def initialize(*args, **keywords):
if "CLTools" == identifiers.name:
# this is the original package
location = os.path.join(vistrails.core.system.current_dot_vistrails(),
"CLTools")
# make sure dir exist
if not os.path.isdir(location):
try:
debug.log("Creating CLTools directory...")
os.mkdir(location)
except:
debug.critical("""Could not create CLTools directory. Make
sure '%s' does not exist and parent directory is writable""" % location)
sys.exit(1)
else:
# this is a standalone package so modules are placed in this directory
location = os.path.dirname(__file__)
reg = vistrails.core.modules.module_registry.get_module_registry()
reg.add_module(CLTools, abstract=True)
for path in os.listdir(location):
if path.endswith(SUFFIX):
try:
add_tool(os.path.join(location, path))
except Exception as exc:
import traceback
debug.critical("Package CLTools failed to create module "
"from '%s': %s" % (os.path.join(location, path), exc),
traceback.format_exc())
def reload_scripts():
remove_all_scripts()
if "CLTools" == identifiers.name:
# this is the original package
location = os.path.join(vistrails.core.system.current_dot_vistrails(),
"CLTools")
# make sure dir exist
if not os.path.isdir(location):
try:
debug.log("Creating CLTools directory...")
os.mkdir(location)
except:
debug.critical("""Could not create CLTools directory. Make
sure '%s' does not exist and parent directory is writable""" % location)
sys.exit(1)
else:
# this is a standalone package so modules are placed in this directory
location = os.path.dirname(__file__)
for path in os.listdir(location):
if path.endswith(SUFFIX):
try:
add_tool(os.path.join(location, path))
except Exception as exc:
import traceback
debug.critical("Package CLTools failed to create module "
"from '%s': %s" % (os.path.join(location, path), exc),
traceback.format_exc())
from vistrails.core.interpreter.cached import CachedInterpreter
CachedInterpreter.clear_package(identifiers.identifier)
from vistrails.gui.vistrails_window import _app
_app.invalidate_pipelines()
def open_workflow(self, locator):
if isinstance(locator, basestring):
locator = BaseLocator.from_url(locator)
vistrail = Vistrail()
try:
if locator is None:
return False
if locator is not None:
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)
vistrail.add_action(action, 0L)
vistrail.update_id_scope()
vistrail.addTag("Imported workflow", action.id)
# FIXME might need different locator?
controller = self.add_vistrail(vistrail, locator)
except VistrailsDBException, e:
import traceback
debug.critical("Exception from the database",
traceback.format_exc())
return None
def execute(self):
""" execute() -> None
Perform the exploration by collecting a list of actions
corresponding to each dimension
"""
# persist the parameter exploration
pe = self.getParameterExploration()
pe.action_id = self.controller.current_version
# check if pe has changed
changed = False
if not self.controller.current_parameter_exploration or \
pe != self.controller.current_parameter_exploration:
changed = True
pe.name = ''
self.controller.current_parameter_exploration = pe
self.controller.vistrail.add_paramexp(pe)
self.controller.set_changed(True)
else:
pe = self.controller.current_parameter_exploration
errors = self.controller.executeParameterExploration(pe,
self.get_param_view().pipeline_view.scene())
if errors:
errors = '\n'.join(['Position %s: %s' % (error[0], error[1]) for error in errors])
debug.critical("Parameter Exploration Execution had errors", errors)
if changed:
from vistrails.gui.vistrails_window import _app
_app.notify('exploration_changed')
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:
import traceback
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,
traceback.format_exc())
workflow = self.vistrail.getPipeline(0)
wf_entity = self.create_workflow_entity(workflow, action)
self.wf_entity_map[version_id] = wf_entity
else:
wf_entity = self.wf_entity_map[version_id]
entity = self.create_wf_exec_entity(wf_exec, wf_entity)
if add_to_map:
self.wf_exec_entity_map[wf_exec.id] = entity
if is_new:
return (entity, wf_entity)
return (entity, None)
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:
import traceback
debug.critical("Failed to construct pipeline '%s'" %
(tag if tag else version_id),
traceback.format_exc())
workflow = self.vistrail.getPipeline(0)
if tag:
workflow.name = tag
# if workflow already exists, we want to update it...
# spin through self.children and look for matching
# workflow entity?
# self.children.append(WorkflowEntity(workflow))
self.wf_entity_map[version_id] = \
self.create_workflow_entity(workflow, action)
# get thumbnail
thumbnail = self.vistrail.get_thumbnail(version_id)
if thumbnail is not None:
cache = ThumbnailCache.getInstance()
path = cache.get_abs_name_entry(thumbnail)
if path:
entity = ThumbnailEntity(path)
self.wf_entity_map[action.id].children.append(entity)
entity.parent = self.wf_entity_map[action.id]
return self.wf_entity_map[version_id]
def updateController(self, controller):
""" updateController(controller: VistrailController) -> None
Construct input forms for a controller's variables
"""
# we shouldn't do this whenver the controller changes...
if self.controller != controller:
self.controller = controller
if self.updateLocked: return
self.vWidget.clear()
if controller:
reg = module_registry.get_module_registry()
for var in [v for v in controller.vistrail.vistrail_vars]:
try:
descriptor = reg.get_descriptor_by_name(var.package,
var.module,
var.namespace)
except module_registry.ModuleRegistryException:
debug.critical("Missing Module Descriptor for vistrail"
" variable %s\nPackage: %s\nType: %s"
"\nNamespace: %s" % \
(var.name, var.package, var.module,
var.namespace))
continue
self.vWidget.addVariable(var.uuid, var.name, descriptor,
var.value)
self.vWidget.showPromptByChildren()
else:
self.vWidget.showPrompt(False)
def import_user_packages_module(self):
"""Imports the 'userspackages' package.
This will need to manipulate the Python path to find it.
"""
if self._userpackages is not None:
return self._userpackages
# Imports user packages directory
old_sys_path = copy.copy(sys.path)
userPackageDir = system.get_vistrails_directory('userPackageDir')
if userPackageDir is not None:
sys.path.insert(0, os.path.join(userPackageDir, os.path.pardir))
try:
import userpackages
except ImportError:
debug.critical('ImportError: "userpackages" sys.path: %s' %
sys.path)
raise
finally:
sys.path = old_sys_path
os.environ['VISTRAILS_USERPACKAGES_DIR'] = userPackageDir
self._userpackages = userpackages
return userpackages
# possible that we don't have userPackageDir set!
return None
def open_workflow(self, locator, version=None):
self.close_first_vistrail_if_necessary()
if self.single_document_mode and self.currentView():
self.closeVistrail()
vistrail = Vistrail()
try:
if locator is not None:
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)
vistrail.add_action(action, 0L)
vistrail.update_id_scope()
vistrail.addTag("Imported workflow", action.id)
# FIXME might need different locator?
except ModuleRegistryException, e:
msg = ('Cannot find module "%s" in package "%s". '
'Make sure package is '
'enabled in the Preferences dialog.' % \
(e._name, e._identifier))
debug.critical(msg)
def updateContents(self, conn_id=-1):
"""updateContents(connection_id: int) -> None
Reloads vistrails from the given connection
"""
self.clear()
if conn_id != -1:
parent = self.parent()
try:
objs = parent.connectionList.getDBObjectList(int(conn_id),
self.obj_type)
for (id,obj,date) in objs:
item = QDBObjectListItem(CurrentTheme.FILE_ICON,
int(id),
str(obj),
str(date))
self.addItem(item)
except VistrailsDBException, e:
#show connection setup
error = str(e)
if "Couldn't get list of vistrails objects" in error:
debug.critical('An error has occurred', error)
raise e
config = parent.connectionList.getConnectionInfo(int(conn_id))
if config != None:
config["create"] = False
if not parent.showConnConfig(**config):
raise e
else:
raise e
def __init__(self, address):
""" Process WSDL and add all Types and Methods
"""
self.address = address
self.signature = toSignature(self.address)
self.wsdlHash = '-1'
self.modules = []
self.package = None
debug.log("Installing Web Service from WSDL: %s"% address)
options = dict(cachingpolicy=1, cache=package_cache)
proxy_types = ['http']
for t in proxy_types:
key = 'proxy_%s'%t
if configuration.check(key):
proxy = getattr(configuration, key)
debug.log("Using proxy: %s" % proxy)
if len(proxy):
options['proxy'] = {t:proxy}
try:
self.service = suds.client.Client(address, **options)
self.backUpCache()
except Exception, e:
self.service = None
# We may be offline and the cache may have expired,
# try to use backup
if self.restoreFromBackup():
try:
self.service = suds.client.Client(address, **options)
except Exception, e:
self.service = None
debug.critical("Could not load WSDL: %s" % address,
str(e) + '\n' + str(traceback.format_exc()))
def install_default_startupxml_if_needed():
fname = os.path.join(self.temp_configuration.dotVistrails,
'startup.xml')
root_dir = system.vistrails_root_directory()
origin = os.path.join(root_dir, 'core','resources',
'default_vistrails_startup_xml')
def skip():
if os.path.isfile(fname):
try:
d = self.startup_dom()
v = str(d.getElementsByTagName('startup')[0].attributes['version'].value)
return LooseVersion('0.1') <= LooseVersion(v)
except Exception:
return False
else:
return False
if skip():
return
try:
shutil.copyfile(origin, fname)
debug.log('Succeeded!')
except Exception, e:
debug.critical("""Failed to copy default configuration
file to %s. This could be an indication of a
permissions problem. Please make sure '%s' is writable."""
% (fname,
self.temp_configuration.dotVistrails), e)
def save_as(self, save_bundle, version=None):
save_bundle = _DBLocator.save(self, save_bundle, True, version)
for obj in save_bundle.get_db_objs():
klass = self.get_convert_klass(obj.vtType)
klass.convert(obj)
obj.locator = self
# Need to copy images into thumbnail cache directory so references
# won't become invalid if they are in a temp dir that gets destroyed
# when the previous locator is closed
import shutil
thumb_cache = ThumbnailCache.getInstance()
thumb_cache_dir = thumb_cache.get_directory()
new_thumbnails = []
for thumbnail in save_bundle.thumbnails:
if os.path.dirname(thumbnail) == thumb_cache_dir:
new_thumbnails.append(thumbnail)
else:
cachedir_thumbnail = os.path.join(thumb_cache_dir, os.path.basename(thumbnail))
try:
shutil.copyfile(thumbnail, cachedir_thumbnail)
new_thumbnails.append(cachedir_thumbnail)
except Exception, e:
debug.critical("copying %s -> %s failed" % (
thumbnail, cachedir_thumbnail),
e)
def updateCells(self, info=None):
# check if we should create a sequence
if self.cb_loop_sequence.isChecked():
return self.updateCellsLoop(info)
self.is_executing = True
(cellEvents, errors) = self.runAndGetCellEvents()
if errors is True:
debug.critical("Mashup job is still running. Run again to check "
"if it has completed.")
self.is_executing = False
if self.numberOfCells is not None and len(cellEvents) != self.numberOfCells:
raise RuntimeError(
"The number of cells has changed (unexpectedly) "
"(%d vs. %d)!\n"
"Pipeline results: %s" % (len(cellEvents),
self.numberOfCells,
errors))
elif self.numberOfCells is None and not errors:
self.numberOfCells = len(cellEvents)
if cellEvents:
self.initCells(cellEvents)
#self.SaveCamera()
for i in xrange(self.numberOfCells):
camera = []
if (hasattr(self.cellWidgets[i],"getRendererList") and
self.cb_keep_camera.isChecked()):
for ren in self.cellWidgets[i].getRendererList():
camera.append(ren.GetActiveCamera())
self.cellWidgets[i].updateContents(cellEvents[i].inputPorts, camera)
#self.cellWidgets[i].updateContents(cellEvents[i].inputPorts)
else:
self.cellWidgets[i].updateContents(cellEvents[i].inputPorts)
def interpolate(self, ranges, stepCount):
""" interpolate(ranges: tuple, stepCount: int) -> list
This function takes a number of (min,max) or (s1,...sn) to
interpolate exact stepCount number of step. The output will be
a list of stepCount elements where each of them is (a1,...,an).
a{i} is either int or string and n is the number of arguments.
"""
params = []
for r in ranges:
interpolatedValues = []
argumentType = type(r[0])
if argumentType in [int, float]:
for i in xrange(stepCount):
if stepCount>1: t = i/float(stepCount-1)
else: t = 0
interpolatedValues.append(argumentType(r[0]+t*(r[1]-r[0])))
elif argumentType==str:
interpolatedValues = list(r)
else:
debug.critical('Cannot interpolate non-cardinal types')
assert False
params.append(interpolatedValues)
return zip(*params)
def create_startupxml_if_needed(self):
needs_create = True
fname = self.get_startup_xml_fname()
if os.path.isfile(fname):
try:
tree = ElementTree.parse(fname)
startup_version = \
vistrails.db.services.io.get_version_for_xml(tree.getroot())
version_list = version_string_to_list(startup_version)
if version_list >= [0,1]:
needs_create = False
except:
debug.warning("Unable to read startup.xml file, "
"creating a new one")
if needs_create:
root_dir = system.vistrails_root_directory()
origin = os.path.join(root_dir, 'core','resources',
'default_vistrails_startup_xml')
try:
shutil.copyfile(origin, fname)
debug.log('Succeeded!')
self.first_run = True
except:
debug.critical("""Failed to copy default configuration
file to %s. This could be an indication of a
permissions problem. Please make sure '%s' is writable."""
% (fname, self._dot_vistrails))
raise
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",
traceback.format_exc())
return None
controller.select_latest_version()
controller.set_changed(True)
return controller
def createPackage(self):
reg = vistrails.core.modules.module_registry.get_module_registry()
if self.signature in reg.packages:
reg.remove_package(reg.packages[self.signature])
# create a document hash integer from the cached sax tree
# "name" is what suds use as the cache key
name = '%s-%s' % (abs(hash(self.address)), "wsdl")
wsdl = package_cache.get(name)
if not wsdl:
debug.critical("File not found in SUDS cache: '%s'" % name)
self.wsdlHash = '0'
return
self.wsdlHash = str(int(hashlib.md5(str(wsdl.root)).hexdigest(), 16))
package_id = reg.idScope.getNewId(Package.vtType)
package = Package(id=package_id,
load_configuration=False,
name="SUDS#" + self.address,
identifier=self.signature,
version=self.wsdlHash,
)
suds_package = reg.get_package_by_name(identifier)
package._module = suds_package.module
package._init_module = suds_package.init_module
self.package = package
reg.add_package(package)
reg.signals.emit_new_package(self.signature)
self.module = new_module(Module, str(self.signature))
reg.add_module(self.module, **{'package':self.signature,
'package_version':self.wsdlHash,
'abstract':True})
def updateVistrail(self):
"""updateVistrail() -> None
Update vistrail to contain changes to the python source
"""
deleted_ports = []
added_ports = []
if self.has_inputs:
(input_deleted_ports, input_added_ports) = \
self.getPortDiff('input', self.inputPortTable)
deleted_ports.extend(input_deleted_ports)
added_ports.extend(input_added_ports)
if self.has_outputs:
(output_deleted_ports, output_added_ports) = \
self.getPortDiff('output', self.outputPortTable)
deleted_ports.extend(output_deleted_ports)
added_ports.extend(output_added_ports)
functions = []
modified = False
if self.codeEditor.__class__.__name__ not in ['_PythonEditor', '_TextEditor']:
modified = self.codeEditor.document().isModified()
else:
modified = self.codeEditor.isModified()
if (self.codeEditor is not None and modified):
try:
code = str(self.codeEditor.toPlainText())
except UnicodeEncodeError, e:
debug.critical('Source Code Editor does not support non-ascii characters', e)
return False
if self.sourceEncode:
code = urllib.quote(code)
functions.append((self.sourcePortName, [code]))
def load_entity(self, *args):
if args[1] in Collection.entity_types:
entity = Collection.entity_types[args[1]].create(*args)
return entity
else:
debug.critical("Cannot find entity type '%s'" % args[1])
return None
def initialize_packages(self, prefix_dictionary={},
report_missing_dependencies=True):
"""initialize_packages(prefix_dictionary={}): None
Initializes all installed packages. If prefix_dictionary is
not {}, then it should be a dictionary from package names to
the prefix such that prefix + package_name is a valid python
import."""
failed = []
# import the modules
app = get_vistrails_application()
for package in self._package_list.itervalues():
# print '+ initializing', package.codepath, id(package)
if package.initialized():
# print '- already initialized'
continue
try:
prefix = prefix_dictionary.get(package.codepath)
if prefix is None:
prefix = self._default_prefix_dict.get(package.codepath)
package.load(prefix)
except Package.LoadFailed, e:
debug.critical("Package %s failed to load and will be "
"disabled" % package.name, e)
# We disable the package manually to skip over things
# we know will not be necessary - the only thing needed is
# the reference in the package list
self._startup.set_package_to_disabled(package.codepath)
failed.append(package)
except MissingRequirement, e:
debug.critical("Package <codepath %s> is missing a "
"requirement: %s" % (
package.codepath, e.requirement),
e)
def import_user_packages_module(self):
"""Imports the packages module using path trickery to find it
in the right place.
"""
if self._userpackages is not None:
return self._userpackages
# Imports user packages directory
conf = self._startup.temp_configuration
old_sys_path = copy.copy(sys.path)
userPackageDir = system.get_vistrails_directory('userPackageDir')
if userPackageDir is not None:
sys.path.insert(0, os.path.join(userPackageDir, os.path.pardir))
try:
import userpackages
except ImportError:
debug.critical('ImportError: "userpackages" sys.path: %s' %
sys.path)
raise
finally:
sys.path = old_sys_path
os.environ['VISTRAILS_USERPACKAGES_DIR'] = userPackageDir
self._userpackages = userpackages
return userpackages
# possible that we don't have userPackageDir set!
return None
def reload_scripts(initial=False, name=None):
reg = vistrails.core.modules.module_registry.get_module_registry()
if not initial:
from vistrails.core.interpreter.cached import CachedInterpreter
CachedInterpreter.clear_package(identifiers.identifier)
if name is None:
remove_all_scripts()
else:
del cl_tools[name]
reg.delete_module(identifiers.identifier, name)
if "CLTools" == identifiers.name:
# this is the original package
location = os.path.join(vistrails.core.system.current_dot_vistrails(),
"CLTools")
# make sure dir exist
if not os.path.isdir(location): # pragma: no cover # pragma: no branch
try:
debug.log("Creating CLTools directory...")
os.mkdir(location)
except Exception, e:
debug.critical("Could not create CLTools directory. Make "
"sure '%s' does not exist and parent directory "
"is writable" % location,
e)
sys.exit(1)
def save_vistrail(self, locator_class,
vistrailView=None,
force_choose_locator=False):
"""
force_choose_locator=True triggers 'save as' behavior
"""
global bobo
if not vistrailView:
vistrailView = self.currentWidget()
vistrailView.flush_changes()
if vistrailView:
gui_get = locator_class.save_from_gui
# get a locator to write to
if force_choose_locator:
locator = gui_get(self, Vistrail.vtType,
vistrailView.controller.locator)
else:
locator = (vistrailView.controller.locator or
gui_get(self, Vistrail.vtType,
vistrailView.controller.locator))
if locator == untitled_locator():
locator = gui_get(self, Vistrail.vtType,
vistrailView.controller.locator)
# if couldn't get one, ignore the request
if not locator:
return False
# update collection
vistrailView.controller.flush_delayed_actions()
try:
vistrailView.controller.write_vistrail(locator)
except Exception, e:
debug.critical('An error has occurred', str(e))
raise
return False
try:
thumb_cache = ThumbnailCache.getInstance()
vistrailView.controller.vistrail.thumbnails = \
vistrailView.controller.find_thumbnails(
tags_only=thumb_cache.conf.tagsOnly)
vistrailView.controller.vistrail.abstractions = \
vistrailView.controller.find_abstractions(
vistrailView.controller.vistrail, True)
collection = Collection.getInstance()
url = locator.to_url()
# create index if not exist
entity = collection.fromUrl(url)
if entity:
# find parent vistrail
while entity.parent:
entity = entity.parent
else:
entity = collection.updateVistrail(url, vistrailView.controller.vistrail)
# add to relevant workspace categories
collection.add_to_workspace(entity)
collection.commit()
except Exception, e:
debug.critical('Failed to index vistrail', str(e))
def updateCellsLoop(self, info=None):
""" Run workflow for each step in the loop sequence and collect results.
"""
interactive = self.cb_loop_int.isChecked()
slider = self.sequenceOption.value
if info and info[1][0] == slider:
# User is moving the slider, so we use the existing result
if interactive:
if slider.value() < len(self.steps):
self.updateRenderedCells(slider.value())
else:
for i in xrange(self.numberOfCells):
self.cellWidgets[i].setPlayerFrame(slider.value())
return
if not interactive:
for i in xrange(self.numberOfCells):
self.cellWidgets[i].clearHistory()
self.is_executing = True
self.steps = []
old_value = slider.value()
value = slider.minimum()
slider.setValue(value)
while True:
(cellEvents, errors) = self.runAndGetCellEvents()
if errors is True:
debug.critical("Mashup job is still running. Run again to check "
"if it has completed.")
if self.numberOfCells is not None and len(cellEvents) != self.numberOfCells:
raise RuntimeError(
"The number of cells has changed (unexpectedly) "
"(%d vs. %d)!\n"
"Pipeline results: %s" % (len(cellEvents),
self.numberOfCells,
errors))
elif self.numberOfCells is None and not errors:
self.numberOfCells = len(cellEvents)
if cellEvents:
self.initCells(cellEvents)
if interactive:
self.steps.append([])
else:
self.steps = [[]]
for i in xrange(self.numberOfCells):
self.steps[-1].append(cellEvents[i].inputPorts)
# show the result
self.updateRenderedCells(value if interactive else 0)
self.is_executing = True
if value >= slider.maximum():
break
value += slider.singleStep()
slider.setValue(value)
self.is_executing = False
slider.setValue(old_value)
self.loopButton.setEnabled(True)
def run(self, useDefaultValues=False):
# Building the list of parameter values
params = []
if useDefaultValues:
for alias in self.currentMashup.alias_list:
params.append((alias.component.vttype, alias.component.vtid,
alias.component.val))
else:
for (aliasName, edit) in self.cellControls.iteritems():
alias = self.currentMashup.getAliasByName(aliasName)
if hasattr(edit, 'contents'):
val = str(edit.contents())
else:
val =str(edit.text())
params.append((alias.component.vttype, alias.component.vtid,
val))
# reset job view
from vistrails.gui.job_monitor import QJobView
jobView = QJobView.instance()
if jobView.updating_now:
debug.critical("Execution Aborted: Job Monitor is updating. "
"Please wait a few seconds and try again.")
return [False, []]
jobView.updating_now = True
job_id = 'Mashup %s %s' % (self.currentMashup.version, self.currentMashup.id)
current_workflow = None
for wf in self.view.controller.jobMonitor.workflows.itervalues():
if job_id == wf.version:
current_workflow = wf
self.view.controller.jobMonitor.startWorkflow(wf)
if not current_workflow:
current_workflow = JobWorkflow(job_id)
self.view.controller.jobMonitor.startWorkflow(current_workflow)
self.view.controller.progress = ExecutionProgressDialog(self.view)
self.view.controller.progress.show()
try:
results = self.controller.execute(params)[0]
finally:
self.view.controller.jobMonitor.finishWorkflow()
jobView.updating_now = False
self.view.controller.progress.setValue(100)
self.view.controller.progress.hide()
self.view.controller.progress.deleteLater()
self.view.controller.progress = None
result = results[0]
objs, errors, executed, suspended = \
result.objects, result.errors, result.executed, result.suspended
if len(errors) > 0:
print '=== ERROR EXECUTING PIPELINE ==='
print errors
return (False, errors)
return (not suspended, [])
def saveToPNG(self, filename):
""" saveToPNG(filename: str) -> Bool
Abtract function for saving the current widget contents to an
image file
Returns True when succesful
"""
debug.critical('saveToPNG() is unimplemented by the inherited cell')
def module_documentation(self, module=None):
doc = pydoc.getdoc(self.module)
if hasattr(self.module, "get_documentation"):
try:
doc = self.module.get_documentation(doc, module)
except Exception, e:
debug.critical("Exception calling get_documentation on %r" % self.module, e)
doc = doc or "(Error getting documentation)"
def add_tool(path):
try:
_add_tool(path)
except Exception as exc: # pragma: no cover
import traceback
debug.critical("Package CLTools failed to create module "
"from '%s': %s" % (path, exc),
traceback.format_exc())
def saveVistrailFileHook(self, vistrail, tmp_dir):
if hasattr(self._init_module, 'saveVistrailFileHook'):
try:
self._init_module.saveVistrailFileHook(vistrail, tmp_dir)
except Exception, e:
debug.critical("Got exception in %s's saveVistrailFileHook(): "
"%s: %s" % (self.name, type(e).__name__,
', '.join(e.args)))
def setup_init_file(self, dir_name):
name = os.path.join(dir_name, '__init__.py')
try:
f = open(name, 'w')
f.write('pass\n')
f.close()
except:
msg = ("""Failed to create file '%s'. This could indicate a
rare combination of a race condition and a permissions problem.
Please make sure it is writable.""" % name)
debug.critical(msg)
sys.exit(1)
def getInstance():
if Collection._instance is False:
debug.critical("Collection.getInstance() called but the "
"Collection has been deleted!")
raise RuntimeError("Collection has been deleted!")
elif Collection._instance is None:
dotVistrails = vistrails.core.system.current_dot_vistrails()
path = os.path.join(dotVistrails, "index.db")
obj = Collection(path)
Collection._instance = obj
return Collection._instance
def testConnection(self):
"""testConnection() -> None """
config = {'host': str(self.hostEdt.text()),
'port': int(self.portEdt.value()),
'user': str(self.userEdt.text()),
'passwd': str(self.passwdEdt.text()),
'db': str(self.databaseEdt.text())}
try:
vistrails.db.services.io.test_db_connection(config)
show_info('Vistrails',"Connection succeeded!")
except Exception, e:
debug.critical('An error has occurred', e)
def create_directory(self, dir_name):
if not os.path.isdir(dir_name):
debug.warning('Will try to create directory "%s"' % dir_name)
try:
os.mkdir(dir_name)
return True
except Exception, e:
msg = ("Failed to create directory: '%s'."
"This could be an indication of a permissions problem."
"Make sure directory '%s' in writable." %
(str(e), dir_name))
debug.critical(msg)
sys.exit(1)
def enable_current_package(self):
av = self._available_packages_list
item = av.currentItem()
codepath = str(item.text())
pm = get_package_manager()
try:
new_deps = self._current_package.dependencies()
except Exception, e:
debug.critical(
"Failed getting dependencies of package %s, "
"so it will not be enabled" % self._current_package.name, e)
return
def menu_items(self):
try:
callable_ = self._module.menu_items
except AttributeError:
return None
else:
try:
return callable_()
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Couldn't load menu items for %s: %s\n%s" %
(self.name, debug.format_exception(e),
traceback.format_exc()))
def can_handle_identifier(self, identifier):
""" Asks package if it can handle this package
"""
try:
return (hasattr(self.init_module, 'can_handle_identifier')
and self.init_module.can_handle_identifier(identifier))
except Exception, e:
debug.unexpected_exception(e)
debug.critical(
"Got exception calling %s's can_handle_identifier: "
"%s\n%s" %
(self.name, debug.format_exception(e), traceback.format_exc()))
return False
def can_handle_vt_file(self, name):
""" Asks package if it can handle a file inside a zipped vt file
"""
try:
return (hasattr(self.init_module, 'can_handle_vt_file')
and self.init_module.can_handle_vt_file(name))
except Exception, e:
debug.unexpected_exception(e)
debug.critical(
"Got exception calling %s's can_handle_vt_file: "
"%s\n%s" %
(self.name, debug.format_exception(e), traceback.format_exc()))
return False
def dependencies(self):
deps = []
try:
callable_ = self._module.package_dependencies
except AttributeError:
pass
else:
try:
deps = callable_()
except Exception, e:
debug.critical(
"Couldn't get dependencies of %s: %s: %s" %
(self.name, type(e).__name__, ', '.join(e.args)))
def clicked_on_login(self):
"""
Attempts to log into web repository
stores auth cookie for session
"""
from vistrails.gui.application import get_vistrails_application
self.dialog.loginUser = self.loginUser.text()
params = urllib.urlencode({'username':self.dialog.loginUser,
'password':self.loginPassword.text()})
self.dialog.cookiejar = cookielib.CookieJar()
# set base url used for cookie
self.dialog.cookie_url = self.config.webRepositoryURL
self.loginOpener = urllib2.build_opener(urllib2.HTTPCookieProcessor(self.dialog.cookiejar))
# FIXME doesn't use https
login_url = "%s/account/login/" % self.config.webRepositoryURL
request = urllib2.Request(login_url, params)
url = self.loginOpener.open(request)
# login failed
if not 'sessionid' in [cookie.name for cookie in self.dialog.cookiejar]:
debug.critical("Incorrect username or password")
self.dialog.cookiejar = None
else: # login successful
self._login_status = "login successful"
self.loginUser.setEnabled(False)
self.loginPassword.setEnabled(False)
self._login_button.setEnabled(False)
self.saveLogin.setEnabled(False)
# add association between VisTrails user and web repository user
if self.saveLogin.checkState():
if not (self.config.check('webRepositoryUser') and self.config.webRepositoryUser == self.loginUser.text()):
self.config.webRepositoryUser = str(self.loginUser.text())
pers_config = get_vistrails_persistent_configuration()
pers_config.webRepositoryUser = self.config.webRepositoryUser
get_vistrails_application().save_configuration()
# remove association between VisTrails user and web repository user
else:
if self.config.check('webRepositoryUser') and self.config.webRepositoryUser:
self.config.webRepositoryUser = ""
pers_config = get_vistrails_persistent_configuration()
pers_config.webRepositoryUser = ""
get_vistrails_application().save_configuration()
self.close_dialog(0)
def getChildTypes(type):
schema = self.service.wsdl.schema
if type in schema.elements:
if schema.elements[type].type is not None:
return [(schema.elements[type].name,
schema.elements[type].type)]
else:
return [(c[0].name, c[0].type)
for c in schema.elements[type].children()]
elif type in schema.types:
return [(c[0].name, c[0].type)
for c in schema.types[type].children()]
debug.critical("Could not resolve type in WSDL:" + str(type))
return []
def dependencies(self):
deps = []
try:
callable_ = self._module.package_dependencies
except AttributeError:
pass
else:
try:
deps = callable_()
except Exception, e:
debug.critical("Couldn't get dependencies of %s: %s\n%s" %
(self.name, debug.format_exception(e),
traceback.format_exc()))
deps = []
def update_jobs(self):
"""Called via a timer.
Checks jobs for all workflows both with and without monitors.
"""
for i in xrange(self.jobView.topLevelItemCount()):
vistrail = self.jobView.topLevelItem(i)
jm = vistrail.jobMonitor
for workflow_item in vistrail.workflowItems.values():
workflow = workflow_item.workflow
# jobs without a handle can also be checked
if not workflow_item.has_handle:
# restart job and execute
jm.startWorkflow(workflow)
self.updating_now = False
workflow_item.execute()
self.updating_now = True
continue
if workflow_item.workflowFinished:
continue
for job in workflow_item.jobs.itervalues():
if job.jobFinished:
continue
try:
# call monitor
job.jobFinished = jm.isDone(job.handle)
if job.jobFinished:
job.setText(1, "Finished")
except Exception, e:
debug.critical("Error checking job %s: %s" %
(workflow_item.text(0), e))
workflow_item.updateJobs()
if workflow_item.workflowFinished:
if self.autorun.isChecked():
jm.startWorkflow(workflow)
self.updating_now = False
workflow_item.execute()
self.updating_now = True
continue
ret = QtGui.QMessageBox.information(
self, "Job Ready",
'Pending Jobs in workflow "%s" have finished, '
'continue execution now?' % workflow_item.text(0),
QtGui.QMessageBox.Ok, QtGui.QMessageBox.Cancel)
if ret == QtGui.QMessageBox.Ok:
jm.startWorkflow(workflow)
self.updating_now = False
workflow_item.execute()
self.updating_now = True
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 finalize(self):
if not self._initialized:
return
debug.log("Finalizing %s" % self.name)
try:
callable_ = self._module.finalize
except AttributeError:
pass
else:
try:
callable_()
except Exception, e:
debug.critical(
"Couldn't finalize %s: %s: %s" %
(self.name, type(e).__name__, ', '.join(e.args)))
def setParameterExplorationOld(self, xmlString):
""" setParameterExploration(xmlString: string) -> None
Sets the current parameter exploration to the one
defined by 'xmlString'.
"""
if not xmlString:
return
# Parse/validate the xml
try:
xmlDoc = parseString(xmlString).documentElement
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Parameter Exploration load failed because of "
"invalid XML:\n\n%s" % xmlString)
return
def finalize(self):
if not self._initialized:
return
debug.log("Finalizing %s" % self.name)
try:
callable_ = self._module.finalize
except AttributeError:
pass
else:
try:
callable_()
except Exception, e:
debug.unexpected_exception(e)
debug.critical("Couldn't finalize %s: %s\n%s" %
(self.name, debug.format_exception(e),
traceback.format_exc()))
def disable_current_package(self):
inst = self._enabled_packages_list
item = inst.currentItem()
codepath = str(item.text())
pm = get_package_manager()
dependency_graph = pm.dependency_graph()
identifier = pm.get_package_by_codepath(codepath).identifier
if dependency_graph.in_degree(identifier) > 0:
rev_deps = dependency_graph.inverse_adjacency_list[identifier]
debug.critical("Missing dependency",
("There are other packages that depend on this:\n %s" +
"Please disable those first.") % rev_deps)
else:
pm.late_disable_package(codepath)
self.invalidate_current_pipeline()
def initialize(*args, **keywords):
# import core.packagemanager
global webServicesDict
global package_cache
#Create a directory for the SUDSWebServices package
location = os.path.join(vistrails.core.system.current_dot_vistrails(),
"SUDSWebServices")
if not os.path.isdir(location):
try:
debug.log("Creating SUDS cache directory...")
os.mkdir(location)
except OSError, e:
debug.critical(
"""Could not create SUDS cache directory. Make sure
'%s' does not exist and parent directory is writable""" % location, e)
sys.exit(1)
def set_key(self, key, value):
""" set_key(key: str, value: str) -> None
Sets a key value pair in the internal dictionary
"""
#get the arguments of the frame that called us
args = inspect.getargvalues(inspect.currentframe().f_back)[3]
try:
#this will return the instance of the object that called us
caller = id(args['self'])
newkey = str(caller) + str(key)
hashkey = md5_hash(newkey).hexdigest()[:16]
cryptvalue = crypt(hashkey, value)
self.__keys[hashkey] = cryptvalue
except KeyError:
debug.critical("KeyChain: You need to call this method inside "
"another a object's method")
def setup_debug(self):
if (self.temp_configuration.has('debugLevel')
and self.temp_configuration.debugLevel != -1):
verbose = self.temp_configuration.debugLevel
if verbose < 0:
msg = ("""Don't know how to set verboseness level to %s - "
"setting to the lowest one I know of: 0""" % verbose)
debug.critical(msg)
verbose = self.temp_configuration.debugLevel = 0
if verbose > 2:
msg = ("""Don't know how to set verboseness level to %s - "
"setting to the highest one I know of: 2""" % verbose)
debug.critical(msg)
verbose = self.temp_configuration.debugLevel = 2
dbg = debug.DebugPrint.getInstance()
levels = [dbg.WARNING, dbg.INFO, dbg.DEBUG]
dbg.set_message_level(levels[verbose])
debug.log("Set verboseness level to %s" % verbose)
def set_package_information(self):
"""Looks at current package and sets all labels (name,
dependencies, etc.) appropriately.
"""
assert self._current_package
p = self._current_package
try:
p.load()
except Exception, e:
msg = 'ERROR: Could not load package.'
self._name_label.setText(msg)
self._version_label.setText(msg)
self._identifier_label.setText(msg)
self._dependencies_label.setText(msg)
self._description_label.setText(msg)
self._reverse_dependencies_label.setText(msg)
debug.critical('Cannot load package', e)
def updateVistrail(self):
"""updateVistrail() -> None
Update vistrail to contain changes to the python source
"""
deleted_ports = []
added_ports = []
if self.has_inputs:
(input_deleted_ports, input_added_ports) = \
self.getPortDiff('input', self.inputPortTable)
deleted_ports.extend(input_deleted_ports)
added_ports.extend(input_added_ports)
if self.has_outputs:
(output_deleted_ports, output_added_ports) = \
self.getPortDiff('output', self.outputPortTable)
deleted_ports.extend(output_deleted_ports)
added_ports.extend(output_added_ports)
functions = []
modified = False
if self.codeEditor.__class__.__name__ not in [
'_PythonEditor', '_TextEditor'
]:
modified = self.codeEditor.document().isModified()
else:
modified = self.codeEditor.isModified()
if (self.codeEditor is not None and modified):
code = self.codeEditor.toPlainText().encode('utf-8')
if self.sourceEncode:
code = urllib.quote(code)
functions.append((self.sourcePortName, [code]))
if len(deleted_ports) + len(added_ports) + len(functions) == 0:
# nothing changed
return True
try:
self.controller.update_ports_and_functions(self.module.id,
deleted_ports,
added_ports, functions)
except PortAlreadyExists, e:
debug.critical('Port Already Exists %s' % e)
return False
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 create_dot_vistrails_if_necessary(self):
if os.path.exists(self._dot_vistrails):
if not os.path.isdir(self._dot_vistrails):
raise ValueError('The .vistrails directory cannot be used or '
'created because the specified path "%s" is '
'a file not a directory.' %
self._dot_vistrails)
else:
return
debug.log('Will try to create default directory')
try:
os.mkdir(self._dot_vistrails)
debug.log('Succeeded!')
except:
debug.critical("""Failed to create initialization directory.
This could be an indication of a permissions problem.
Make sure parent directory of '%s' is writable.""" %
self._dot_vistrails)
raise
def show_dialog(parent, id, name, host, port, user,
passwd, databaseb, create):
dialog = QConnectionDBSetupWindow(parent, id, name, host, port, user,
passwd, database, create)
config = None
if dialog.exec_() == QtGui.QDialog.Accepted:
config = {'host': str(dialog.hostEdt.text()),
'port': int(dialog.portEdt.value()),
'user': unicode(dialog.userEdt.text()),
'passwd': unicode(dialog.passwdEdt.text()),
'db': str(dialog.databaseEdt.text())
}
try:
vistrails.db.services.io.test_db_connection(config)
config['succeeded'] = True
config['name'] = str(dialog.nameEdt.text())
config['id'] = dialog.id
except VistrailsDBException, e:
debug.critical('VisTrails DB Exception', e)
config['succeeded'] = False
def import_packages_module(self):
"""Imports the 'vistrails.packages' package.
This might need to manipulate the Python path to find it.
"""
if self._packages is not None:
return self._packages
# Imports standard packages directory
conf = self._startup.temp_configuration
old_sys_path = copy.copy(sys.path)
if conf.check('packageDirectory'):
sys.path.insert(0, conf.packageDirectory)
try:
import vistrails.packages
except ImportError:
debug.critical('ImportError: "packages" sys.path: %s' % sys.path)
raise
finally:
sys.path = old_sys_path
self._packages = vistrails.packages
return vistrails.packages
def import_packages_module(self):
"""Imports the packages module using path trickery to find it
in the right place.
"""
if self._packages is not None:
return self._packages
# Imports standard packages directory
conf = self._startup.temp_configuration
old_sys_path = copy.copy(sys.path)
if conf.check('packageDirectory'):
sys.path.insert(0, conf.packageDirectory)
try:
import vistrails.packages
except ImportError:
debug.critical('ImportError: "packages" sys.path: %s' % sys.path)
raise
finally:
sys.path = old_sys_path
self._packages = vistrails.packages
return vistrails.packages
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