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bugged stringlengths 4 228k	fixed stringlengths 0 96.3M	__index_level_0__ int64 0 481k
def setupScene(self, pipeline): """ setupScene(pipeline: Pipeline) -> None Construct the scene to view a pipeline """ old_pipeline = self.pipeline self.pipeline = pipeline	def setupScene(self, pipeline): """ setupScene(pipeline: Pipeline) -> None Construct the scene to view a pipeline """ old_pipeline = self.pipeline self.pipeline = pipeline	477,500
def initialize(): global global_db, local_db, search_dbs, compress_by_default, db_access, \ git_bin, tar_bin, debug if configuration.check('git_bin'): git_bin = configuration.git_bin if git_bin.startswith("@executable_path/"): non_expand_path = git_bin git_bin = get_executable_path(git_bin[len("@executable_path/"):]) ...	def initialize(): global global_db, local_db, search_dbs, compress_by_default, db_access, \ git_bin, tar_bin, debug if configuration.check('git_bin'): git_bin = configuration.git_bin if git_bin.startswith("@executable_path/"): non_expand_path = git_bin git_bin = get_executable_path(git_bin[len("@executable_path/"):]) ...	477,501
def _import(self, name, globals=None, locals=None, fromlist=None, level=-1): # if name != 'core.modules.module_registry': # print 'running import', name, fromlist res = apply(self._real_import, (name, globals, locals, fromlist, level)) if len(name) > len(res.__name__): res_name = name else: res_name = res.__name__ ...	def _import(self, name, globals=None, locals=None, fromlist=None, level=-1): # if name != 'core.modules.module_registry': # print 'running import', name, fromlist res = apply(self._real_import, (name, globals, locals, fromlist, level)) if len(name) > len(res.__name__): res_name = name else: res_name = res.__name__ ...	477,502
def populate_table(self): self._unrunnable_table.clear()	defpopulate_table(self):self._unrunnable_table.clear()	477,503
def check_dependencies(self, index): """ determines if current VisTrail will be supported by the repository's VisTrail server """	def check_dependencies(self, index): """ determines if current VisTrail will be supported by the repository's VisTrail server """	477,504
def check_dependencies(self, index): """ determines if current VisTrail will be supported by the repository's VisTrail server """	def check_dependencies(self, index): """ determines if current VisTrail will be supported by the repository's VisTrail server """	477,505
def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	477,506
def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	477,507
def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	477,508
def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	477,509
def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	def clicked_on_login(self): """ Attempts to log into web repository stores auth cookie for session """ from gui.application import VistrailsApplication	477,510
def create_ungroup(self, full_pipeline, module_id):	def create_ungroup(self, full_pipeline, module_id):	477,511
def open_vistrail_bundle_from_zip_xml(filename): """open_vistrail_bundle_from_zip_xml(filename) -> SaveBundle Open a vistrail from a zip compressed format. It expects that the vistrail file inside archive has name 'vistrail', the log inside archive has name 'log', abstractions inside archive have prefix 'abstraction_',...	def open_vistrail_bundle_from_zip_xml(filename): """open_vistrail_bundle_from_zip_xml(filename) -> SaveBundle Open a vistrail from a zip compressed format. It expects that the vistrail file inside archive has name 'vistrail', the log inside archive has name 'log', abstractions inside archive have prefix 'abstraction_',...	477,512
def open_vistrail_bundle_from_zip_xml(filename): """open_vistrail_bundle_from_zip_xml(filename) -> SaveBundle Open a vistrail from a zip compressed format. It expects that the vistrail file inside archive has name 'vistrail', the log inside archive has name 'log', abstractions inside archive have prefix 'abstraction_',...	def open_vistrail_bundle_from_zip_xml(filename): """open_vistrail_bundle_from_zip_xml(filename) -> SaveBundle Open a vistrail from a zip compressed format. It expects that the vistrail file inside archive has name 'vistrail', the log inside archive has name 'log', abstractions inside archive have prefix 'abstraction_',...	477,513
def __init__(self): """ DefaultTheme() -> DefaultTheme This is for initializing all Qt objects """ ###################### #### MEASUREMENTS ####	def __init__(self): """ DefaultTheme() -> DefaultTheme This is for initializing all Qt objects """ ###################### #### MEASUREMENTS ####	477,514
def name(self): return 'transparent'	def name(self): return 'transparent'	477,515
def git_get_dir(self, name, version="HEAD", out_dirname=None): global temp_persist_files if out_dirname is None: # create a temporary directory out_dirname = tempfile.mkdtemp(prefix='vt_persist') temp_persist_files.append(out_dirname) cmd_list = [self.git_command() + \ ["archive", str(version + ':' + name)], ['tar', '...	def git_get_dir(self, name, version="HEAD", out_dirname=None): global temp_persist_files if out_dirname is None: # create a temporary directory out_dirname = tempfile.mkdtemp(prefix='vt_persist') temp_persist_files.append(out_dirname) if systemType == "Windows": cmd_list = [self.git_command() + \ ["archive", str(versio...	477,516
def find_abstractions(self, vistrail, recurse=False): abstractions = [] for action in vistrail.actions: for operation in action.operations: if operation.vtType == 'add' or \ operation.vtType == 'change': if operation.data.vtType == Abstraction.vtType: abstraction = operation.data if abstraction.package == abstraction_p...	def find_abstractions(self, vistrail, recurse=False): abstractions = [] for action in vistrail.actions: for operation in action.operations: if operation.vtType == 'add' or \ operation.vtType == 'change': if operation.data is not None and operation.data.vtType == Abstraction.vtType: abstraction = operation.data if abstr...	477,517
def add_parameter_changes_from_execution(self, pipeline, version, parameter_changes): """add_parameter_changes_from_execution(pipeline, version, parameter_changes) -> int.	def add_parameter_changes_from_execution(self, pipeline, version, parameter_changes): """add_parameter_changes_from_execution(pipeline, version, parameter_changes) -> int.	477,518
def add_parameter_changes_from_execution(self, pipeline, version, parameter_changes): """add_parameter_changes_from_execution(pipeline, version, parameter_changes) -> int.	def add_parameter_changes_from_execution(self, pipeline, version, parameter_changes): """add_parameter_changes_from_execution(pipeline, version, parameter_changes) -> int.	477,519
def init(self): """ init() -> None Initialize VisTrails with optionsDict. optionsDict can be another VisTrails Configuration object, e.g. ConfigurationObject """ if self._do_load_packages: self.load_packages() self.setupDefaultFolders() if self._do_load_packages: # don't call this anymore since we do an add_package fo...	def init(self): """ init() -> None Initialize VisTrails with optionsDict. optionsDict can be another VisTrails Configuration object, e.g. ConfigurationObject """ if self._do_load_packages: self.load_packages() if self._do_load_packages: # don't call this anymore since we do an add_package for it now # self.setupBaseMo...	477,520
def focusNextPrevChild(self, next): """focusNextPrevChild(next) -> None Suppress tabbing to the next window in multi-line commands. """ if next and self.more: return 0 return QtGui.QTextEdit.focusNextPrevChild(self, next)	def focusNextPrevChild(self, next): """focusNextPrevChild(next) -> None Suppress tabbing to the next window in multi-line commands. """ if next and self.more: return 0 return QtGui.QTextEdit.focusNextPrevChild(self, next)	477,521
def bool_conv(x): s = str(x).upper() if s == 'TRUE': return True if s == 'FALSE': return False	def bool_conv(x): s = str(x).upper() if s == 'TRUE': return True if s == 'FALSE': return False	477,522
def translateVistrail(_vistrail): vistrail = DBVistrail() for _action in _vistrail.db_actions.itervalues(): ops = [] for op in _action.db_operations: if op.vtType == 'add': data = convert_data(op.db_data) ops.append(DBAdd(id=op.db_id, what=op.db_what, objectId=op.db_objectId, parentObjId=op.db_parentObjId, parentObjTy...	def translateVistrail(_vistrail): vistrail = DBVistrail() for _action in _vistrail.db_actions.itervalues(): ops = [] for op in _action.db_operations: if op.vtType == 'add': data = convert_data(op.db_data, op.db_parentObjType, op.db_parentObjId) ops.append(DBAdd(id=op.db_id, what=op.db_what, objectId=op.db_objectId, pa...	477,523
def translateVistrail(_vistrail): vistrail = DBVistrail() for _action in _vistrail.db_actions.itervalues(): ops = [] for op in _action.db_operations: if op.vtType == 'add': data = convert_data(op.db_data) ops.append(DBAdd(id=op.db_id, what=op.db_what, objectId=op.db_objectId, parentObjId=op.db_parentObjId, parentObjTy...	def translateVistrail(_vistrail): vistrail = DBVistrail() for _action in _vistrail.db_actions.itervalues(): ops = [] for op in _action.db_operations: if op.vtType == 'add': data = convert_data(op.db_data, op.db_parentObjType, op.db_parentObjId) ops.append(DBAdd(id=op.db_id, what=op.db_what, objectId=op.db_objectId, pa...	477,524
def typeMap(name, package=None): """ typeMap(name: str) -> Module Convert from C/C++ types into VisTrails Module type """ if package is None: package = identifier if type(name) == tuple: return [typeMap(x, package) for x in name] if name in typeMapDict: return typeMapDict[name] else: registry = get_module_registry() i...	def typeMap(name, package=None): """ typeMap(name: str) -> Module Convert from C/C++ types into VisTrails Module type """ if package is None: package = identifier if type(name) == tuple: return [typeMap(x, package) for x in name] if name in typeMapDict: return typeMapDict[name] else: registry = get_module_registry() i...	477,525
def get_method_signature(method): """ get_method_signature(method: vtkmethod) -> [ret, arg] Re-wrap Prabu's method to increase performance	def get_method_signature(method): """ get_method_signature(method: vtkmethod) -> [ret, arg] Re-wrap Prabu's method to increase performance	477,526
def get_method_signature(method): """ get_method_signature(method: vtkmethod) -> [ret, arg] Re-wrap Prabu's method to increase performance	def get_method_signature(method): """ get_method_signature(method: vtkmethod) -> [ret, arg] Re-wrap Prabu's method to increase performance	477,527
def resizeEvent(self, e): """ resizeEvent(e: QEvent) -> None Re-adjust the vtkRenderWindow size then QVTKWidget resized """ qt_super(QVTKWidget, self).resizeEvent(e) if not self.mRenWin: return	def resizeEvent(self, e): """ resizeEvent(e: QEvent) -> None Re-adjust the vtkRenderWindow size then QVTKWidget resized """ qt_super(QVTKWidget, self).resizeEvent(e) if not self.mRenWin: return	477,528
def paintEvent(self, e): """ paintEvent(e: QPaintEvent) -> None Paint the QVTKWidget with vtkRenderWindow """ iren = None if self.mRenWin: iren = self.mRenWin.GetInteractor()	def paintEvent(self, e): """ paintEvent(e: QPaintEvent) -> None Paint the QVTKWidget with vtkRenderWindow """ iren = None if self.mRenWin: iren = self.mRenWin.GetInteractor()	477,529
def saveToPNG(self, filename): """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray Save the current widget contents to an image file. If str==None, then it returns the vtkUnsignedCharArray containing the PNG image. Otherwise, the filename is returned. """ w2i = vtk.vtkWindowToImageFilter() w2i.ReadFrontB...	def saveToPNG(self, filename): """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray Save the current widget contents to an image file. If str==None, then it returns the vtkUnsignedCharArray containing the PNG image. Otherwise, the filename is returned. """ w2i = vtk.vtkWindowToImageFilter() w2i.ReadFrontB...	477,530
def create_ungroup(self, module_id): (modules, connections) = \ BaseController.create_ungroup(self, self.current_pipeline, module_id) pipeline = self.current_pipeline old_conn_ids = self.get_module_connection_ids([module_id], pipeline.graph) op_list = [] op_list.extend(('delete', pipeline.connections[c_id]) for c_id in...	def create_ungroup(self, module_id): (modules, connections) = \ BaseController.create_ungroup(self, self.current_pipeline, module_id) pipeline = self.current_pipeline old_conn_ids = self.get_module_connection_ids([module_id], pipeline.graph) op_list = [] op_list.extend(('delete', pipeline.connections[c_id]) for c_id in...	477,531
def git_get_type(self, name, version="HEAD"): cmd_list = [["echo", str(version + ':' + name)], self.git_command() + ["cat-file", "--batch-check"]] debug_print('executing commands', cmd_list) result, output, errs = execute_piped_cmdlines(cmd_list) debug_print('stdout:', type(output), output) debug_print('stderr:', type(...	def git_get_type(self, name, version="HEAD"): cmd_list = [self.git_command() + ["cat-file", "-t", str(version + ':' + name)]] debug_print('executing commands', cmd_list) result, output, errs = execute_piped_cmdlines(cmd_list) debug_print('stdout:', type(output), output) debug_print('stderr:', type(errs), errs) if res...	477,532
def git_get_type(self, name, version="HEAD"): cmd_list = [["echo", str(version + ':' + name)], self.git_command() + ["cat-file", "--batch-check"]] debug_print('executing commands', cmd_list) result, output, errs = execute_piped_cmdlines(cmd_list) debug_print('stdout:', type(output), output) debug_print('stderr:', type(...	def git_get_type(self, name, version="HEAD"): cmd_list = [["echo", str(version + ':' + name)], self.git_command() + ["cat-file", "--batch-check"]] debug_print('executing commands', cmd_list) result, output, errs = execute_piped_cmdlines(cmd_list) debug_print('stdout:', type(output), output) debug_print('stderr:', type(...	477,533
def attempt_automatic_upgrade(controller, pipeline, module_id, function_remap={}, src_port_remap={}, dst_port_remap={}, annotation_remap={}): """attempt_automatic_upgrade(module_id, pipeline): [Action]	def attempt_automatic_upgrade(controller, pipeline, module_id, function_remap={}, src_port_remap={}, dst_port_remap={}, annotation_remap={}): """attempt_automatic_upgrade(module_id, pipeline): [Action]	477,534
def attempt_automatic_upgrade(controller, pipeline, module_id, function_remap={}, src_port_remap={}, dst_port_remap={}, annotation_remap={}): """attempt_automatic_upgrade(module_id, pipeline): [Action]	def attempt_automatic_upgrade(controller, pipeline, module_id, function_remap={}, src_port_remap={}, dst_port_remap={}, annotation_remap={}): """attempt_automatic_upgrade(module_id, pipeline): [Action]	477,535
def paintEngine(self): """ paintEvent(e: QPaintEvent) -> QPaintEngine On Windows, this has to return None to fully disable double-buffer (we let vtkRenderWindow handle this instead). """ if system.systemType=='Win32': return None else: return QCellWidget.paintEngine(self)	def paintEngine(self): """ paintEngine() -> QPaintEngine On Windows, this has to return None to fully disable double-buffer (we let vtkRenderWindow handle this instead). """ if system.systemType=='Win32': return None else: return QCellWidget.paintEngine(self)	477,536
def paintEngine(self): """ paintEvent(e: QPaintEvent) -> QPaintEngine On Windows, this has to return None to fully disable double-buffer (we let vtkRenderWindow handle this instead). """ if system.systemType=='Win32': return None else: return QCellWidget.paintEngine(self)	def paintEngine(self): """ paintEvent(e: QPaintEvent) -> QPaintEngine On Windows, this has to return None to fully disable double-buffer (we let vtkRenderWindow handle this instead). """ if system.systemType in ['Windows', 'Microsoft']: return None else: return QCellWidget.paintEngine(self)	477,537
def compute(self): exPipe = self.forceGetInputFromPort('ExternalPipe') if exPipe: self.setResult('InternalPipe', exPipe) else: self.setResult('InternalPipe', InvalidOutput)	def compute(self): exPipe = self.forceGetInputFromPort('ExternalPipe') if exPipe is not None: self.setResult('InternalPipe', exPipe) else: self.setResult('InternalPipe', InvalidOutput)	477,538
def canonicalize(sig_item): if type(sig_item) == __builtin__.type: return (sig_item, '<no description>') elif type(sig_item) == __builtin__.tuple: # assert len(sig_item) == 2 # assert type(sig_item[0]) == __builtin__.type # assert type(sig_item[1]) == __builtin__.str return sig_item elif type(sig_item) == __builtin__.l...	def canonicalize(sig_item): if type(sig_item) == __builtin__.tuple: # assert len(sig_item) == 2 # assert type(sig_item[0]) == __builtin__.type # assert type(sig_item[1]) == __builtin__.str return sig_item elif type(sig_item) == __builtin__.list: return (registry.get_descriptor_by_name('edu.utah.sci.vistrails.basic', 'L...	477,539