Merge pull request #2420 from nsoranzo/log_warn

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

lib/galaxy/auth/providers/ldap_ad.py

@@ -135,7 +135,7 @@ def authenticate(self, email, username, password, options):
 
                 # 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 @@ def authenticate(self, email, username, password, options):
             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

@@ -509,7 +509,7 @@ def get_cram_version( self, filename):
                 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 @@ def set_index_file(self, dataset, index_file):
                 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 @@ def set_meta( self, dataset, overwrite=True, **kwd ):
                     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 @@ def set_meta( self, dataset, overwrite=True, **kwd ):
                 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 @@ def sniff( self, filename ):
                         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 @@ def sniff( self, filename ):
                         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 @@ def sniff( self, filename ):
                         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 @@ def set_meta( self, dataset, overwrite=True, **kwd ):
                     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 @@ def sniff( self, filename ):
                 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

@@ -301,7 +301,7 @@ def set_meta(self, dataset, overwrite=True, skip=0, **kwd):
                     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 @@ def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd):
             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

@@ -129,11 +129,11 @@ def __import_module( full_path, datatype_module, datatype_class_name ):
                 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

@@ -528,14 +528,14 @@ def set_meta( self, dataset, overwrite=True, **kwd ):
                             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

@@ -185,7 +185,7 @@ def get_statistics( self ):
             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

@@ -107,7 +107,7 @@ def queue_job( self, job_wrapper ):
             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

@@ -377,7 +377,7 @@ def _populate_parameter_defaults( self, job_destination ):
         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 @@ def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, r
             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

@@ -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

@@ -136,7 +136,7 @@ def apply_item_tag( self, user, item, name, value=None ):
             # 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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -428,7 +428,7 @@ def parse( self, tool_source, guid=None ):
         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

@@ -340,7 +340,7 @@ def configure_and_load( self, config_element, tool_data_path, from_shed_config=F
                 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 @@ def parse_file_fields( self, reader, errors=None, here="__HERE__" ):
                     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 @@ def _remove_entry( self, values):
                 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

@@ -78,9 +78,9 @@ def __init__( self, default_base_path, conf_file=None, **extra_config ):
         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 @@ def dependency_shell_commands( self, requirements, **kwds ):
                                             **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

@@ -102,7 +102,7 @@ def resolve(self, name, version, type, **kwds):
 
         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

@@ -97,7 +97,7 @@ def exact(self):
     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

@@ -74,7 +74,7 @@ def __init__(self, module_dependency_resolver, modulepath, prefetch):
         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

@@ -109,7 +109,7 @@ def record_success( self, job, outputs ):
     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 @@ def create_output_collections( self, trans, history, params ):
             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

@@ -26,7 +26,7 @@
 
 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(