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Python3: use log.warning() instead of deprecated log.warn()

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$ python3 -Wd -c 'import logging; logging.warn("foo")'
-c:1: DeprecationWarning: The 'warn' function is deprecated, use 'warning' instead
WARNING:root:foo
This commit is contained in:
Nicola Soranzo
2016-05-26 17:11:36 +01:00
parent 4eeb73ec8c
commit 03a92abdb6
38 changed files with 68 additions and 68 deletions
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lib/galaxy/auth/providers/ldap_ad.py
+2 -2
View File
@@ -135,7 +135,7 @@ class LDAP(AuthProvider):
# parse results
if suser is None or len(suser) == 0:
log.warn('LDAP authenticate: search returned no results')
log.warning('LDAP authenticate: search returned no results')
return (failure_mode, '', '')
dn, attrs = suser[0]
log.debug(("LDAP authenticate: dn is %s" % dn))
@@ -169,7 +169,7 @@ class LDAP(AuthProvider):
if whoami is None:
raise RuntimeError('LDAP authenticate: anonymous bind')
except Exception:
log.warn('LDAP authenticate: bind exception', exc_info=True)
log.warning('LDAP authenticate: bind exception', exc_info=True)
return (failure_mode, '', '')
log.debug('LDAP authentication successful')
lib/galaxy/datatypes/binary.py
+12 -12
View File
@@ -509,7 +509,7 @@ class CRAM( Binary ):
header = fh.read(6)
return ord( header[4] ), ord( header[5] )
except Exception as exc:
log.warn( '%s, get_cram_version Exception: %s', self, exc )
log.warning( '%s, get_cram_version Exception: %s', self, exc )
return -1, -1
def set_index_file(self, dataset, index_file):
@@ -530,10 +530,10 @@ class CRAM( Binary ):
return index_file.file_name
else:
os.unlink( dataset_symlink )
log.warn( '%s, expected crai index not created for: %s', self, dataset.file_name )
log.warning( '%s, expected crai index not created for: %s', self, dataset.file_name )
return False
except Exception as exc:
log.warn( '%s, set_index_file Exception: %s', self, exc )
log.warning( '%s, set_index_file Exception: %s', self, exc )
return False
def set_peek( self, dataset, is_multi_byte=False ):
@@ -821,18 +821,18 @@ class SQlite ( Binary ):
cols = [col[0] for col in cur.description]
columns[table] = cols
except Exception as exc:
log.warn( '%s, set_meta Exception: %s', self, exc )
log.warning( '%s, set_meta Exception: %s', self, exc )
for table in tables:
try:
row_query = "SELECT count(*) FROM %s" % table
rowcounts[table] = c.execute(row_query).fetchone()[0]
except Exception as exc:
log.warn( '%s, set_meta Exception: %s', self, exc )
log.warning( '%s, set_meta Exception: %s', self, exc )
dataset.metadata.tables = tables
dataset.metadata.table_columns = columns
dataset.metadata.table_row_count = rowcounts
except Exception as exc:
log.warn( '%s, set_meta Exception: %s', self, exc )
log.warning( '%s, set_meta Exception: %s', self, exc )
def sniff( self, filename ):
# The first 16 bytes of any SQLite3 database file is 'SQLite format 3\0', and the file is binary. For details
@@ -903,7 +903,7 @@ class GeminiSQLite( SQlite ):
dataset.metadata.gemini_version = version
# TODO: Can/should we detect even more attributes, such as use of PED file, what was input annotation type, etc.
except Exception as e:
log.warn( '%s, set_meta Exception: %s', self, e )
log.warning( '%s, set_meta Exception: %s', self, e )
def sniff( self, filename ):
if super( GeminiSQLite, self ).sniff( filename ):
@@ -920,7 +920,7 @@ class GeminiSQLite( SQlite ):
return False
return True
except Exception as e:
log.warn( '%s, sniff Exception: %s', self, e )
log.warning( '%s, sniff Exception: %s', self, e )
return False
def set_peek( self, dataset, is_multi_byte=False ):
@@ -959,7 +959,7 @@ class MzSQlite( SQlite ):
return False
return True
except Exception as e:
log.warn( '%s, sniff Exception: %s', self, e )
log.warning( '%s, sniff Exception: %s', self, e )
return False
@@ -994,7 +994,7 @@ class IdpDB( SQlite ):
return False
return True
except Exception as e:
log.warn( '%s, sniff Exception: %s', self, e )
log.warning( '%s, sniff Exception: %s', self, e )
return False
def set_peek( self, dataset, is_multi_byte=False ):
@@ -1274,7 +1274,7 @@ class SearchGuiArchive ( CompressedArchive ):
fh.close()
tempzip.close()
except Exception as e:
log.warn( '%s, set_meta Exception: %s', self, e )
log.warning( '%s, set_meta Exception: %s', self, e )
def sniff( self, filename ):
try:
@@ -1284,7 +1284,7 @@ class SearchGuiArchive ( CompressedArchive ):
tempzip.close()
return is_searchgui
except Exception as e:
log.warn( '%s, sniff Exception: %s', self, e )
log.warning( '%s, sniff Exception: %s', self, e )
return False
def set_peek( self, dataset, is_multi_byte=False ):
lib/galaxy/datatypes/mothur.py
+2 -2
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@@ -301,7 +301,7 @@ class DistanceMatrix(Text):
dataset.metadata.sequence_count = int(''.join(line)) # seq count sometimes preceded by tab
break
except Exception as e:
log.warn("DistanceMatrix set_meta %s" % e)
log.warning("DistanceMatrix set_meta %s" % e)
class LowerTriangleDistanceMatrix(DistanceMatrix):
@@ -902,7 +902,7 @@ class SffFlow(Tabular):
flow_values = int(headers[0][0])
dataset.metadata.flow_values = flow_values
except Exception as e:
log.warn("SffFlow set_meta %s" % e)
log.warning("SffFlow set_meta %s" % e)
def make_html_table(self, dataset, skipchars=[]):
"""Create HTML table, used for displaying peek"""
lib/galaxy/datatypes/registry.py
+2 -2
View File
@@ -129,11 +129,11 @@ class Registry( object ):
make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) )
edam_format = elem.get( 'edam_format', None )
if edam_format and not make_subclass:
self.log.warn("Cannot specify edam_format without setting subclass to True, skipping datatype.")
self.log.warning("Cannot specify edam_format without setting subclass to True, skipping datatype.")
continue
edam_data = elem.get( 'edam_data', None )
if edam_data and not make_subclass:
self.log.warn("Cannot specify edam_data without setting subclass to True, skipping datatype.")
self.log.warning("Cannot specify edam_data without setting subclass to True, skipping datatype.")
continue
# Proprietary datatypes included in installed tool shed repositories will include two special attributes
# (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes.
lib/galaxy/datatypes/text.py
+2 -2
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@@ -528,14 +528,14 @@ class SnpSiftDbNSFP( Text ):
headers = lines[0].split('\t')
dataset.metadata.annotation = headers[4:]
except Exception as e:
log.warn("set_meta fname: %s %s" % (fname, str(e)))
log.warning("set_meta fname: %s %s" % (fname, str(e)))
finally:
fh.close()
if fname.endswith('.tbi'):
dataset.metadata.index = fname
self.regenerate_primary_file(dataset)
except Exception as e:
log.warn("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
lib/galaxy/jobs/metrics/collectl/processes.py
+1 -1
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@@ -185,7 +185,7 @@ class CollectlProcessSummarizer( object ):
if column == "AccumT":
# Only thing that makes sense is sum
if statistic_type != "max":
log.warn( "Only statistic max makes sense for AccumT" )
log.warning( "Only statistic max makes sense for AccumT" )
continue
value = sum( [ v.max for v in self.process_accum_statistics.itervalues() ] )
lib/galaxy/jobs/runners/local.py
+1 -1
View File
@@ -107,7 +107,7 @@ class LocalJobRunner( BaseJobRunner ):
try:
exit_code = int( open( exit_code_path, 'r' ).read() )
except Exception:
log.warn( "Failed to read exit code from path %s" % exit_code_path )
log.warning( "Failed to read exit code from path %s" % exit_code_path )
pass
stdout_file.seek( 0 )
stderr_file.seek( 0 )
lib/galaxy/jobs/runners/pulsar.py
+2 -2
View File
@@ -377,7 +377,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
for key, value in self.destination_defaults.iteritems():
if key in params:
if value is PARAMETER_SPECIFICATION_IGNORED:
log.warn( "Pulsar runner in selected configuration ignores parameter %s" % key )
log.warning( "Pulsar runner in selected configuration ignores parameter %s" % key )
continue
# if self.runner_params.get( key, None ):
# # Let plugin define defaults for some parameters -
@@ -668,7 +668,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
if PulsarJobRunner.__use_remote_datatypes_conf( client ):
remote_datatypes_config = remote_system_properties.get('galaxy_datatypes_config_file', None)
if not remote_datatypes_config:
log.warn(NO_REMOTE_DATATYPES_CONFIG)
log.warning(NO_REMOTE_DATATYPES_CONFIG)
remote_datatypes_config = os.path.join(remote_galaxy_home, 'datatypes_conf.xml')
metadata_kwds['datatypes_config'] = remote_datatypes_config
else:
lib/galaxy/managers/citations.py
+1 -1
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@@ -65,7 +65,7 @@ def parse_citation( elem, directory, citation_manager ):
citation_type = elem.attrib.get( 'type', None )
citation_class = CITATION_CLASSES.get( citation_type, None )
if not citation_class:
log.warn("Unknown or unspecified citation type: %s" % citation_type)
log.warning("Unknown or unspecified citation type: %s" % citation_type)
return None
return citation_class( elem, directory, citation_manager )
lib/galaxy/managers/tags.py
+1 -1
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@@ -136,7 +136,7 @@ class TagManager( object ):
# Create tag; if None, skip the tag (and log error).
tag = self._get_or_create_tag( lc_name )
if not tag:
log.warn( "Failed to create tag with name %s" % lc_name )
log.warning( "Failed to create tag with name %s" % lc_name )
return
# Create tag association based on item class.
item_tag_assoc_class = self.get_tag_assoc_class( item.__class__ )
lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
+1 -1
View File
@@ -37,7 +37,7 @@ def upgrade(migrate_engine):
try:
table.create()
except:
log.warn( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
log.warning( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
def downgrade(migrate_engine):
lib/galaxy/model/migrate/versions/0046_post_job_actions.py
+1 -1
View File
@@ -37,7 +37,7 @@ def upgrade(migrate_engine):
try:
table.create()
except:
log.warn( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
log.warning( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
def downgrade(migrate_engine):
lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
+1 -1
View File
@@ -26,7 +26,7 @@ def upgrade(migrate_engine):
try:
table.create()
except:
log.warn( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
log.warning( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
def downgrade(migrate_engine):
lib/galaxy/model/migrate/versions/0061_tasks.py
+1 -1
View File
@@ -38,7 +38,7 @@ def upgrade(migrate_engine):
try:
table.create()
except:
log.warn( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
log.warning( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
def downgrade(migrate_engine):
lib/galaxy/tools/__init__.py
+1 -1
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@@ -428,7 +428,7 @@ class Tool( object, Dictifiable ):
if self.profile >= 16.04 and VERSION_MAJOR < self.profile:
template = "The tool %s targets version %s of Galaxy, you should upgrade Galaxy to ensure proper functioning of this tool."
message = template % (self.id, self.profile)
log.warn(message)
log.warning(message)
# Get the (user visible) name of the tool
self.name = tool_source.parse_name()
lib/galaxy/tools/data/__init__.py
+3 -3
View File
@@ -340,7 +340,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
self._update_version()
else:
self.missing_index_file = filename
log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) )
log.warning( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) )
if filename not in self.filenames or not self.filenames[ filename ][ 'found' ]:
self.filenames[ filename ] = dict( found=found, filename=filename, from_shed_config=from_shed_config, tool_data_path=tool_data_path,
@@ -461,7 +461,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
line_error = "Line %i in tool data table '%s' is invalid (HINT: '%s' characters must be used to separate fields):\n%s" % ( ( i + 1 ), self.name, separator_char, line )
if errors is not None:
errors.append( line_error )
log.warn( line_error )
log.warning( line_error )
return rval
def get_column_name_list( self ):
@@ -590,7 +590,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
values = self._replace_field_separators( values )
self.filter_file_fields( filename, values )
else:
log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) )
log.warning( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) )
self.reload_from_files()
lib/galaxy/tools/deps/__init__.py
+3 -3
View File
@@ -78,9 +78,9 @@ class DependencyManager( object ):
in `base_paths`. The default base path is app.config.tool_dependency_dir.
"""
if not os.path.exists( default_base_path ):
log.warn( "Path '%s' does not exist, ignoring", default_base_path )
log.warning( "Path '%s' does not exist, ignoring", default_base_path )
if not os.path.isdir( default_base_path ):
log.warn( "Path '%s' is not directory, ignoring", default_base_path )
log.warning( "Path '%s' is not directory, ignoring", default_base_path )
self.extra_config = extra_config
self.default_base_path = os.path.abspath( default_base_path )
self.resolver_classes = self.__resolvers_dict()
@@ -98,7 +98,7 @@ class DependencyManager( object ):
**kwds )
dependency_commands = dependency.shell_commands( requirement )
if not dependency_commands:
log.warn( "Failed to resolve dependency on '%s', ignoring", requirement.name )
log.warning( "Failed to resolve dependency on '%s', ignoring", requirement.name )
else:
commands.append( dependency_commands )
return commands
lib/galaxy/tools/deps/resolvers/conda.py
+1 -1
View File
@@ -102,7 +102,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
job_directory = kwds.get("job_directory", None)
if job_directory is None:
log.warn("Conda dependency resolver not sent job directory.")
log.warning("Conda dependency resolver not sent job directory.")
return INDETERMINATE_DEPENDENCY
exact = not self.versionless or version is None
lib/galaxy/tools/deps/resolvers/galaxy_packages.py
+1 -1
View File
@@ -97,7 +97,7 @@ class GalaxyPackageDependency(Dependency):
def shell_commands( self, requirement ):
base_path = self.path
if self.script is None and base_path is None:
log.warn( "Failed to resolve dependency on '%s', ignoring", requirement.name )
log.warning( "Failed to resolve dependency on '%s', ignoring", requirement.name )
commands = None
elif requirement.type == 'package' and self.script is None:
commands = 'PACKAGE_BASE=%s; export PACKAGE_BASE; PATH="%s/bin:$PATH"; export PATH' % ( base_path, base_path )
lib/galaxy/tools/deps/resolvers/modules.py
+1 -1
View File
@@ -74,7 +74,7 @@ class DirectoryModuleChecker(object):
self.module_dependency_resolver = module_dependency_resolver
self.directories = modulepath.split(pathsep)
if prefetch:
log.warn("Created module dependency resolver with prefetch enabled, but directory module checker does not support this.")
log.warning("Created module dependency resolver with prefetch enabled, but directory module checker does not support this.")
def has_module(self, module, version):
has_module = False
lib/galaxy/tools/execute.py
+2 -2
View File
@@ -109,7 +109,7 @@ class ToolExecutionTracker( object ):
def record_error( self, error ):
self.failed_jobs += 1
message = "There was a failure executing a job for tool [%s] - %s"
log.warn(message, self.tool.id, error)
log.warning(message, self.tool.id, error)
self.execution_errors.append( error )
def create_output_collections( self, trans, history, params ):
@@ -137,7 +137,7 @@ class ToolExecutionTracker( object ):
if not len( structure ) == len( outputs ):
# Output does not have the same structure, if all jobs were
# successfully submitted this shouldn't have happened.
log.warn( "Problem matching up datasets while attempting to create implicit dataset collections")
log.warning( "Problem matching up datasets while attempting to create implicit dataset collections")
continue
output = self.tool.outputs[ output_name ]
element_identifiers = structure.element_identifiers_for_outputs( trans, outputs )
lib/galaxy/tools/loader_directory.py
+1 -1
View File
@@ -26,7 +26,7 @@ CWL_EXTENSIONS = YAML_EXTENSIONS + [".cwl"]
def load_exception_handler(path, exc_info):
"""Default exception handler for use by load_tool_elements_from_path."""
log.warn(LOAD_FAILURE_ERROR % path, exc_info=exc_info)
log.warning(LOAD_FAILURE_ERROR % path, exc_info=exc_info)
def find_possible_tools_from_path(
lib/galaxy/tools/parameters/dynamic_options.py
+3 -3
View File
@@ -491,7 +491,7 @@ class DynamicOptions( object ):
self.missing_index_file = self.tool_data_table.missing_index_file
else:
self.missing_tool_data_table_name = tool_data_table_name
log.warn( "Data table named '%s' is required by tool but not configured" % tool_data_table_name )
log.warning( "Data table named '%s' is required by tool but not configured" % tool_data_table_name )
# Options are defined by parsing tabular text data from a data file
# on disk, a dataset, or the value of another parameter
elif data_file is not None or dataset_file is not None or from_parameter is not None:
@@ -556,7 +556,7 @@ class DynamicOptions( object ):
except AttributeError:
name = "a configuration file"
# Perhaps this should be an error, but even a warning is useful.
log.warn( "Inconsistent number of fields (%i vs %i) in %s using separator %r, check line: %r" %
log.warning( "Inconsistent number of fields (%i vs %i) in %s using separator %r, check line: %r" %
( field_count, len( fields ), name, self.separator, line ) )
rval.append( fields )
return rval
@@ -587,7 +587,7 @@ class DynamicOptions( object ):
else:
# Pass just the first megabyte to parse_file_fields.
import StringIO
log.warn( "Attempting to load options from large file, reading just first megabyte" )
log.warning( "Attempting to load options from large file, reading just first megabyte" )
contents = open( path, 'r' ).read( 1048576 )
options = self.parse_file_fields( StringIO.StringIO( contents ) )
elif self.tool_data_table:
lib/galaxy/tools/parser/xml.py
+1 -1
View File
@@ -129,7 +129,7 @@ class XmlToolSource(ToolSource):
command_el = self._command_el
interpreter = (command_el is not None) and command_el.get("interpreter", None)
if not self.legacy_defaults:
log.warn("Deprecated interpeter attribute on command element is now ignored.")
log.warning("Deprecated interpeter attribute on command element is now ignored.")
interpreter = None
return interpreter
lib/galaxy/util/__init__.py
+2 -2
View File
@@ -729,7 +729,7 @@ def rst_to_html( s ):
class FakeStream( object ):
def write( self, str ):
if len( str ) > 0 and not str.isspace():
log.warn( str )
log.warning( str )
settings_overrides = {
"embed_stylesheet": False,
@@ -1351,7 +1351,7 @@ def config_directories_from_setting( directories_setting, galaxy_root=galaxy_roo
if not directory.startswith( '/' ):
directory = os.path.join( galaxy_root, directory )
if not os.path.exists( directory ):
log.warn( 'directory not found: %s', directory )
log.warning( 'directory not found: %s', directory )
continue
directories.append( directory )
return directories
lib/galaxy/visualization/plugins/config_parser.py
+1 -1
View File
@@ -283,7 +283,7 @@ class DataSourceParser( object ):
test_type = test_elem.get( 'type', 'eq' )
test_result = test_elem.text.strip() if test_elem.text else None
if not test_type or not test_result:
log.warn( 'Skipping test. Needs both type attribute and text node to be parsed: ' +
log.warning( 'Skipping test. Needs both type attribute and text node to be parsed: ' +
'%s, %s' % ( test_type, test_elem.text ) )
continue
test_result = test_result.strip()
lib/galaxy/visualization/plugins/registry.py
+1 -1
View File
@@ -203,7 +203,7 @@ class VisualizationsRegistry( pluginframework.PageServingPluginManager ):
if not test_result:
# but continue (with other tests) if can't find class by that name
# if self.debug:
# log.warn( 'visualizations_registry cannot find class (%s)' +
# log.warning( 'visualizations_registry cannot find class (%s)' +
# ' for applicability test on: %s, id: %s', datatype_class_name,
# target_object, getattr( target_object, 'id', '' ) )
continue
lib/galaxy/visualization/plugins/resource_parser.py
+2 -2
View File
@@ -78,7 +78,7 @@ class ResourceParser( object ):
if trans.debug:
raise
else:
log.warn( 'Exception parsing visualization param from query: %s, %s, (%s) %s',
log.warning( 'Exception parsing visualization param from query: %s, %s, (%s) %s',
param_name, query_val, str( type( exception ) ), str( exception ) )
resource = None
@@ -109,7 +109,7 @@ class ResourceParser( object ):
config_val = self.parse_parameter( trans, param_config, config_val )
except Exception as exception:
log.warn( 'Exception parsing visualization param from query: ' +
log.warning( 'Exception parsing visualization param from query: ' +
'%s, %s, (%s) %s' % ( param_name, config_val, str( type( exception ) ), str( exception ) ))
config_val = None
lib/galaxy/web/base/controller.py
+1 -1
View File
@@ -80,7 +80,7 @@ class BaseController( object ):
# this should be here - but catching errors from sharable item controllers that *should* have SharableItemMixin
# but *don't* then becomes difficult
# def security_check( self, trans, item, check_ownership=False, check_accessible=False ):
# log.warn( 'BaseController.security_check: %s, %b, %b', str( item ), check_ownership, check_accessible )
# log.warning( 'BaseController.security_check: %s, %b, %b', str( item ), check_ownership, check_accessible )
# # meant to be overridden in SharableSecurityMixin
# return item
lib/galaxy/web/base/pluginframework.py
+1 -1
View File
@@ -93,7 +93,7 @@ class PluginManager( object ):
# NOTE: prevent silent, implicit overwrite here (two plugins in two diff directories)
# TODO: overwriting may be desired
elif plugin and plugin.name in self.plugins:
log.warn( '%s, plugin with name already exists: %s. Skipping...', self, plugin.name )
log.warning( '%s, plugin with name already exists: %s. Skipping...', self, plugin.name )
except Exception:
if not self.skip_bad_plugins:
lib/galaxy/webapps/galaxy/controllers/dataset.py
+1 -1
View File
@@ -473,7 +473,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
assert trans.user.id == hda.history.user_id, "HistoryDatasetAssocation does not belong to current user"
hdas.append( hda )
else:
log.warn( "Invalid history_dataset_association id '%r' passed to list", hda_id )
log.warning( "Invalid history_dataset_association id '%r' passed to list", hda_id )
if hdas:
if operation == "switch" or operation == "switch_history":
lib/galaxy/webapps/galaxy/controllers/history.py
+1 -1
View File
@@ -283,7 +283,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
assert trans.user.id == history.user_id, "History does not belong to current user"
histories.append( history )
else:
log.warn( "Invalid history id '%r' passed to list", history_id )
log.warning( "Invalid history id '%r' passed to list", history_id )
if histories:
if operation == "switch":
status, message = self._list_switch( trans, histories )
lib/galaxy/workflow/extract.py
+3 -3
View File
@@ -97,7 +97,7 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_
# Tool steps
for job_id in job_ids:
if job_id not in jobs_by_id:
log.warn( "job_id %s not found in jobs_by_id %s" % ( job_id, jobs_by_id ) )
log.warning( "job_id %s not found in jobs_by_id %s" % ( job_id, jobs_by_id ) )
raise AssertionError( "Attempt to create workflow with job not connected to current history" )
job = jobs_by_id[ job_id ]
tool_inputs, associations = step_inputs( trans, job )
@@ -141,7 +141,7 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_
if hid is None:
template = "Failed to find matching implicit job - job is %s, jobs are %s, assoc_name is %s."
message = template % ( job.id, jobs, assoc.name )
log.warn( message )
log.warning( message )
raise Exception( "Failed to extract job." )
else:
if hasattr( assoc, "dataset" ):
@@ -241,7 +241,7 @@ class WorkflowSummary( object ):
job_hda = self.__original_hda( dataset_instance )
if not job_hda.creating_job_associations:
log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" )
log.warning( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" )
job = DatasetCollectionCreationJob( dataset_collection )
self.jobs[ job ] = [ ( None, dataset_collection ) ]
lib/tool_shed/galaxy_install/install_manager.py
+2 -2
View File
@@ -465,7 +465,7 @@ class InstallRepositoryManager( object ):
message = "Error attempting to retrieve installation information from tool shed "
message += "%s for revision %s of repository %s owned by %s: %s" % \
( str( tool_shed_url ), str( changeset_revision ), str( name ), str( owner ), str( e ) )
log.warn( message )
log.warning( message )
raise exceptions.InternalServerError( message )
if raw_text:
# If successful, the response from get_repository_revision_install_info will be 3
@@ -478,7 +478,7 @@ class InstallRepositoryManager( object ):
else:
message = "Unable to retrieve installation information from tool shed %s for revision %s of repository %s owned by %s: %s" % \
( str( tool_shed_url ), str( changeset_revision ), str( name ), str( owner ), str( e ) )
log.warn( message )
log.warning( message )
raise exceptions.InternalServerError( message )
# Make sure the tool shed returned everything we need for installing the repository.
if not repository_revision_dict or not repo_info_dict:
lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
+2 -2
View File
@@ -119,10 +119,10 @@ class InstallEnvironment( object ):
stdout = output.stdout
stderr = output.stderr
if len( stdout ) > DATABASE_MAX_STRING_SIZE:
log.warn( "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) )
log.warning( "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) )
stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
if len( stderr ) > DATABASE_MAX_STRING_SIZE:
log.warn( "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) )
log.warning( "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) )
stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
if output.return_code not in [ 0 ]:
status = self.app.install_model.ToolDependency.installation_status.ERROR
lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+1 -1
View File
@@ -82,7 +82,7 @@ class CompressedFile( object ):
if os.path.exists( absolute_filepath ):
os.chmod( absolute_filepath, unix_permissions )
else:
log.warn("Unable to change permission on extracted file '%s' as it does not exist" % absolute_filepath)
log.warning("Unable to change permission on extracted file '%s' as it does not exist" % absolute_filepath)
return os.path.abspath( os.path.join( extraction_path, common_prefix ) )
def getmembers_tar( self ):
lib/tool_shed/util/common_util.py
+2 -2
View File
@@ -161,7 +161,7 @@ def get_repository_dependencies( app, tool_shed_url, repository_name, repository
tool_shed_accessible = True
except Exception as e:
tool_shed_accessible = False
log.warn( "The URL\n%s\nraised the exception:\n%s\n", util.build_url( tool_shed_url, pathspec=pathspec, params=params ), e )
log.warning( "The URL\n%s\nraised the exception:\n%s\n", util.build_url( tool_shed_url, pathspec=pathspec, params=params ), e )
if tool_shed_accessible:
if len( raw_text ) > 2:
encoded_text = json.loads( raw_text )
@@ -193,7 +193,7 @@ def get_tool_dependencies( app, tool_shed_url, repository_name, repository_owner
tool_shed_accessible = True
except Exception as e:
tool_shed_accessible = False
log.warn( "The URL\n%s\nraised the exception:\n%s\n", util.build_url( tool_shed_url, pathspec=pathspec, params=params ), e )
log.warning( "The URL\n%s\nraised the exception:\n%s\n", util.build_url( tool_shed_url, pathspec=pathspec, params=params ), e )
if tool_shed_accessible:
if text:
tool_dependencies_dict = encoding_util.tool_shed_decode( text )
lib/tool_shed/util/tool_dependency_util.py
+1 -1
View File
@@ -366,7 +366,7 @@ def remove_tool_dependency_installation_directory( dependency_install_dir ):
except Exception as e:
removed = False
error_message = "Error removing tool dependency installation directory %s: %s" % ( str( dependency_install_dir ), str( e ) )
log.warn( error_message )
log.warning( error_message )
else:
removed = True
error_message = ''