def run_parameter_exploration(
locator,
pe_id,
extra_info={},
reason="Console Mode Parameter Exploration Execution"):
"""run_parameter_exploration(w_list: (locator, version),
pe_id: str/int,
reason: str) -> (pe_id, [error msg])
Run parameter exploration in w, and returns an interpreter result object.
version can be a tag name or a version id.
"""
if is_running_gui():
from vistrails.gui.vistrail_controller import VistrailController as \
GUIVistrailController
try:
(v, abstractions, thumbnails, mashups) = load_vistrail(locator)
controller = GUIVistrailController(v, locator, abstractions,
thumbnails, mashups)
try:
pe_id = int(pe_id)
pe = controller.vistrail.get_paramexp(pe_id)
except ValueError:
pe = controller.vistrail.get_named_paramexp(pe_id)
controller.change_selected_version(pe.action_id)
controller.executeParameterExploration(pe,
extra_info=extra_info,
showProgress=False)
except Exception, e:
return (locator, pe_id, debug.format_exception(e),
debug.format_exc())
def open_workflow(self, locator):
if isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
new_locator = UntitledLocator()
controller = self.open_vistrail(new_locator)
try:
if locator is None:
return False
workflow = locator.load(Pipeline)
action_list = []
for module in workflow.module_list:
action_list.append(('add', module))
for connection in workflow.connection_list:
action_list.append(('add', connection))
action = vistrails.core.db.action.create_action(action_list)
controller.add_new_action(action)
controller.perform_action(action)
controller.vistrail.set_tag(action.id, "Imported workflow")
controller.change_selected_version(action.id)
except VistrailsDBException as e:
debug.unexpected_exception(e)
debug.critical("Exception from the database: %s" % e,
debug.format_exc())
return None
controller.select_latest_version()
controller.set_changed(True)
return controller
def open_workflow(self, locator):
if isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
new_locator = UntitledLocator()
controller = self.open_vistrail(new_locator)
try:
if locator is None:
return False
workflow = locator.load(Pipeline)
action_list = []
for module in workflow.module_list:
action_list.append(('add', module))
for connection in workflow.connection_list:
action_list.append(('add', connection))
action = vistrails.core.db.action.create_action(action_list)
controller.add_new_action(action)
controller.perform_action(action)
controller.vistrail.set_tag(action.id, "Imported workflow")
controller.change_selected_version(action.id)
except VistrailsDBException:
debug.critical("Exception from the database", debug.format_exc())
return None
controller.select_latest_version()
controller.set_changed(True)
return controller
def run_parameter_exploration(locator, pe_id, extra_info = {},
reason="Console Mode Parameter Exploration Execution"):
"""run_parameter_exploration(w_list: (locator, version),
pe_id: str/int,
reason: str) -> (pe_id, [error msg])
Run parameter exploration in w, and returns an interpreter result object.
version can be a tag name or a version id.
"""
if is_running_gui():
from vistrails.gui.vistrail_controller import VistrailController as \
GUIVistrailController
try:
(v, abstractions , thumbnails, mashups) = load_vistrail(locator)
controller = GUIVistrailController(v, locator, abstractions,
thumbnails, mashups)
try:
pe_id = int(pe_id)
pe = controller.vistrail.get_paramexp(pe_id)
except ValueError:
pe = controller.vistrail.get_named_paramexp(pe_id)
controller.change_selected_version(pe.action_id)
controller.executeParameterExploration(pe, extra_info=extra_info,
showProgress=False)
except Exception, e:
return (locator, pe_id,
debug.format_exception(e), debug.format_exc())
def runAndGetCellEvents(self, useDefaultValues=False):
spreadsheetController.setEchoMode(True)
#will run to get Spreadsheet Cell events
cellEvents = []
errors = []
try:
(res, errors) = self.run(useDefaultValues)
if res:
cellEvents = spreadsheetController.getEchoCellEvents()
except Exception, e:
debug.unexpected_exception(e)
print "Executing pipeline failed:", debug.format_exc()
def runAndGetCellEvents(self, useDefaultValues=False):
spreadsheetController.setEchoMode(True)
# will run to get Spreadsheet Cell events
cellEvents = []
errors = []
try:
(res, errors) = self.run(useDefaultValues)
if res:
cellEvents = spreadsheetController.getEchoCellEvents()
except Exception, e:
debug.unexpected_exception(e)
print "Executing pipeline failed:", debug.format_exc()
def reload(self, vistrail):
if vistrail is not None:
self.set_vistrail(vistrail)
for version_id in self.vistrail.get_tagMap():
self.add_workflow_entity(version_id)
#mashups
if hasattr(self.vistrail, 'mashups'):
self._mshp_tag_map = {}
for mashuptrail in self.vistrail.mashups:
self._mshp_tag_map[mashuptrail.id] = \
self.add_mashup_entities_from_mashuptrail(mashuptrail)
#parameter explorations
if hasattr(self.vistrail, 'parameter_explorations'):
self.pe_entity_map = {}
# find named pe's
#max_pe = {}
for pe in self.vistrail.parameter_explorations:
if pe.name:
self.pe_entity_map[pe.name] = \
self.add_parameter_exploration_entity(pe)
# if pe.action_id not in max_pe or max_pe[pe.action_id]<pe.id:
# max_pe[pe.action_id] = pe
#for pe in max_pe.values():
# if pe.id not in self.pe_entity_map:
# self.pe_entity_map[pe.id] = \
# self.add_parameter_exploration_entity(pe)
# read persisted log entries
log = None
try:
log = vistrail.get_persisted_log()
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Failed to read log", debug.format_exc())
if log is not None:
for wf_exec in log.workflow_execs:
self.add_wf_exec_entity(wf_exec, False)
# read unpersisted log entries
if vistrail.log is not None:
for wf_exec in self.vistrail.log.workflow_execs:
self.add_wf_exec_entity(wf_exec, True)
self._vt_tag_map = copy.copy(self.vistrail.get_tagMap())
def reload(self, vistrail):
if vistrail is not None:
self.set_vistrail(vistrail)
for version_id in self.vistrail.get_tagMap():
self.add_workflow_entity(version_id)
#mashups
if hasattr(self.vistrail, 'mashups'):
self._mshp_tag_map = {}
for mashuptrail in self.vistrail.mashups:
self._mshp_tag_map[mashuptrail.id] = \
self.add_mashup_entities_from_mashuptrail(mashuptrail)
#parameter explorations
if hasattr(self.vistrail, 'parameter_explorations'):
self.pe_entity_map = {}
# find named pe's
#max_pe = {}
for pe in self.vistrail.parameter_explorations:
if pe.name:
self.pe_entity_map[pe.name] = \
self.add_parameter_exploration_entity(pe)
# if pe.action_id not in max_pe or max_pe[pe.action_id]<pe.id:
# max_pe[pe.action_id] = pe
#for pe in max_pe.values():
# if pe.id not in self.pe_entity_map:
# self.pe_entity_map[pe.id] = \
# self.add_parameter_exploration_entity(pe)
# read persisted log entries
log = None
try:
log = vistrail.get_persisted_log()
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Failed to read log", debug.format_exc())
if log is not None:
for wf_exec in log.workflow_execs:
self.add_wf_exec_entity(wf_exec, False)
# read unpersisted log entries
if vistrail.log is not None:
for wf_exec in self.vistrail.log.workflow_execs:
self.add_wf_exec_entity(wf_exec, True)
self._vt_tag_map = copy.copy(self.vistrail.get_tagMap())
def add_workflow_entity(self, version_id):
if version_id not in self.vistrail.actionMap:
return
action = self.vistrail.actionMap[version_id]
tag = None
if self.vistrail.has_tag(version_id):
tag = self.vistrail.get_tag(version_id)
try:
workflow = self.vistrail.getPipeline(version_id)
except Exception, e:
debug.unexpected_exception(e)
debug.critical(
"Failed to construct pipeline '%s'" %
(tag if tag else version_id), debug.format_exc())
workflow = self.vistrail.getPipeline(0)
def add_workflow_entity(self, version_id):
if version_id not in self.vistrail.actionMap:
return
action = self.vistrail.actionMap[version_id]
tag = None
if self.vistrail.has_tag(version_id):
tag = self.vistrail.get_tag(version_id)
try:
workflow = self.vistrail.getPipeline(version_id)
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Failed to construct pipeline '%s'" %
(tag if tag else version_id),
debug.format_exc())
workflow = self.vistrail.getPipeline(0)
def getVersionDAO(version=None):
if version is None:
version = currentVersion
persistence_dir = 'vistrails.db.versions.' + get_version_name(version) + \
'.persistence'
try:
persistence = __import__(persistence_dir, {}, {}, [''])
except ImportError as e:
if str(e).startswith('No module named v'):
# assume version is not available
msg = "Cannot find DAO for version '%s'" % version
raise VistrailsDBException(msg)
# assume other error
import traceback
raise VistrailsDBException(debug.format_exc())
return persistence.DAOList()
def getVersionDAO(version=None):
if version is None:
version = currentVersion
persistence_dir = 'vistrails.db.versions.' + get_version_name(version) + \
'.persistence'
try:
persistence = __import__(persistence_dir, {}, {}, [''])
except ImportError as e:
if str(e).startswith('No module named v'):
# assume version is not available
msg = "Cannot find DAO for version '%s'" % version
raise VistrailsDBException(msg)
# assume other error
import traceback
raise VistrailsDBException(debug.format_exc())
return persistence.DAOList()
def open_vistrail(self, locator=None, version=None, is_abstraction=False):
if isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
elif locator is None:
locator = UntitledLocator()
controller = self.ensure_vistrail(locator)
if controller is None:
# vistrail is not already open
try:
loaded_objs = vistrails.core.db.io.load_vistrail(
locator, is_abstraction)
controller = self.add_vistrail(loaded_objs[0], locator,
*loaded_objs[1:])
if locator.is_untitled():
return controller
controller.is_abstraction = is_abstraction
thumb_cache = ThumbnailCache.getInstance()
controller.vistrail.thumbnails = controller.find_thumbnails(
tags_only=thumb_cache.conf.tagsOnly)
controller.vistrail.abstractions = controller.find_abstractions(
controller.vistrail, True)
controller.vistrail.mashups = controller._mashups
collection = Collection.getInstance()
url = locator.to_url()
entity = collection.updateVistrail(url, controller.vistrail)
# add to relevant workspace categories
if not controller.is_abstraction:
collection.add_to_workspace(entity)
collection.commit()
except VistrailsDBException as e:
debug.unexpected_exception(e)
debug.critical("Exception from the database: %s" % e,
debug.format_exc())
return None
version = self.convert_version(version)
if version is None:
controller.select_latest_version()
version = controller.current_version
self.select_version(version)
return controller
def open_vistrail(self, locator=None, version=None, is_abstraction=False):
if isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
elif locator is None:
locator = UntitledLocator()
controller = self.ensure_vistrail(locator)
if controller is None:
# vistrail is not already open
try:
loaded_objs = vistrails.core.db.io.load_vistrail(locator, is_abstraction)
controller = self.add_vistrail(loaded_objs[0], locator,
*loaded_objs[1:])
if locator.is_untitled():
return controller
controller.is_abstraction = is_abstraction
thumb_cache = ThumbnailCache.getInstance()
controller.vistrail.thumbnails = controller.find_thumbnails(
tags_only=thumb_cache.conf.tagsOnly)
controller.vistrail.abstractions = controller.find_abstractions(
controller.vistrail, True)
controller.vistrail.mashups = controller._mashups
collection = Collection.getInstance()
url = locator.to_url()
entity = collection.updateVistrail(url, controller.vistrail)
# add to relevant workspace categories
if not controller.is_abstraction:
collection.add_to_workspace(entity)
collection.commit()
except VistrailsDBException as e:
debug.unexpected_exception(e)
debug.critical("Exception from the database: %s" % e,
debug.format_exc())
return None
version = self.convert_version(version)
if version is None:
controller.select_latest_version()
version = controller.current_version
self.select_version(version)
return controller
def save_vistrail(self, locator=None, controller=None, export=False):
if controller is None:
controller = self.get_current_controller()
if controller is None:
return False
if locator is None and controller is not None:
locator = controller.locator
elif isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
if not locator:
return False
old_locator = controller.locator
controller.flush_delayed_actions()
try:
controller.write_vistrail(locator, export=export)
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Failed to save vistrail", debug.format_exc())
raise
def save_vistrail(self, locator=None, controller=None, export=False):
if controller is None:
controller = self.get_current_controller()
if controller is None:
return False
if locator is None and controller is not None:
locator = controller.locator
elif isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
if not locator:
return False
old_locator = controller.locator
controller.flush_delayed_actions()
try:
controller.write_vistrail(locator, export=export)
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Failed to save vistrail", debug.format_exc())
raise
def add_wf_exec_entity(self, wf_exec, add_to_map=False):
version_id = wf_exec.parent_version
is_new = False
if version_id not in self.wf_entity_map:
is_new = True
# FIXME add new workflow entity for this version
if version_id not in self.vistrail.actionMap:
raise LookupError("Version %d does not occur in vistrail." %
version_id)
action = self.vistrail.actionMap[version_id]
try:
workflow = self.vistrail.getPipeline(version_id)
except Exception, e:
debug.unexpected_exception(e)
if self.vistrail.has_tag(version_id):
tag_str = self.vistrail.get_tag(version_id)
else:
tag_str = str(version_id)
debug.critical("Failed to construct pipeline '%s'" % tag_str,
debug.format_exc())
workflow = self.vistrail.getPipeline(0)
wf_entity = self.create_workflow_entity(workflow, action)
self.wf_entity_map[version_id] = wf_entity
def add_wf_exec_entity(self, wf_exec, add_to_map=False):
version_id = wf_exec.parent_version
is_new = False
if version_id not in self.wf_entity_map:
is_new = True
# FIXME add new workflow entity for this version
if version_id not in self.vistrail.actionMap:
raise LookupError("Version %d does not occur in vistrail." %
version_id)
action = self.vistrail.actionMap[version_id]
try:
workflow = self.vistrail.getPipeline(version_id)
except Exception, e:
debug.unexpected_exception(e)
if self.vistrail.has_tag(version_id):
tag_str = self.vistrail.get_tag(version_id)
else:
tag_str = str(version_id)
debug.critical("Failed to construct pipeline '%s'" % tag_str,
debug.format_exc())
workflow = self.vistrail.getPipeline(0)
wf_entity = self.create_workflow_entity(workflow, action)
self.wf_entity_map[version_id] = wf_entity
for me in mes.module_errors:
me.module.logging.end_update(me.module, me)
logging_obj.signalError(me.module, me)
abort = abort or me.abort
except ModuleError, me:
me.module.logging.end_update(me.module, me, me.errorTrace)
logging_obj.signalError(me.module, me)
abort = me.abort
except ModuleBreakpoint, mb:
mb.module.logging.end_update(mb.module)
logging_obj.signalError(mb.module, mb)
abort = True
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Exception running generators: %s" % e,
debug.format_exc())
abort = True
if stop_on_error or abort:
break
Generator.generators = self._streams.pop()
if self.done_update_hook:
self.done_update_hook(self._persistent_pipeline, self._objects)
# objs, errs, and execs are mappings that use the local ids as keys,
# as opposed to the persistent ids.
# They are thus ideal to external consumption.
objs = {}
# dict([(i, self._objects[tmp_to_persistent_module_map[i]])
# for i in tmp_to_persistent_module_map.keys()])
try:
thumb_cache = ThumbnailCache.getInstance()
controller.vistrail.thumbnails = controller.find_thumbnails(
tags_only=thumb_cache.conf.tagsOnly)
controller.vistrail.abstractions = controller.find_abstractions(
controller.vistrail, True)
controller.vistrail.mashups = controller._mashups
collection = Collection.getInstance()
url = locator.to_url()
entity = collection.updateVistrail(url, controller.vistrail)
# add to relevant workspace categories
collection.add_to_workspace(entity)
collection.commit()
except Exception, e:
debug.critical('Failed to index vistrail', debug.format_exc())
return controller.locator
def close_vistrail(self, locator=None, controller=None):
if controller is None:
controller = self.get_current_controller()
if controller is None:
return False
if locator is None and controller is not None:
locator = controller.locator
elif isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
controller.close_vistrail(locator)
controller.cleanup()
self.remove_vistrail(locator)
try:
thumb_cache = ThumbnailCache.getInstance()
controller.vistrail.thumbnails = controller.find_thumbnails(
tags_only=thumb_cache.conf.tagsOnly)
controller.vistrail.abstractions = controller.find_abstractions(
controller.vistrail, True)
controller.vistrail.mashups = controller._mashups
collection = Collection.getInstance()
url = locator.to_url()
entity = collection.updateVistrail(url, controller.vistrail)
# add to relevant workspace categories
collection.add_to_workspace(entity)
collection.commit()
except Exception, e:
debug.critical('Failed to index vistrail', debug.format_exc())
return controller.locator
def close_vistrail(self, locator=None, controller=None):
if controller is None:
controller = self.get_current_controller()
if controller is None:
return False
if locator is None and controller is not None:
locator = controller.locator
elif isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
controller.close_vistrail(locator)
controller.cleanup()
self.remove_vistrail(locator)
for me in mes.module_errors:
me.module.logging.end_update(me.module, me)
logging_obj.signalError(me.module, me)
abort = abort or me.abort
except ModuleError, me:
me.module.logging.end_update(me.module, me, me.errorTrace)
logging_obj.signalError(me.module, me)
abort = me.abort
except ModuleBreakpoint, mb:
mb.module.logging.end_update(mb.module)
logging_obj.signalError(mb.module, mb)
abort = True
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Exception running generators: %s" % e,
debug.format_exc())
abort = True
if stop_on_error or abort:
break
Generator.generators = self._streams.pop()
if self.done_update_hook:
self.done_update_hook(self._persistent_pipeline, self._objects)
# objs, errs, and execs are mappings that use the local ids as keys,
# as opposed to the persistent ids.
# They are thus ideal to external consumption.
objs = {}
# dict([(i, self._objects[tmp_to_persistent_module_map[i]])
# for i in tmp_to_persistent_module_map.keys()])
