def process_move( self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd ):
if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[ data_table_name ]:
move_dict = self.move_by_data_table_column[ data_table_name ][ column_name ]
source = move_dict[ 'source_base' ]
if source is None:
source = source_base_path
else:
source = fill_template( source, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd )
if move_dict[ 'source_value' ]:
source = os.path.join( source, fill_template( move_dict[ 'source_value' ], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd ) )
target = move_dict[ 'target_base' ]
if target is None:
target = self.data_managers.app.config.galaxy_data_manager_data_path
else:
target = fill_template( target, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd )
if move_dict[ 'target_value' ]:
target = os.path.join( target, fill_template( move_dict[ 'target_value' ], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd ) )
if move_dict[ 'type' ] == 'file':
dirs = os.path.split( target )[0]
try:
os.makedirs( dirs )
except OSError as e:
if e.errno != errno.EEXIST:
raise e
# moving a directory and the target already exists, we move the contents instead
util.move_merge( source, target )
if move_dict.get( 'relativize_symlinks', False ):
util.relativize_symlinks( target )
return True
return False
def process_move(self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd):
if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[data_table_name]:
move_dict = self.move_by_data_table_column[data_table_name][column_name]
source = move_dict['source_base']
if source is None:
source = source_base_path
else:
source = fill_template(source, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip()
if move_dict['source_value']:
source = os.path.join(source, fill_template(move_dict['source_value'], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip())
target = move_dict['target_base']
if target is None:
target = self.data_managers.app.config.galaxy_data_manager_data_path
else:
target = fill_template(target, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip()
if move_dict['target_value']:
target = os.path.join(target, fill_template(move_dict['target_value'], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip())
if move_dict['type'] == 'file':
dirs = os.path.split(target)[0]
try:
os.makedirs(dirs)
except OSError as e:
if e.errno != errno.EEXIST:
raise e
# moving a directory and the target already exists, we move the contents instead
if os.path.exists(source):
util.move_merge(source, target)
if move_dict.get('relativize_symlinks', False):
util.relativize_symlinks(target)
return True
return False
def process_move(self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd):
if (
data_table_name in self.move_by_data_table_column
and column_name in self.move_by_data_table_column[data_table_name]
):
move_dict = self.move_by_data_table_column[data_table_name][column_name]
source = move_dict["source_base"]
if source is None:
source = source_base_path
else:
source = fill_template(
source,
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
**kwd
)
if move_dict["source_value"]:
source = os.path.join(
source,
fill_template(
move_dict["source_value"],
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
**kwd
),
)
target = move_dict["target_base"]
if target is None:
target = self.data_managers.app.config.galaxy_data_manager_data_path
else:
target = fill_template(
target,
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
**kwd
)
if move_dict["target_value"]:
target = os.path.join(
target,
fill_template(
move_dict["target_value"],
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
**kwd
),
)
if move_dict["type"] == "file":
dirs, filename = os.path.split(target)
try:
os.makedirs(dirs)
except OSError, e:
if e.errno != errno.EEXIST:
raise e
# log.debug( 'Error creating directory "%s": %s' % ( dirs, e ) )
# moving a directory and the target already exists, we move the contents instead
util.move_merge(source, target)
if move_dict.get("relativize_symlinks", False):
util.relativize_symlinks(target)
return True
def process_result(self, out_data):
data_manager_dicts = {}
data_manager_dict = {}
# TODO: fix this merging below
for output_name, output_dataset in out_data.items():
try:
output_dict = json.loads(open(output_dataset.file_name).read())
except Exception as e:
log.warning('Error reading DataManagerTool json for "%s": %s' % (output_name, e))
continue
data_manager_dicts[output_name] = output_dict
for key, value in output_dict.items():
if key not in data_manager_dict:
data_manager_dict[key] = {}
data_manager_dict[key].update(value)
data_manager_dict.update(output_dict)
data_tables_dict = data_manager_dict.get('data_tables', {})
for data_table_name in self.data_tables.keys():
data_table_values = data_tables_dict.pop(data_table_name, None)
if not data_table_values:
log.warning('No values for data table "%s" were returned by the data manager "%s".' % (data_table_name, self.id))
continue # next data table
data_table = self.data_managers.app.tool_data_tables.get(data_table_name, None)
if data_table is None:
log.error('The data manager "%s" returned an unknown data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % (self.id, data_table_name, data_table_values, data_table_name, 'tool_data_table_conf.xml'))
continue # next table name
if not isinstance(data_table, SUPPORTED_DATA_TABLE_TYPES):
log.error('The data manager "%s" returned an unsupported data table "%s" with type "%s" with new entries "%s". These entries will not be created. Please confirm that the data table is of a supported type (%s).' % (self.id, data_table_name, type(data_table), data_table_values, SUPPORTED_DATA_TABLE_TYPES))
continue # next table name
output_ref_values = {}
if data_table_name in self.output_ref_by_data_table:
for data_table_column, output_ref in self.output_ref_by_data_table[data_table_name].items():
output_ref_dataset = out_data.get(output_ref, None)
assert output_ref_dataset is not None, "Referenced output was not found."
output_ref_values[data_table_column] = output_ref_dataset
if not isinstance(data_table_values, list):
data_table_values = [data_table_values]
for data_table_row in data_table_values:
data_table_value = dict(**data_table_row) # keep original values here
for name, value in data_table_row.items(): # FIXME: need to loop through here based upon order listed in data_manager config
if name in output_ref_values:
self.process_move(data_table_name, name, output_ref_values[name].extra_files_path, **data_table_value)
data_table_value[name] = self.process_value_translation(data_table_name, name, **data_table_value)
data_table.add_entry(data_table_value, persist=True, entry_source=self)
send_control_task(self.data_managers.app,
'reload_tool_data_tables',
noop_self=True,
kwargs={'table_name': data_table_name})
if self.undeclared_tables and data_tables_dict:
# We handle the data move, by just moving all the data out of the extra files path
# moving a directory and the target already exists, we move the contents instead
log.debug('Attempting to add entries for undeclared tables: %s.', ', '.join(data_tables_dict.keys()))
for ref_file in out_data.values():
if ref_file.extra_files_path_exists():
util.move_merge(ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path)
path_column_names = ['path']
for data_table_name, data_table_values in data_tables_dict.items():
data_table = self.data_managers.app.tool_data_tables.get(data_table_name, None)
if not isinstance(data_table_values, list):
data_table_values = [data_table_values]
for data_table_row in data_table_values:
data_table_value = dict(**data_table_row) # keep original values here
for name, value in data_table_row.items():
if name in path_column_names:
data_table_value[name] = os.path.abspath(os.path.join(self.data_managers.app.config.galaxy_data_manager_data_path, value))
data_table.add_entry(data_table_value, persist=True, entry_source=self)
send_control_task(self.data_managers.app, 'reload_tool_data_tables',
noop_self=True,
kwargs={'table_name': data_table_name})
else:
for data_table_name, data_table_values in data_tables_dict.items():
# tool returned extra data table entries, but data table was not declared in data manager
# do not add these values, but do provide messages
log.warning('The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % (self.id, data_table_name, data_table_values, data_table_name, self.data_managers.filename))
for data_table_row in data_table_values:
data_table_value = dict( **data_table_row ) # keep original values here
for name, value in data_table_row.iteritems(): # FIXME: need to loop through here based upon order listed in data_manager config
if name in output_ref_values:
self.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value )
data_table_value[ name ] = self.process_value_translation( data_table_name, name, **data_table_value )
data_table.add_entry( data_table_value, persist=True, entry_source=self )
galaxy.queue_worker.send_control_task(self.data_managers.app, 'reload_tool_data_tables',
noop_self=True,
kwargs={'table_name': data_table_name} )
if self.undeclared_tables and data_tables_dict:
# We handle the data move, by just moving all the data out of the extra files path
# moving a directory and the target already exists, we move the contents instead
log.debug( 'Attempting to add entries for undeclared tables: %s.', ', '.join( data_tables_dict.keys() ) )
for ref_file in out_data.values():
util.move_merge( ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path )
path_column_names = [ 'path' ]
for data_table_name, data_table_values in data_tables_dict.iteritems():
data_table = self.data_managers.app.tool_data_tables.get( data_table_name, None )
if not isinstance( data_table_values, list ):
data_table_values = [ data_table_values ]
for data_table_row in data_table_values:
data_table_value = dict( **data_table_row ) # keep original values here
for name, value in data_table_row.iteritems():
if name in path_column_names:
data_table_value[ name ] = os.path.abspath( os.path.join( self.data_managers.app.config.galaxy_data_manager_data_path, value ) )
data_table.add_entry( data_table_value, persist=True, entry_source=self )
galaxy.queue_worker.send_control_task(self.data_managers.app, 'reload_tool_data_tables',
noop_self=True,
kwargs={'table_name': data_table_name} )
else:
output_ref_values[name].extra_files_path,
**data_table_value)
data_table_value[
name] = self.process_value_translation(
data_table_name, name, **data_table_value)
data_table.add_entry(data_table_value,
persist=True,
entry_source=self)
if self.undeclared_tables and data_tables_dict:
# We handle the data move, by just moving all the data out of the extra files path
# moving a directory and the target already exists, we move the contents instead
log.debug('Attempting to add entries for undeclared tables: %s.',
', '.join(data_tables_dict.keys()))
for ref_file in out_data.values():
util.move_merge(
ref_file.extra_files_path, self.data_managers.app.config.
galaxy_data_manager_data_path)
path_column_names = ['path']
for data_table_name, data_table_values in data_tables_dict.iteritems(
):
data_table = self.data_managers.app.tool_data_tables.get(
data_table_name, None)
if not isinstance(data_table_values, list):
data_table_values = [data_table_values]
for data_table_row in data_table_values:
data_table_value = dict(
**data_table_row) #keep original values here
for name, value in data_table_row.iteritems():
if name in path_column_names:
data_table_value[name] = os.path.abspath(
os.path.join(
def process_result(self, out_data):
data_manager_dicts = {}
data_manager_dict = {}
# TODO: fix this merging below
for output_name, output_dataset in out_data.items():
try:
output_dict = json.loads(open(output_dataset.file_name).read())
except Exception as e:
log.warning('Error reading DataManagerTool json for "%s": %s' %
(output_name, e))
continue
data_manager_dicts[output_name] = output_dict
for key, value in output_dict.items():
if key not in data_manager_dict:
data_manager_dict[key] = {}
data_manager_dict[key].update(value)
data_manager_dict.update(output_dict)
data_tables_dict = data_manager_dict.get('data_tables', {})
for data_table_name in self.data_tables.keys():
data_table_values = None
data_table_remove_values = None
# Add/Remove option for data tables
if isinstance(data_tables_dict.get(data_table_name), dict):
data_table_data = data_tables_dict.get(data_table_name, None)
# Validate results
if not data_table_data:
log.warning('Data table seems invalid: "%s".' %
data_table_name)
continue
data_table_values = data_table_data.pop('add', None)
data_table_remove_values = data_table_data.pop('remove', None)
# Remove it as well here
data_tables_dict.pop(data_table_name, None)
else:
data_table_values = data_tables_dict.pop(data_table_name, None)
if not data_table_values and not data_table_remove_values:
log.warning(
'No values for data table "%s" were returned by the data manager "%s".'
% (data_table_name, self.id))
continue # next data table
data_table = self.data_managers.app.tool_data_tables.get(
data_table_name, None)
if data_table is None:
log.error(
'The data manager "%s" returned an unknown data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.'
% (self.id, data_table_name, data_table_values,
data_table_name, 'tool_data_table_conf.xml'))
continue # next table name
if not isinstance(data_table, SUPPORTED_DATA_TABLE_TYPES):
log.error(
'The data manager "%s" returned an unsupported data table "%s" with type "%s" with new entries "%s". These entries will not be created. Please confirm that the data table is of a supported type (%s).'
% (self.id, data_table_name, type(data_table),
data_table_values, SUPPORTED_DATA_TABLE_TYPES))
continue # next table name
output_ref_values = {}
if data_table_name in self.output_ref_by_data_table:
for data_table_column, output_ref in self.output_ref_by_data_table[
data_table_name].items():
output_ref_dataset = out_data.get(output_ref, None)
assert output_ref_dataset is not None, "Referenced output was not found."
output_ref_values[data_table_column] = output_ref_dataset
if not isinstance(data_table_values, list):
data_table_values = [data_table_values
] if data_table_values else []
if not isinstance(data_table_remove_values, list):
data_table_remove_values = [
data_table_remove_values
] if data_table_remove_values else []
for data_table_row in data_table_values:
data_table_value = dict(
**data_table_row) # keep original values here
for name, value in data_table_row.items(
): # FIXME: need to loop through here based upon order listed in data_manager config
if name in output_ref_values:
self.process_move(
data_table_name, name,
output_ref_values[name].extra_files_path,
**data_table_value)
data_table_value[
name] = self.process_value_translation(
data_table_name, name, **data_table_value)
data_table.add_entry(data_table_value,
persist=True,
entry_source=self)
# Removes data table entries
for data_table_row in data_table_remove_values:
data_table_value = dict(
**data_table_row) # keep original values here
data_table.remove_entry(list(data_table_value.values()))
self.data_managers.app.queue_worker.send_control_task(
'reload_tool_data_tables',
noop_self=True,
kwargs={'table_name': data_table_name})
if self.undeclared_tables and data_tables_dict:
# We handle the data move, by just moving all the data out of the extra files path
# moving a directory and the target already exists, we move the contents instead
log.debug('Attempting to add entries for undeclared tables: %s.',
', '.join(data_tables_dict.keys()))
for ref_file in out_data.values():
if ref_file.extra_files_path_exists():
util.move_merge(
ref_file.extra_files_path, self.data_managers.app.
config.galaxy_data_manager_data_path)
path_column_names = ['path']
for data_table_name, data_table_values in data_tables_dict.items():
data_table = self.data_managers.app.tool_data_tables.get(
data_table_name, None)
if not isinstance(data_table_values, list):
data_table_values = [data_table_values]
for data_table_row in data_table_values:
data_table_value = dict(
**data_table_row) # keep original values here
for name, value in data_table_row.items():
if name in path_column_names:
data_table_value[name] = os.path.abspath(
os.path.join(
self.data_managers.app.config.
galaxy_data_manager_data_path, value))
data_table.add_entry(data_table_value,
persist=True,
entry_source=self)
self.data_managers.app.queue_worker.send_control_task(
'reload_tool_data_tables',
noop_self=True,
kwargs={'table_name': data_table_name})
else:
for data_table_name, data_table_values in data_tables_dict.items():
# tool returned extra data table entries, but data table was not declared in data manager
# do not add these values, but do provide messages
log.warning(
'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.'
% (self.id, data_table_name, data_table_values,
data_table_name, self.data_managers.filename))