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Merge pull request #6921 from nsoranzo/dependencies_update

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Update all dependencies
This commit is contained in:
Marius van den Beek
2018-10-26 13:14:42 +02:00
committed by GitHub
parent 79da3e554c a38a0add24
commit 2be4f3b2a1
74 changed files with 245 additions and 267 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/containers/docker.py
+2 -2
View File
@@ -276,12 +276,12 @@ class DockerAPIClient(object):
if tries > 1:
log.info('%s() succeeded on attempt %s', qualname, tries)
return r
except ConnectionError as exc:
except ConnectionError:
reinit = True
except docker.errors.APIError as exc:
if not DockerAPIClient._should_retry_request(exc.response.status_code):
raise
except ReadTimeout as exc:
except ReadTimeout:
reinit = True
retry_time = 0
finally:
lib/galaxy/containers/docker_model.py
+1 -1
View File
@@ -189,7 +189,7 @@ class DockerService(Container):
def from_cli(cls, interface, s, task_list):
service = cls(interface, s['ID'], name=s['NAME'], image=s['IMAGE'])
for task_dict in task_list:
if task_dict['NAME'].strip().startswith('\_'):
if task_dict['NAME'].strip().startswith(r'\_'):
continue # historical task
service.task_add(DockerTask.from_cli(interface, task_dict, service=service))
return service
lib/galaxy/containers/docker_swarm.py
+1 -1
View File
@@ -280,7 +280,7 @@ class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
def service_tasks(self, service):
for task_dict in self.service_ps(service.id):
if task_dict['NAME'].strip().startswith('\_'):
if task_dict['NAME'].strip().startswith(r'\_'):
continue # historical task
yield DockerTask.from_cli(self, task_dict, service=service)
lib/galaxy/datatypes/assembly.py
+5 -5
View File
@@ -174,15 +174,15 @@ class Velvet(Html):
log_path = os.path.join(efp, 'Log')
with open(log_path, 'r') as f:
log_content = f.read(1000)
log_msg = re.sub('/\S*/', '', log_content)
log_msg = re.sub(r'/\S*/', '', log_content)
log.debug("Velveth log info %s" % log_msg)
paired_end_reads = re.search('-(short|long)Paired', log_msg) is not None
paired_end_reads = re.search(r'-(short|long)Paired', log_msg) is not None
dataset.metadata.paired_end_reads = paired_end_reads
long_reads = re.search('-long', log_msg) is not None
long_reads = re.search(r'-long', log_msg) is not None
dataset.metadata.long_reads = long_reads
short2_reads = re.search('-short(Paired)?2', log_msg) is not None
short2_reads = re.search(r'-short(Paired)?2', log_msg) is not None
dataset.metadata.short2_reads = short2_reads
dataset.info = re.sub('.*velveth \S+', 'hash_length', re.sub('\n', ' ', log_msg))
dataset.info = re.sub(r'.*velveth \S+', 'hash_length', re.sub(r'\n', ' ', log_msg))
if paired_end_reads:
gen_msg = gen_msg + ' Paired-End Reads'
if long_reads:
lib/galaxy/datatypes/genetics.py
+2 -2
View File
@@ -32,8 +32,8 @@ gal_Log = logging.getLogger(__name__)
verbose = False
# https://genome.ucsc.edu/goldenpath/help/hgGenomeHelp.html
VALID_GENOME_GRAPH_MARKERS = re.compile('^(chr.*|RH.*|rs.*|SNP_.*|CN.*|A_.*)')
VALID_GENOTYPES_LINE = re.compile('^([a-zA-Z0-9]+)(\\s([0-9]{2}|[A-Z]{2}|NC|\?\?))+\\s*$')
VALID_GENOME_GRAPH_MARKERS = re.compile(r'^(chr.*|RH.*|rs.*|SNP_.*|CN.*|A_.*)')
VALID_GENOTYPES_LINE = re.compile(r'^([a-zA-Z0-9]+)(\s([0-9]{2}|[A-Z]{2}|NC|\?\?))+\s*$')
@build_sniff_from_prefix
lib/galaxy/datatypes/isa.py
+8 -22
View File
@@ -2,11 +2,10 @@
ISA datatype
See https://github.com/ISA-tools
"""
from __future__ import print_function
import io
import json
import logging
import os
@@ -16,14 +15,14 @@ import shutil
import sys
import tempfile
from cgi import escape
from json import dumps # noqa: F401
# Imports isatab after turning off warnings inside logger settings to avoid pandas warning making uploads fail.
logging.getLogger("isatools.isatab").setLevel(logging.ERROR)
from isatools import isajson
from isatools import isatab_meta
from isatools import (
isajson,
isatab_meta
)
from galaxy import model
from galaxy import util
from galaxy.datatypes import data
from galaxy.util.compression_utils import CompressedFile
@@ -89,22 +88,9 @@ class _Isa(data.Data):
################################################################
def _get_isa_folder_path(self, dataset):
isa_folder = None
if dataset:
if isinstance(dataset, model.Dataset):
isa_folder = dataset.extra_files_path
if isinstance(dataset, model.HistoryDatasetAssociation):
# XXX With this loop the dataset name is reset inside the history to the ISA archive ID. Why?
for attr, value in dataset.__dict__.iteritems():
if str(attr) == '_metadata_collection':
datatype = value.parent.datatype # noqa: F841
isa_folder = dataset.dataset.extra_files_path
if isa_folder is None:
isa_folder = dataset.extra_files_path
if not isa_folder:
raise Exception('Unvalid dataset object, or no extra files path found for this dataset.')
return isa_folder
# Get main file {{{2
@@ -176,7 +162,7 @@ class _Isa(data.Data):
raise RuntimeError("Unable to find the main file within the 'files_path' folder")
# Read first lines of main file
with open(main_file, "r") as f:
with io.open(main_file, encoding='utf-8') as f:
data = []
for line in f:
if len(data) < _MAX_LINES_HISTORY_PEEK:
lib/galaxy/datatypes/molecules.py
+3 -3
View File
@@ -45,7 +45,7 @@ def count_lines(filename, non_empty=False):
"""
try:
if non_empty:
out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE)
out = subprocess.Popen(['grep', '-cve', r'^\s*$', filename], stdout=subprocess.PIPE)
else:
out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
return int(out.communicate()[0].split()[0])
@@ -136,7 +136,7 @@ class SDF(GenericMolFile):
"""
Set the number of molecules in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$$", dataset.file_name)
dataset.metadata.number_of_molecules = count_special_lines(r"^\$\$\$\$$", dataset.file_name)
def split(cls, input_datasets, subdir_generator_function, split_params):
"""
@@ -717,7 +717,7 @@ class CML(GenericXml):
"""
Set the number of lines of data in dataset.
"""
dataset.metadata.number_of_molecules = count_special_lines('^\s*<molecule', dataset.file_name)
dataset.metadata.number_of_molecules = count_special_lines(r'^\s*<molecule', dataset.file_name)
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
lib/galaxy/datatypes/proteomics.py
+1 -1
View File
@@ -106,7 +106,7 @@ class ProteomicsXml(GenericXml):
if line is None or not line.startswith('<?'):
break
# pattern match <root or <ns:root for any ns string
pattern = '^<(\w*:)?%s' % self.root
pattern = r'^<(\w*:)?%s' % self.root
return line is not None and re.match(pattern, line) is not None
def set_peek(self, dataset, is_multi_byte=False):
lib/galaxy/datatypes/registry.py
+6 -6
View File
@@ -204,7 +204,7 @@ class Registry(object):
fields = dtype.split(':')
datatype_module = fields[0]
datatype_class_name = fields[1]
except Exception as e:
except Exception:
self.log.exception('Error parsing datatype definition for dtype %s', str(dtype))
ok = False
if ok:
@@ -234,13 +234,13 @@ class Registry(object):
module = getattr(module, mod)
datatype_class = getattr(module, datatype_class_name)
self.log.debug('Retrieved datatype module %s:%s from the datatype registry.' % (str(datatype_module), datatype_class_name))
except Exception as e:
except Exception:
self.log.exception('Error importing datatype module %s', str(datatype_module))
ok = False
elif type_extension is not None:
try:
datatype_class = self.datatypes_by_extension[type_extension].__class__
except Exception as e:
except Exception:
self.log.exception('Error determining datatype_class for type_extension %s', str(type_extension))
ok = False
if ok:
@@ -461,7 +461,7 @@ class Registry(object):
datatype_module = fields[0]
datatype_class_name = fields[1]
module = None
except Exception as e:
except Exception:
self.log.exception('Error determining datatype class or module for dtype %s', str(dtype))
ok = False
if ok:
@@ -477,13 +477,13 @@ class Registry(object):
module = __import__(datatype_module)
for comp in datatype_module.split('.')[1:]:
module = getattr(module, comp)
except Exception as e:
except Exception:
self.log.exception("Error importing datatype class for '%s'", str(dtype))
ok = False
if ok:
try:
aclass = getattr(module, datatype_class_name)()
except Exception as e:
except Exception:
self.log.exception('Error calling method %s from class %s', str(datatype_class_name), str(module))
ok = False
if ok:
lib/galaxy/datatypes/sequence.py
+4 -4
View File
@@ -366,7 +366,7 @@ class Fasta(Sequence):
# If there is a third line, and it isn't a header line, it may not contain chars like '()[].' otherwise it's most likely a DotBracket file
line = fh.readline()
if not line.startswith('>') and re.search("[\(\)\[\]\.]", line):
if not line.startswith('>') and re.search(r"[\(\)\[\]\.]", line):
break
return True
else:
@@ -529,7 +529,7 @@ class csFasta(Sequence):
break
elif line[0] not in string.ascii_uppercase:
return False
elif len(line) > 1 and not re.search('^[\d.]+$', line[1:]):
elif len(line) > 1 and not re.search(r'^[\d.]+$', line[1:]):
return False
return True
else:
@@ -1013,8 +1013,8 @@ class DotBracket(Sequence):
edam_format = "format_1457"
file_ext = "dbn"
sequence_regexp = re.compile("^[ACGTURYKMSWBDHVN]+$", re.I)
structure_regexp = re.compile("^[\(\)\.\[\]{}]+$")
sequence_regexp = re.compile(r"^[ACGTURYKMSWBDHVN]+$", re.I)
structure_regexp = re.compile(r"^[\(\)\.\[\]{}]+$")
def set_meta(self, dataset, **kwd):
"""
lib/galaxy/datatypes/tabular.py
+2 -2
View File
@@ -1124,12 +1124,12 @@ class ConnectivityTable(Tabular):
if not self.header_regexp.match(line):
return False
else:
length = int(re.split('\W+', line, 1)[0])
length = int(re.split(r'\W+', line, 1)[0])
else:
if not self.structure_regexp.match(line.upper()):
return False
else:
if j != int(re.split('\W+', line, 1)[0]):
if j != int(re.split(r'\W+', line, 1)[0]):
return False
elif j == length: # Last line of first sequence has been recheached
return True
lib/galaxy/datatypes/text.py
+1 -1
View File
@@ -416,7 +416,7 @@ class SnpEffDb(Text):
with gzip.open(path, 'rb') as fh:
buf = fh.read(100)
lines = buf.splitlines()
m = re.match('^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip())
m = re.match(r'^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip())
if m:
snpeff_version = m.groups()[0] + m.groups()[1]
except Exception:
lib/galaxy/datatypes/util/gff_util.py
+1 -1
View File
@@ -217,7 +217,7 @@ class GFFReaderWrapper(NiceReaderWrapper):
try:
interval = super(GenomicIntervalReader, self).__next__()
raw_size += len(self.current_line)
except StopIteration as e:
except StopIteration:
# No more intervals to read, but last feature needs to be
# returned.
interval = None
lib/galaxy/datatypes/xml.py
+1 -1
View File
@@ -39,7 +39,7 @@ class GenericXml(data.Text):
if line is None or not line.startswith('<?'):
break
# pattern match <root or <ns:root for any ns string
pattern = '^<(\w*:)?%s' % root
pattern = r'^<(\w*:)?%s' % root
return line is not None and re.match(pattern, line) is not None
def sniff_prefix(self, file_prefix):
lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+20 -22
View File
@@ -1,18 +1,18 @@
-i https://wheels.galaxyproject.org/simple
--extra-index-url https://pypi.python.org/simple
alabaster==0.7.11
alabaster==0.7.12
argh==0.26.2
atomicwrites==1.2.1; python_version != '3.3.*'
atomicwrites==1.2.1
attrs==18.2.0
babel==2.6.0
certifi==2018.8.24
certifi==2018.10.15
chardet==3.0.4
commonmark==0.5.4
docutils==0.14
funcsigs==1.0.2; python_version < '3.3'
funcsigs==1.0.2 ; python_version < '3.3'
gunicorn==19.9.0
idna==2.7
imagesize==1.1.0; python_version != '3.3.*'
imagesize==1.1.0
jinja2==2.10
lxml==4.2.5
markupsafe==1.0
@@ -20,32 +20,30 @@ mock==2.0.0
more-itertools==4.3.0
nose==1.3.7
nosehtml==0.4.5
packaging==17.1
pathlib2==2.3.2; python_version < '3.6'
pathlib2==2.3.2 ; python_version < '3.6'
pathtools==0.1.2
pbr==4.2.0
pluggy==0.7.1; python_version != '3.3.*'
py==1.6.0; python_version != '3.3.*'
pygithub3==0.5.1; python_version < '3'
pbr==5.1.0
pluggy==0.8.0
py==1.7.0
pygithub3==0.5.1 ; python_version < '3'
pygments==2.2.0
pyparsing==2.2.0
pytest-html==1.19.0
pytest-metadata==1.7.0
pytest-pythonpath==0.7.3
pytest==3.8.0
pytz==2018.5
pytest==3.9.2
pytz==2018.6
pyyaml==3.13
recommonmark==0.4.0
requests==2.19.1
scandir==1.9.0; python_version < '3.5'
selenium==3.14.0
requests==2.20.0
scandir==1.9.0 ; python_version < '3.5'
selenium==3.14.1
six==1.11.0
snowballstemmer==1.2.1
sphinx-rtd-theme==0.4.1
sphinx-rtd-theme==0.4.2
sphinx==1.6.7
sphinxcontrib-websupport==1.1.0; python_version != '3.3.*'
sphinxcontrib-websupport==1.1.0
testfixtures==6.3.0
twill==0.9.1; python_version < '3'
typing==3.6.6; python_version < '3.5'
urllib3==1.23; python_version >= '2.6'
twill==0.9.1 ; python_version < '3'
typing==3.6.6 ; python_version < '3.5'
urllib3==1.24
watchdog==0.9.0
lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+54 -54
View File
@@ -1,6 +1,6 @@
-i https://wheels.galaxyproject.org/simple
--extra-index-url https://pypi.python.org/simple
adal==1.1.0
adal==1.2.0
amqp==2.3.2
appdirs==1.4.3
asn1crypto==0.24.0
@@ -10,56 +10,56 @@ azure-cosmosdb-table==1.0.4
azure-mgmt-compute==4.0.1
azure-mgmt-devtestlabs==2.2.0
azure-mgmt-network==2.1.0
azure-mgmt-nspkg==2.0.0
azure-mgmt-nspkg==3.0.2
azure-mgmt-resource==2.0.0
azure-mgmt-storage==2.0.0
azure-nspkg==2.0.0
azure-nspkg==3.0.2
azure-storage-blob==1.3.1
azure-storage-common==1.3.0
azure-storage-nspkg==3.0.0
babel==2.6.0
bagit==1.6.4
bagit==1.7.0
bcrypt==3.1.4
bdbag==1.4.1
bdbag==1.5.0
beaker==1.10.0
bioblend==0.11.0
bleach==2.1.4
bleach==3.0.2
boltons==18.0.1
boto3==1.7.84
boto==2.49.0
botocore==1.10.84
bunch==1.0.1
bx-python==0.8.2
bz2file==0.98; python_version < '3.3'
certifi==2018.8.24
bz2file==0.98 ; python_version < '3.3'
cachetools==2.1.0
certifi==2018.10.15
cffi==1.11.5
chardet==3.0.4
cheetah3==3.1.0
cliff==2.13.0; python_version >= '2.6'
cliff==2.13.0
cloudauthz==0.2.0
cloudbridge==1.0.1
cloudbridge==1.0.2
cmd2==0.8.9
contextlib2==0.5.5; python_version < '3.5'
contextlib2==0.5.5 ; python_version < '3.5'
cryptography==2.3.1
debtcollector==1.20.0
decorator==4.3.0
deprecation==2.0.5
deprecation==2.0.6
dictobj==0.4
docopt==0.6.2
docutils==0.14
dogpile.cache==0.6.7
enum34==1.1.6; python_version < '3.4'
enum34==1.1.6 ; python_version < '3.4'
fabric3==1.14.post1
funcsigs==1.0.2; python_version < '3.3'
functools32==3.2.3.post2; python_version == '2.7'
funcsigs==1.0.2 ; python_version < '3.3'
functools32==3.2.3.post2 ; python_version == '2.7'
future==0.16.0
futures==3.2.0; python_version == '2.6' or python_version == '2.7'
futures==3.2.0 ; python_version == '2.6' or python_version == '2.7'
galaxy-sequence-utils==1.1.3
gxformat2==0.6.0
gxformat2==0.7.1
h5py==2.8.0
html5lib==1.0.1
idna==2.7
ipaddress==1.0.22; python_version < '3.3'
ipaddress==1.0.22 ; python_version < '3.3'
isa-rwval==0.10.7
iso8601==0.1.12
isodate==0.6.0
@@ -71,8 +71,8 @@ keystoneauth1==3.11.0
kombu==4.2.1
mako==1.0.7
markupsafe==1.0
mercurial==3.7.3; python_version < '3'
monotonic==1.5; python_version == '2.7'
mercurial==3.7.3 ; python_version < '3'
monotonic==1.5
msgpack==0.5.6
msrest==0.5.5
msrestazure==0.5.0
@@ -82,44 +82,44 @@ netifaces==0.10.7
networkx==1.11
nodeenv==1.3.2
nose==1.3.7
numpy==1.15.1
numpy==1.15.3
oauthlib==2.1.0
openstacksdk==0.17.0; python_version >= '2.6'
os-client-config==1.31.2; python_version >= '2.6'
openstacksdk==0.17.0
os-client-config==1.31.2
os-service-types==1.3.0
osc-lib==1.11.1
oslo.config==6.4.0
oslo.config==6.6.2
oslo.context==2.21.0
oslo.i18n==3.21.0
oslo.log==3.39.0
oslo.serialization==2.27.0; python_version != '3.3.*'
oslo.utils==3.37.0; python_version != '3.3.*'
packaging==17.1
oslo.i18n==3.22.1
oslo.log==3.40.1
oslo.serialization==2.28.1
oslo.utils==3.37.1
packaging==18.0
paramiko==2.4.2
parsley==1.3
paste==2.0.3
paste==3.0.0
pastedeploy==1.5.2
pastescript==2.0.2
pbr==4.2.0
pbr==5.1.0
prettytable==0.7.2
psutil==5.4.7
pulsar-galaxy-lib==0.8.3
pyasn1==0.4.4
pycparser==2.18
pycparser==2.19
pycryptodome==3.6.6
pycryptodomex==3.6.6
pyinotify==0.9.6; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
pyjwkest==1.4.0
pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
pyjwkest==1.4.0 ; extra == 'openidconnect'
pyjwt==1.6.4
pykwalify==1.6.1
pynacl==1.2.1
pykwalify==1.7.0
pynacl==1.3.0
pyopenssl==18.0.0
pyparsing==2.2.0
pyperclip==1.6.4
pyparsing==2.2.2
pyperclip==1.7.0
pysam==0.14.1
pysftp==0.2.9
python-cinderclient==4.0.0
python-dateutil==2.7.3; python_version >= '2.7'
python-dateutil==2.7.3
python-genomespaceclient==1.1.0
python-glanceclient==2.12.0
python-keystoneclient==3.17.0
@@ -127,37 +127,37 @@ python-neutronclient==6.9.0
python-novaclient==11.0.0
python-openid==2.2.5
python-swiftclient==3.6.0
pytz==2018.5
pytz==2018.6
pyyaml==3.13
repoze.lru==0.7
requests-oauthlib==1.0.0
requests-toolbelt==0.8.0
requests==2.19.1
requests==2.20.0
requestsexceptions==1.4.0
rfc3986==1.1.0
routes==2.4.1
s3transfer==0.1.13
simplejson==3.16.0
six==1.11.0
social-auth-core==1.5.0
social-auth-core[openidconnect]==1.5.0
sqlalchemy-migrate==0.11.0
sqlalchemy-utils==0.33.4
sqlalchemy==1.2.11
sqlalchemy-utils==0.33.6
sqlalchemy==1.2.12
sqlparse==0.2.4
stevedore==1.29.0
subprocess32==3.5.2; python_version < '3.0'
stevedore==1.30.0
subprocess32==3.5.3 ; python_version < '3.0'
svgwrite==1.1.12
tempita==0.5.2
tenacity==4.12.0; python_version >= '2.6'
typing==3.6.6; python_version < '3.5'
tenacity==4.12.0
typing==3.6.6 ; python_version < '3.5'
tzlocal==1.5.1
unicodecsv==0.14.1; python_version < '3.0'
urllib3==1.23; python_version >= '2.6'
unicodecsv==0.14.1 ; python_version < '3.0'
urllib3==1.24
uwsgi==2.0.17.1
vine==1.1.4
warlock==1.3.0; python_version != '3.3.*'
wcwidth==0.1.7; sys_platform != 'win32'
warlock==1.3.0
wcwidth==0.1.7 ; sys_platform != 'win32'
webencodings==0.5.1
webob==1.8.2; python_version != '3.2.*'
webob==1.8.3
whoosh==2.7.4
wrapt==1.10.11
lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
+5 -5
View File
@@ -1,8 +1,8 @@
-i https://pypi.python.org/simple
configparser==3.5.0; python_version < '3.2'
enum34==1.1.6; python_version < '3.4'
configparser==3.5.0 ; python_version < '3.2'
enum34==1.1.6 ; python_version < '3.4'
flake8-import-order==0.18
flake8==3.5.0
flake8==3.6.0
mccabe==0.6.1
pycodestyle==2.3.1
pyflakes==1.6.0
pycodestyle==2.4.0
pyflakes==2.0.0
lib/galaxy/dependencies/pipfiles/update.sh
+10 -8
View File
@@ -42,14 +42,16 @@ for env in $ENVS; do
pipenv lock -r | sed -e 's/--hash[^[:space:]]*//g' -e 's/[[:space:]]*$//' > pinned-requirements.txt
pipenv lock -r --dev | sed -e 's/--hash[^[:space:]]*//g' -e 's/[[:space:]]*$//' > pinned-dev-requirements.txt
# Fix oscillating environment markers
sed -i.orig -e "s/^cffi==\([^;]\{1,\}\).*$/cffi==\1/" \
-e "s/^cmd2==\([^;]\{1,\}\).*$/cmd2==\1/" \
-e "s/^enum34==\([^;]\{1,\}\).*$/enum34==\1; python_version < '3.4'/" \
-e "s/^funcsigs==\([^;]\{1,\}\).*$/funcsigs==\1; python_version < '3.3'/" \
-e "s/^futures==\([^;]\{1,\}\).*$/futures==\1; python_version == '2.6' or python_version == '2.7'/" \
-e "s/^py2-ipaddress==\([^;]\{1,\}\).*$/py2-ipaddress==\1; python_version < '3'/" \
-e "s/^pyinotify==\([^;]\{1,\}\).*$/pyinotify==\1; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'/" \
-e "s/^subprocess32==\([^;]\{1,\}\).*$/subprocess32==\1; python_version < '3.0'/" \
sed -i.orig -e "s/^cffi==\([^ ;]\{1,\}\).*$/cffi==\1/" \
-e "s/^cmd2==\([^ ;]\{1,\}\).*$/cmd2==\1/" \
-e "s/^enum34==\([^ ;]\{1,\}\).*$/enum34==\1 ; python_version < '3.4'/" \
-e "s/^funcsigs==\([^ ;]\{1,\}\).*$/funcsigs==\1 ; python_version < '3.3'/" \
-e "s/^futures==\([^ ;]\{1,\}\).*$/futures==\1 ; python_version == '2.6' or python_version == '2.7'/" \
-e "s/^monotonic==\([^ ;]\{1,\}\).*$/monotonic==\1/" \
-e "s/^py2-ipaddress==\([^ ;]\{1,\}\).*$/py2-ipaddress==\1 ; python_version < '3'/" \
-e "s/^pyinotify==\([^ ;]\{1,\}\).*$/pyinotify==\1 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'/" \
-e "s/^python-dateutil==\([^ ;]\{1,\}\).*$/python-dateutil==\1/" \
-e "s/^subprocess32==\([^ ;]\{1,\}\).*$/subprocess32==\1 ; python_version < '3.0'/" \
pinned-requirements.txt pinned-dev-requirements.txt
done
lib/galaxy/jobs/dynamic_tool_destination.py
+1 -1
View File
@@ -644,7 +644,7 @@ class RuleValidator(object):
@return: validated rule and result of validation
"""
emailregex = "^[A-Za-z0-9\.\+_-]+@[A-Za-z0-9\._-]+\.[a-zA-Z]*$"
emailregex = r"^[A-Za-z0-9\.\+_-]+@[A-Za-z0-9\._-]+\.[a-zA-Z]*$"
if "users" in rule:
if isinstance(rule["users"], list):
lib/galaxy/jobs/handler.py
+1 -1
View File
@@ -494,7 +494,7 @@ class JobHandlerQueue(Monitors):
usage = self.app.quota_agent.get_usage(user=job.user, history=job.history)
if usage > quota:
return JOB_USER_OVER_QUOTA, job_destination
except AssertionError as e:
except AssertionError:
pass # No history, should not happen with an anon user
# Check total walltime limits
if (state == JOB_READY and
lib/galaxy/jobs/metrics/instrumenters/env.py
+1 -1
View File
@@ -48,7 +48,7 @@ class EnvPlugin(InstrumentPlugin):
# We use '\n\}\n' as regex termination because shell
# functions can be nested.
# We use the non-greedy '.+?' because of re.DOTALL .
m = re.match('([^=]+)=(\(\) \{.+?\n\})\n', env_string, re.DOTALL)
m = re.match(r'([^=]+)=(\(\) \{.+?\n\})\n', env_string, re.DOTALL)
if m is None:
m = re.match('([^=]+)=(.*)\n', env_string)
if m is None:
lib/galaxy/jobs/runners/kubernetes.py
+1 -1
View File
@@ -188,7 +188,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
:rtype:
"""
if "k8s_galaxy_instance_id" in self.runner_params:
if re.match("(?!-)[a-z\d-]{1,20}(?<!-)$", self.runner_params['k8s_galaxy_instance_id']):
if re.match(r"(?!-)[a-z\d-]{1,20}(?<!-)$", self.runner_params['k8s_galaxy_instance_id']):
return self.runner_params['k8s_galaxy_instance_id']
else:
log.error("Galaxy instance '" + self.runner_params['k8s_galaxy_instance_id'] + "' is either too long "
lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
+1 -1
View File
@@ -19,7 +19,7 @@ class SlurmTorque(Torque):
for line in status.strip().splitlines():
if line.startswith("Job ID"):
continue
line_parts = re.compile("\s+").split(line)
line_parts = re.compile(r"\s+").split(line)
if len(line_parts) < 5:
continue
id = line_parts[0]
lib/galaxy/managers/collections.py
+1 -1
View File
@@ -548,7 +548,7 @@ class DatasetCollectionManager(object):
def __get_library_collection_instance(self, trans, id, check_ownership=False, check_accessible=True):
if check_ownership:
raise NotImplemented("Functionality (getting library dataset collection with ownership check) unimplemented.")
raise NotImplementedError("Functionality (getting library dataset collection with ownership check) unimplemented.")
instance_id = int(trans.security.decode_id(id))
collection_instance = trans.sa_session.query(trans.app.model.LibraryDatasetCollectionAssociation).get(instance_id)
if check_accessible:
lib/galaxy/managers/rbac_secured.py
+1 -1
View File
@@ -16,7 +16,7 @@ class RBACPermissionFailedException(galaxy.exceptions.InsufficientPermissionsExc
class RBACPermission(object):
"""
Base class for wrangling/controlling the permissions ORM models (\*Permissions, Roles)
Base class for wrangling/controlling the permissions ORM models (*Permissions, Roles)
that control which users can perform certain actions on their associated models
(Libraries, Datasets).
"""
lib/galaxy/managers/sharable.py
+3 -3
View File
@@ -244,7 +244,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
"""
Returns true if `slug` is valid.
"""
VALID_SLUG_RE = re.compile("^[a-z0-9\-]+$")
VALID_SLUG_RE = re.compile(r"^[a-z0-9\-]+$")
return VALID_SLUG_RE.match(slug)
def _existing_set_of_slugs(self, user):
@@ -259,9 +259,9 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
def _slugify(self, start_with):
# Replace whitespace with '-'
slug_base = re.sub("\s+", "-", start_with)
slug_base = re.sub(r"\s+", "-", start_with)
# Remove all non-alphanumeric characters.
slug_base = re.sub("[^a-zA-Z0-9\-]", "", slug_base)
slug_base = re.sub(r"[^a-zA-Z0-9\-]", "", slug_base)
# Remove trailing '-'.
if slug_base.endswith('-'):
slug_base = slug_base[:-1]
lib/galaxy/managers/tags.py
+2 -2
View File
@@ -281,7 +281,7 @@ class TagManager(object):
if not value:
return None
# Remove whitespace from value.
reg_exp = re.compile('\s')
reg_exp = re.compile(r'\s')
scrubbed_value = re.sub(reg_exp, "", value)
return scrubbed_value
@@ -291,7 +291,7 @@ class TagManager(object):
if not name:
return None
# Remove whitespace from name.
reg_exp = re.compile('\s')
reg_exp = re.compile(r'\s')
scrubbed_name = re.sub(reg_exp, "", name)
# Ignore starting ':' char.
if scrubbed_name.startswith(self.hierarchy_separator):
lib/galaxy/model/search.py
+1 -1
View File
@@ -553,7 +553,7 @@ view_mapping = {
# The GQL gramar is defined in Parsley syntax ( https://parsley.readthedocs.io/ )
gqlGrammar = """
gqlGrammar = r"""
expr = 'select' bs field_desc:f bs 'from' bs word:t (
bs 'where' bs conditional:c ws -> GalaxyQuery(f,t,c)
| ws -> GalaxyQuery(f, t, None) )
lib/galaxy/security/validate_user_input.py
+3 -3
View File
@@ -10,14 +10,14 @@ import re
log = logging.getLogger(__name__)
# Email validity parameters
VALID_EMAIL_RE = re.compile("[^@]+@[^@]+\.[^@]+")
VALID_EMAIL_RE = re.compile(r"[^@]+@[^@]+\.[^@]+")
EMAIL_MAX_LEN = 255
# Public name validity parameters
PUBLICNAME_MIN_LEN = 3
PUBLICNAME_MAX_LEN = 255
VALID_PUBLICNAME_RE = re.compile("^[a-z0-9._\-]+$")
VALID_PUBLICNAME_SUB = re.compile("[^a-z0-9._\-]")
VALID_PUBLICNAME_RE = re.compile(r"^[a-z0-9._\-]+$")
VALID_PUBLICNAME_SUB = re.compile(r"[^a-z0-9._\-]")
FILL_CHAR = '-'
# Password validity parameters
lib/galaxy/tools/__init__.py
+2 -2
View File
@@ -1703,7 +1703,7 @@ class Tool(Dictifiable):
tool_help = tool.help._source
# Check each line of the rendered tool help for an image tag that points to a location under static/
for help_line in tool_help.split('\n'):
image_regex = re.compile('img alt="[^"]+" src="\${static_path}/([^"]+)"')
image_regex = re.compile(r'img alt="[^"]+" src="\${static_path}/([^"]+)"')
matches = re.search(image_regex, help_line)
if matches is not None:
tool_help_image = matches.group(1)
@@ -2760,7 +2760,7 @@ class RelabelFromFileTool(DatabaseOperationTool):
dce_object = dce.element_object
add_copied_value_to_new_elements(new_labels[i], dce_object)
for key in new_elements.keys():
if not re.match("^[\w\-_]+$", key):
if not re.match(r"^[\w\-_]+$", key):
raise Exception("Invalid new colleciton identifier [%s]" % key)
self._add_datasets_to_history(history, itervalues(new_elements))
output_collections.create_collection(
lib/galaxy/tools/deps/brew_exts.py
+1 -1
View File
@@ -31,7 +31,7 @@ import string
import subprocess
import sys
WHITESPACE_PATTERN = re.compile("[\s]+")
WHITESPACE_PATTERN = re.compile(r"[\s]+")
DESCRIPTION = "Script built on top of linuxbrew to operate on isolated, versioned brew installed environments."
lib/galaxy/tools/deps/containers.py
+2 -2
View File
@@ -39,7 +39,7 @@ SINGULARITY_CONTAINER_TYPE = "singularity"
DEFAULT_CONTAINER_TYPE = DOCKER_CONTAINER_TYPE
ALL_CONTAINER_TYPES = [DOCKER_CONTAINER_TYPE, SINGULARITY_CONTAINER_TYPE]
LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = '''
LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = r'''
python << EOF
from __future__ import print_function
@@ -57,7 +57,7 @@ cmd = "${images_cmd}"
proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
stdo, stde = proc.communicate()
found = False
for line in stdo.split("\\n"):
for line in stdo.split("\n"):
tmp = re.split(r'\s+', line)
if tmp[0] == tag and tmp[1] == rev and tmp[2] == rev_value:
found = True
lib/galaxy/tools/deps/views.py
+5 -8
View File
@@ -1,7 +1,4 @@
from galaxy.exceptions import (
NotImplemented,
RequestParameterMissingException
)
from galaxy import exceptions
class DependencyResolversView(object):
@@ -34,7 +31,7 @@ class DependencyResolversView(object):
requirements = []
resolver = self._dependency_resolver(index)
if not hasattr(resolver, "list_dependencies"):
raise NotImplemented()
raise exceptions.NotImplemented()
for requirement in resolver.list_dependencies():
requirements.append(requirement.to_dict())
return requirements
@@ -128,7 +125,7 @@ class DependencyResolversView(object):
"""
resolver = self._dependency_resolver(index)
if not hasattr(resolver, "install_dependency"):
raise NotImplemented()
raise exceptions.NotImplemented()
name, version, type, extra_kwds = self._parse_dependency_info(payload)
return resolver.install_dependency(
@@ -157,7 +154,7 @@ class DependencyResolversView(object):
extra_kwds = kwds.copy()
name = extra_kwds.pop("name", None)
if name is None:
raise RequestParameterMissingException("Missing 'name' parameter required for resolution.")
raise exceptions.RequestParameterMissingException("Missing 'name' parameter required for resolution.")
version = extra_kwds.pop("version", None)
type = extra_kwds.pop("type", "package")
return name, version, type, extra_kwds
@@ -227,7 +224,7 @@ class DependencyResolversView(object):
if index:
resolver = self._dependency_resolver(index)
if not hasattr(resolver, "clean"):
raise NotImplemented()
raise exceptions.NotImplemented()
else:
resolver.clean()
return "OK"
lib/galaxy/tools/parameters/basic.py
+2 -2
View File
@@ -41,7 +41,7 @@ log = logging.getLogger(__name__)
workflow_building_modes = Bunch(DISABLED=False, ENABLED=True, USE_HISTORY=1)
WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile('''\$\{.+?\}''')
WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile(r'\$\{.+?\}')
def contains_workflow_parameter(value, search=False):
@@ -529,7 +529,7 @@ class FileToolParameter(ToolParameter):
# handle api upload
session_id = value["session_id"]
upload_store = trans.app.config.new_file_path
if re.match('^[\w-]+$', session_id) is None:
if re.match(r'^[\w-]+$', session_id) is None:
raise ValueError("Invald session id format.")
local_filename = os.path.abspath(os.path.join(upload_store, session_id))
else:
lib/galaxy/tools/parser/xml.py
+4 -4
View File
@@ -744,8 +744,8 @@ class StdioParser(object):
# Also note that whitespace is eliminated.
# TODO: Turn this into a single match - it should be
# more efficient.
code_range = re.sub("\s", "", code_range)
code_ranges = re.split(":", code_range)
code_range = re.sub(r"\s", "", code_range)
code_ranges = re.split(r":", code_range)
if (len(code_ranges) == 2):
if (code_ranges[0] is None or '' == code_ranges[0]):
exit_code.range_start = float("-inf")
@@ -827,8 +827,8 @@ class StdioParser(object):
output_srcs = regex_elem.get("sources")
if output_srcs is None:
output_srcs = "output,error"
output_srcs = re.sub("\s", "", output_srcs)
src_list = re.split(",", output_srcs)
output_srcs = re.sub(r"\s", "", output_srcs)
src_list = re.split(r",", output_srcs)
# Just put together anything to do with "out", including
# "stdout", "output", etc. Repeat for "stderr", "error",
# and anything to do with "err". If neither stdout nor
lib/galaxy/tools/verify/asserts/__init__.py
+1 -1
View File
@@ -21,7 +21,7 @@ for assertion_module_name in assertion_module_names:
__import__(full_assertion_module_name)
assertion_module = sys.modules[full_assertion_module_name]
assertion_modules.append(assertion_module)
except Exception as e:
except Exception:
log.exception('Failed to load assertion module: %s', assertion_module_name)
lib/galaxy/tools/verify/test_data.py
+1 -1
View File
@@ -23,7 +23,7 @@ UPDATE_FAILED_TEMPLATE = Template(
)
LIST_SEP = re.compile("\s*,\s*")
LIST_SEP = re.compile(r"\s*,\s*")
class TestDataResolver(object):
lib/galaxy/util/__init__.py
+7 -7
View File
@@ -640,9 +640,9 @@ def ready_name_for_url(raw_name):
"""
# Replace whitespace with '-'
slug_base = re.sub("\s+", "-", raw_name)
slug_base = re.sub(r"\s+", "-", raw_name)
# Remove all non-alphanumeric characters.
slug_base = re.sub("[^a-zA-Z0-9\-]", "", slug_base)
slug_base = re.sub(r"[^a-zA-Z0-9\-]", "", slug_base)
# Remove trailing '-'.
if slug_base.endswith('-'):
slug_base = slug_base[:-1]
@@ -957,7 +957,7 @@ def listify(item, do_strip=False):
def commaify(amount):
orig = amount
new = re.sub("^(-?\d+)(\d{3})", '\g<1>,\g<2>', amount)
new = re.sub(r"^(-?\d+)(\d{3})", r'\g<1>,\g<2>', amount)
if orig == new:
return new
else:
@@ -1256,7 +1256,7 @@ def umask_fix_perms(path, umask, unmasked_perms, gid=None):
perms = unmasked_perms & ~umask
try:
st = os.stat(path)
except OSError as e:
except OSError:
log.exception('Unable to set permissions or group on %s', path)
return
# fix modes
@@ -1364,8 +1364,8 @@ def size_to_bytes(size):
except ValueError:
pass
# Otherwise it must have non-numeric characters
size_re = re.compile('([\d\.]+)\s*([eptgmk]b?|b|bytes?)$')
size_match = re.match(size_re, size.lower())
size_re = re.compile(r'([\d\.]+)\s*([eptgmk]b?|b|bytes?)$')
size_match = size_re.match(size.lower())
assert size_match is not None
size = float(size_match.group(1))
multiple = size_match.group(2)
@@ -1557,7 +1557,7 @@ def parse_int(value, min_val=None, max_val=None, default=None, allow_none=False)
def parse_non_hex_float(s):
"""
r"""
Parse string `s` into a float but throw a `ValueError` if the string is in
the otherwise acceptable format `\d+e\d+` (e.g. 40000000000000e5.)
lib/galaxy/util/checkers.py
+5 -5
View File
@@ -30,11 +30,11 @@ def check_html(file_path, chunk=None):
temp = chunk.splitlines()
else:
temp = chunk
regexp1 = re.compile("<A\s+[^>]*HREF[^>]+>", re.I)
regexp2 = re.compile("<IFRAME[^>]*>", re.I)
regexp3 = re.compile("<FRAMESET[^>]*>", re.I)
regexp4 = re.compile("<META[\W][^>]*>", re.I)
regexp5 = re.compile("<SCRIPT[^>]*>", re.I)
regexp1 = re.compile(r"<A\s+[^>]*HREF[^>]+>", re.I)
regexp2 = re.compile(r"<IFRAME[^>]*>", re.I)
regexp3 = re.compile(r"<FRAMESET[^>]*>", re.I)
regexp4 = re.compile(r"<META[\W][^>]*>", re.I)
regexp5 = re.compile(r"<SCRIPT[^>]*>", re.I)
lineno = 0
# TODO: Potentially reading huge lines into string here, this should be
# reworked.
lib/galaxy/util/inflection.py
+3 -3
View File
@@ -45,9 +45,9 @@ class Base(object):
"underscored_word".
This can be really useful for creating friendly URLs.'''
return re.sub('[^A-Z^a-z^0-9^\/]+', '_',
re.sub('([a-z\d])([A-Z])', '\\1_\\2',
re.sub('([A-Z]+)([A-Z][a-z])', '\\1_\\2', re.sub('::', '/', word)))).lower()
return re.sub(r'[^A-Z^a-z^0-9^\/]+', r'_',
re.sub(r'([a-z\d])([A-Z])', r'\1_\2',
re.sub(r'([A-Z]+)([A-Z][a-z])', r'\1_\2', re.sub(r'::', r'/', word)))).lower()
def humanize(self, word, uppercase=''):
'''Returns a human-readable string from word
lib/galaxy/util/json.py
+4 -4
View File
@@ -109,7 +109,7 @@ def validate_jsonrpc_request(request, regular_methods, notification_methods):
data=str(e)))
try:
assert request['method'] in (regular_methods + notification_methods)
except AssertionError as e:
except AssertionError:
return False, request, jsonrpc_response(request=request,
error=dict(code=-32601,
message='Method not found',
@@ -142,14 +142,14 @@ def validate_jsonrpc_response(response, id=None):
'The "code" member of the "error" object in the Response is missing or not an integer.'
assert 'message' in response, \
'The "message" member of the "error" object in the Response is missing.'
except Exception as e:
log.error('Response was not valid JSON-RPC: %s' % str(e))
except Exception:
log.exception('Response was not valid JSON-RPC')
log.debug('Response was: %s' % response)
return False, response
if id is not None:
try:
assert 'id' in response and response['id'] == id
except Exception as e:
except Exception:
log.error('The response id "%s" does not match the request id "%s"' % (response['id'], id))
return False, response
return True, response
lib/galaxy/visualization/data_providers/genome.py
+1 -1
View File
@@ -653,7 +653,7 @@ class VcfDataProvider(GenomeDataProvider):
return ref_in_alt_index, alt[ref_in_alt_index + 1:], [[cig_ops.find("I"), alt_len - ref_len]]
# Pack data.
genotype_re = re.compile('/|\|')
genotype_re = re.compile(r'/|\|')
for count, line in enumerate(iterator):
if count < start_val:
continue
lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
+2 -2
View File
@@ -36,8 +36,8 @@ class Newick_Parser(Base_Parser):
return self.phyloTree.generateJsonableDict()
def cleanNewickString(self, rawNewick):
"""removing semi colon, and illegal json characters (\,',") and white spaces"""
return re.sub(r'\s|;|\"|\'|\\', '', rawNewick)
r"""removing semi colon, and illegal json characters (\,',") and white spaces"""
return re.sub(r'\s|;|\"|\'|\\', r'', rawNewick)
def _makeNodesFromString(self, string, depth):
"""elements separated by comma could be empty"""
lib/galaxy/web/base/controller.py
+1 -1
View File
@@ -57,7 +57,7 @@ SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
def _is_valid_slug(slug):
""" Returns true if slug is valid. """
VALID_SLUG_RE = re.compile("^[a-z0-9\-]+$")
VALID_SLUG_RE = re.compile(r"^[a-z0-9\-]+$")
return VALID_SLUG_RE.match(slug)
lib/galaxy/web/framework/middleware/batch.py
+3 -3
View File
@@ -58,9 +58,9 @@ class BatchMiddleware(object):
DEFAULT_CONFIG = {
'route' : '/api/batch',
'allowed_routes' : [
'^api\/users.*',
'^api\/histories.*',
'^api\/jobs.*',
r'^api\/users.*',
r'^api\/histories.*',
r'^api\/jobs.*',
]
}
lib/galaxy/webapps/galaxy/api/uploads.py
+8 -8
View File
@@ -5,7 +5,7 @@ import logging
import os
import re
from galaxy.exceptions import MessageException, NotImplemented
from galaxy import exceptions
from galaxy.web import expose_api_anonymous
from galaxy.web.base.controller import BaseAPIController
@@ -18,7 +18,7 @@ class UploadsAPIController(BaseAPIController):
@expose_api_anonymous
def index(self, trans, **kwd):
raise NotImplemented("Listing uploads is not implemented.")
raise exceptions.NotImplemented("Listing uploads is not implemented.")
@expose_api_anonymous
def create(self, trans, payload, **kwd):
@@ -28,21 +28,21 @@ class UploadsAPIController(BaseAPIController):
session_id = payload.get("session_id")
session_start = payload.get("session_start")
session_chunk = payload.get("session_chunk")
if re.match('^[\w-]+$', session_id) is None:
raise MessageException("Requires a session id.")
if re.match(r'^[\w-]+$', session_id) is None:
raise exceptions.MessageException("Requires a session id.")
if session_start is None:
raise MessageException("Requires a session start.")
raise exceptions.MessageException("Requires a session start.")
if not hasattr(session_chunk, "file"):
raise MessageException("Requires a session chunk.")
raise exceptions.MessageException("Requires a session chunk.")
target_file = os.path.join(trans.app.config.new_file_path, session_id)
target_size = 0
if os.path.exists(target_file):
target_size = os.path.getsize(target_file)
if session_start != target_size:
raise MessageException("Incorrect session start.")
raise exceptions.MessageException("Incorrect session start.")
chunk_size = os.fstat(session_chunk.file.fileno()).st_size
if chunk_size > trans.app.config.chunk_upload_size:
raise MessageException("Invalid chunk size.")
raise exceptions.MessageException("Invalid chunk size.")
with open(target_file, "ab") as f:
while True:
read_chunk = session_chunk.file.read(self.READ_CHUNK_SIZE)
lib/galaxy/webapps/galaxy/api/users.py
+2 -2
View File
@@ -568,13 +568,13 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cre
''' Validate email and username using regex '''
if email == '' or not isinstance(email, six.string_types):
return 'Please provide your email address.'
if not re.match('^(([^<>()[\]\\.,;:\s@\"]+(\.[^<>()[\]\\.,;:\s@\"]+)*)|(\".+\"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$', email):
if not re.match(r'^(([^<>()[\]\.,;:\s@"]+(\.[^<>()[\]\.,;:\s@"]+)*)|(".+"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$', email):
return 'Please provide your valid email address.'
if len(email) > 255:
return 'Email cannot be more than 255 characters in length.'
def _validate_publicname(self, username):
if not re.match('^[a-z0-9\-]{3,255}$', username):
if not re.match(r'^[a-z0-9\-]{3,255}$', username):
return 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 2.'
@expose_api
lib/galaxy/webapps/galaxy/controllers/forms.py
+1 -1
View File
@@ -11,7 +11,7 @@ from galaxy.web.framework.helpers import grids, iff, time_ago
log = logging.getLogger(__name__)
VALID_FIELDNAME_RE = re.compile("^[a-zA-Z0-9\_]+$")
VALID_FIELDNAME_RE = re.compile(r"^[a-zA-Z0-9\_]+$")
class FormsGrid(grids.Grid):
lib/galaxy/webapps/galaxy/controllers/page.py
+1 -1
View File
@@ -305,7 +305,7 @@ class _PageContentProcessor(HTMLParser, object):
Processes page content to produce HTML that is suitable for display.
For now, processor renders embedded objects.
"""
bare_ampersand = re.compile("&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)")
bare_ampersand = re.compile(r"&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)")
elements_no_end_tag = set([
'area', 'base', 'basefont', 'br', 'col', 'command', 'embed', 'frame',
'hr', 'img', 'input', 'isindex', 'keygen', 'link', 'meta', 'param',
lib/galaxy/webapps/tool_shed/api/tools.py
+6 -10
View File
@@ -3,14 +3,10 @@ import logging
from collections import namedtuple
from galaxy import (
exceptions,
util,
web
)
from galaxy.exceptions import (
ConfigDoesNotAllowException,
NotImplemented,
RequestParameterInvalidException
)
from galaxy.tools.parameters import params_to_strings
from galaxy.tools.repositories import ValidationContext
from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless
@@ -62,7 +58,7 @@ class ToolsController(BaseAPIController):
"""
q = kwd.get('q', '')
if not q:
raise NotImplemented('Listing of all the tools is not implemented. Provide parameter "q" to search instead.')
raise exceptions.NotImplemented('Listing of all the tools is not implemented. Provide parameter "q" to search instead.')
else:
page = kwd.get('page', 1)
page_size = kwd.get('page_size', 10)
@@ -70,7 +66,7 @@ class ToolsController(BaseAPIController):
page = int(page)
page_size = int(page_size)
except ValueError:
raise RequestParameterInvalidException('The "page" and "page_size" have to be integers.')
raise exceptions.RequestParameterInvalidException('The "page" and "page_size" have to be integers.')
return_jsonp = util.asbool(kwd.get('jsonp', False))
callback = kwd.get('callback', 'callback')
search_results = self._search(trans, q, page, page_size)
@@ -90,12 +86,12 @@ class ToolsController(BaseAPIController):
"""
conf = self.app.config
if not conf.toolshed_search_on:
raise ConfigDoesNotAllowException('Searching the TS through the API is turned off for this instance.')
raise exceptions.ConfigDoesNotAllowException('Searching the TS through the API is turned off for this instance.')
if not conf.whoosh_index_dir:
raise ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.')
raise exceptions.ConfigDoesNotAllowException('There is no directory for the search index specified. Please contact the administrator.')
search_term = q.strip()
if len(search_term) < 3:
raise RequestParameterInvalidException('The search term has to be at least 3 characters long.')
raise exceptions.RequestParameterInvalidException('The search term has to be at least 3 characters long.')
tool_search = ToolSearch()
lib/galaxy/webapps/tool_shed/controllers/repository.py
+2 -2
View File
@@ -2380,7 +2380,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
if os.path.isdir(absolute_selected_file):
try:
os.rmdir(absolute_selected_file)
except OSError as e:
except OSError:
# The directory is not empty
pass
elif os.path.isfile(absolute_selected_file):
@@ -2388,7 +2388,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
dir = os.path.split(absolute_selected_file)[0]
try:
os.rmdir(dir)
except OSError as e:
except OSError:
# The directory is not empty
pass
# Commit the change set.
lib/galaxy/webapps/tool_shed/controllers/upload.py
+1 -1
View File
@@ -116,7 +116,7 @@ class UploadController(BaseUIController):
else:
tar = tarfile.open(uploaded_file_name)
istar = True
except tarfile.ReadError as e:
except tarfile.ReadError:
tar = None
istar = False
else:
lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+1 -1
View File
@@ -768,7 +768,7 @@ class RegexReplace(RecipeStep):
def execute_step(self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False):
"""
r"""
Search and replace text in a file using regular expressions. Since this class is not used in the initial
download stage, no recipe step filtering is performed here, and None values are always returned for
filtered_actions and dir.
lib/tool_shed/util/commit_util.py
+2 -2
View File
@@ -192,7 +192,7 @@ def handle_directory_changes(app, host, username, repository, full_path, filenam
if os.path.isdir(absolute_selected_file):
try:
os.rmdir(absolute_selected_file)
except OSError as e:
except OSError:
# The directory is not empty.
pass
elif os.path.isfile(absolute_selected_file):
@@ -200,7 +200,7 @@ def handle_directory_changes(app, host, username, repository, full_path, filenam
dir = os.path.split(absolute_selected_file)[0]
try:
os.rmdir(dir)
except OSError as e:
except OSError:
# The directory is not empty.
pass
# See if any admin users have chosen to receive email alerts when a repository is updated.
lib/tool_shed/util/repository_util.py
+3 -3
View File
@@ -16,7 +16,7 @@ from tool_shed.util.web_util import escape
log = logging.getLogger(__name__)
VALID_REPOSITORYNAME_RE = re.compile("^[a-z0-9\_]+$")
VALID_REPOSITORYNAME_RE = re.compile(r"^[a-z0-9\_]+$")
def change_repository_name_in_hgrc_file(hgrc_file, new_name):
@@ -813,10 +813,10 @@ def get_tool_shed_status_for_installed_repository(app, repository):
# The value of text will be 'true' or 'false', depending upon whether there is an update available for the installed revision.
text = util.url_get(tool_shed_url, password_mgr=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
return dict(revision_update=text)
except Exception as e:
except Exception:
# The required tool shed may be unavailable, so default the revision_update value to 'false'.
return dict(revision_update='false')
except Exception as e:
except Exception:
log.exception("Error attempting to get tool shed status for installed repository %s", str(repository.name))
return {}
scripts/bootstrap_history.py
+1 -1
View File
@@ -626,7 +626,7 @@ def get_first_sentence(message):
def process_sentence(message):
# Strip tags like [15.07].
message = re.sub("^\s*\[.*\]\s*", "", message)
message = re.sub(r"^\s*\[.*\]\s*", r"", message)
# Link issues and pull requests...
issue_url = "https://github.com/%s/%s/issues" % (PROJECT_OWNER, PROJECT_NAME)
message = re.sub(r'#(\d+)', r'`#\1 <%s/\1>`__' % issue_url, message)
scripts/check_python.py
+1 -1
View File
@@ -39,5 +39,5 @@ def check_python():
if __name__ == '__main__':
try:
check_python()
except Exception as e:
except Exception:
sys.exit(1)
scripts/runtime_stats.py
+1 -1
View File
@@ -163,7 +163,7 @@ def query(tool_id=None, user=None, like=None, source='metrics',
if like:
query_tool_id = '%%/%s/%%' % tool_id
elif '/' in tool_id and not re.match('\d+\.\d+', tool_id.split('/')[-1]):
elif '/' in tool_id and not re.match(r'\d+\.\d+', tool_id.split('/')[-1]):
query_tool_id = '%s%%' % tool_id
like = True
else:
scripts/summarize_timings.py
+1 -1
View File
@@ -9,7 +9,7 @@ import numpy
DESCRIPTION = ""
TIMING_LINE_PATTERN = re.compile("\((\d+.\d+) ms\)")
TIMING_LINE_PATTERN = re.compile(r"\((\d+.\d+) ms\)")
def main(argv=None):
scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
+2 -2
View File
@@ -20,8 +20,8 @@ from bootstrap_util import admin_user_info # noqa: I100,I201
log = logging.getLogger(__name__)
VALID_PUBLICNAME_RE = re.compile("^[a-z0-9\-]+$")
VALID_EMAIL_RE = re.compile("[^@]+@[^@]+\.[^@]+")
VALID_PUBLICNAME_RE = re.compile(r"^[a-z0-9\-]+$")
VALID_EMAIL_RE = re.compile(r"[^@]+@[^@]+\.[^@]+")
class BootstrapApplication(object):
scripts/transfer.py
+1 -1
View File
@@ -282,7 +282,7 @@ def scp_transfer(transfer_job):
# TODO: add the ability to determine progress of the copy here like we do in the http_transfer above.
cmd = "scp %s@%s:'%s' '%s'" % (user_name,
host,
file_path.replace(' ', '\ '),
file_path.replace(' ', r'\ '),
fn)
pexpect.run(cmd, events={'.ssword:*': password + '\r\n',
pexpect.TIMEOUT: print_ticks},
setup.cfg
+1 -1
View File
@@ -7,7 +7,7 @@
# E741 do not use variables named 'l', 'O' or 'I'
# W503 is line breaks before binary operators, which has been reversed in PEP 8.
# D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
ignore = E128,E203,E501,E402,E741,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
ignore = E128,E203,E501,E402,E741,W503,W504,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
exclude = lib/galaxy/util/jstree.py
# For flake8-import-order
# https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py
test/functional/webhooks/phdcomics/__init__.py
+2 -2
View File
@@ -24,7 +24,7 @@ def main(trans, webhook, params):
url = 'http://phdcomics.com/gradfeed.php'
content = urlopen(url).read()
soap = BeautifulSoup(content, 'html.parser')
pattern = '(?:http://www\.phdcomics\.com/comics\.php\?f=)(\d+)'
pattern = r'(?:http://www\.phdcomics\.com/comics\.php\?f=)(\d+)'
webhook.config['latest_id'] = max([
int(re.search(pattern, link.text).group(1))
for link in soap.find_all('link', text=re.compile(pattern))
@@ -40,7 +40,7 @@ def main(trans, webhook, params):
try:
comic_src = comic_img[0].attrs.get('src')
except IndexError:
pattern = '<img id=comic2 name=comic2 src=([\w:\/\.]+)'
pattern = r'<img id=comic2 name=comic2 src=([\w:\/\.]+)'
comic_src = re.search(pattern, content).group(1)
except Exception as e:
test/selenium_tests/test_uploads.py
+3 -3
View File
@@ -190,13 +190,13 @@ PRJDA60709 SAMD00016382 DRX000480 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
self.rule_builder_set_mapping("list-identifiers", "C")
self.rule_builder_set_extension("fastqsanger.gz")
self.screenshot("rules_example_3_3_old_rules")
self.rule_builder_add_regex_groups("D", 2, "(.*);(.*)", screenshot_name="rules_example_3_4_regex")
self.rule_builder_add_regex_groups("D", 2, r"(.*);(.*)", screenshot_name="rules_example_3_4_regex")
self.screenshot("rules_example_3_6_with_regexes")
# Remove A also?
self.rule_builder_remove_columns(["D"], screenshot_name="rules_example_3_7_removed_column")
self.rule_builder_split_columns(["D"], ["E"], screenshot_name="rules_example_3_8_split_columns")
self.screenshot("rules_example_3_9_columns_are_split")
self.rule_builder_add_regex_groups("D", 1, ".*_(\d).fastq.gz", screenshot_name="rules_example_3_10_regex_paired")
self.rule_builder_add_regex_groups("D", 1, r".*_(\d).fastq.gz", screenshot_name="rules_example_3_10_regex_paired")
self.screenshot("rules_example_3_11_has_paired_id")
self.rule_builder_swap_columns("D", "E", screenshot_name="rules_example_3_12_swap_columns")
self.screenshot("rules_example_3_13_swapped_columns")
@@ -288,7 +288,7 @@ PRJDA60709 SAMD00016382 DRX000480 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
self.rule_builder_set_extension("sra")
self._scroll_to_end_of_table()
self.screenshot("rules_example_6_3_end_of_table")
self.rule_builder_add_regex_groups("L", 1, "([^\d]+)\d+", screenshot_name="rules_example_6_4_regex")
self.rule_builder_add_regex_groups("L", 1, r"([^\d]+)\d+", screenshot_name="rules_example_6_4_regex")
self.rule_builder_set_mapping("list-identifiers", ["M", "A"], screenshot_name="rules_example_6_5_multiple_identifiers_edit")
self._scroll_to_end_of_table()
self.screenshot("rules_example_6_6_multiple_identifiers")
test/shed_functional/base/twilltestcase.py
+1 -1
View File
@@ -1390,7 +1390,7 @@ class ShedTwillTestCase(FunctionalTestCase):
# installation process. This regex will return the tool shed repository IDs in group(1), the encoded_kwd parameter in
# group(2), and the reinstalling flag in group(3) and pass them to the manage_repositories method in the Galaxy
# admin_toolshed controller.
install_parameters = re.search('initiate_repository_installation\( "([^"]+)", "([^"]+)", "([^"]+)" \);', html)
install_parameters = re.search(r'initiate_repository_installation\( "([^"]+)", "([^"]+)", "([^"]+)" \);', html)
if install_parameters:
iri_ids = install_parameters.group(1)
# In some cases, the returned iri_ids are of the form: "[u'<encoded id>', u'<encoded id>']"
test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
-1
View File
@@ -324,7 +324,6 @@ class TestDynamicToolDestination(unittest.TestCase):
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'lame_cluster'.")
)
# ================================Invalid yaml files==============================
@log_capture()
def test_no_file(self, l):
test/unit/web/framework/test_webapp.py
+4 -4
View File
@@ -56,7 +56,7 @@ class GalaxyWebTransaction_Headers_TestCase(unittest.TestCase):
# should parse regex if using fwd slashes, string otherwise
hostnames = config._parse_allowed_origin_hostnames({
"allowed_origin_hostnames": "/host\d{2}/,geocities.com,miskatonic.edu"
"allowed_origin_hostnames": r"/host\d{2}/,geocities.com,miskatonic.edu"
})
self.assertTrue(isinstance(hostnames[0], re._pattern_type))
self.assertTrue(isinstance(hostnames[1], str))
@@ -80,13 +80,13 @@ class GalaxyWebTransaction_Headers_TestCase(unittest.TestCase):
self.assert_cors_header_equals(trans.response.headers, 'http://xxdarkhackerxx.disney.com')
# subdomains should pass
trans = self._new_trans(allowed_origin_hostnames='something.com,/^[\w\.]*beep\.com/')
trans = self._new_trans(allowed_origin_hostnames=r'something.com,/^[\w\.]*beep\.com/')
trans.request.headers['Origin'] = 'http://boop.beep.com'
trans.set_cors_headers()
self.assert_cors_header_equals(trans.response.headers, 'http://boop.beep.com')
# ports should work
trans = self._new_trans(allowed_origin_hostnames='somethingelse.com,/^[\w\.]*beep\.com/')
trans = self._new_trans(allowed_origin_hostnames=r'somethingelse.com,/^[\w\.]*beep\.com/')
trans.request.headers['Origin'] = 'http://boop.beep.com:8080'
trans.set_cors_headers()
self.assert_cors_header_equals(trans.response.headers, 'http://boop.beep.com:8080')
@@ -104,7 +104,7 @@ class GalaxyWebTransaction_Headers_TestCase(unittest.TestCase):
self.assert_cors_header_missing(trans.response.headers)
# unicode should work
trans = self._new_trans(allowed_origin_hostnames='/öbb\.at/')
trans = self._new_trans(allowed_origin_hostnames=r'/öbb\.at/')
trans.request.headers['Origin'] = 'http://öbb.at'
trans.set_cors_headers()
self.assertEqual(
tools/data_source/upload.py
+1 -1
View File
@@ -177,7 +177,7 @@ def add_composite_file(dataset, registry, output_path, files_path):
if dataset.file_type is not None:
try:
datatype = registry.get_datatype_by_extension(dataset.file_type)
except Exception as e:
except Exception:
print("Unable to instantiate the datatype object for the file type '%s'" % dataset.file_type)
if dataset.composite_files:
tools/extract/extract_genomic_dna.py
+1 -1
View File
@@ -212,7 +212,7 @@ def __main__():
nibs[chrom] = nib = bx.seq.nib.NibFile(open("%s/%s.nib" % (seq_path, chrom)))
try:
sequence = nib.get(start, end - start)
except Exception as e:
except Exception:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (start, end - start, dbkey)
warnings.append(warning)
if not invalid_lines:
tools/filters/convert_characters.py
+3 -3
View File
@@ -18,12 +18,12 @@ def __main__():
char_dict = {
'T': '\t',
's': '\s',
'Dt': '\.',
's': r'\s',
'Dt': r'\.',
'C': ',',
'D': '-',
'U': '_',
'P': '\|',
'P': r'\|',
'Co': ':',
'Sc': ';'
}
tools/filters/grep.py
+2 -2
View File
@@ -85,8 +85,8 @@ def main():
pattern = pattern.replace(value, key)
# match filename and invert flag
fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$")
invertRegEx = re.compile("(true)|(false)")
fileRegEx = re.compile(r"^[A-Za-z0-9./\-_]+$")
invertRegEx = re.compile(r"(true)|(false)")
# verify that filename and inversion flag are in the correct format
if not fileRegEx.match(outputfile):
tools/filters/uniq.py
+4 -4
View File
@@ -83,7 +83,7 @@ def main():
return -5
# All inputs have been specified at this point, now validate.
fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$")
fileRegEx = re.compile(r"^[A-Za-z0-9./\-_]+$")
columnRegEx = re.compile("([0-9]{1,},?)+")
if not columnRegEx.match(columns):
@@ -118,9 +118,9 @@ def main():
commandline += "-f " + columns
# we want to remove *trailing* spaces from each field,
# so look for spaces then tab (for first and middle selected columns)
# and replacw with just tab, and remove any spaces at end of the line
# and replace with just tab, and remove any spaces at end of the line
# (for the final selected column):
commandline += " " + inputfile + " | sed 's/\ *\t/\t/' | sed 's/\ *$//'"
commandline += " " + inputfile + r" | sed 's/\ *\t/\t/' | sed 's/\ *$//'"
commandline += " | sort | uniq -c"
# uniq -C puts counts at the start, so we can sort lines by numerical value
if sorting == "largest":
@@ -130,7 +130,7 @@ def main():
# uniq -C produces lines with leading spaces, use sed to remove that
# uniq -C puts a space between the count and the field, want a tab.
# To replace just first tab, use sed again with 1 as the index
commandline += " | sed 's/^\ *//' | sed 's/ /\t/1' > " + outputfile
commandline += r" | sed 's/^\ *//' | sed 's/ /\t/1' > " + outputfile
errorcode = subprocess.call(commandline, shell=True)
print("Count of unique values in " + columns_for_display)
tools/stats/filtering.py
+1 -1
View File
@@ -185,7 +185,7 @@ if not check_expression(cond_text):
# Work out which columns are used in the filter (save using 1 based counting)
used_cols = sorted(set(int(match.group()[1:])
for match in re.finditer('c(\d)+', cond_text)))
for match in re.finditer(r'c(\d)+', cond_text)))
largest_col_index = max(used_cols)
# Prepare the column variable names and wrappers for column data types. Only
tools/stats/gsummary.py
+1 -1
View File
@@ -42,7 +42,7 @@ def main():
if word and word not in math_allowed:
stop_err("Invalid expression '%s': term '%s' is not recognized or allowed" % (expression, word))
symbols = set()
for symbol in re.compile('[^a-z0-9\s]+').findall(expression):
for symbol in re.compile(r'[^a-z0-9\s]+').findall(expression):
if symbol and symbol not in ops_allowed:
stop_err("Invalid expression '%s': operator '%s' is not recognized or allowed" % (expression, symbol))
else: