def reload(self, trans, payload={}, **kwd):
"""
POST /api/display_applications/reload
Reloads the list of display applications.
:param ids: list containing ids of display to be reloaded
:type ids: list
"""
ids = payload.get('ids')
queue_worker.send_control_task(trans.app,
'reload_display_application',
noop_self=True,
kwargs={'display_application_ids': ids})
reloaded, failed = trans.app.datatypes_registry.reload_display_applications(
ids)
if not reloaded and failed:
message = 'Unable to reload any of the %i requested display applications ("%s").' % (
len(failed), '", "'.join(failed))
elif failed:
message = 'Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").' % (
len(reloaded), '", "'.join(reloaded), len(failed),
'", "'.join(failed))
elif not reloaded:
message = 'You need to request at least one display application to reload.'
else:
message = 'Reloaded %i requested display applications ("%s").' % (
len(reloaded), '", "'.join(reloaded))
return {'message': message, 'reloaded': reloaded, 'failed': failed}
def test_send_control_task_to_many_listeners(queue_worker_factory):
app1 = queue_worker_factory()
app2 = queue_worker_factory()
app3 = queue_worker_factory()
app4 = queue_worker_factory()
app5 = queue_worker_factory()
send_control_task(app=app1, task='echo')
for app in [app1, app2, app3, app4, app5]:
wait_for_var(app, 'some_var', 'bar')
assert len(app.tasks_executed) == 1
def test_send_control_task_noop_self(queue_worker_factory):
app = queue_worker_factory()
assert app.some_var == 'foo'
response = send_control_task(app=app, task='echo', noop_self=True, get_response=True)
assert response == 'NO_OP'
assert app.some_var == 'foo'
assert len(app.tasks_executed) == 0
def reload(self, trans, payload={}, **kwd):
"""
POST /api/display_applications/reload
Reloads the list of display applications.
:param ids: list containing ids of display to be reloaded
:type ids: list
"""
ids = payload.get('ids')
queue_worker.send_control_task(trans.app,
'reload_display_application',
noop_self=True,
kwargs={'display_application_ids': ids})
reloaded, failed = trans.app.datatypes_registry.reload_display_applications(ids)
if not reloaded and failed:
message = 'Unable to reload any of the %i requested display applications ("%s").' % (len(failed), '", "'.join(failed))
elif failed:
message = 'Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").' % (len(reloaded), '", "'.join(reloaded), len(failed), '", "'.join(failed))
elif not reloaded:
message = 'You need to request at least one display application to reload.'
else:
message = 'Reloaded %i requested display applications ("%s").' % (len(reloaded), '", "'.join(reloaded))
return {'message': message, 'reloaded': reloaded, 'failed': failed}
def reload_toolbox(self, trans, **kwds):
"""
PUT /api/configuration/toolbox
Reload the Galaxy toolbox (but not individual tools).
"""
send_control_task(self.app.toolbox.app, 'reload_toolbox')
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))
def reload_toolbox(self, trans, **kwds):
"""
PUT /api/configuration/toolbox
Reload the Galaxy toolbox (but not individual tools).
"""
send_control_task(self.app.toolbox.app, 'reload_toolbox')
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))
def test_send_control_task_get_result(queue_worker_factory):
app = queue_worker_factory()
response = send_control_task(app=app, task='echo', get_response=True)
assert response == 'bar'
assert app.some_var == 'bar'
assert len(app.tasks_executed) == 1
def test_send_control_task(queue_worker_factory):
app = queue_worker_factory()
send_control_task(app=app, task='echo')
wait_for_var(app, 'some_var', 'bar')
assert len(app.tasks_executed) == 1
