def pipeline_from_generator(variable_gen):
# Get the original OutputPort module
orig_controller = variable_gen._generator.controller
base_pipeline = orig_controller.vistrail.getPipeline('dat-vars')
if len(base_pipeline.module_list) != 1:
raise ValueError("dat-vars version is invalid")
output_port = base_pipeline.module_list[0]
controller = VistrailController(Vistrail())
# OutputPort
operations = [('add', output_port)]
# Rest of the pipeline
operations += variable_gen._generator.operations
# Connection
connection = controller.create_connection(
variable_gen._output_module,
variable_gen._outputport_name,
output_port,
'InternalPipe')
operations.append(('add', connection))
# Materialize this
action = create_action(operations)
controller.add_new_action(action)
version = controller.perform_action(action)
controller.change_selected_version(version)
assert version == controller.current_version == 1
return controller.current_pipeline, 1
def pipeline_from_generator(variable_gen):
# Get the original OutputPort module
orig_controller = variable_gen._generator.controller
base_pipeline = orig_controller.vistrail.getPipeline('dat-vars')
if len(base_pipeline.module_list) != 1:
raise ValueError("dat-vars version is invalid")
output_port = base_pipeline.module_list[0]
controller = VistrailController(Vistrail())
# OutputPort
operations = [('add', output_port)]
# Rest of the pipeline
operations += variable_gen._generator.operations
# Connection
connection = controller.create_connection(
variable_gen._output_module, variable_gen._outputport_name,
output_port, 'InternalPipe')
operations.append(('add', connection))
# Materialize this
action = create_action(operations)
controller.add_new_action(action)
version = controller.perform_action(action)
controller.change_selected_version(version)
assert version == controller.current_version == 1
return controller.current_pipeline, 1
def handle_module_upgrade_request(controller, module_id, pipeline):
old_module = pipeline.modules[module_id]
if old_module.name == "JSONFile" and old_module.version != "0.1.5" and old_module.namespace == "read":
from vistrails.core.db.action import create_action
from vistrails.core.modules.module_registry import get_module_registry
from .read.read_json import JSONObject
reg = get_module_registry()
new_desc = reg.get_descriptor(JSONObject)
new_module = controller.create_module_from_descriptor(new_desc, old_module.location.x, old_module.location.y)
actions = UpgradeWorkflowHandler.replace_generic(controller, pipeline, old_module, new_module)
new_function = controller.create_function(new_module, "key_name", ["_key"])
actions.append(create_action([("add", new_function, "module", new_module.id)]))
return actions
module_remap = {
"read|csv|CSVFile": [(None, "0.1.1", "read|CSVFile", {"src_port_remap": {"self": "value"}})],
"read|numpy|NumPyArray": [(None, "0.1.1", "read|NumPyArray", {"src_port_remap": {"self": "value"}})],
"read|CSVFile": [("0.1.1", "0.1.2", None, {"src_port_remap": {"self": "value"}}), ("0.1.3", "0.1.5", None, {})],
"read|NumPyArray": [("0.1.1", "0.1.2", None, {"src_port_remap": {"self": "value"}})],
"read|ExcelSpreadsheet": [
("0.1.1", "0.1.2", None, {"src_port_remap": {"self": "value"}}),
("0.1.3", "0.1.4", None, {}),
],
"read|JSONFile": [(None, "0.1.5", "read|JSONObject")],
}
return UpgradeWorkflowHandler.remap_module(controller, module_id, pipeline, module_remap)
def handle_module_upgrade_request(controller, module_id, pipeline):
# Before 0.0.3, SQLSource's resultSet output was type ListOfElements (which
# doesn't exist anymore)
# In 0.0.3, SQLSource's resultSet output was type List
# In 0.1.0, SQLSource's output was renamed to result and is now a Table;
# this is totally incompatible and no upgrade code is possible
# the resultSet is kept for now for compatibility
# Up to 0.0.4, DBConnection would ask for a password if one was necessary;
# this behavior has not been kept. There is now a password input port, to
# which you can connect a PasswordDialog from package dialogs if needed
old_module = pipeline.modules[module_id]
# DBConnection module from before 0.1.0: automatically add the password
# prompt module
if (old_module.name == 'DBConnection'
and versions_increasing(old_module.version, '0.1.0')):
reg = get_module_registry()
# Creates the new module
new_module = controller.create_module_from_descriptor(
reg.get_descriptor(DBConnection))
# Create the password module
mod_desc = reg.get_descriptor_by_name(
'org.vistrails.vistrails.dialogs', 'PasswordDialog')
mod = controller.create_module_from_descriptor(mod_desc)
# Adds a 'label' function to the password module
ops = [('add', mod)]
ops.extend(
controller.update_function_ops(mod, 'label', ['Server password']))
# Connects the password module to the new module
conn = controller.create_connection(mod, 'result', new_module,
'password')
ops.append(('add', conn))
# Replaces the old module with the new one
upgrade_actions = UpgradeWorkflowHandler.replace_generic(
controller,
pipeline,
old_module,
new_module,
src_port_remap={'self': 'connection'})
password_fix_action = create_action(ops)
return upgrade_actions + [password_fix_action]
return UpgradeWorkflowHandler.attempt_automatic_upgrade(
controller, pipeline, module_id)
def handle_module_upgrade_request(controller, module_id, pipeline):
# Before 0.0.3, SQLSource's resultSet output was type ListOfElements (which
# doesn't exist anymore)
# In 0.0.3, SQLSource's resultSet output was type List
# In 0.1.0, SQLSource's output was renamed to result and is now a Table;
# this is totally incompatible and no upgrade code is possible
# the resultSet is kept for now for compatibility
# Up to 0.0.4, DBConnection would ask for a password if one was necessary;
# this behavior has not been kept. There is now a password input port, to
# which you can connect a PasswordDialog from package dialogs if needed
old_module = pipeline.modules[module_id]
# DBConnection module from before 0.1.0: automatically add the password
# prompt module
if (old_module.name == 'DBConnection' and
versions_increasing(old_module.version, '0.1.0')):
reg = get_module_registry()
# Creates the new module
new_module = controller.create_module_from_descriptor(
reg.get_descriptor(DBConnection))
# Create the password module
mod_desc = reg.get_descriptor_by_name(
'org.vistrails.vistrails.dialogs', 'PasswordDialog')
mod = controller.create_module_from_descriptor(mod_desc)
# Adds a 'label' function to the password module
ops = [('add', mod)]
ops.extend(controller.update_function_ops(mod,
'label', ['Server password']))
# Connects the password module to the new module
conn = controller.create_connection(mod, 'result',
new_module, 'password')
ops.append(('add', conn))
# Replaces the old module with the new one
upgrade_actions = UpgradeWorkflowHandler.replace_generic(
controller, pipeline,
old_module, new_module,
src_port_remap={'self': 'connection'})
password_fix_action = create_action(ops)
return upgrade_actions + [password_fix_action]
return UpgradeWorkflowHandler.attempt_automatic_upgrade(
controller, pipeline,
module_id)
def _get_variables_root(controller=None):
"""Create or get the version tagged 'dat-vars'
This is the base version of all DAT variables. It consists of a single
OutputPort module with name 'value'.
"""
if controller is None:
controller = get_vistrails_application().get_controller()
assert controller is not None
if controller.vistrail.has_tag_str('dat-vars'):
root_version = controller.vistrail.get_version_number('dat-vars')
else:
# Create the 'dat-vars' version
controller.change_selected_version(0)
reg = get_module_registry()
operations = []
# Add an OutputPort module
descriptor = reg.get_descriptor_by_name(
'org.vistrails.vistrails.basic', 'OutputPort')
out_mod = controller.create_module_from_descriptor(descriptor)
operations.append(('add', out_mod))
# Add a function to this module
operations.extend(
controller.update_function_ops(
out_mod,
'name',
['value']))
# Perform the operations
action = create_action(operations)
controller.add_new_action(action)
root_version = controller.perform_action(action)
# Tag as 'dat-vars'
controller.vistrail.set_tag(root_version, 'dat-vars')
controller.change_selected_version(root_version)
pipeline = controller.current_pipeline
outmod_id = pipeline.modules.keys()
assert len(outmod_id) == 1
outmod_id = outmod_id[0]
return controller, root_version, outmod_id
def test_delete(to_delete, expected_survivors,
controller=None, modules=None,
**kwargs):
if controller is None:
controller, modules = self.make_pipeline()
rmodules = {m.id: i for i, m in enumerate(modules)}
to_delete = [modules[i] for i in to_delete]
operations = []
delete_linked(controller, to_delete, operations, **kwargs)
action = create_action(operations)
controller.add_new_action(action)
controller.change_selected_version(
controller.perform_action(action))
survivors = [rmodules[m.id]
for m in controller.current_pipeline.module_list]
survivors.sort()
self.assertEqual(survivors, expected_survivors)
def updateVistrail(self):
""" updateVistrail() -> None
Update functions on the metadata port of the module
"""
# Remove the keys that we loaded
ops = [('delete', func) for func in self._loaded_keys]
# Add the metadata in the list
for i in xrange(self._list_layout.count()):
widget = self._list_layout.itemAt(i).widget()
ops.extend(self.controller.update_function_ops(
self.module, 'metadata',
[widget.to_string()]))
# This code should really be in VistrailController
self.controller.flush_delayed_actions()
action = create_action(ops)
self.controller.add_new_action(action,
"Updated PersistedPath metadata")
self.controller.perform_action(action)
return True
def perform_action(self):
"""Layout all the modules and create the action.
"""
self._ensure_version()
pipeline = self.controller.current_pipeline
self.operations.extend(self.controller.layout_modules_ops(
old_modules=[m
for m in self.all_modules
if m.id in pipeline.modules],
new_modules=[m
for m in self.all_modules
if m.id not in pipeline.modules],
new_connections=[c
for c in self.all_connections
if c.id not in pipeline.connections],
preserve_order=True))
action = create_action(self.operations)
self.controller.add_new_action(action)
return self.controller.perform_action(action)
def perform_action(self):
"""Layout all the modules and create the action.
"""
self._ensure_version()
pipeline = self.controller.current_pipeline
self.operations.extend(self.controller.layout_modules_ops(
old_modules=[m
for m in self.all_modules
if m.id in pipeline.modules],
new_modules=[m
for m in self.all_modules
if m.id not in pipeline.modules],
new_connections=[c
for c in self.all_connections
if c.id not in pipeline.connections],
preserve_order=True))
action = create_action(self.operations)
self.controller.add_new_action(action)
return self.controller.perform_action(action)
def updateVistrail(self):
""" updateVistrail() -> None
Update functions on the metadata port of the module
"""
# Remove the keys that we loaded
ops = [('delete', func) for func in self._loaded_keys]
# Add the metadata in the list
for i in xrange(self._list_layout.count()):
widget = self._list_layout.itemAt(i).widget()
ops.extend(
self.controller.update_function_ops(self.module, 'metadata',
[widget.to_string()]))
# This code should really be in VistrailController
self.controller.flush_delayed_actions()
action = create_action(ops)
self.controller.add_new_action(action,
"Updated PersistedPath metadata")
self.controller.perform_action(action)
return True
def test_delete(to_delete,
expected_survivors,
controller=None,
modules=None,
**kwargs):
if controller is None:
controller, modules = self.make_pipeline()
rmodules = {m.id: i for i, m in enumerate(modules)}
to_delete = [modules[i] for i in to_delete]
operations = []
delete_linked(controller, to_delete, operations, **kwargs)
action = create_action(operations)
controller.add_new_action(action)
controller.change_selected_version(
controller.perform_action(action))
survivors = [
rmodules[m.id] for m in controller.current_pipeline.module_list
]
survivors.sort()
self.assertEqual(survivors, expected_survivors)