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Merge pull request #3933 from dannon/exception_logging_fixes

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Standardize usage of log.exception
This commit is contained in:
John Chilton
2017-04-21 08:54:24 -04:00
committed by GitHub
parent 01b3eb42d8 d43d7aa140
commit 386afbb4f6
60 changed files with 162 additions and 162 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/datatypes/data.py
+7 -7
View File
@@ -129,7 +129,7 @@ class Data( object ):
try:
return open(dataset.file_name, 'rb').read(-1)
except OSError:
log.exception('%s reading a file that does not exist %s' % (self.__class__.__name__, dataset.file_name))
log.exception('%s reading a file that does not exist %s', self.__class__.__name__, dataset.file_name)
return ''
def dataset_content_needs_grooming( self, file_name ):
@@ -229,7 +229,7 @@ class Data( object ):
archive.add(data_filename, archname)
except IOError:
error = True
log.exception("Unable to add composite parent %s to temporary library download archive" % data_filename)
log.exception("Unable to add composite parent %s to temporary library download archive", data_filename)
msg = "Unable to create archive for download, please report this error"
messagetype = "error"
return error, msg, messagetype
@@ -284,7 +284,7 @@ class Data( object ):
archive.add( fpath, rpath )
except IOError:
error = True
log.exception( "Unable to add %s to temporary library download archive" % rpath)
log.exception( "Unable to add %s to temporary library download archive", rpath)
msg = "Unable to create archive for download, please report this error"
continue
if not error:
@@ -439,7 +439,7 @@ class Data( object ):
try:
del self.supported_display_apps[app_id]
except:
log.exception('Tried to remove display app %s from datatype %s, but this display app is not declared.' % ( type, self.__class__.__name__ ) )
log.exception('Tried to remove display app %s from datatype %s, but this display app is not declared.', type, self.__class__.__name__ )
def clear_display_apps( self ):
self.supported_display_apps = {}
@@ -477,7 +477,7 @@ class Data( object ):
if type in self.get_display_types():
return getattr(self, self.supported_display_apps[type]['file_function'])(dataset, **kwd)
except:
log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible' % (self.supported_display_apps[type]['file_function'], self.__class__.__name__, type) )
log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible', self.supported_display_apps[type]['file_function'], self.__class__.__name__, type )
return "This display type (%s) is not implemented for this datatype (%s)." % ( type, dataset.ext)
def get_display_links( self, dataset, type, app, base_url, target_frame='_blank', **kwd ):
@@ -491,8 +491,8 @@ class Data( object ):
if app.config.enable_old_display_applications and type in self.get_display_types():
return target_frame, getattr( self, self.supported_display_apps[type]['links_function'] )( dataset, type, app, base_url, **kwd )
except:
log.exception( 'Function %s is referred to in datatype %s for generating links for type %s, but is not accessible'
% ( self.supported_display_apps[type]['links_function'], self.__class__.__name__, type ) )
log.exception( 'Function %s is referred to in datatype %s for generating links for type %s, but is not accessible',
self.supported_display_apps[type]['links_function'], self.__class__.__name__, type )
return target_frame, []
def get_converter_types(self, original_dataset, datatypes_registry):
lib/galaxy/datatypes/registry.py
+13 -13
View File
@@ -187,7 +187,7 @@ class Registry( object ):
datatype_module = fields[ 0 ]
datatype_class_name = fields[ 1 ]
except Exception as e:
self.log.exception( 'Error parsing datatype definition for dtype %s: %s' % ( str( dtype ), str( e ) ) )
self.log.exception( 'Error parsing datatype definition for dtype %s', str( dtype ) )
ok = False
if ok:
datatype_class = None
@@ -217,13 +217,13 @@ class Registry( object ):
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:
self.log.exception( 'Error importing datatype module %s: %s' % ( str( datatype_module ), str( e ) ) )
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:
self.log.exception( 'Error determining datatype_class for type_extension %s: %s' % ( str( type_extension ), str( e ) ) )
self.log.exception( 'Error determining datatype_class for type_extension %s', str( type_extension ) )
ok = False
if ok:
if not deactivate:
@@ -324,7 +324,7 @@ class Registry( object ):
def load_build_site( build_site_config ):
# Take in either an XML element or simple dictionary from YAML and add build site for this.
if not (build_site_config.get( 'type' ) and build_site_config.get( 'file' )):
self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" )
self.log.exception( "Site is missing required 'type' and 'file' attributes" )
return
site_type = build_site_config.get( 'type' )
@@ -397,7 +397,7 @@ class Registry( object ):
datatype_class_name = fields[ 1 ]
module = None
except Exception as e:
self.log.exception( 'Error determining datatype class or module for dtype %s: %s' % ( str( dtype ), str( e ) ) )
self.log.exception( 'Error determining datatype class or module for dtype %s', str( dtype ) )
ok = False
if ok:
if handling_proprietary_datatypes:
@@ -413,13 +413,13 @@ class Registry( object ):
for comp in datatype_module.split( '.' )[ 1: ]:
module = getattr( module, comp )
except Exception as e:
self.log.exception( "Error importing datatype class for '%s': %s" % ( str( dtype ), str( e ) ) )
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:
self.log.exception( 'Error calling method %s from class %s: %s', str( datatype_class_name ), str( module ), str( e ) )
self.log.exception( 'Error calling method %s from class %s', str( datatype_class_name ), str( module ) )
ok = False
if ok:
if deactivate:
@@ -560,11 +560,11 @@ class Registry( object ):
self.datatype_converters[ source_datatype ] = odict()
self.datatype_converters[ source_datatype ][ target_datatype ] = converter
self.log.debug( "Loaded converter: %s", converter.id )
except Exception as e:
except Exception:
if deactivate:
self.log.exception( "Error deactivating converter from (%s): %s" % ( converter_path, str( e ) ) )
self.log.exception( "Error deactivating converter from (%s)" % converter_path )
else:
self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) )
self.log.exception( "Error loading converter (%s)" % converter_path )
def load_display_applications( self, app, installed_repository_dict=None, deactivate=False ):
"""
@@ -628,11 +628,11 @@ class Registry( object ):
if inherit and ( self.datatypes_by_extension[ extension ], display_app ) not in self.inherit_display_application_by_class:
self.inherit_display_application_by_class.append( ( self.datatypes_by_extension[ extension ], display_app ) )
self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s." % ( display_app.id, extension, inherit ) )
except Exception as e:
except Exception:
if deactivate:
self.log.exception( "Error deactivating display application (%s): %s" % ( config_path, str( e ) ) )
self.log.exception( "Error deactivating display application (%s)" % config_path )
else:
self.log.exception( "Error loading display application (%s): %s" % ( config_path, str( e ) ) )
self.log.exception( "Error loading display application (%s)" % config_path )
# Handle display_application subclass inheritance.
for extension, d_type1 in self.datatypes_by_extension.iteritems():
for d_type2, display_app in self.inherit_display_application_by_class:
lib/galaxy/datatypes/tabular.py
+2 -2
View File
@@ -167,7 +167,7 @@ class TabularData( data.Text ):
out.append( '</th>' )
out.append( '</tr>' )
except Exception as exc:
log.exception( 'make_html_peek_header failed on HDA %s' % dataset.id )
log.exception( 'make_html_peek_header failed on HDA %s', dataset.id )
raise Exception( "Can't create peek header %s" % str( exc ) )
return "".join( out )
@@ -198,7 +198,7 @@ class TabularData( data.Text ):
out.append( '<td>%s</td>' % escape( elem ) )
out.append( '</tr>' )
except Exception as exc:
log.exception( 'make_html_peek_rows failed on HDA %s' % dataset.id )
log.exception( 'make_html_peek_rows failed on HDA %s', dataset.id )
raise Exception( "Can't create peek rows %s" % str( exc ) )
return "".join( out )
lib/galaxy/datatypes/text.py
+1 -1
View File
@@ -150,7 +150,7 @@ class Ipynb( Json ):
ofilename = '%s.html' % ofilename
except:
ofilename = dataset.file_name
log.exception( 'Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.' % cmd )
log.exception( 'Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.', cmd )
return open( ofilename )
def set_meta( self, dataset, **kwd ):
lib/galaxy/jobs/__init__.py
+3 -3
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@@ -631,8 +631,8 @@ class JobConfiguration( object, ConfiguresHandlers ):
try:
rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
except TypeError:
log.exception( "Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load"
% ( module_name, class_name ) )
log.exception( "Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load",
module_name, class_name )
rval[id] = runner_class( self.app )
log.debug( "Loaded job runner '%s:%s' as '%s'" % ( module_name, class_name, id ) )
return rval
@@ -1443,7 +1443,7 @@ class JobWrapper( object, HasResourceParameters ):
if delete_files:
self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, obj_dir=True)
except:
log.exception( "Unable to cleanup job %d" % self.job_id )
log.exception( "Unable to cleanup job %d", self.job_id )
def _collect_extra_files(self, dataset, job_working_directory):
temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( dataset.id ) )
lib/galaxy/jobs/deferred/__init__.py
+5 -5
View File
@@ -40,7 +40,7 @@ class DeferredJobQueue( object ):
try:
module = __import__( module_name )
except:
log.exception( 'Deferred job plugin appears to exist but is not loadable: %s' % module_name )
log.exception( 'Deferred job plugin appears to exist but is not loadable: %s', module_name )
continue
for comp in module_name.split( "." )[1:]:
module = getattr( module, comp )
@@ -105,16 +105,16 @@ class DeferredJobQueue( object ):
if job.is_check_time:
try:
job_state = self.plugins[job.plugin].check_job( job )
except Exception as e:
except Exception:
self.__fail_job( job )
log.exception( 'Set deferred job %s to error because of an exception in check_job(): %s' % ( job.id, str( e ) ) )
log.exception( 'Set deferred job %s to error because of an exception in check_job()' % job.id )
continue
if job_state == self.job_states.READY:
try:
self.plugins[job.plugin].run_job( job )
except Exception as e:
except Exception:
self.__fail_job( job )
log.exception( 'Set deferred job %s to error because of an exception in run_job(): %s' % ( job.id, str( e ) ) )
log.exception( 'Set deferred job %s to error because of an exception in run_job()' % job.id )
continue
elif job_state == self.job_states.INVALID:
self.__fail_job( job )
lib/galaxy/jobs/handler.py
+3 -3
View File
@@ -309,7 +309,7 @@ class JobHandlerQueue( object ):
log.error( "(%d) Job in unknown state '%s'" % ( job.id, job_state ) )
new_waiting_jobs.append( job.id )
except Exception:
log.exception( "failure running job %d" % job.id )
log.exception( "failure running job %d", job.id )
# Update the waiting list
if not self.track_jobs_in_database:
self.waiting_jobs = new_waiting_jobs
@@ -784,8 +784,8 @@ class DefaultJobDispatcher( object ):
runner_name = url.split(':', 1)[0]
try:
return self.job_runners[runner_name].url_to_destination(url)
except Exception as e:
log.exception("Unable to convert legacy job runner URL '%s' to job destination, destination will be the '%s' runner with no params: %s" % (url, runner_name, e))
except Exception:
log.exception("Unable to convert legacy job runner URL '%s' to job destination, destination will be the '%s' runner with no params", url, runner_name)
return JobDestination(runner=runner_name)
def put( self, job_wrapper ):
lib/galaxy/jobs/metrics/__init__.py
+3 -3
View File
@@ -94,7 +94,7 @@ class JobInstrumenter(object):
if plugin_commands:
commands.extend(util.listify(plugin_commands))
except Exception:
log.exception("Failed to generate pre-execute commands for plugin %s" % plugin)
log.exception("Failed to generate pre-execute commands for plugin %s", plugin)
return "\n".join([ c for c in commands if c ])
def post_execute_commands(self, job_directory):
@@ -105,7 +105,7 @@ class JobInstrumenter(object):
if plugin_commands:
commands.extend(util.listify(plugin_commands))
except Exception:
log.exception("Failed to generate post-execute commands for plugin %s" % plugin)
log.exception("Failed to generate post-execute commands for plugin %s", plugin)
return "\n".join([ c for c in commands if c ])
def collect_properties(self, job_id, job_directory):
@@ -116,7 +116,7 @@ class JobInstrumenter(object):
if properties:
per_plugin_properites[ plugin.plugin_type ] = properties
except Exception:
log.exception("Failed to collect job properties for plugin %s" % plugin)
log.exception("Failed to collect job properties for plugin %s", plugin)
return per_plugin_properites
def __plugins_from_source(self, plugins_source):
lib/galaxy/jobs/runners/__init__.py
+1 -1
View File
@@ -247,7 +247,7 @@ class BaseJobRunner( object ):
output_pairs.append( ( source_file, destination ) )
else:
# Security violation.
log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) )
log.exception( "from_work_dir specified a location not in the working directory: %s, %s", source_file, job_wrapper.working_directory )
return output_pairs
def _walk_dataset_outputs( self, job ):
lib/galaxy/jobs/runners/local.py
+1 -1
View File
@@ -120,7 +120,7 @@ class LocalJobRunner( BaseJobRunner ):
stderr_file.close()
log.debug('execution finished: %s' % command_line)
except Exception:
log.exception("failure running job %d" % job_wrapper.job_id)
log.exception("failure running job %d", job_wrapper.job_id)
self._fail_job_local(job_wrapper, "failure running job")
return
lib/galaxy/jobs/runners/pulsar.py
+5 -5
View File
@@ -299,7 +299,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
job_wrapper.change_state( model.Job.states.QUEUED )
except Exception:
job_wrapper.fail( "failure running job", exception=True )
log.exception("failure running job %d" % job_wrapper.job_id)
log.exception("failure running job %d", job_wrapper.job_id)
return
pulsar_job_state = AsynchronousJobState()
@@ -366,10 +366,10 @@ class PulsarJobRunner( AsynchronousJobRunner ):
)
except UnsupportedPulsarException as e:
job_wrapper.fail( e.message, exception=False )
log.exception("failure running job %d" % job_wrapper.job_id)
log.exception("failure running job %d", job_wrapper.job_id)
except Exception:
job_wrapper.fail( "failure preparing job", exception=True )
log.exception("failure running job %d" % job_wrapper.job_id)
log.exception("failure running job %d", job_wrapper.job_id)
# If we were able to get a command line, run the job
if not command_line:
@@ -488,7 +488,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
except Exception:
message = GENERIC_REMOTE_ERROR
job_wrapper.fail( message, exception=True )
log.exception("failure finishing job %d" % job_wrapper.job_id)
log.exception("failure finishing job %d", job_wrapper.job_id)
return
if not PulsarJobRunner.__remote_metadata( client ):
self._handle_metadata_externally( job_wrapper, resolve_requirements=True )
@@ -730,7 +730,7 @@ class PulsarMQJobRunner( PulsarJobRunner ):
job_state = self._job_state( job, job_wrapper )
self._update_job_state_for_status(job_state, full_status[ "status" ] )
except Exception:
log.exception( "Failed to update Pulsar job status for job_id %s" % job_id )
log.exception( "Failed to update Pulsar job status for job_id %s", job_id )
raise
# Nothing else to do? - Attempt to fail the job?
lib/galaxy/jobs/runners/tasks.py
+1 -1
View File
@@ -115,7 +115,7 @@ class TaskedJobRunner( BaseJobRunner ):
stdout, stderr = splitter.do_merge(job_wrapper, task_wrappers)
except Exception:
job_wrapper.fail( "failure running job", exception=True )
log.exception("failure running job %d" % job_wrapper.job_id)
log.exception("failure running job %d", job_wrapper.job_id)
return
# run the metadata setting script here
lib/galaxy/managers/citations.py
+1 -1
View File
@@ -150,7 +150,7 @@ class DoiCitation( BaseCitation ):
try:
self.raw_bibtex = self.doi_cache.get_bibtex(self.__doi)
except Exception:
log.exception("Failed to fetch bibtex for DOI %s" % self.__doi)
log.exception("Failed to fetch bibtex for DOI %s", self.__doi)
if self.raw_bibtex is DoiCitation.BIBTEX_UNSET:
return """@MISC{%s,
lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
+2 -2
View File
@@ -42,7 +42,7 @@ def upgrade(migrate_engine):
col.create( dataset_instance_table, index_name=index_name)
assert col is dataset_instance_table.c.state
except Exception:
log.exception("Adding column 'state' to %s table failed." % table_name)
log.exception("Adding column 'state' to %s table failed.", table_name)
def downgrade(migrate_engine):
@@ -60,4 +60,4 @@ def downgrade(migrate_engine):
col = dataset_instance_table.c.state
col.drop()
except Exception:
log.exception("Dropping column 'state' from %s table failed." % table_name)
log.exception("Dropping column 'state' from %s table failed.", table_name)
lib/galaxy/model/migrate/versions/0062_user_openid_table.py
+1 -1
View File
@@ -44,7 +44,7 @@ def upgrade(migrate_engine):
try:
i.create()
except Exception:
log.exception("Adding index '%s' failed." % ix_name)
log.exception("Adding index '%s' failed.", ix_name)
def downgrade(migrate_engine):
lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
+1 -1
View File
@@ -73,7 +73,7 @@ def upgrade(migrate_engine):
cmd = "ALTER TABLE sequencer RENAME TO external_service"
migrate_engine.execute( cmd )
except Exception:
log.exception("Exception executing SQL command: %s" % cmd)
log.exception("Exception executing SQL command: %s", cmd)
# if running postgres then rename the primary key sequence too
if migrate_engine.name in ['postgres', 'postgresql']:
cmd = "ALTER TABLE sequencer_id_seq RENAME TO external_service_id_seq"
lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
+2 -2
View File
@@ -24,7 +24,7 @@ def upgrade(migrate_engine):
c.create( t, index_name="ix_%s_object_store_id" % t_name)
assert c is t.c.object_store_id
except Exception:
log.exception("Adding object_store_id column to %s table failed." % t_name)
log.exception("Adding object_store_id column to %s table failed.", t_name)
def downgrade(migrate_engine):
@@ -35,4 +35,4 @@ def downgrade(migrate_engine):
try:
t.c.object_store_id.drop()
except Exception:
log.exception("Dropping object_store_id column from %s table failed." % t_name)
log.exception("Dropping object_store_id column from %s table failed.", t_name)
lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
+3 -3
View File
@@ -36,19 +36,19 @@ def upgrade(migrate_engine):
try:
migrate_engine.execute( cmd )
except Exception:
log.exception("Exception executing SQL command: %s" % cmd)
log.exception("Exception executing SQL command: %s", cmd)
# Update the status column for tool_shed_repositories that have been uninstalled.
cmd = "UPDATE tool_shed_repository SET status = 'Uninstalled' WHERE uninstalled;"
try:
migrate_engine.execute( cmd )
except Exception:
log.exception("Exception executing SQL command: %s" % cmd)
log.exception("Exception executing SQL command: %s", cmd)
# Update the status column for tool_shed_repositories that have been deactivated.
cmd = "UPDATE tool_shed_repository SET status = 'Deactivated' where deleted and not uninstalled;"
try:
migrate_engine.execute( cmd )
except Exception:
log.exception("Exception executing SQL command: %s" % cmd)
log.exception("Exception executing SQL command: %s", cmd)
def downgrade(migrate_engine):
lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
+2 -2
View File
@@ -65,7 +65,7 @@ def upgrade(migrate_engine):
else:
pass # Index already exists, don't recreate.
except Exception:
log.exception("Unable to create index '%s'." % ix)
log.exception("Unable to create index '%s'.", ix)
def downgrade(migrate_engine):
@@ -78,4 +78,4 @@ def downgrade(migrate_engine):
t = Table( table, metadata, autoload=True )
Index( ix, t.c[col] ).drop()
except Exception:
log.exception("Unable to drop index '%s'." % ix)
log.exception("Unable to drop index '%s'.", ix)
lib/galaxy/model/migrate/versions/0119_job_metrics.py
+2 -2
View File
@@ -85,11 +85,11 @@ def __create(table):
try:
table.create()
except Exception:
log.exception("Creating %s table failed." % table.name)
log.exception("Creating %s table failed.", table.name)
def __drop(table):
try:
table.drop()
except Exception:
log.exception("Dropping %s table failed." % table.name)
log.exception("Dropping %s table failed.", table.name)
lib/galaxy/model/migrate/versions/0120_dataset_collections.py
+2 -2
View File
@@ -162,11 +162,11 @@ def __create(table):
try:
table.create()
except Exception:
log.exception("Creating %s table failed." % table.name)
log.exception("Creating %s table failed.", table.name)
def __drop(table):
try:
table.drop()
except Exception:
log.exception("Dropping %s table failed." % table.name)
log.exception("Dropping %s table failed.", table.name)
lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
+1 -1
View File
@@ -45,7 +45,7 @@ def upgrade(migrate_engine):
try:
migrate_engine.execute( cmd )
except Exception:
log.exception("Failed to grow column %s.%s" % (table, column))
log.exception("Failed to grow column %s.%s", table, column)
def downgrade(migrate_engine):
lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
+4 -4
View File
@@ -112,7 +112,7 @@ def __add_column(column, table_name, metadata, **kwds):
table = Table( table_name, metadata, autoload=True )
column.create( table, **kwds )
except Exception:
log.exception("Adding column %s column failed." % column)
log.exception("Adding column %s column failed.", column)
def __drop_column( column_name, table_name, metadata ):
@@ -120,18 +120,18 @@ def __drop_column( column_name, table_name, metadata ):
table = Table( table_name, metadata, autoload=True )
getattr( table.c, column_name ).drop()
except Exception:
log.exception("Dropping column %s failed." % column_name)
log.exception("Dropping column %s failed.", column_name)
def __create(table):
try:
table.create()
except Exception:
log.exception("Creating %s table failed." % table.name)
log.exception("Creating %s table failed.", table.name)
def __drop(table):
try:
table.drop()
except Exception:
log.exception("Dropping %s table failed." % table.name)
log.exception("Dropping %s table failed.", table.name)
lib/galaxy/model/migrate/versions/0124_job_state_history.py
+2 -2
View File
@@ -31,7 +31,7 @@ def upgrade(migrate_engine):
try:
JobStateHistory_table.create()
except Exception:
log.exception("Creating %s table failed." % JobStateHistory_table.name)
log.exception("Creating %s table failed.", JobStateHistory_table.name)
def downgrade(migrate_engine):
@@ -41,4 +41,4 @@ def downgrade(migrate_engine):
try:
JobStateHistory_table.drop()
except Exception:
log.exception("Dropping %s table failed." % JobStateHistory_table.name)
log.exception("Dropping %s table failed.", JobStateHistory_table.name)
lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
+2 -2
View File
@@ -37,7 +37,7 @@ def __add_column(column, table_name, metadata, **kwds):
table = Table( table_name, metadata, autoload=True )
column.create( table, **kwds )
except Exception:
log.exception("Adding column %s failed." % column)
log.exception("Adding column %s failed.", column)
def __drop_column( column_name, table_name, metadata ):
@@ -45,4 +45,4 @@ def __drop_column( column_name, table_name, metadata ):
table = Table( table_name, metadata, autoload=True )
getattr( table.c, column_name ).drop()
except Exception:
log.exception("Dropping column %s failed." % column_name)
log.exception("Dropping column %s failed.", column_name)
lib/galaxy/model/migrate/versions/0126_password_reset.py
+2 -2
View File
@@ -23,7 +23,7 @@ def upgrade(migrate_engine):
try:
PasswordResetToken_table.create()
except Exception:
log.exception("Creating %s table failed." % PasswordResetToken_table.name)
log.exception("Creating %s table failed.", PasswordResetToken_table.name)
def downgrade(migrate_engine):
@@ -32,4 +32,4 @@ def downgrade(migrate_engine):
try:
PasswordResetToken_table.drop()
except Exception:
log.exception("Dropping %s table failed." % PasswordResetToken_table.name)
log.exception("Dropping %s table failed.", PasswordResetToken_table.name)
lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
+2 -2
View File
@@ -67,11 +67,11 @@ def __create(table):
try:
table.create()
except Exception:
log.exception("Creating %s table failed." % table.name)
log.exception("Creating %s table failed.", table.name)
def __drop(table):
try:
table.drop()
except Exception:
log.exception("Dropping %s table failed." % table.name)
log.exception("Dropping %s table failed.", table.name)
lib/galaxy/model/migrate/versions/0128_session_timeout.py
+2 -2
View File
@@ -32,7 +32,7 @@ def __add_column(column, table_name, metadata, **kwds):
table = Table( table_name, metadata, autoload=True )
column.create( table, **kwds )
except Exception:
log.exception("Adding column %s failed." % column)
log.exception("Adding column %s failed.", column)
def __drop_column( column_name, table_name, metadata ):
@@ -40,4 +40,4 @@ def __drop_column( column_name, table_name, metadata ):
table = Table( table_name, metadata, autoload=True )
getattr( table.c, column_name ).drop()
except Exception:
log.exception("Dropping column %s failed." % column_name)
log.exception("Dropping column %s failed.", column_name)
lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
+2 -2
View File
@@ -33,7 +33,7 @@ def __add_column(column, table_name, metadata, **kwds):
table = Table( table_name, metadata, autoload=True )
column.create( table, **kwds )
except Exception:
log.exception("Adding column %s failed." % column)
log.exception("Adding column %s failed.", column)
def __drop_column( column_name, table_name, metadata ):
@@ -41,4 +41,4 @@ def __drop_column( column_name, table_name, metadata ):
table = Table( table_name, metadata, autoload=True )
getattr( table.c, column_name ).drop()
except Exception:
log.exception("Dropping column %s failed." % column_name)
log.exception("Dropping column %s failed.", column_name)
lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
+5 -5
View File
@@ -95,7 +95,7 @@ def __alter_column(table_name, column_name, metadata, **kwds):
table = Table( table_name, metadata, autoload=True )
getattr( table.c, column_name ).alter(**kwds)
except Exception:
log.exception("Adding column %s failed." % column_name)
log.exception("Adding column %s failed.", column_name)
def __add_column(column, table_name, metadata, **kwds):
@@ -103,7 +103,7 @@ def __add_column(column, table_name, metadata, **kwds):
table = Table( table_name, metadata, autoload=True )
column.create( table, **kwds )
except Exception:
log.exception("Adding column %s failed." % column)
log.exception("Adding column %s failed.", column)
def __drop_column( column_name, table_name, metadata ):
@@ -111,18 +111,18 @@ def __drop_column( column_name, table_name, metadata ):
table = Table( table_name, metadata, autoload=True )
getattr( table.c, column_name ).drop()
except Exception:
log.exception("Dropping column %s failed." % column_name)
log.exception("Dropping column %s failed.", column_name)
def __create(table):
try:
table.create()
except Exception:
log.exception("Creating %s table failed." % table.name)
log.exception("Creating %s table failed.", table.name)
def __drop(table):
try:
table.drop()
except Exception:
log.exception("Dropping %s table failed." % table.name)
log.exception("Dropping %s table failed.", table.name)
lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
+1 -1
View File
@@ -24,7 +24,7 @@ def upgrade(migrate_engine):
try:
migrate_engine.execute(cmd)
except Exception:
log.exception("Exception executing SQL command: %s" % cmd)
log.exception("Exception executing SQL command: %s", cmd)
def downgrade(migrate_engine):
lib/galaxy/queue_worker.py
+3 -3
View File
@@ -34,7 +34,7 @@ def send_local_control_task(app, task, kwargs={}):
declare=[galaxy.queues.galaxy_exchange] + [galaxy.queues.control_queue_from_config(app.config)],
routing_key='control.%s' % app.config.server_name)
except Exception:
log.exception("Error queueing async task: %s." % payload)
log.exception("Error queueing async task: %s.", payload)
def send_control_task(app, task, noop_self=False, kwargs={}):
@@ -58,7 +58,7 @@ def send_control_task(app, task, noop_self=False, kwargs={}):
except Exception:
# This is likely connection refused.
# TODO Use the specific Exception above.
log.exception("Error sending control task: %s." % payload)
log.exception("Error sending control task: %s.", payload)
# Tasks -- to be reorganized into a separate module as appropriate. This is
@@ -232,7 +232,7 @@ class GalaxyQueueWorker(ConsumerMixin, threading.Thread):
f(self.app, **body['kwargs'])
except Exception:
# this shouldn't ever throw an exception, but...
log.exception("Error running control task type: %s" % body['task'])
log.exception("Error running control task type: %s", body['task'])
else:
log.warning("Received a malformed task message:\n%s" % body)
message.ack()
lib/galaxy/sample_tracking/external_service_types.py
+1 -1
View File
@@ -38,7 +38,7 @@ class ExternalServiceTypesCollection( object ):
if visible:
self.visible_external_service_types.append( external_service_type.id )
except:
log.exception( "error reading external_service_type from path: %s" % file_path )
log.exception( "error reading external_service_type from path: %s", file_path )
def load_external_service_type( self, config_file, visible=True ):
# Parse XML configuration file and get the root element
lib/galaxy/tools/__init__.py
+4 -4
View File
@@ -1102,14 +1102,14 @@ class Tool( object, Dictifiable ):
# Handle tool help image display for tools that are contained in repositories in the tool shed or installed into Galaxy.
try:
help_text = tool_shed.util.shed_util_common.set_image_paths( self.app, self.repository_id, help_text )
except Exception as e:
log.exception( "Exception in parse_help, so images may not be properly displayed:\n%s" % str( e ) )
except Exception:
log.exception( "Exception in parse_help, so images may not be properly displayed" )
try:
self.__help = Template( rst_to_html(help_text), input_encoding='utf-8',
output_encoding='utf-8', default_filters=[ 'decode.utf8' ],
encoding_errors='replace' )
except:
log.exception( "error in help for tool %s" % self.name )
log.exception( "error in help for tool %s", self.name )
# Handle deprecated multi-page help text in XML case.
if hasattr(tool_source, "root"):
@@ -1129,7 +1129,7 @@ class Tool( object, Dictifiable ):
encoding_errors='replace' )
for x in self.__help_by_page ]
except:
log.exception( "error in multi-page help for tool %s" % self.name )
log.exception( "error in multi-page help for tool %s", self.name )
# Pad out help pages to match npages ... could this be done better?
while len( self.__help_by_page ) < self.npages:
self.__help_by_page.append( self.__help )
lib/galaxy/tools/toolbox/base.py
+3 -3
View File
@@ -567,7 +567,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
except IOError:
log.error( "Error reading tool configuration file from path: %s" % path )
except Exception:
log.exception( "Error reading tool from path: %s" % path )
log.exception( "Error reading tool from path: %s", path )
def get_tool_repository_from_xml_item(self, item, path):
tool_shed = item.elem.find("tool_shed").text
@@ -630,7 +630,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
# Always load workflows into the integrated_panel_dict.
integrated_panel_dict.update_or_append( index, key, workflow )
except:
log.exception( "Error loading workflow: %s" % workflow_id )
log.exception( "Error loading workflow: %s", workflow_id )
def _load_label_tag_set( self, item, panel_dict, integrated_panel_dict, load_panel_dict, index=None ):
label = ToolSectionLabel( item )
@@ -697,7 +697,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
self._save_integrated_tool_panel()
return tool.id
except Exception:
log.exception("Failed to load potential tool %s." % tool_file)
log.exception("Failed to load potential tool %s.", tool_file)
return None
tool_loaded = False
lib/galaxy/tools/verify/asserts/__init__.py
+1 -1
View File
@@ -20,7 +20,7 @@ for assertion_module_name in assertion_module_names:
assertion_module = sys.modules[full_assertion_module_name]
assertion_modules.append(assertion_module)
except Exception as e:
log.exception('Failed to load assertion module: %s %s' % (assertion_module_name, str(e)))
log.exception('Failed to load assertion module: %s', assertion_module_name)
def verify_assertions(data, assertion_description_list):
lib/galaxy/tours/__init__.py
+2 -2
View File
@@ -74,7 +74,7 @@ class ToursRegistry(object):
log.info("Loaded tour '%s'" % tour_id)
return tour
except IOError:
log.exception("Tour '%s' could not be loaded, error reading file." % tour_id)
log.exception("Tour '%s' could not be loaded, error reading file.", tour_id)
except yaml.error.YAMLError:
log.exception("Tour '%s' could not be loaded, error within file. Please check your yaml syntax." % tour_id)
log.exception("Tour '%s' could not be loaded, error within file. Please check your yaml syntax.", tour_id)
return None
lib/galaxy/util/__init__.py
+2 -2
View File
@@ -899,7 +899,7 @@ def unicodify(value, encoding=DEFAULT_ENCODING, error='replace', default=None):
if not isinstance(value, text_type):
value = text_type(value, encoding, error)
except Exception:
log.exception("value %s could not be coerced to unicode" % value)
log.exception("value %s could not be coerced to unicode", value)
return default
return value
@@ -1139,7 +1139,7 @@ def umask_fix_perms( path, umask, unmasked_perms, gid=None ):
try:
st = os.stat( path )
except OSError as e:
log.exception( 'Unable to set permissions or group on %s' % path )
log.exception( 'Unable to set permissions or group on %s', path )
return
# fix modes
if stat.S_IMODE( st.st_mode ) != perms:
lib/galaxy/visualization/genomes.py
+3 -3
View File
@@ -214,9 +214,9 @@ class Genomes( object ):
if len( val ) == 2:
key, path = val
twobit_fields[ key ] = path
except IOError as e:
except IOError:
# Thrown if twobit.loc does not exist.
log.exception( "Error reading twobit.loc: %s", e )
log.exception( "Error reading twobit.loc" )
for key, description in self.app.genome_builds.get_genome_build_names():
self.genomes[ key ] = Genome( key, description )
# Add len files to genomes.
@@ -329,7 +329,7 @@ class Genomes( object ):
if genome:
rval = genome.to_dict( num=num, chrom=chrom, low=low )
else:
log.exception( 'genome not found for key %s' % dbkey )
log.exception( 'genome not found for key %s', dbkey )
return rval
lib/galaxy/web/base/controller.py
+2 -2
View File
@@ -164,7 +164,7 @@ class BaseUIController( BaseController ):
except exceptions.MessageException:
raise # handled in the caller
except:
log.exception( "Exception in get_object check for %s %s:" % ( class_name, str( id ) ) )
log.exception( "Exception in get_object check for %s %s:", class_name, str( id ) )
raise Exception( 'Server error retrieving %s id ( %s ).' % ( class_name, str( id ) ) )
@@ -180,7 +180,7 @@ class BaseAPIController( BaseController ):
except exceptions.MessageException as e:
raise HTTPBadRequest( detail=e.err_msg )
except Exception as e:
log.exception( "Exception in get_object check for %s %s." % ( class_name, str( id ) ) )
log.exception( "Exception in get_object check for %s %s.", class_name, str( id ) )
raise HTTPInternalServerError( comment=str( e ) )
def validate_in_users_and_groups( self, trans, payload ):
lib/galaxy/webapps/galaxy/api/history_contents.py
+1 -1
View File
@@ -162,7 +162,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
)
return self.__collection_dict( trans, dataset_collection_instance, view="element" )
except Exception as e:
log.exception( "Error in history API at listing dataset collection: %s", e )
log.exception( "Error in history API at listing dataset collection" )
trans.response.status = 500
return { 'error': str( e ) }
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+10 -10
View File
@@ -607,7 +607,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
log.exception( "Unable to create archive for download" )
raise exceptions.InternalServerError( "Unable to create archive for download." )
except Exception:
log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[ 0 ] )
log.exception( "Unexpected error %s in create archive for download", sys.exc_info()[ 0 ] )
raise exceptions.InternalServerError( "Unable to create archive for download." )
composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
seen = []
@@ -640,13 +640,13 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
else:
archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set
except IOError:
log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name )
log.exception( "Unable to add composite parent %s to temporary library download archive", ldda.dataset.file_name )
raise exceptions.InternalServerError( "Unable to create archive for download." )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
log.exception( "Requested dataset %s does not exist on the host.", ldda.dataset.file_name )
raise exceptions.ObjectNotFound( "Requested dataset not found. " )
except Exception as e:
log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name )
log.exception( "Unable to add composite parent %s to temporary library download archive", ldda.dataset.file_name )
raise exceptions.InternalServerError( "Unable to add composite parent to temporary library download archive. " + str( e ) )
flist = glob.glob(os.path.join(ldda.dataset.extra_files_path, '*.*')) # glob returns full paths
@@ -660,13 +660,13 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
else:
archive.add( fpath, fname, check_file=True )
except IOError:
log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname) )
log.exception( "Unable to add %s to temporary library download archive %s", fname, outfname )
raise exceptions.InternalServerError( "Unable to create archive for download." )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % fpath )
log.exception( "Requested dataset %s does not exist on the host.", fpath )
raise exceptions.ObjectNotFound( "Requested dataset not found." )
except Exception as e:
log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname ) )
log.exception( "Unable to add %s to temporary library download archive %s", fname, outfname )
raise exceptions.InternalServerError( "Unable to add dataset to temporary library download archive . " + str( e ) )
else: # simple case
@@ -676,13 +676,13 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
else:
archive.add( ldda.dataset.file_name, path, check_file=True )
except IOError:
log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name )
log.exception( "Unable to write %s to temporary library download archive", ldda.dataset.file_name )
raise exceptions.InternalServerError( "Unable to create archive for download" )
except ObjectNotFound:
log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
log.exception( "Requested dataset %s does not exist on the host.", ldda.dataset.file_name )
raise exceptions.ObjectNotFound( "Requested dataset not found." )
except Exception as e:
log.exception( "Unable to add %s to temporary library download archive %s" % ( fname, outfname ) )
log.exception( "Unable to add %s to temporary library download archive %s", fname, outfname )
raise exceptions.InternalServerError( "Unknown error. " + str( e ) )
lname = 'selected_dataset'
fname = lname.replace( ' ', '_' ) + '_files'
lib/galaxy/webapps/galaxy/api/library_contents.py
+5 -5
View File
@@ -390,15 +390,15 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
trans.sa_session.flush()
rval[ 'deleted' ] = True
except exceptions.httpexceptions.HTTPInternalServerError as http_server_err:
log.exception( 'Library_contents API, delete: uncaught HTTPInternalServerError: %s, %s\n%s',
id, str( kwd ), str( http_server_err ) )
except exceptions.httpexceptions.HTTPInternalServerError:
log.exception( 'Library_contents API, delete: uncaught HTTPInternalServerError: %s, %s',
id, str( kwd ) )
raise
except exceptions.httpexceptions.HTTPException:
raise
except Exception as exc:
log.exception( 'library_contents API, delete: uncaught exception: %s, %s\n%s',
id, str( kwd ), str( exc ) )
log.exception( 'library_contents API, delete: uncaught exception: %s, %s',
id, str( kwd ) )
trans.response.status = 500
rval.update({ 'error': str( exc ) })
return rval
lib/galaxy/webapps/galaxy/controllers/history.py
+1 -1
View File
@@ -630,7 +630,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
except Exception as exc:
user_id = str( trans.user.id ) if trans.user else '(anonymous)'
log.exception( 'Error bootstrapping history for user %s: %s', user_id, exc )
log.exception( 'Error bootstrapping history for user %s', user_id )
if isinstance( exc, exceptions.ItemAccessibilityException ):
error_msg = 'You do not have permission to view this history.'
else:
lib/galaxy/webapps/galaxy/controllers/library_common.py
+5 -5
View File
@@ -51,7 +51,7 @@ for comptype in ( 'gz', 'bz2' ):
archive.close()
comptypes.append( comptype )
except tarfile.CompressionError:
log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads." % comptype )
log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads.", comptype )
try:
os.unlink( tmpf )
except OSError:
@@ -1863,7 +1863,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status = 'error'
except:
error = True
log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] )
log.exception( "Unexpected error %s in create archive for download", sys.exc_info()[0] )
message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0]
status = 'error'
if not error:
@@ -1897,7 +1897,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
archive.add(ldda.dataset.file_name, zpath) # add the primary of a composite set
except IOError:
error = True
log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name)
log.exception( "Unable to add composite parent %s to temporary library download archive", ldda.dataset.file_name)
message = "Unable to create archive for download, please report this error"
status = 'error'
continue
@@ -1910,7 +1910,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
archive.add( fpath, fname )
except IOError:
error = True
log.exception( "Unable to add %s to temporary library download archive %s" % (fname, outfname))
log.exception( "Unable to add %s to temporary library download archive %s", fname, outfname)
message = "Unable to create archive for download, please report this error"
status = 'error'
continue
@@ -1919,7 +1919,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
archive.add( ldda.dataset.file_name, path )
except IOError:
error = True
log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name)
log.exception( "Unable to write %s to temporary library download archive", ldda.dataset.file_name)
message = "Unable to create archive for download, please report this error"
status = 'error'
if not error:
lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
+2 -2
View File
@@ -24,7 +24,7 @@ def upgrade(migrate_engine):
PasswordResetToken_table.create()
except Exception as e:
print str(e)
log.exception("Creating %s table failed: %s" % (PasswordResetToken_table.name, str( e ) ) )
log.exception("Creating %s table failed", PasswordResetToken_table.name )
def downgrade(migrate_engine):
@@ -34,4 +34,4 @@ def downgrade(migrate_engine):
PasswordResetToken_table.drop()
except Exception as e:
print str(e)
log.exception("Dropping %s table failed: %s" % (PasswordResetToken_table.name, str( e ) ) )
log.exception("Dropping %s table failed", PasswordResetToken_table.name )
lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
+2 -2
View File
@@ -33,7 +33,7 @@ def __add_column(column, table_name, metadata, **kwds):
column.create( table, **kwds )
except Exception as e:
print str(e)
log.exception( "Adding column %s failed." % column)
log.exception( "Adding column %s failed.", column)
def __drop_column( column_name, table_name, metadata ):
@@ -42,4 +42,4 @@ def __drop_column( column_name, table_name, metadata ):
getattr( table.c, column_name ).drop()
except Exception as e:
print str(e)
log.exception( "Dropping column %s failed." % column_name )
log.exception( "Dropping column %s failed.", column_name )
lib/tool_shed/capsule/capsule_manager.py
+2 -2
View File
@@ -507,8 +507,8 @@ class ImportRepositoryManager( object ):
tar_archive.extractall( path=file_path )
try:
tar_archive.close()
except Exception as e:
log.exception( "Cannot close tar_archive: %s" % str( e ) )
except Exception:
log.exception( "Cannot close tar_archive" )
del return_dict[ 'tar_archive' ]
return return_dict
lib/tool_shed/galaxy_install/tool_migration_manager.py
+2 -2
View File
@@ -412,8 +412,8 @@ class ToolMigrationManager( object ):
lock.acquire( True )
try:
self.filter_and_persist_proprietary_tool_panel_configs( tool_configs_to_filter )
except Exception as e:
log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) )
except Exception:
log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs" )
finally:
lock.release()
irmm = InstalledRepositoryMetadataManager( app=self.app,
lib/tool_shed/galaxy_install/tools/data_manager.py
+2 -2
View File
@@ -28,8 +28,8 @@ class DataManagerHandler( object ):
fh.write( xml_util.xml_to_string( elem ) )
fh.write( '</data_managers>\n' )
fh.close()
except Exception as e:
log.exception( "Exception in DataManagerHandler.data_manager_config_elems_to_xml_file: %s" % str( e ) )
except Exception:
log.exception( "Exception in DataManagerHandler.data_manager_config_elems_to_xml_file" )
finally:
lock.release()
lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
+2 -2
View File
@@ -89,8 +89,8 @@ class ToolPanelManager( object ):
fh.write( xml_util.xml_to_string( elem, use_indent=True ) )
fh.write( '</toolbox>\n' )
fh.close()
except Exception as e:
log.exception( "Exception in ToolPanelManager.config_elems_to_xml_file: %s" % str( e ) )
except Exception:
log.exception( "Exception in ToolPanelManager.config_elems_to_xml_file: %s" )
finally:
lock.release()
lib/tool_shed/metadata/metadata_generator.py
+3 -3
View File
@@ -450,9 +450,9 @@ class MetadataGenerator( object ):
valid_exported_galaxy_workflow = True
try:
exported_workflow_dict = json.loads( workflow_text )
except Exception as e:
log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s"
% ( str( relative_path ), str( e ) ) )
except Exception:
log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow",
str( relative_path ) )
valid_exported_galaxy_workflow = False
if valid_exported_galaxy_workflow and \
'a_galaxy_workflow' in exported_workflow_dict and \
lib/tool_shed/metadata/repository_metadata_manager.py
+1 -1
View File
@@ -885,7 +885,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
( str( repository.name ), str( repository.user.username ) ) )
successful_count += 1
except:
log.exception( "Error attempting to reset metadata on repository %s" % str( repository.name ) )
log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) )
unsuccessful_count += 1
message = "Successfully reset metadata on %d %s. " % \
( successful_count, inflector.cond_plural( successful_count, "repository" ) )
lib/tool_shed/repository_registry.py
+4 -4
View File
@@ -93,11 +93,11 @@ class Registry( object ):
self.load_repository_and_suite_tuple( repository )
if is_level_one_certified:
self.load_certified_level_one_repository_and_suite_tuple( repository )
except Exception as e:
except Exception:
# The viewable repository numbers and the categorized (filtered) lists of repository tuples
# may be slightly skewed, but that is no reason to result in a potential server error. All
# will be corrected at next server start.
log.exception( "Handled error adding entry to repository registry: %s." % str( e ) )
log.exception( "Handled error adding entry to repository registry" )
def edit_category_entry( self, old_name, new_name ):
if old_name in self.viewable_repositories_and_suites_by_category:
@@ -341,11 +341,11 @@ class Registry( object ):
self.unload_repository_and_suite_tuple( repository )
if is_level_one_certified:
self.unload_certified_level_one_repository_and_suite_tuple( repository )
except Exception as e:
except Exception:
# The viewable repository numbers and the categorized (filtered) lists of repository tuples
# may be slightly skewed, but that is no reason to result in a potential server error. All
# will be corrected at next server start.
log.exception( "Handled error removing entry from repository registry: %s." % str( e ) )
log.exception( "Handled error removing entry from repository registry: %s." )
@property
def sa_session( self ):
lib/tool_shed/util/commit_util.py
+3 -3
View File
@@ -138,7 +138,7 @@ def handle_bz2( repository, uploaded_file_name ):
except IOError:
os.close( fd )
os.remove( uncompressed )
log.exception( 'Problem uncompressing bz2 data "%s"' % uploaded_file_name )
log.exception( 'Problem uncompressing bz2 data "%s"', uploaded_file_name )
return
if not chunk:
break
@@ -235,10 +235,10 @@ def handle_gzip( repository, uploaded_file_name ):
while 1:
try:
chunk = gzipped_file.read( basic_util.CHUNK_SIZE )
except IOError as e:
except IOError:
os.close( fd )
os.remove( uncompressed )
log.exception( 'Problem uncompressing gz data "%s": %s' % ( uploaded_file_name, str( e ) ) )
log.exception( 'Problem uncompressing gz data "%s"', uploaded_file_name )
return
if not chunk:
break
lib/tool_shed/util/common_util.py
+6 -6
View File
@@ -174,11 +174,11 @@ def get_protocol_from_tool_shed_url( tool_shed_url ):
try:
if tool_shed_url.find( '://' ) > 0:
return tool_shed_url.split( '://' )[0].lower()
except Exception as e:
except Exception:
# We receive a lot of calls here where the tool_shed_url is None. The container_util uses
# that value when creating a header row. If the tool_shed_url is not None, we have a problem.
if tool_shed_url is not None:
log.exception( "Handled exception getting the protocol from Tool Shed URL %s:\n%s", str( tool_shed_url ), e )
log.exception( "Handled exception getting the protocol from Tool Shed URL %s", str( tool_shed_url ) )
# Default to HTTP protocol.
return 'http'
@@ -272,11 +272,11 @@ def handle_tool_shed_url_protocol( app, shed_url ):
else:
tool_shed_url = str( url_for( '/', qualified=True ) ).rstrip( '/' )
return tool_shed_url
except Exception as e:
except Exception:
# We receive a lot of calls here where the tool_shed_url is None. The container_util uses
# that value when creating a header row. If the tool_shed_url is not None, we have a problem.
if shed_url is not None:
log.exception( "Handled exception removing protocol from URL %s:\n%s", str( shed_url ), e )
log.exception( "Handled exception removing protocol from URL %s", str( shed_url ) )
return shed_url
@@ -313,11 +313,11 @@ def remove_port_from_tool_shed_url( tool_shed_url ):
else:
new_tool_shed_url = tool_shed_url
return new_tool_shed_url.rstrip( '/' )
except Exception as e:
except Exception:
# We receive a lot of calls here where the tool_shed_url is None. The container_util uses
# that value when creating a header row. If the tool_shed_url is not None, we have a problem.
if tool_shed_url is not None:
log.exception( "Handled exception removing the port from Tool Shed URL %s:\n%s", str( tool_shed_url ), e )
log.exception( "Handled exception removing the port from Tool Shed URL %s", str( tool_shed_url ) )
return tool_shed_url
lib/tool_shed/util/readme_util.py
+2 -2
View File
@@ -45,7 +45,7 @@ def build_readme_files_dict( app, repository, changeset_revision, metadata, tool
text = unicodify( f.read() )
f.close()
except Exception as e:
log.exception( "Error reading README file '%s' from disk: %s" % ( str( relative_path_to_readme_file ), str( e ) ) )
log.exception( "Error reading README file '%s' from disk", str( relative_path_to_readme_file ) )
text = None
if text:
text_of_reasonable_length = basic_util.size_string( text )
@@ -58,7 +58,7 @@ def build_readme_files_dict( app, repository, changeset_revision, metadata, tool
app.security.encode_id( repository.id ),
text_of_reasonable_length )
except Exception as e:
log.exception( "Exception in build_readme_files_dict, so images may not be properly displayed:\n%s" % str( e ) )
log.exception( "Exception in build_readme_files_dict, so images may not be properly displayed" )
finally:
lock.release()
if readme_file_name.endswith( '.rst' ):
lib/tool_shed/util/repository_util.py
+1 -1
View File
@@ -813,7 +813,7 @@ def get_tool_shed_status_for_installed_repository( app, repository ):
# The required tool shed may be unavailable, so default the revision_update value to 'false'.
return dict( revision_update='false' )
except Exception as e:
log.exception( "Error attempting to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) )
log.exception( "Error attempting to get tool shed status for installed repository %s", str( repository.name ) )
return {}
lib/tool_shed/util/workflow_util.py
+1 -1
View File
@@ -88,7 +88,7 @@ class RepoToolModule( ToolModule ):
except:
# TODO have this actually use default parameters? Fix at
# refactor, needs to be discussed wrt: reproducibility though.
log.exception("Tool parse failed for %s -- this indicates incompatibility of local tool version with expected version by the workflow." % self.tool.id)
log.exception("Tool parse failed for %s -- this indicates incompatibility of local tool version with expected version by the workflow.", self.tool.id)
return data_inputs
def get_data_outputs( self ):
lib/tool_shed/utility_containers/__init__.py
+2 -2
View File
@@ -350,8 +350,8 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine
error_messages,
label="Invalid Data Managers" )
containers_dict[ 'invalid_data_managers' ] = data_managers_root_folder
except Exception as e:
log.exception( "Exception in build_repository_containers: %s" % str( e ) )
except Exception:
log.exception( "Exception in build_repository_containers" )
finally:
lock.release()
return containers_dict