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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/"):]) if git_bin is not None: configuration.git_bin = non_expand_path if git_bin is None: git_bin = 'git' configuration.git_bin = git_bin if configuration.check('tar_bin'): tar_bin = configuration.git_bin if tar_bin.startswith("@executable_path/"): non_expand_path = tar_bin tar_bin = get_executable_path(tar_bin[len("@executable_path/"):]) if tar_bin is not None: configuration.tar_bin = non_expand_path if tar_bin is None: tar_bin = 'tar' configuration.tar_bin = tar_bin if configuration.check('compress_by_default'): compress_by_default = configuration.compress_by_default if configuration.check('debug'): debug = configuration.debug if configuration.check('global_db'): global_db = configuration.global_db if configuration.check('local_db'): local_db = configuration.local_db if not os.path.exists(local_db): raise Exception('local_db "%s" does not exist' % local_db) else: local_db = os.path.join(default_dot_vistrails(), 'persistent_files') if not os.path.exists(local_db): try: os.mkdir(local_db) except: raise Exception('local_db "%s" does not exist' % local_db) git_init(local_db) debug_print('creating DatabaseAccess') db_path = os.path.join(local_db, '.files.db') db_access = DatabaseAccessSingleton(db_path) debug_print('done', db_access) search_dbs = [local_db,] if configuration.check('search_dbs'): try: check_paths = eval(configuration.search_dbs) except: print "* persistence error: cannot parse search_dbs " for path in check_paths: if os.path.exists(path): search_dbs.append(path) else: print '** persistence warning: cannot find path "%s"' % 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/"):]) if git_bin is not None: configuration.git_bin = non_expand_path if git_bin is None: git_bin = 'git' configuration.git_bin = git_bin if configuration.check('tar_bin'): tar_bin = configuration.tar_bin if tar_bin.startswith("@executable_path/"): non_expand_path = tar_bin tar_bin = get_executable_path(tar_bin[len("@executable_path/"):]) if tar_bin is not None: configuration.tar_bin = non_expand_path if tar_bin is None: tar_bin = 'tar' configuration.tar_bin = tar_bin if configuration.check('compress_by_default'): compress_by_default = configuration.compress_by_default if configuration.check('debug'): debug = configuration.debug if configuration.check('global_db'): global_db = configuration.global_db if configuration.check('local_db'): local_db = configuration.local_db if not os.path.exists(local_db): raise Exception('local_db "%s" does not exist' % local_db) else: local_db = os.path.join(default_dot_vistrails(), 'persistent_files') if not os.path.exists(local_db): try: os.mkdir(local_db) except: raise Exception('local_db "%s" does not exist' % local_db) git_init(local_db) debug_print('creating DatabaseAccess') db_path = os.path.join(local_db, '.files.db') db_access = DatabaseAccessSingleton(db_path) debug_print('done', db_access) search_dbs = [local_db,] if configuration.check('search_dbs'): try: check_paths = eval(configuration.search_dbs) except: print "* persistence error: cannot parse search_dbs " for path in check_paths: if os.path.exists(path): search_dbs.append(path) else: print '** persistence warning: cannot find path "%s"' % 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__ qual_name = '' for m in res_name.split('.'): qual_name += m if qual_name not in self._existing_paths and not qual_name.endswith('_rc'): # print ' adding', name, qual_name self._imported_paths.add(qual_name) # else: # if name != 'core.modules.module_registry': # print ' already exists', 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__ qual_name = '' for m in res_name.split('.'): qual_name += m if qual_name not in self._existing_paths and not qual_name.endswith('_rc'): # print ' adding', name, qual_name self._imported_paths.add(qual_name) # else: # if name != 'core.modules.module_registry': # print ' already exists', 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_', and thumbnails inside archive are '.png' files in 'thumbs' dir """ core.requirements.require_executable('unzip') vt_save_dir = tempfile.mkdtemp(prefix='vt_save') output = [] cmdline = ['unzip', '-q','-o','-d', vt_save_dir, filename] result = execute_cmdline(cmdline, output) if result != 0 and len(output) != 0: raise VistrailsDBException("Unzip of '%s' failed" % filename) vistrail = None log = None log_fname = None abstraction_files = [] unknown_files = [] thumbnail_files = [] try: for root, dirs, files in os.walk(vt_save_dir): for fname in files: if fname == 'vistrail' and root == vt_save_dir: vistrail = open_vistrail_from_xml(os.path.join(root, fname)) elif fname == 'log' and root == vt_save_dir: # FIXME read log to get execution info # right now, just ignore the file log = None log_fname = os.path.join(root, fname) # log = open_log_from_xml(os.path.join(root, fname)) # objs.append(DBLog.vtType, log) elif fname.startswith('abstraction_'): abstraction_file = os.path.join(root, fname) abstraction_files.append(abstraction_file) elif (fname.endswith('.png') and root == os.path.join(vt_save_dir,'thumbs')): thumbnail_file = os.path.join(root, fname) thumbnail_files.append(thumbnail_file) else: unknown_files.append(os.path.join(root, fname)) except OSError, e: raise VistrailsDBException("Error when reading vt file") if len(unknown_files) > 0: raise VistrailsDBException("Unknown files in vt file: %s" % \ unknown_files) if vistrail is None: raise VistrailsDBException("vt file does not contain vistrail") vistrail.db_log_filename = log_fname save_bundle = SaveBundle(DBVistrail.vtType, vistrail, log, abstractions=abstraction_files, thumbnails=thumbnail_files) return (save_bundle, vt_save_dir)	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_', and thumbnails inside archive are '.png' files in 'thumbs' dir """ core.requirements.require_executable('unzip') vt_save_dir = tempfile.mkdtemp(prefix='vt_save') output = [] cmdline = ['unzip', '-q','-o','-d', vt_save_dir, shell_quote(filename)] result = execute_cmdline(cmdline, output) if result != 0 and len(output) != 0: raise VistrailsDBException("Unzip of '%s' failed" % filename) vistrail = None log = None log_fname = None abstraction_files = [] unknown_files = [] thumbnail_files = [] try: for root, dirs, files in os.walk(vt_save_dir): for fname in files: if fname == 'vistrail' and root == vt_save_dir: vistrail = open_vistrail_from_xml(os.path.join(root, fname)) elif fname == 'log' and root == vt_save_dir: # FIXME read log to get execution info # right now, just ignore the file log = None log_fname = os.path.join(root, fname) # log = open_log_from_xml(os.path.join(root, fname)) # objs.append(DBLog.vtType, log) elif fname.startswith('abstraction_'): abstraction_file = os.path.join(root, fname) abstraction_files.append(abstraction_file) elif (fname.endswith('.png') and root == os.path.join(vt_save_dir,'thumbs')): thumbnail_file = os.path.join(root, fname) thumbnail_files.append(thumbnail_file) else: unknown_files.append(os.path.join(root, fname)) except OSError, e: raise VistrailsDBException("Error when reading vt file") if len(unknown_files) > 0: raise VistrailsDBException("Unknown files in vt file: %s" % \ unknown_files) if vistrail is None: raise VistrailsDBException("vt file does not contain vistrail") vistrail.db_log_filename = log_fname save_bundle = SaveBundle(DBVistrail.vtType, vistrail, log, abstractions=abstraction_files, thumbnails=thumbnail_files) return (save_bundle, vt_save_dir)	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_', and thumbnails inside archive are '.png' files in 'thumbs' dir """ core.requirements.require_executable('unzip') vt_save_dir = tempfile.mkdtemp(prefix='vt_save') output = [] cmdline = ['unzip', '-q','-o','-d', vt_save_dir, filename] result = execute_cmdline(cmdline, output) if result != 0 and len(output) != 0: raise VistrailsDBException("Unzip of '%s' failed" % filename) vistrail = None log = None log_fname = None abstraction_files = [] unknown_files = [] thumbnail_files = [] try: for root, dirs, files in os.walk(vt_save_dir): for fname in files: if fname == 'vistrail' and root == vt_save_dir: vistrail = open_vistrail_from_xml(os.path.join(root, fname)) elif fname == 'log' and root == vt_save_dir: # FIXME read log to get execution info # right now, just ignore the file log = None log_fname = os.path.join(root, fname) # log = open_log_from_xml(os.path.join(root, fname)) # objs.append(DBLog.vtType, log) elif fname.startswith('abstraction_'): abstraction_file = os.path.join(root, fname) abstraction_files.append(abstraction_file) elif (fname.endswith('.png') and root == os.path.join(vt_save_dir,'thumbs')): thumbnail_file = os.path.join(root, fname) thumbnail_files.append(thumbnail_file) else: unknown_files.append(os.path.join(root, fname)) except OSError, e: raise VistrailsDBException("Error when reading vt file") if len(unknown_files) > 0: raise VistrailsDBException("Unknown files in vt file: %s" % \ unknown_files) if vistrail is None: raise VistrailsDBException("vt file does not contain vistrail") vistrail.db_log_filename = log_fname save_bundle = SaveBundle(DBVistrail.vtType, vistrail, log, abstractions=abstraction_files, thumbnails=thumbnail_files) return (save_bundle, vt_save_dir)	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_', and thumbnails inside archive are '.png' files in 'thumbs' dir """ core.requirements.require_executable('unzip') vt_save_dir = tempfile.mkdtemp(prefix='vt_save') output = [] cmdline = ['unzip', '-q','-o','-d', vt_save_dir, filename] result = execute_cmdline(cmdline, output) if result != 0 and len(output) != 0: raise VistrailsDBException("Unzip of '%s' failed" % filename) vistrail = None log = None log_fname = None abstraction_files = [] unknown_files = [] thumbnail_files = [] try: for root, dirs, files in os.walk(vt_save_dir): for fname in files: if fname == 'vistrail' and root == vt_save_dir: vistrail = open_vistrail_from_xml(os.path.join(root, fname)) elif fname == 'log' and root == vt_save_dir: # FIXME read log to get execution info # right now, just ignore the file log = None log_fname = os.path.join(root, fname) # log = open_log_from_xml(os.path.join(root, fname)) # objs.append(DBLog.vtType, log) elif fname.startswith('abstraction_'): abstraction_file = os.path.join(root, fname) abstraction_files.append(abstraction_file) elif (fname.endswith('.png') and root == os.path.join(vt_save_dir,'thumbs')): thumbnail_file = os.path.join(root, fname) thumbnail_files.append(thumbnail_file) else: unknown_files.append(os.path.join(root, fname)) except OSError, e: raise VistrailsDBException("Error when reading vt file") if len(unknown_files) > 0: raise VistrailsDBException("Unknown files in vt file: %s" % \ unknown_files) if vistrail is None: raise VistrailsDBException("vt file does not contain vistrail") vistrail.db_log_filename = log_fname save_bundle = SaveBundle(DBVistrail.vtType, vistrail, log, abstractions=abstraction_files, thumbnails=thumbnail_files) return (save_bundle, vt_save_dir)	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', '-C', out_dirname, '-xf-']] 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 result != 0: # check output for error messages raise ModuleError(self, "Error retrieving file '%s'\n" % name + errs) return out_dirname	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(version + ':' + name)], ["%s:" % out_dirname[0], "&&", "cd", "%s"%out_dirname, "&&", 'tar', '-xf-']] else: cmd_list = [self.git_command() + \ ["archive", str(version + ':' + name)], ['tar', '-C', out_dirname, '-xf-']] 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 result != 0: # check output for error messages raise ModuleError(self, "Error retrieving file '%s'\n" % name + errs) return out_dirname	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_pkg: abstractions.append(abstraction) if recurse: for abstraction in abstractions: try: vistrail = abstraction.vistrail except MissingPackageVersion, e: reg = core.modules.module_registry.get_module_registry() abstraction._module_descriptor = \ reg.get_similar_descriptor(*abstraction.descriptor_info) vistrail = abstraction.vistrail abstractions.extend(self.find_abstractions(vistrail, recurse)) return abstractions	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 abstraction.package == abstraction_pkg: abstractions.append(abstraction) if recurse: for abstraction in abstractions: try: vistrail = abstraction.vistrail except MissingPackageVersion, e: reg = core.modules.module_registry.get_module_registry() abstraction._module_descriptor = \ reg.get_similar_descriptor(*abstraction.descriptor_info) vistrail = abstraction.vistrail abstractions.extend(self.find_abstractions(vistrail, recurse)) return abstractions	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 for it now # self.setupBaseModules() self.installPackages() self.runStartupHooks()	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.setupBaseModules() self.installPackages() self.runStartupHooks()	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, parentObjType=op.db_parentObjType, data=data)) elif op.vtType == 'change': data = convert_data(op.db_data) ops.append(DBChange(id=op.db_id, what=op.db_what, oldObjId=op.db_oldObjId, newObjId=op.db_newObjId, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType, data=data)) elif op.vtType == 'delete': ops.append(DBDelete(id=op.db_id, what=op.db_what, objectId=op.db_objectId, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType)) action = DBAction(id=_action.db_id, prevId=_action.db_prevId, date=_action.db_date, user=_action.db_user, operations=ops, annotations=_action.db_annotations.values()) vistrail.db_add_action(action) for _tag in _vistrail.db_tags.itervalues(): tag = DBTag(id=_tag.db_id, name=_tag.db_name) vistrail.db_add_tag(tag) vistrail.db_version = '0.7.0' return vistrail	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, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType, data=data)) elif op.vtType == 'change': data = convert_data(op.db_data, op.db_parentObjType, op.db_parentObjId) ops.append(DBChange(id=op.db_id, what=op.db_what, oldObjId=op.db_oldObjId, newObjId=op.db_newObjId, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType, data=data)) elif op.vtType == 'delete': ops.append(DBDelete(id=op.db_id, what=op.db_what, objectId=op.db_objectId, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType)) action = DBAction(id=_action.db_id, prevId=_action.db_prevId, date=_action.db_date, user=_action.db_user, operations=ops, annotations=_action.db_annotations.values()) vistrail.db_add_action(action) for _tag in _vistrail.db_tags.itervalues(): tag = DBTag(id=_tag.db_id, name=_tag.db_name) vistrail.db_add_tag(tag) vistrail.db_version = '0.7.0' return vistrail	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, parentObjType=op.db_parentObjType, data=data)) elif op.vtType == 'change': data = convert_data(op.db_data) ops.append(DBChange(id=op.db_id, what=op.db_what, oldObjId=op.db_oldObjId, newObjId=op.db_newObjId, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType, data=data)) elif op.vtType == 'delete': ops.append(DBDelete(id=op.db_id, what=op.db_what, objectId=op.db_objectId, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType)) action = DBAction(id=_action.db_id, prevId=_action.db_prevId, date=_action.db_date, user=_action.db_user, operations=ops, annotations=_action.db_annotations.values()) vistrail.db_add_action(action) for _tag in _vistrail.db_tags.itervalues(): tag = DBTag(id=_tag.db_id, name=_tag.db_name) vistrail.db_add_tag(tag) vistrail.db_version = '0.7.0' return vistrail	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, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType, data=data)) elif op.vtType == 'change': data = convert_data(op.db_data, op.db_parentObjType, op.db_parentObjId) ops.append(DBChange(id=op.db_id, what=op.db_what, oldObjId=op.db_oldObjId, newObjId=op.db_newObjId, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType, data=data)) elif op.vtType == 'delete': ops.append(DBDelete(id=op.db_id, what=op.db_what, objectId=op.db_objectId, parentObjId=op.db_parentObjId, parentObjType=op.db_parentObjType)) action = DBAction(id=_action.db_id, prevId=_action.db_prevId, date=_action.db_date, user=_action.db_user, operations=ops, annotations=_action.db_annotations.values()) vistrail.db_add_action(action) for _tag in _vistrail.db_tags.itervalues(): tag = DBTag(id=_tag.db_id, name=_tag.db_name) vistrail.db_add_tag(tag) vistrail.db_version = '0.7.0' return vistrail	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() if not registry.has_descriptor_with_name(package, name): return None else: return registry.get_descriptor_by_name(package, name).module	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() if not registry.has_descriptor_with_name(package, name): return None else: return registry.get_descriptor_by_name(package, name).module	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.ReadFrontBufferOff() w2i.SetInput(self.mRenWin) # Render twice to get a clean image on the back buffer self.mRenWin.Render() self.mRenWin.Render() w2i.Update() writer = vtk.vtkPNGWriter() writer.SetInputConnection(w2i.GetOutputPort()) if filename!=None: writer.SetFileName(filename) else: writer.WriteToMemoryOn() writer.Write() if filename: return filename else: return writer.GetResult()	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.ReadFrontBufferOff() w2i.SetInput(self.mRenWin) # Render twice to get a clean image on the back buffer if self.mRenWin.GetInteractor(): self.mRenWin.GetInteractor().Render() self.mRenWin.GetInteractor().Render() else: self.mRenWin.Render() self.mRenWin.Render() w2i.Update() writer = vtk.vtkPNGWriter() writer.SetInputConnection(w2i.GetOutputPort()) if filename!=None: writer.SetFileName(filename) else: writer.WriteToMemoryOn() writer.Write() if filename: return filename else: return writer.GetResult()	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 old_conn_ids) op_list.append(('delete', pipeline.modules[module_id])) op_list.extend(('add', m) for m in modules) op_list.extend(('add', c) for c in connections) action = core.db.action.create_action(op_list) self.add_new_action(action) return self.perform_action(action)	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 old_conn_ids) op_list.append(('delete', pipeline.modules[module_id])) op_list.extend(('add', m) for m in modules) op_list.extend(('add', c) for c in connections) action = core.db.action.create_action(op_list) self.add_new_action(action) return self.perform_action(action)	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(errs), errs) if result != 0: # check output for error messages raise ModuleError(self, "Error retrieving file '%s'" % name + errs) return output.split(None, 2)[1]	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 result != 0: # check output for error messages raise ModuleError(self, "Error retrieving file '%s'" % name + errs) return output.split(None, 2)[1]	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(errs), errs) if result != 0: # check output for error messages raise ModuleError(self, "Error retrieving file '%s'" % name + errs) return output.split(None, 2)[1]	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(errs), errs) if result != 0: # check output for error messages raise ModuleError(self, "Error retrieving file '%s'" % name + errs) return output.split(None, 2)[1]	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__.list: return (registry.get_descriptor_by_name('edu.utah.sci.vistrails.basic', 'List').module, '<no description>')	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', 'List').module, '<no description>')	477,539