repository_grid(trans, **kwd)
pyproject.toml
+1 -1
View File
@@ -106,7 +106,7 @@ requests = "*"
rocrate = "*"
Routes = "*"
schema-salad = "!=8.3.20220721194857" # https://github.com/common-workflow-language/schema_salad/issues/575
social-auth-core = {version = "*", extras = ["openidconnect"]}
social-auth-core = ">=4.5.0" # to drop dependency on abandoned python-jose
sortedcontainers = "*"
SQLAlchemy = ">=1.4.25,<2"
sqlitedict = "*"
test/unit/app/jobs/test_command_factory.py
+1 -6
View File
@@ -64,12 +64,7 @@ class TestCommandFactory(TestCase):
dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
self.job_wrapper.dependency_shell_commands = dep_commands
self._assert_command_is(
self._surround_command(
"{} {}/tool_script.sh".format(
self.job_wrapper.shell,
self.job_wrapper.working_directory,
)
)
self._surround_command(f"{self.job_wrapper.shell} {self.job_wrapper.working_directory}/tool_script.sh")
)
self.__assert_tool_script_is(f"#!/bin/sh\n{dep_commands[0]}; {MOCK_COMMAND_LINE}")
test/unit/app/queue_worker/conftest.py
+1 -1
View File
@@ -50,7 +50,7 @@ def sqlite_app(sqlite_connection):
@pytest.fixture()
def postgres_app(postgresql_proc):
connection = "postgresql://{p.user}@{p.host}:{p.port}/".format(p=postgresql_proc)
connection = f"postgresql://{postgresql_proc.user}@{postgresql_proc.host}:{postgresql_proc.port}/"
def create_app():
return create_base_test(connection, amqp_type="postgres")
test/unit/files/_util.py
+4 -10
View File
@@ -94,23 +94,17 @@ def realize_to_temp_file(file_sources, uri, user_context=None):
def assert_realizes_as(file_sources, uri, expected, user_context=None):
realized_contents = realize_to_temp_file(file_sources, uri, user_context=user_context)
if realized_contents != expected:
message = "Expected to realize contents at [{}] as [{}], instead found [{}]".format(
uri,
expected,
realized_contents,
raise AssertionError(
f"Expected to realize contents at [{uri}] as [{expected}], instead found [{realized_contents}]"
)
raise AssertionError(message)
def assert_realizes_contains(file_sources, uri, expected, user_context=None):
realized_contents = realize_to_temp_file(file_sources, uri, user_context=user_context)
if expected not in realized_contents:
message = "Expected to realize contents at [{}] to contain [{}], instead found [{}]".format(
uri,
expected,
realized_contents,
raise AssertionError(
f"Expected to realize contents at [{uri}] to contain [{expected}], instead found [{realized_contents}]"
)
raise AssertionError(message)
def assert_realizes_throws_exception(file_sources, uri, user_context=None) -> Exception: