bugged
stringlengths 4
228k
| fixed
stringlengths 0
96.3M
| __index_level_0__
int64 0
481k
|
|---|---|---|
def modified(event): """When an object is modified, execute rules assigned to its parent """ if is_portal_factory(event.object): return # Let the special handler take care of IObjectInitializedEvent if not IObjectInitializedEvent.providedBy(event): execute(aq_parent(aq_inner(event.object)), event)
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def modified(event): """When an object is modified, execute rules assigned to its parent """ if is_portal_factory(event.object): return # Let the special handler take care of IObjectInitializedEvent if not IObjectInitializedEvent.providedBy(event): execute(aq_parent(aq_inner(event.object)), event)
| 477,200
|
def modified(event): """When an object is modified, execute rules assigned to its parent """ if is_portal_factory(event.object): return # Let the special handler take care of IObjectInitializedEvent if not IObjectInitializedEvent.providedBy(event): execute(aq_parent(aq_inner(event.object)), event)
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def modified(event): """When an object is modified, execute rules assigned to its parent """ if is_portal_factory(event.object): return # Let the special handler take care of IObjectInitializedEvent if not IObjectInitializedEvent.providedBy(event): execute(aq_parent(aq_inner(event.object)), event)
| 477,201
|
def modified(event): """When an object is modified, execute rules assigned to its parent """ if is_portal_factory(event.object): return # Let the special handler take care of IObjectInitializedEvent if not IObjectInitializedEvent.providedBy(event): execute(aq_parent(aq_inner(event.object)), event)
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def modified(event): """When an object is modified, execute rules assigned to its parent """ if is_portal_factory(event.object): return # Let the special handler take care of IObjectInitializedEvent if not IObjectInitializedEvent.providedBy(event): execute(aq_parent(aq_inner(event.object)), event)
| 477,202
|
def calc_global(problem_data): """ Calculates global stiffness matrix, assembly of elemental systems are included here instead of defining an extra function for assembly """ print("Calculating global system...") global NEN, NEN_range, functions, a, V1, V2, c, f, shape_funcs #Defining global variables NEN = problem_data["NEN"] NEN_range = range(NEN) #Taking coefficient functions of DE out of problem data functions = problem_data["functions"] a = functions["a"] V1 = functions["V1"] V2 = functions["V2"] c = functions["c"] f = functions["f"] #Defining shape functions shape_funcs = problem_data["shapefunc"] print(" * Creating matrixes...") NN = problem_data["NN"] K = sparse.lil_matrix((NN, NN)) F = zeros((NN, 1)) print(" * Calculating K and F matrixes...") for e_nodes in problem_data["LtoG"]: Ke, Fe = calc_elem(problem_data, e_nodes) for i, node_i in enumerate(e_nodes): F[node_i] += Fe[i] for j, node_j in enumerate(e_nodes): K[node_i, node_j] += Ke[i][j] print(" * Freeing up memory (1/2)...") del problem_data["GQ"] del problem_data["UV"] del problem_data["functions"] if problem_data["BCs"] != "null": K, F = apply_bc(problem_data, K, F) print (" * Freeing up memory (2/2)...") del problem_data["LtoG"] del problem_data["BCs"] print(" * Converting LIL to CSR format...") K = K.tocsr() return K, F
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def calc_global(problem_data): """ Calculates global stiffness matrix, assembly of elemental systems are included here instead of defining an extra function for assembly """ print("Calculating global system...") global NEN, NEN_range, functions, a, V1, V2, c, f, shape_funcs #Defining global variables NEN = problem_data["NEN"] NEN_range = range(NEN) #Taking coefficient functions of DE out of problem data functions = problem_data["functions"] a = functions["a"] V1 = functions["V1"] V2 = functions["V2"] c = functions["c"] f = functions["f"] #Defining shape functions shape_funcs = problem_data["shapefunc"] print(" * Creating matrixes...") NN = problem_data["NN"] K = sparse.lil_matrix((NN, NN)) F = zeros((NN, 1)) print(" * Calculating K and F matrixes...") for e_nodes in problem_data["LtoG"]: Ke, Fe = calc_elem(problem_data, e_nodes) for i, node_i in enumerate(e_nodes): F[node_i] += Fe[i] for j, node_j in enumerate(e_nodes): K[node_i, node_j] += Ke[i][j] print(" * Freeing up memory (1/2)...") del problem_data["GQ"] del problem_data["UV"] del problem_data["functions"] if problem_data["BCs"]: K, F = apply_bc(problem_data, K, F) print (" * Freeing up memory (2/2)...") del problem_data["LtoG"] del problem_data["BCs"] print(" * Converting LIL to CSR format...") K = K.tocsr() return K, F
| 477,203
|
def check_dependencies(self): """ determines if current VisTrail will be supported by the repository's VisTrail server """
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def check_dependencies(self): """ determines if current VisTrail will be supported by the repository's VisTrail server """
| 477,204
|
def check_dependencies(self): """ determines if current VisTrail will be supported by the repository's VisTrail server """
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def check_dependencies(self): """ determines if current VisTrail will be supported by the repository's VisTrail server """
| 477,205
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def push_vistrail_to_repository(self, branching=False): """ uploads current VisTrail to web repository """
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def push_vistrail_to_repository(self, branching=False): """ uploads current VisTrail to web repository """
| 477,206
|
def check_url(url): try: p = urlparse(url) h = HTTP(p[1]) h.putrequest('HEAD', p[2]) h.endheaders() if h.getreply()[0] == 200: return True else: return False except: return False
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def check_url(url): try: p = urlparse(url) h = HTTP(p[1]) h.putrequest('HEAD', p[2]) h.endheaders() if h.getreply()[0] == 200: return True else: return False except Exception, e: log(str(e)) return False
| 477,207
|
def check_url(url): try: p = urlparse(url) h = HTTP(p[1]) h.putrequest('HEAD', p[2]) h.endheaders() if h.getreply()[0] == 200: return True else: return False except: return False
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def check_url(url): try: p = urlparse(url) h = HTTP(p[1]) h.putrequest('HEAD', p[2]) h.endheaders() if h.getreply()[0] == 200: return True else: return False except: return False
| 477,208
|
def check_url(url): try: p = urlparse(url) h = HTTP(p[1]) h.putrequest('HEAD', p[2]) h.endheaders() if h.getreply()[0] == 200: return True else: return False except: return False
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def check_url(url): try: p = urlparse(url) h = HTTP(p[1]) h.putrequest('HEAD', p[2]) h.endheaders() if h.getreply()[0] == 200: return True else: return False except: return False
| 477,209
|
def attempt_automatic_upgrade(controller, pipeline, module_id): """attempt_automatic_upgrade(module_id, pipeline): [Action]
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def attempt_automatic_upgrade(controller, pipeline, module_id): """attempt_automatic_upgrade(module_id, pipeline): [Action]
| 477,210
|
def attempt_automatic_upgrade(controller, pipeline, module_id): """attempt_automatic_upgrade(module_id, pipeline): [Action]
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def attempt_automatic_upgrade(controller, pipeline, module_id): """attempt_automatic_upgrade(module_id, pipeline): [Action]
| 477,211
|
def check_connection_port(port): try: port_type = PortSpec.port_type_map.inverse[port.type] s = reg.get_port_spec_from_descriptor(d, port.name, port_type)
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def check_connection_port(port): try: port_type = PortSpec.port_type_map.inverse[port.type] s = reg.get_port_spec_from_descriptor(d, port.name, port_type)
| 477,212
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def check_connection_port(port): try: port_type = PortSpec.port_type_map.inverse[port.type] s = reg.get_port_spec_from_descriptor(d, port.name, port_type)
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def check_connection_port(port): try: port_type = PortSpec.port_type_map.inverse[port.type] s = reg.get_port_spec_from_descriptor(d, port.name, port_type)
| 477,213
|
def create_new_connection(src_module, src_port, dst_module, dst_port): # spec -> name, type, signature output_port_id = controller.id_scope.getNewId(Port.vtType) if type(src_port) == type(""): output_port_spec = \ src_module.get_port_spec(src_port, 'output') output_port = Port(id=output_port_id, spec=output_port_spec, moduleId=src_module.id, moduleName=src_module.name) else: output_port = Port(id=output_port_id, name=src_port.name, type=src_port.type, signature=src_port.signature, moduleId=src_module.id, moduleName=src_module.name)
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def create_new_connection(src_module, src_port, dst_module, dst_port): # spec -> name, type, signature output_port_id = controller.id_scope.getNewId(Port.vtType) if type(src_port) == type(""): if ((src_port, 'output')) in local_port_specs: output_port_spec = local_port_specs[(src_port, 'output')] else: output_port_spec = \ src_module.get_port_spec(src_port, 'output') output_port = Port(id=output_port_id, spec=output_port_spec, moduleId=src_module.id, moduleName=src_module.name) else: output_port = Port(id=output_port_id, name=src_port.name, type=src_port.type, signature=src_port.signature, moduleId=src_module.id, moduleName=src_module.name)
| 477,214
|
def create_new_connection(src_module, src_port, dst_module, dst_port): # spec -> name, type, signature output_port_id = controller.id_scope.getNewId(Port.vtType) if type(src_port) == type(""): output_port_spec = \ src_module.get_port_spec(src_port, 'output') output_port = Port(id=output_port_id, spec=output_port_spec, moduleId=src_module.id, moduleName=src_module.name) else: output_port = Port(id=output_port_id, name=src_port.name, type=src_port.type, signature=src_port.signature, moduleId=src_module.id, moduleName=src_module.name)
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def create_new_connection(src_module, src_port, dst_module, dst_port): # spec -> name, type, signature output_port_id = controller.id_scope.getNewId(Port.vtType) if type(src_port) == type(""): output_port_spec = \ src_module.get_port_spec(src_port, 'output') output_port = Port(id=output_port_id, spec=output_port_spec, moduleId=src_module.id, moduleName=src_module.name) else: output_port = Port(id=output_port_id, name=src_port.name, type=src_port.type, signature=src_port.signature, moduleId=src_module.id, moduleName=src_module.name)
| 477,215
|
def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails Messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,216
|
def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('currentItemChanged(QListWidgetItem *, QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,217
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,218
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,219
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,220
|
def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,221
|
def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,222
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,223
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,224
|
def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
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def __init__(self, parent = None): QtGui.QDialog.__init__(self, parent) core.debug.DebugPrint.getInstance().set_stream(debugStream(self.write)) self.setWindowTitle('VisTrails messages') layout = QtGui.QVBoxLayout() self.setLayout(layout) self.list = QtGui.QListWidget() self.connect(self.list, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.showMessage) self.msg_box = None
| 477,225
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def copyAll(self): """ copy selected message to clipboard """
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defcopyAll(self):"""copyselectedmessagetoclipboard"""
| 477,226
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def showMessage(self, item): """ show item data in a messagebox """ self.showMessageBox(str(item.data(32).toString()))
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def showMessage(self, item, olditem): """ show item data in a messagebox """ self.showMessageBox(str(item.data(32).toString()))
| 477,227
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def showMessage(self, item): """ show item data in a messagebox """ self.showMessageBox(str(item.data(32).toString()))
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def showMessage(self, item): """ show item data in a messagebox """ self.showMessageBox(str(item.data(32).toString()))
| 477,228
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def showMessageBox(self, s): s = str(s).strip() msgs = s.split('\n') if self.msg_box and self.msg_box.isVisible(): self.msg_box.close() msg_box = QtGui.QMessageBox(self.parent()) self.msg_box = msg_box if msgs[0] == "INFO": msg_box.setIcon(QtGui.QMessageBox.Information) msg_box.setWindowTitle("Information") elif msgs[0] == "WARNING": msg_box.setIcon(QtGui.QMessageBox.Warning) msg_box.setWindowTitle("Warning") elif msgs[0] == "CRITICAL": msg_box.setIcon(QtGui.QMessageBox.Critical) msg_box.setWindowTitle("Critical error") msg_box.setText(msgs[3]) text = "Time: %s\n Location: %s\n Message:\n%s" % \ (msgs[1], msgs[2], '\n'.join(msgs[3:])) msg_box.setInformativeText('\n'.join(msgs[4:])) msg_box.setStandardButtons(QtGui.QMessageBox.Ok) msg_box.setDefaultButton(QtGui.QMessageBox.Ok) msg_box.setDetailedText(text) msg_box.show()
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def updateMessageBox(self, item): self.currentItem = item msg_box = self.msg_box s = str(item.data(32).toString()) msgs = s.split('\n') if self.msg_box and self.msg_box.isVisible(): self.msg_box.close() msg_box = QtGui.QMessageBox(self.parent()) self.msg_box = msg_box if msgs[0] == "INFO": msg_box.setIcon(QtGui.QMessageBox.Information) msg_box.setWindowTitle("Information") elif msgs[0] == "WARNING": msg_box.setIcon(QtGui.QMessageBox.Warning) msg_box.setWindowTitle("Warning") elif msgs[0] == "CRITICAL": msg_box.setIcon(QtGui.QMessageBox.Critical) msg_box.setWindowTitle("Critical error") msg_box.setText(msgs[3]) text = "Time: %s\n Location: %s\n Message:\n%s" % \ (msgs[1], msgs[2], '\n'.join(msgs[3:])) msg_box.setInformativeText('\n'.join(msgs[4:])) msg_box.setStandardButtons(QtGui.QMessageBox.Ok) msg_box.setDefaultButton(QtGui.QMessageBox.Ok) msg_box.setDetailedText(text) msg_box.show()
| 477,229
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def showMessageBox(self, s): s = str(s).strip() msgs = s.split('\n') if self.msg_box and self.msg_box.isVisible(): self.msg_box.close() msg_box = QtGui.QMessageBox(self.parent()) self.msg_box = msg_box if msgs[0] == "INFO": msg_box.setIcon(QtGui.QMessageBox.Information) msg_box.setWindowTitle("Information") elif msgs[0] == "WARNING": msg_box.setIcon(QtGui.QMessageBox.Warning) msg_box.setWindowTitle("Warning") elif msgs[0] == "CRITICAL": msg_box.setIcon(QtGui.QMessageBox.Critical) msg_box.setWindowTitle("Critical error") msg_box.setText(msgs[3]) text = "Time: %s\n Location: %s\n Message:\n%s" % \ (msgs[1], msgs[2], '\n'.join(msgs[3:])) msg_box.setInformativeText('\n'.join(msgs[4:])) msg_box.setStandardButtons(QtGui.QMessageBox.Ok) msg_box.setDefaultButton(QtGui.QMessageBox.Ok) msg_box.setDetailedText(text) msg_box.show()
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def showMessageBox(self, s): s = str(s).strip() msgs = s.split('\n') if msgs[0] == "INFO": msg_box.setIcon(QtGui.QMessageBox.Information) msg_box.setWindowTitle("Information") elif msgs[0] == "WARNING": msg_box.setIcon(QtGui.QMessageBox.Warning) msg_box.setWindowTitle("Warning") elif msgs[0] == "CRITICAL": msg_box.setIcon(QtGui.QMessageBox.Critical) msg_box.setWindowTitle("Critical error") msg_box.setText(msgs[3]) text = "Time: %s\n Location: %s\n Message:\n%s" % \ (msgs[1], msgs[2], '\n'.join(msgs[3:])) msg_box.setInformativeText('\n'.join(msgs[4:])) msg_box.setStandardButtons(QtGui.QMessageBox.Ok) msg_box.setDefaultButton(QtGui.QMessageBox.Ok) msg_box.setDetailedText(text) msg_box.show()
| 477,230
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def showMessageBox(self, s): s = str(s).strip() msgs = s.split('\n') if self.msg_box and self.msg_box.isVisible(): self.msg_box.close() msg_box = QtGui.QMessageBox(self.parent()) self.msg_box = msg_box if msgs[0] == "INFO": msg_box.setIcon(QtGui.QMessageBox.Information) msg_box.setWindowTitle("Information") elif msgs[0] == "WARNING": msg_box.setIcon(QtGui.QMessageBox.Warning) msg_box.setWindowTitle("Warning") elif msgs[0] == "CRITICAL": msg_box.setIcon(QtGui.QMessageBox.Critical) msg_box.setWindowTitle("Critical error") msg_box.setText(msgs[3]) text = "Time: %s\n Location: %s\n Message:\n%s" % \ (msgs[1], msgs[2], '\n'.join(msgs[3:])) msg_box.setInformativeText('\n'.join(msgs[4:])) msg_box.setStandardButtons(QtGui.QMessageBox.Ok) msg_box.setDefaultButton(QtGui.QMessageBox.Ok) msg_box.setDetailedText(text) msg_box.show()
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def showMessageBox(self, s): s = str(s).strip() msgs = s.split('\n') if self.msg_box and self.msg_box.isVisible(): self.msg_box.close() msg_box = QtGui.QMessageBox(self.parent()) self.msg_box = msg_box if msgs[0] == "INFO": msg_box.setIcon(QtGui.QMessageBox.Information) msg_box.setWindowTitle("Information") elif msgs[0] == "WARNING": msg_box.setIcon(QtGui.QMessageBox.Warning) msg_box.setWindowTitle("Warning") elif msgs[0] == "CRITICAL": msg_box.setIcon(QtGui.QMessageBox.Critical) msg_box.setWindowTitle("Critical error") msg_box.setText(msgs[3]) text = "Time: %s\n Location: %s\n Message:\n%s" % \ (msgs[1], msgs[2], '\n'.join(msgs[3:])) msg_box.setInformativeText('\n'.join(msgs[4:])) msg_box.setStandardButtons(QtGui.QMessageBox.Ok) msg_box.setDefaultButton(QtGui.QMessageBox.Ok) msg_box.setDetailedText(text) msg_box.show()
| 477,231
|
def write(self, s):
|
def write(self, s):
| 477,232
|
def write(self, s):
|
def write(self, s):
| 477,233
|
def write(self, s):
|
def write(self, s):
| 477,234
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def showEvent(self, e): """closeEvent(e) -> None Event handler called when the dialog is about to close.""" count = self.list.count() if count: self.list.scrollToItem(self.list.item(count-1)) self.emit(QtCore.SIGNAL("messagesView(bool)"), True)
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def showEvent(self, e): """closeEvent(e) -> None Event handler called when the dialog is about to close.""" self.emit(QtCore.SIGNAL("messagesView(bool)"), True)
| 477,235
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def load_vistrail(locator, is_abstraction=False): abstraction_files = [] thumbnail_files = [] vistrail = None if locator is None: vistrail = Vistrail() else: res = locator.load() if type(res) == type(SaveBundle(None)): vistrail = res.vistrail abstraction_files.extend(res.abstractions) thumbnail_files.extend(res.thumbnails) else: vistrail = res vistrail.is_abstraction = is_abstraction return (vistrail, abstraction_files, thumbnail_files)
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def load_vistrail(locator, is_abstraction=False): from core.vistrail.vistrail import Vistrail abstraction_files = [] thumbnail_files = [] vistrail = None if locator is None: vistrail = Vistrail() else: res = locator.load() if type(res) == type(SaveBundle(None)): vistrail = res.vistrail abstraction_files.extend(res.abstractions) thumbnail_files.extend(res.thumbnails) else: res = locator.load() if type(res) == type(SaveBundle(None)): vistrail = res.vistrail abstraction_files.extend(res.abstractions) thumbnail_files.extend(res.thumbnails) else: vistrail = res vistrail.is_abstraction = is_abstraction return (vistrail, abstraction_files, thumbnail_files)
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def load_vistrail(locator, is_abstraction=False): abstraction_files = [] thumbnail_files = [] vistrail = None if locator is None: vistrail = Vistrail() else: res = locator.load() if type(res) == type(SaveBundle(None)): vistrail = res.vistrail abstraction_files.extend(res.abstractions) thumbnail_files.extend(res.thumbnails) else: vistrail = res vistrail.is_abstraction = is_abstraction return (vistrail, abstraction_files, thumbnail_files)
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def load_vistrail(locator, is_abstraction=False): abstraction_files = [] thumbnail_files = [] vistrail = None if locator is None: vistrail = Vistrail() else: vistrail = res vistrail.is_abstraction = is_abstraction return (vistrail, abstraction_files, thumbnail_files)
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def get_vt_graph_png(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_png(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_png(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_png(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def is_image_stale(filename, host, port, db_name, vt_id): statinfo = os.stat(filename) image_time = datetime.fromtimestamp(statinfo.st_mtime) locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None) vt_mod_time = locator.get_db_modification_time() self.server_logger.info("image time: %s, vt time: %s"%(image_time, vt_mod_time)) if image_time < vt_mod_time: return True else: return False
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def is_image_stale(filename, host, port, db_name, vt_id): statinfo = os.stat(filename) image_time = datetime.fromtimestamp(statinfo.st_mtime) locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None) vt_mod_time = locator.get_db_modification_time() self.server_logger.info("image time: %s, vt time: %s"%(image_time, vt_mod_time)) if image_time < vt_mod_time: return True else: return False
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def is_image_stale(filename, host, port, db_name, vt_id): statinfo = os.stat(filename) image_time = datetime.fromtimestamp(statinfo.st_mtime) locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None) vt_mod_time = locator.get_db_modification_time() self.server_logger.info("image time: %s, vt time: %s"%(image_time, vt_mod_time)) if image_time < vt_mod_time: return True else: return False
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def is_image_stale(filename, host, port, db_name, vt_id): statinfo = os.stat(filename) image_time = datetime.fromtimestamp(statinfo.st_mtime) locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None) vt_mod_time = locator.get_db_modification_time() self.server_logger.info("image time: %s, vt time: %s"%(image_time, vt_mod_time)) if image_time < vt_mod_time: return True else: return False
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def get_vt_graph_pdf(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_pdf(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_pdf(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_pdf(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_pdf(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_pdf(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_pdf(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_pdf(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_pdf(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_pdf(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_pdf(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_pdf(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def keyPressEvent(self, e): """keyPressEvent(e) -> None Handle user input a key at a time.
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def keyPressEvent(self, e): """keyPressEvent(e) -> None Handle user input a key at a time.
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def keyPressEvent(self, e): """keyPressEvent(e) -> None Handle user input a key at a time.
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def keyPressEvent(self, e): """keyPressEvent(e) -> None Handle user input a key at a time.
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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)
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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)
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# def mousePressEvent(self, e):
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#return return return return defreturn mousePressEvent(self,return e):
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def flush_delayed_actions(self): start_version = self.current_version desc_key = Action.ANNOTATION_DESCRIPTION for action in self._delayed_actions: self.vistrail.add_action(action, start_version, self.current_session) # HACK to populate upgrade information if (action.has_annotation_with_key(desc_key) and action.get_annotation_by_key(desc_key).value == 'Upgrade'): self.vistrail.set_upgrade(start_version, str(action.id)) self.current_version = action.id start_version = action.id
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def flush_delayed_actions(self): start_version = self.current_version desc_key = Action.ANNOTATION_DESCRIPTION for action in self._delayed_actions: self.vistrail.add_action(action, start_version, self.current_session) # HACK to populate upgrade information if (action.has_annotation_with_key(desc_key) and action.get_annotation_by_key(desc_key).value == 'Upgrade'): self.vistrail.set_upgrade(start_version, str(action.id)) self.current_version = action.id start_version = action.id
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def load_wsdl_with_config(wsdlList): """load_wsdl_with_config(wsdlList: list of urls) -> (bool,list) This loads the wsdl list creating config files. Returns a tuple with two values. The first is a boolean that is True in case of success. The second is a list with problematic urls""" global schema global webServicesmodulesDict global complexsdict reg = core.modules.module_registry.get_module_registry() basic = core.modules.basic_modules not_loaded = [] result = True for w in wsdlList: #Validation if the user introduces a blank space in the list of #web services if w == '': continue complexsdict = {} #This dictionary stores the complex types for #a webservice w w = w.strip() #Check to see if the element is not repeated in the web services list numtimes = 0 for element in wsdlList: if w == element.strip(): numtimes = numtimes + 1 if numtimes > 1: print "The following web service is repeated in the list and won't \
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def load_wsdl_with_config(wsdlList): """load_wsdl_with_config(wsdlList: list of urls) -> (bool,list) This loads the wsdl list creating config files. Returns a tuple with two values. The first is a boolean that is True in case of success. The second is a list with problematic urls""" global schema global webServicesmodulesDict global complexsdict reg = core.modules.module_registry.get_module_registry() basic = core.modules.basic_modules not_loaded = [] result = True for w in wsdlList: #Validation if the user introduces a blank space in the list of #web services if w == '': continue complexsdict = {} #This dictionary stores the complex types for #a webservice w w = w.strip() #Check to see if the element is not repeated in the web services list numtimes = 0 for element in wsdlList: if w == element.strip(): numtimes = numtimes + 1 if numtimes > 1: print "The following web service is repeated in the list and won't \
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def update_workflow(old_obj, translate_dict): return DBWorkflow.update_version(old_obj.db_workflow, translate_dict, DBWorkflow())
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def update_workflow(old_obj, translate_dict): return DBWorkflow.update_version(old_obj.db_workflow, translate_dict, DBWorkflow())
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def update_workflow(old_obj, translate_dict): return DBWorkflow.update_version(old_obj.db_workflow, translate_dict, DBWorkflow())
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def update_workflow(old_obj, translate_dict): return DBWorkflow.update_version(old_obj.db_workflow, translate_dict, DBWorkflow())
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def connectSignals(self): """ connectSignals() -> None Map signals between GUI components """ self.connect(self.cancelButton, QtCore.SIGNAL('clicked()'), self.reject) self.connect(self.openButton, QtCore.SIGNAL('clicked()'), self.accept) self.connect(self.addAct, QtCore.SIGNAL('triggered()'), self.showConnConfig) self.connect(self.removeAct, QtCore.SIGNAL('triggered()'), self.connectionList.removeConnection) self.connect(self.connectionList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateDBObjectsList) self.connect(self.connectionList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateButtons) self.connect(self.connectionList, QtCore.SIGNAL('itemClicked(QListWidgetItem *)'), self.updateDBObjectsList) self.connect(self.connectionList, QtCore.SIGNAL("reloadConnections"), self.updateDBObjectsList) self.connect(self.objectList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateButtons) self.connect(self.saveasEdt, QtCore.SIGNAL('textChanged(QString)'), self.updateButtons) self.connect(self.objectList, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.accept)
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def connectSignals(self): """ connectSignals() -> None Map signals between GUI components """ self.connect(self.cancelButton, QtCore.SIGNAL('clicked()'), self.reject) self.connect(self.openButton, QtCore.SIGNAL('clicked()'), self.accept) self.connect(self.addAct, QtCore.SIGNAL('triggered()'), self.showConnConfig) self.connect(self.removeAct, QtCore.SIGNAL('triggered()'), self.connectionList.removeConnection) self.connect(self.connectionList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateDBObjectsList) self.connect(self.connectionList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateButtons) self.connect(self.connectionList, QtCore.SIGNAL("reloadConnections"), self.updateDBObjectsList) self.connect(self.objectList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateButtons) self.connect(self.saveasEdt, QtCore.SIGNAL('textChanged(QString)'), self.updateButtons) self.connect(self.objectList, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.accept)
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def connectSignals(self): """ connectSignals() -> None Map signals between GUI components """ self.connect(self.cancelButton, QtCore.SIGNAL('clicked()'), self.reject) self.connect(self.openButton, QtCore.SIGNAL('clicked()'), self.accept) self.connect(self.addAct, QtCore.SIGNAL('triggered()'), self.showConnConfig) self.connect(self.removeAct, QtCore.SIGNAL('triggered()'), self.connectionList.removeConnection) self.connect(self.connectionList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateDBObjectsList) self.connect(self.connectionList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateButtons) self.connect(self.connectionList, QtCore.SIGNAL('itemClicked(QListWidgetItem *)'), self.updateDBObjectsList) self.connect(self.connectionList, QtCore.SIGNAL("reloadConnections"), self.updateDBObjectsList) self.connect(self.objectList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateButtons) self.connect(self.saveasEdt, QtCore.SIGNAL('textChanged(QString)'), self.updateButtons) self.connect(self.objectList, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.accept)
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def connectSignals(self): """ connectSignals() -> None Map signals between GUI components """ self.connect(self.cancelButton, QtCore.SIGNAL('clicked()'), self.reject) self.connect(self.openButton, QtCore.SIGNAL('clicked()'), self.accept) self.connect(self.addAct, QtCore.SIGNAL('triggered()'), self.showConnConfig) self.connect(self.removeAct, QtCore.SIGNAL('triggered()'), self.connectionList.removeConnection) self.connect(self.connectionList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateDBObjectsList) self.connect(self.connectionList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateButtons) self.connect(self.connectionList, QtCore.SIGNAL('itemClicked(QListWidgetItem *)'), self.updateDBObjectsList) self.connect(self.connectionList, QtCore.SIGNAL("reloadConnections"), self.updateDBObjectsList) self.connect(self.objectList, QtCore.SIGNAL('itemSelectionChanged()'), self.updateButtons) self.connect(self.saveasEdt, QtCore.SIGNAL('textChanged(QString)'), self.updateButtons) self.connect(self.objectList, QtCore.SIGNAL('itemDoubleClicked(QListWidgetItem *)'), self.accept)
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def __init__(self, parent): QToolWindow.__init__(self, parent=parent) #locals() returns the original dictionary, not a copy as #the docs say app = gui.application.VistrailsApplication self.firstLocals = copy.copy(locals()) self.shell = QShell(self.firstLocals,None) self.setWidget(self.shell) self.setWindowTitle(self.shell.windowTitle()) self.monitorWindowTitle(self.shell) self.vistrails_interpreter = get_default_interpreter()
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def __init__(self, parent): QToolWindow.__init__(self, parent=parent) #locals() returns the original dictionary, not a copy as #the docs say self.firstLocals = copy.copy(locals()) self.shell = QShell(self.firstLocals,None) self.setWidget(self.shell) self.setWindowTitle(self.shell.windowTitle()) self.monitorWindowTitle(self.shell) self.vistrails_interpreter = get_default_interpreter()
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def __init__(self, locals=None, parent=None): """Constructor.
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def __init__(self, locals=None, parent=None): """Constructor.
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def __init__(self, locals=None, parent=None): """Constructor.
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def __init__(self, locals=None, parent=None): """Constructor.
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def verify_wsdl(wsdlList): """verify_wsdl(wsdlList: list of urls) -> (list,list,list) This checks for the wsdls that need to be updated or the files need to be generated and splits them in 3 lists: files that are outdated, updated and ones that an error was generated. """ outdated_list = [] updated_list = [] error_list = [] for w in wsdlList: if w == '': continue try: s = w.split('/') host = s[2] except: msg = "Malformed URL." error_list.append((w,msg)) continue location = w reader = WSDLTools.WSDLReader() load = reader.loadFromURL try: wsdl = load(location) except Exception, e: msg = "Couldn't load wsdl from the web: %s."%str(e) error_list.append((w,msg)) continue directoryname = urllib.quote_plus(w) directoryname = directoryname.replace(".","_") directoryname = directoryname.replace("%","_") directoryname = directoryname.replace("+","_") package_subdirectory = os.path.join(core.system.default_dot_vistrails(), "webServices", directoryname) wsm = WriteServiceModule(wsdl) client_mod = wsm.getClientModuleName() client_file = os.path.join(package_subdirectory, '%s.py' %client_mod) conn = httplib.HTTPConnection(host) filename = '/' + '/'.join(s[3:]) request = conn.request("GET", filename) response = conn.getresponse() remoteHeader = response.msg.getheader('last-modified') isoutdated = False if remoteHeader != None: localFile = client_file reg = core.modules.module_registry.get_module_registry() httpfile = reg.get_descriptor_by_name('edu.utah.sci.vistrails.http', 'HTTPFile').module() try: isoutdated = httpfile.is_outdated(remoteHeader, localFile) except OSError: print "File doesn't exist" isoutdated = True if isoutdated or remoteHeader == None: outdated_list.append(w) else: updated_list.append(w) return (outdated_list,updated_list, error_list)
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def verify_wsdl(wsdlList): """verify_wsdl(wsdlList: list of urls) -> (list,list,list) This checks for the wsdls that need to be updated or the files need to be generated and splits them in 3 lists: files that are outdated, updated and ones that an error was generated. """ outdated_list = [] updated_list = [] error_list = [] for w in wsdlList: if w == '': continue try: s = w.split('/') host = s[2] except: msg = "Malformed URL." error_list.append((w,msg)) continue location = w reader = WSDLTools.WSDLReader() load = reader.loadFromURL try: wsdl = load(location) except Exception, e: msg = "Couldn't load wsdl from the web: %s."%str(e) error_list.append((w,msg)) continue directoryname = urllib.quote_plus(w) directoryname = directoryname.replace(".","_") directoryname = directoryname.replace("%","_") directoryname = directoryname.replace("+","_") package_subdirectory = os.path.join(core.system.default_dot_vistrails(), "webServices", directoryname) wsm = WriteServiceModule(wsdl) client_mod = wsm.getClientModuleName() client_file = os.path.join(package_subdirectory, '%s.py' %client_mod) conn = httplib.HTTPConnection(host) filename = '/' + '/'.join(s[3:]) request = conn.request("GET", filename) response = conn.getresponse() remoteHeader = response.msg.getheader('last-modified') isoutdated = False if remoteHeader != None: localFile = client_file reg = core.modules.module_registry.get_module_registry() httpfile = reg.get_descriptor_by_name('edu.utah.sci.vistrails.http', 'HTTPFile').module() try: isoutdated = httpfile._is_outdated(remoteHeader, localFile) except OSError: print "File doesn't exist" isoutdated = True if isoutdated or remoteHeader == None: outdated_list.append(w) else: updated_list.append(w) return (outdated_list,updated_list, error_list)
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def keyPressEvent(self, event): """ keyPressEvent(event: QKeyEvent) -> None Capture 'Del', 'Backspace' for pruning versions when not editing a tag """ selectedItems = self.selectedItems() versions = [item.id for item in selectedItems if type(item)==QGraphicsVersionItem and not item.text.hasFocus()] if (self.controller and len(versions)>0 and event.key() in [QtCore.Qt.Key_Backspace, QtCore.Qt.Key_Delete]): versions = [item.id for item in selectedItems] res = gui.utils.show_question("VisTrails", "Are you sure that you want to " "prune the selected version(s)?", [gui.utils.YES_BUTTON, gui.utils.NO_BUTTON], gui.utils.NO_BUTTON) if res == gui.utils.YES_BUTTON: self.controller.prune_versions(versions) qt_super(QVersionTreeScene, self).keyPressEvent(event)
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def keyPressEvent(self, event): """ keyPressEvent(event: QKeyEvent) -> None Capture 'Del', 'Backspace' for pruning versions when not editing a tag """ selectedItems = self.selectedItems() versions = [item.id for item in selectedItems if type(item)==QGraphicsVersionItem and not item.text.hasFocus()] if (self.controller and len(versions)>0 and event.key() in [QtCore.Qt.Key_Backspace, QtCore.Qt.Key_Delete]): versions = [item.id for item in selectedItems] res = gui.utils.show_question("VisTrails", "Are you sure that you want to " "prune the selected version(s)?", [gui.utils.YES_BUTTON, gui.utils.NO_BUTTON], gui.utils.NO_BUTTON) if res == gui.utils.YES_BUTTON: self.controller.prune_versions(versions) qt_super(QVersionTreeScene, self).keyPressEvent(event)
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def new_abstraction(name, vistrail, vt_fname=None, internal_version=-1L): """make_abstraction(name: str, vistrail: (str or Vistrail), registry: ModuleRegistry, vt_fname: str, internal_version: long) -> type Creates a new VisTrails module that is a subclass of Abstraction according to the vistrail file provided and the version. The version can either be a tag (string) or an id (long) """ if type(vistrail) == type(""): vt_fname = vistrail vistrail = read_vistrail(vistrail) elif vt_fname is None: raise VistrailsInternalError("Abstraction must provide " "vt_fname with vistrail") if internal_version == -1L: internal_version = vistrail.get_latest_version() action = vistrail.actionMap[internal_version] pipeline = vistrail.getPipeline(internal_version) # try to make the subworkflow work with the package versions we have pipeline.ensure_modules_are_on_registry() pipeline.ensure_connection_specs() uuid = vistrail.get_annotation('__abstraction_uuid__').value if action.notes is not None: docstring = action.notes else: docstring = None d = {} input_modules = [] output_modules = [] for module in pipeline.module_list: #FIXME make this compare more robust if module.name == 'InputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': input_modules.append(module) elif module.name == 'OutputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': output_modules.append(module) input_ports = [] output_ports = [] input_remap = {} output_remap = {} for module in input_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) input_ports.append((port_name, sigstring, optional)) input_remap[port_name] = module for module in output_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) output_ports.append((port_name, sigstring, optional)) output_remap[port_name] = module # necessary for group d['_input_ports'] = input_ports d['_output_ports'] = output_ports d['input_remap'] = input_remap d['output_remap'] = output_remap d['pipeline'] = pipeline # abstraction specific d['vt_fname'] = vt_fname d['vistrail'] = vistrail d['internal_version'] = internal_version d['uuid'] = uuid # print "input_ports", d['_input_ports'] # print "output_ports", d['_output_ports'] return new_module(Abstraction, name, d, docstring)
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def new_abstraction(name, vistrail, vt_fname=None, internal_version=-1L, pipeline=None): """make_abstraction(name: str, vistrail: (str or Vistrail), registry: ModuleRegistry, vt_fname: str, internal_version: long) -> type Creates a new VisTrails module that is a subclass of Abstraction according to the vistrail file provided and the version. The version can either be a tag (string) or an id (long) """ if type(vistrail) == type(""): vt_fname = vistrail vistrail = read_vistrail(vistrail) elif vt_fname is None: raise VistrailsInternalError("Abstraction must provide " "vt_fname with vistrail") if internal_version == -1L: internal_version = vistrail.get_latest_version() action = vistrail.actionMap[internal_version] pipeline = vistrail.getPipeline(internal_version) # try to make the subworkflow work with the package versions we have pipeline.ensure_modules_are_on_registry() pipeline.ensure_connection_specs() uuid = vistrail.get_annotation('__abstraction_uuid__').value if action.notes is not None: docstring = action.notes else: docstring = None d = {} input_modules = [] output_modules = [] for module in pipeline.module_list: #FIXME make this compare more robust if module.name == 'InputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': input_modules.append(module) elif module.name == 'OutputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': output_modules.append(module) input_ports = [] output_ports = [] input_remap = {} output_remap = {} for module in input_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) input_ports.append((port_name, sigstring, optional)) input_remap[port_name] = module for module in output_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) output_ports.append((port_name, sigstring, optional)) output_remap[port_name] = module # necessary for group d['_input_ports'] = input_ports d['_output_ports'] = output_ports d['input_remap'] = input_remap d['output_remap'] = output_remap d['pipeline'] = pipeline # abstraction specific d['vt_fname'] = vt_fname d['vistrail'] = vistrail d['internal_version'] = internal_version d['uuid'] = uuid # print "input_ports", d['_input_ports'] # print "output_ports", d['_output_ports'] return new_module(Abstraction, name, d, docstring)
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def new_abstraction(name, vistrail, vt_fname=None, internal_version=-1L): """make_abstraction(name: str, vistrail: (str or Vistrail), registry: ModuleRegistry, vt_fname: str, internal_version: long) -> type Creates a new VisTrails module that is a subclass of Abstraction according to the vistrail file provided and the version. The version can either be a tag (string) or an id (long) """ if type(vistrail) == type(""): vt_fname = vistrail vistrail = read_vistrail(vistrail) elif vt_fname is None: raise VistrailsInternalError("Abstraction must provide " "vt_fname with vistrail") if internal_version == -1L: internal_version = vistrail.get_latest_version() action = vistrail.actionMap[internal_version] pipeline = vistrail.getPipeline(internal_version) # try to make the subworkflow work with the package versions we have pipeline.ensure_modules_are_on_registry() pipeline.ensure_connection_specs() uuid = vistrail.get_annotation('__abstraction_uuid__').value if action.notes is not None: docstring = action.notes else: docstring = None d = {} input_modules = [] output_modules = [] for module in pipeline.module_list: #FIXME make this compare more robust if module.name == 'InputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': input_modules.append(module) elif module.name == 'OutputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': output_modules.append(module) input_ports = [] output_ports = [] input_remap = {} output_remap = {} for module in input_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) input_ports.append((port_name, sigstring, optional)) input_remap[port_name] = module for module in output_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) output_ports.append((port_name, sigstring, optional)) output_remap[port_name] = module # necessary for group d['_input_ports'] = input_ports d['_output_ports'] = output_ports d['input_remap'] = input_remap d['output_remap'] = output_remap d['pipeline'] = pipeline # abstraction specific d['vt_fname'] = vt_fname d['vistrail'] = vistrail d['internal_version'] = internal_version d['uuid'] = uuid # print "input_ports", d['_input_ports'] # print "output_ports", d['_output_ports'] return new_module(Abstraction, name, d, docstring)
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def new_abstraction(name, vistrail, vt_fname=None, internal_version=-1L): """make_abstraction(name: str, vistrail: (str or Vistrail), registry: ModuleRegistry, vt_fname: str, internal_version: long, pipeline: Pipeline) -> type Creates a new VisTrails module that is a subclass of Abstraction according to the vistrail file provided and the version. The version can either be a tag (string) or an id (long) """ if type(vistrail) == type(""): vt_fname = vistrail vistrail = read_vistrail(vistrail) elif vt_fname is None: raise VistrailsInternalError("Abstraction must provide " "vt_fname with vistrail") if internal_version == -1L: internal_version = vistrail.get_latest_version() action = vistrail.actionMap[internal_version] pipeline = vistrail.getPipeline(internal_version) # try to make the subworkflow work with the package versions we have pipeline.ensure_modules_are_on_registry() pipeline.ensure_connection_specs() uuid = vistrail.get_annotation('__abstraction_uuid__').value if action.notes is not None: docstring = action.notes else: docstring = None d = {} input_modules = [] output_modules = [] for module in pipeline.module_list: #FIXME make this compare more robust if module.name == 'InputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': input_modules.append(module) elif module.name == 'OutputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': output_modules.append(module) input_ports = [] output_ports = [] input_remap = {} output_remap = {} for module in input_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) input_ports.append((port_name, sigstring, optional)) input_remap[port_name] = module for module in output_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) output_ports.append((port_name, sigstring, optional)) output_remap[port_name] = module # necessary for group d['_input_ports'] = input_ports d['_output_ports'] = output_ports d['input_remap'] = input_remap d['output_remap'] = output_remap d['pipeline'] = pipeline # abstraction specific d['vt_fname'] = vt_fname d['vistrail'] = vistrail d['internal_version'] = internal_version d['uuid'] = uuid # print "input_ports", d['_input_ports'] # print "output_ports", d['_output_ports'] return new_module(Abstraction, name, d, docstring)
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def new_abstraction(name, vistrail, vt_fname=None, internal_version=-1L): """make_abstraction(name: str, vistrail: (str or Vistrail), registry: ModuleRegistry, vt_fname: str, internal_version: long) -> type Creates a new VisTrails module that is a subclass of Abstraction according to the vistrail file provided and the version. The version can either be a tag (string) or an id (long) """ if type(vistrail) == type(""): vt_fname = vistrail vistrail = read_vistrail(vistrail) elif vt_fname is None: raise VistrailsInternalError("Abstraction must provide " "vt_fname with vistrail") if internal_version == -1L: internal_version = vistrail.get_latest_version() action = vistrail.actionMap[internal_version] pipeline = vistrail.getPipeline(internal_version) # try to make the subworkflow work with the package versions we have pipeline.ensure_modules_are_on_registry() pipeline.ensure_connection_specs() uuid = vistrail.get_annotation('__abstraction_uuid__').value if action.notes is not None: docstring = action.notes else: docstring = None d = {} input_modules = [] output_modules = [] for module in pipeline.module_list: #FIXME make this compare more robust if module.name == 'InputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': input_modules.append(module) elif module.name == 'OutputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': output_modules.append(module) input_ports = [] output_ports = [] input_remap = {} output_remap = {} for module in input_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) input_ports.append((port_name, sigstring, optional)) input_remap[port_name] = module for module in output_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) output_ports.append((port_name, sigstring, optional)) output_remap[port_name] = module # necessary for group d['_input_ports'] = input_ports d['_output_ports'] = output_ports d['input_remap'] = input_remap d['output_remap'] = output_remap d['pipeline'] = pipeline # abstraction specific d['vt_fname'] = vt_fname d['vistrail'] = vistrail d['internal_version'] = internal_version d['uuid'] = uuid # print "input_ports", d['_input_ports'] # print "output_ports", d['_output_ports'] return new_module(Abstraction, name, d, docstring)
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def new_abstraction(name, vistrail, vt_fname=None, internal_version=-1L): """make_abstraction(name: str, vistrail: (str or Vistrail), registry: ModuleRegistry, vt_fname: str, internal_version: long) -> type Creates a new VisTrails module that is a subclass of Abstraction according to the vistrail file provided and the version. The version can either be a tag (string) or an id (long) """ if type(vistrail) == type(""): vt_fname = vistrail vistrail = read_vistrail(vistrail) elif vt_fname is None: raise VistrailsInternalError("Abstraction must provide " "vt_fname with vistrail") if internal_version == -1L: internal_version = vistrail.get_latest_version() action = vistrail.actionMap[internal_version] pipeline = vistrail.getPipeline(internal_version) # try to make the subworkflow work with the package versions we have pipeline.ensure_modules_are_on_registry() pipeline.ensure_connection_specs() uuid = vistrail.get_annotation('__abstraction_uuid__').value if action.notes is not None: docstring = action.notes else: docstring = None d = {} input_modules = [] output_modules = [] for module in pipeline.module_list: #FIXME make this compare more robust if module.name == 'InputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': input_modules.append(module) elif module.name == 'OutputPort' and \ module.package == 'edu.utah.sci.vistrails.basic': output_modules.append(module) input_ports = [] output_ports = [] input_remap = {} output_remap = {} for module in input_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) input_ports.append((port_name, sigstring, optional)) input_remap[port_name] = module for module in output_modules: (port_name, sigstring, optional, _) = \ get_port_spec_info(pipeline, module) output_ports.append((port_name, sigstring, optional)) output_remap[port_name] = module # necessary for group d['_input_ports'] = input_ports d['_output_ports'] = output_ports d['input_remap'] = input_remap d['output_remap'] = output_remap d['pipeline'] = pipeline # abstraction specific d['vt_fname'] = vt_fname d['vistrail'] = vistrail d['internal_version'] = internal_version d['uuid'] = uuid # print "input_ports", d['_input_ports'] # print "output_ports", d['_output_ports'] return new_module(Abstraction, name, d, docstring)
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def add_vt_to_db(self, host, port, db_name, user, vt_filepath, filename, repository_vt_id, repository_creator): """add_vt_to_db(host:str, port:int, db_name:str, user:str, vt_filepath:str(or datastream), filename:str, repository_vt_id:int, repository_creator:str) -> (return_status, int) This will add a vistrail in vt_filepath to the the database. If running on a remote machine, vt_filepath will contain vt file data stream. Before adding it it will annotate the vistrail with the repository_vt_id and repository_creator.
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def add_vt_to_db(self, host, port, db_name, user, vt_filepath, filename, repository_vt_id, repository_creator, is_local=True): """add_vt_to_db(host:str, port:int, db_name:str, user:str, vt_filepath:str(or datastream), filename:str, repository_vt_id:int, repository_creator:str) -> (return_status, int) This will add a vistrail in vt_filepath to the the database. If running on a remote machine, vt_filepath will contain vt file data stream. Before adding it it will annotate the vistrail with the repository_vt_id and repository_creator.
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def add_vt_to_db(self, host, port, db_name, user, vt_filepath, filename, repository_vt_id, repository_creator): """add_vt_to_db(host:str, port:int, db_name:str, user:str, vt_filepath:str(or datastream), filename:str, repository_vt_id:int, repository_creator:str) -> (return_status, int) This will add a vistrail in vt_filepath to the the database. If running on a remote machine, vt_filepath will contain vt file data stream. Before adding it it will annotate the vistrail with the repository_vt_id and repository_creator.
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def add_vt_to_db(self, host, port, db_name, user, vt_filepath, filename, repository_vt_id, repository_creator): """add_vt_to_db(host:str, port:int, db_name:str, user:str, vt_filepath:str(or datastream), filename:str, repository_vt_id:int, repository_creator:str) -> (return_status, int) This will add a vistrail in vt_filepath to the the database. If running on a remote machine, vt_filepath will contain vt file data stream. Before adding it it will annotate the vistrail with the repository_vt_id and repository_creator.
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def merge_vt(self, host, port, db_name, user, new_vt_filepath, old_db_vt_id): """ Merge new_vt (new_vt_filepath) with current vt (old_db_vt_id)
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def merge_vt(self, host, port, db_name, user, new_vt_filepath, old_db_vt_id, is_local=True): """ Merge new_vt (new_vt_filepath) with current vt (old_db_vt_id)
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def run_from_db(self, host, port, db_name, vt_id, path_to_figures, version=None, pdf=False, vt_tag='',parameters=''): self.server_logger.info("Request: run_vistrail_from_db(%s,%s,%s,%s,%s,%s,%s,%s,%s)" % \ (host, port, db_name, vt_id, path_to_figures, version, pdf, vt_tag, parameters))
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def run_from_db(self, host, port, db_name, vt_id, path_to_figures, version=None, pdf=False, vt_tag='',parameters='', is_local=True): self.server_logger.info("Request: run_vistrail_from_db(%s,%s,%s,%s,%s,%s,%s,%s,%s)" % \ (host, port, db_name, vt_id, path_to_figures, version, pdf, vt_tag, parameters))
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def get_wf_graph_pdf(self, host, port, db_name, vt_id, version): """get_wf_graph_pdf(host:str, port:int, db_name:str, vt_id:int, version:int) -> str Returns the relative url to the generated PDF """ self.server_logger.info("get_wf_graph_pdf(%s,%s,%s,%s,%s) request received" % \ (host, port, db_name, vt_id, version)) try: vt_id = long(vt_id) version = long(version) subdir = 'workflows' filepath = os.path.join(media_dir, 'graphs', subdir) base_fname = "graph_%s_%s.pdf" % (vt_id, version) filename = os.path.join(filepath,base_fname) if ((not os.path.exists(filepath) or os.path.exists(filepath) and not os.path.exists(filename)) and self.proxies_queue is not None): #this server can send requests to other instances proxy = self.proxies_queue.get() try: result = proxy.get_wf_graph_pdf(host,port,db_name, vt_id, version) self.proxies_queue.put(proxy) self.server_logger.info("get_wf_graph_pdf returning %s"% result) return result except Exception, e: self.server_logger.error(str(e)) return (str(e), 0)
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def get_wf_graph_pdf(self, host, port, db_name, vt_id, version, is_local=True): """get_wf_graph_pdf(host:str, port:int, db_name:str, vt_id:int, version:int) -> str Returns the relative url to the generated PDF """ self.server_logger.info("get_wf_graph_pdf(%s,%s,%s,%s,%s) request received" % \ (host, port, db_name, vt_id, version)) try: vt_id = long(vt_id) version = long(version) subdir = 'workflows' filepath = os.path.join(media_dir, 'graphs', subdir) base_fname = "graph_%s_%s.pdf" % (vt_id, version) filename = os.path.join(filepath,base_fname) if ((not os.path.exists(filepath) or os.path.exists(filepath) and not os.path.exists(filename)) and self.proxies_queue is not None): #this server can send requests to other instances proxy = self.proxies_queue.get() try: result = proxy.get_wf_graph_pdf(host,port,db_name, vt_id, version) self.proxies_queue.put(proxy) self.server_logger.info("get_wf_graph_pdf returning %s"% result) return result except Exception, e: self.server_logger.error(str(e)) return (str(e), 0)
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def get_wf_graph_png(self, host, port, db_name, vt_id, version): """get_wf_graph_png(host:str, port:int, db_name:str, vt_id:int, version:int) -> str Returns the relative url to the generated image """ self.server_logger.info("get_wf_graph_png(%s,%s,%s,%s,%s) request received" % \ (host, port, db_name, vt_id, version)) try: vt_id = long(vt_id) version = long(version) subdir = 'workflows' filepath = os.path.join(media_dir, 'graphs', subdir) base_fname = "graph_%s_%s.png" % (vt_id, version) filename = os.path.join(filepath,base_fname) if ((not os.path.exists(filepath) or os.path.exists(filepath) and not os.path.exists(filename)) and self.proxies_queue is not None): #this server can send requests to other instances proxy = self.proxies_queue.get() try: self.server_logger.info("Sending request to %s" % proxy) result = proxy.get_wf_graph_png(host, port, db_name, vt_id, version) self.proxies_queue.put(proxy) self.server_logger.info("returning %s" % result) return result except Exception, e: self.server_logger.error(str(e)) return (str(e), 0) #if it gets here, this means that we will execute on this instance if not os.path.exists(filepath): os.mkdir(filepath)
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def get_wf_graph_png(self, host, port, db_name, vt_id, version, is_local=True): """get_wf_graph_png(host:str, port:int, db_name:str, vt_id:int, version:int) -> str Returns the relative url to the generated image """ self.server_logger.info("get_wf_graph_png(%s,%s,%s,%s,%s) request received" % \ (host, port, db_name, vt_id, version)) try: vt_id = long(vt_id) version = long(version) subdir = 'workflows' filepath = os.path.join(media_dir, 'graphs', subdir) base_fname = "graph_%s_%s.png" % (vt_id, version) filename = os.path.join(filepath,base_fname) if ((not os.path.exists(filepath) or os.path.exists(filepath) and not os.path.exists(filename)) and self.proxies_queue is not None): #this server can send requests to other instances proxy = self.proxies_queue.get() try: self.server_logger.info("Sending request to %s" % proxy) result = proxy.get_wf_graph_png(host, port, db_name, vt_id, version) self.proxies_queue.put(proxy) self.server_logger.info("returning %s" % result) return result except Exception, e: self.server_logger.error(str(e)) return (str(e), 0) #if it gets here, this means that we will execute on this instance if not os.path.exists(filepath): os.mkdir(filepath)
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def get_vt_graph_png(self, host, port, db_name, vt_id): """get_vt_graph_png(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_png(self, host, port, db_name, vt_id, is_local=True): """get_vt_graph_png(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_png(self, host, port, db_name, vt_id): """get_vt_graph_png(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def get_vt_graph_png(self, host, port, db_name, vt_id): """get_vt_graph_png(host:str, port: str, db_name: str, vt_id:str) -> str Returns the relative url of the generated image """
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def getPDFWorkflowMedley(self, m_id): """getPDFWorkflowMedley(m_id:int) -> str Returns the relative url to the generated image """ self.server_logger.info("getPDFWorkflowMedley(%s) request received" % m_id) try: m_id = int(m_id) medley = self.medley_objs[m_id] except Exception, e: self.server_logger.error(str(e))
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def getPDFWorkflowMedley(self, m_id, is_local=True): """getPDFWorkflowMedley(m_id:int) -> str Returns the relative url to the generated image """ self.server_logger.info("getPDFWorkflowMedley(%s) request received" % m_id) try: m_id = int(m_id) medley = self.medley_objs[m_id] except Exception, e: self.server_logger.error(str(e))
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def getPNGWorkflowMedley(self, m_id): self.server_logger.info("getPNGWorkflowMedley(%s) request received" % m_id) try: m_id = int(m_id) medley = self.medley_objs[m_id] except Exception, e: self.server_logger.error(str(e))
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def getPNGWorkflowMedley(self, m_id, is_local=True): self.server_logger.info("getPNGWorkflowMedley(%s) request received" % m_id) try: m_id = int(m_id) medley = self.medley_objs[m_id] except Exception, e: self.server_logger.error(str(e))
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def get_vt_tagged_versions(self, host, port, db_name, vt_id): self.server_logger.info("Request: get_vt_tagged_versions(%s,%s,%s,%s)" % \ (host, port, db_name, vt_id)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_vt_tagged_versions(self, host, port, db_name, vt_id, is_local=True): self.server_logger.info("Request: get_vt_tagged_versions(%s,%s,%s,%s)" % \ (host, port, db_name, vt_id)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
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def updateMethod(self): """ updateMethod() -> None Update the method values to vistrail. We only keep a monotonic version tree of the query pipeline, we can skip the actions here. """ methodBox = self.parent().parent().parent() if methodBox.controller: paramList = [] pipeline = methodBox.controller.current_pipeline f = pipeline.modules[methodBox.module.id].functions[self.fId] p = f.params for i in xrange(len(self.fields)): p[i].strValue = str(self.fields[i].editor.contents()) p[i].queryMethod = self.fields[i].selector.getCurrentMethod()
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def updateMethod(self): """ updateMethod() -> None Update the method values to vistrail. We only keep a monotonic version tree of the query pipeline, we can skip the actions here. """ methodBox = self.parent().parent().parent().parent() if methodBox.controller: paramList = [] pipeline = methodBox.controller.current_pipeline f = pipeline.modules[methodBox.module.id].functions[self.fId] p = f.params for i in xrange(len(self.fields)): p[i].strValue = str(self.fields[i].editor.contents()) p[i].queryMethod = self.fields[i].selector.getCurrentMethod()
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def get_wf_vt_zip(self, host, port, db_name, vt_id, version): """get_wf_vt_zip(host:str, port:str, db_name:str, vt_id:str, version:str) -> str Returns a vt file containing the single workflow defined by version encoded as base64 string """ self.server_logger.info("Request: get_wf_vt_zip(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None) (v, _ , _) = io.load_vistrail(locator) p = v.getPipeline(long(version)) if p: vistrail = Vistrail() action_list = [] for module in self.pipeline.module_list: action_list.append(('add', module)) for connection in self.pipeline.connection_list: action_list.append(('add', connection)) action = core.db.action.create_action(action_list) vistrail.add_action(action, 0L) vistrail.addTag("Imported workflow", action.id) pipxmlstr = io.serialize(vistrail) result = base64.b64encode(pipxmlstr) else: result = "Error: Pipeline was not materialized" self.server_logger.info(result) except Exception, e: result = "Error: %s"%str(e) self.server_logger.info(result) return result
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def get_wf_vt_zip(self, host, port, db_name, vt_id, version): """get_wf_vt_zip(host:str, port:str, db_name:str, vt_id:str, version:str) -> str Returns a vt file containing the single workflow defined by version encoded as base64 string """ self.server_logger.info("Request: get_wf_vt_zip(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None) (v, _ , _) = io.load_vistrail(locator) p = v.getPipeline(long(version)) if p: vistrail = Vistrail() action_list = [] for module in p.module_list: action_list.append(('add', module)) for connection in self.pipeline.connection_list: action_list.append(('add', connection)) action = core.db.action.create_action(action_list) vistrail.add_action(action, 0L) vistrail.addTag("Imported workflow", action.id) pipxmlstr = io.serialize(vistrail) result = base64.b64encode(pipxmlstr) else: result = "Error: Pipeline was not materialized" self.server_logger.info(result) except Exception, e: result = "Error: %s"%str(e) self.server_logger.info(result) return result
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def get_wf_vt_zip(self, host, port, db_name, vt_id, version): """get_wf_vt_zip(host:str, port:str, db_name:str, vt_id:str, version:str) -> str Returns a vt file containing the single workflow defined by version encoded as base64 string """ self.server_logger.info("Request: get_wf_vt_zip(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None) (v, _ , _) = io.load_vistrail(locator) p = v.getPipeline(long(version)) if p: vistrail = Vistrail() action_list = [] for module in self.pipeline.module_list: action_list.append(('add', module)) for connection in self.pipeline.connection_list: action_list.append(('add', connection)) action = core.db.action.create_action(action_list) vistrail.add_action(action, 0L) vistrail.addTag("Imported workflow", action.id) pipxmlstr = io.serialize(vistrail) result = base64.b64encode(pipxmlstr) else: result = "Error: Pipeline was not materialized" self.server_logger.info(result) except Exception, e: result = "Error: %s"%str(e) self.server_logger.info(result) return result
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def get_wf_vt_zip(self, host, port, db_name, vt_id, version): """get_wf_vt_zip(host:str, port:str, db_name:str, vt_id:str, version:str) -> str Returns a vt file containing the single workflow defined by version encoded as base64 string """ self.server_logger.info("Request: get_wf_vt_zip(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None) (v, _ , _) = io.load_vistrail(locator) p = v.getPipeline(long(version)) if p: vistrail = Vistrail() action_list = [] for module in self.pipeline.module_list: action_list.append(('add', module)) for connection in p.connection_list: action_list.append(('add', connection)) action = core.db.action.create_action(action_list) vistrail.add_action(action, 0L) vistrail.addTag("Imported workflow", action.id) pipxmlstr = io.serialize(vistrail) result = base64.b64encode(pipxmlstr) else: result = "Error: Pipeline was not materialized" self.server_logger.info(result) except Exception, e: result = "Error: %s"%str(e) self.server_logger.info(result) return result
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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
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defsetupScene(self,pipeline):"""setupScene(pipeline:Pipeline)->NoneConstructthescenetoviewapipeline"""old_pipeline=self.pipelineself.pipeline=pipeline
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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
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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
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def auto_add_subworkflow(self, subworkflow): if type(subworkflow) == str: return self.add_subworkflow(subworkflow) elif (type(subworkflow) == tuple and len(subworkflow) == 2 and type(subworkflow[0]) == type and type(subworkflow[1]) == dict): descriptor = self.add_subworkflow(subworkflow[0], **subworkflow[1]) return descriptor else: raise TypeError("Expected filename or (filename, kwargs)")
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def auto_add_subworkflow(self, subworkflow): if type(subworkflow) == str: return self.add_subworkflow(subworkflow) elif (type(subworkflow) == tuple and len(subworkflow) == 2 and type(subworkflow[0]) == str and type(subworkflow[1]) == dict): descriptor = self.add_subworkflow(subworkflow[0], **subworkflow[1]) return descriptor else: raise TypeError("Expected filename or (filename, kwargs)")
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def check_connection_port(port): try: s = d.get_port_spec(port.name, PortSpec.port_type_map.inverse[port.type]) # the old port spec doesn't actually exist for # the invalid module so we cannot compare! # if s <> port.spec: # msg = ("%s connection to port %s has mismatched type" % # (PortSpec.port_type_map.inverse[port.type], # port.name)) # raise UpgradeWorkflowError(msg) except Exception, e: import traceback traceback.print_exc() msg = ("%s connection to port %s does not exist." % (PortSpec.port_type_map.inverse[port.type], port.name)) raise UpgradeWorkflowError(msg)
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def check_connection_port(port): try: port_type = PortSpec.port_type_map.inverse[port.type] s = reg.get_port_spec_from_descriptor(d, port.name, port_type) # the old port spec doesn't actually exist for # the invalid module so we cannot compare! # if s <> port.spec: # msg = ("%s connection to port %s has mismatched type" % # (PortSpec.port_type_map.inverse[port.type], # port.name)) # raise UpgradeWorkflowError(msg) except Exception, e: import traceback traceback.print_exc() msg = ("%s connection to port %s does not exist." % (PortSpec.port_type_map.inverse[port.type], port.name)) raise UpgradeWorkflowError(msg)
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def check_connection_port(port): try: s = d.get_port_spec(port.name, PortSpec.port_type_map.inverse[port.type]) # the old port spec doesn't actually exist for # the invalid module so we cannot compare! # if s <> port.spec: # msg = ("%s connection to port %s has mismatched type" % # (PortSpec.port_type_map.inverse[port.type], # port.name)) # raise UpgradeWorkflowError(msg) except Exception, e: import traceback traceback.print_exc() msg = ("%s connection to port %s does not exist." % (PortSpec.port_type_map.inverse[port.type], port.name)) raise UpgradeWorkflowError(msg)
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def check_connection_port(port): try: s = d.get_port_spec(port.name, PortSpec.port_type_map.inverse[port.type]) # the old port spec doesn't actually exist for # the invalid module so we cannot compare! # if s <> port.spec: # msg = ("%s connection to port %s has mismatched type" % # (PortSpec.port_type_map.inverse[port.type], # port.name)) # raise UpgradeWorkflowError(msg) except Exception, e: import traceback traceback.print_exc() msg = ("%s connection to port %s of module %s " "does not exist." % \ (PortSpec.port_type_map.inverse[port.type], port.name, invalid_module.name)) raise UpgradeWorkflowError(msg)
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def check_connection_port(port): try: s = d.get_port_spec(port.name, PortSpec.port_type_map.inverse[port.type]) # the old port spec doesn't actually exist for # the invalid module so we cannot compare! # if s <> port.spec: # msg = ("%s connection to port %s has mismatched type" % # (PortSpec.port_type_map.inverse[port.type], # port.name)) # raise UpgradeWorkflowError(msg) except Exception, e: import traceback traceback.print_exc() msg = ("%s connection to port %s does not exist." % (PortSpec.port_type_map.inverse[port.type], port.name)) raise UpgradeWorkflowError(msg)
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def check_connection_port(port): try: s = d.get_port_spec(port.name, PortSpec.port_type_map.inverse[port.type]) # the old port spec doesn't actually exist for # the invalid module so we cannot compare! # if s <> port.spec: # msg = ("%s connection to port %s has mismatched type" % # (PortSpec.port_type_map.inverse[port.type], # port.name)) # raise UpgradeWorkflowError(msg) except Exception, e: import traceback traceback.print_exc() msg = ("%s connection to port %s does not exist." % (PortSpec.port_type_map.inverse[port.type], port.name)) raise UpgradeWorkflowError(msg)
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pattern = re.compile(r"(^\s*?def vistrails_revision\(\):.*?release = ['\"])([a-fA-F0-9]+?)(['\"].*?return release)", re.DOTALL | re.MULTILINE)
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pattern = re.compile(r"(^\s*?def vistrails_revision\(\):.*?release = ['\"])([a-fA-F0-9]+?)(['\"].*?return release)", re.DOTALL | re.MULTILINE)
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def errexit(errcodeobj, showtrace=True, *args): errcode = errcodeobj[0] errmsg = errcodeobj[1] if args: errmsg = errmsg % args if showtrace: errio = StringIO() errio.write(errmsg + "\n") traceio = StringIO() traceback.print_exc(file=traceio) traceio.seek(0) errio.writelines([INDENT + line for line in traceio.readlines()]) errio.seek(0) errmsg = errio.read() error(errmsg) exit(errcode)
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def errexit(errcodeobj, showtrace=True, *args): errcode = errcodeobj[0] errmsg = errcodeobj[1] if args: errmsg = errmsg % args if showtrace: errio = StringIO() errio.write(errmsg + "\n") traceio = StringIO() traceback.print_exc(file=traceio) traceio.seek(0) errio.writelines([INDENT + line for line in traceio.readlines()]) errio.seek(0) errmsg = errio.read() error(errmsg) exit(errcode)
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def get_wf_modules(self, host, port, db_name, vt_id, version): """get_wf_modules(host:str, port:int, db_name:str, vt_id:int, version:int) -> list of dict Returns a list of information about the modules used in a workflow in a list of dictionaries. The dictionary has the following keys: name, package, documentation. """ self.server_logger.info("Request: get_wf_modules(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_wf_modules(self, host, port, db_name, vt_id, version): """get_wf_modules(host:str, port:int, db_name:str, vt_id:int, version:int) -> list of dict Returns a list of information about the modules used in a workflow in a list of dictionaries. The dictionary has the following keys: name, package, documentation. """ self.server_logger.info("Request: get_wf_modules(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
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def add_vt_to_db(self, host, port, db_name, user, vt_filepath, filename, repository_vt_id, repository_creator): """add_vt_to_db(host:str, port:int, db_name:str, user:str, vt_filepath:str, filename:str, repository_vt_id:int, repository_creator:str) -> int This will add a vistrail in vt_filepath to the the database. Before adding it it will annotate the vistrail with the repository_vt_id and repository_creator. """ try: locator = ZIPFileLocator(vt_filepath).load() if repository_vt_id != -1: vistrail = locator.vistrail vistrail.set_annotation('repository_vt_id', repository_vt_id) vistrail.set_annotation('repository_creator', repository_creator) #print "name=%s"%filename db_locator = DBLocator(host=host, port=int(port), database=db_name, name=filename, user=user, passwd='r3P0:4uTH') #print "db_locator %s" % db_locator db_locator.save_as(locator) return db_locator.obj_id except Exception, e: self.server_logger.info("Error: %s"%str(e)) return "FAILURE: %s" %str(e)
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def add_vt_to_db(self, host, port, db_name, user, vt_filepath, filename, repository_vt_id, repository_creator): """add_vt_to_db(host:str, port:int, db_name:str, user:str, vt_filepath:str, filename:str, repository_vt_id:int, repository_creator:str) -> int This will add a vistrail in vt_filepath to the the database. Before adding it it will annotate the vistrail with the repository_vt_id and repository_creator. """ try: locator = ZIPFileLocator(vt_filepath).load() if repository_vt_id != -1: vistrail = locator.vistrail vistrail.set_annotation('repository_vt_id', repository_vt_id) vistrail.set_annotation('repository_creator', repository_creator) #print "name=%s"%filename db_locator = DBLocator(host=host, port=int(port), database=db_name, name=filename, user=db_write_user, passwd=db_write_pass) #print "db_locator %s" % db_locator db_locator.save_as(locator) return db_locator.obj_id except Exception, e: self.server_logger.info("Error: %s"%str(e)) return "FAILURE: %s" %str(e)
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def remove_vt_from_db(self, host, port, db_name, user, vt_id): """remove_vt_from_db(host:str, port:int, db_name:str, user:str, vt_id:int) -> 0 or 1 Remove a vistrail from the repository """ config = {} config['host'] = host config['port'] = int(port) config['db'] = db_name config['user'] = user config['passwd'] = 'pass' try: conn = db.services.io.open_db_connection(config) db.services.io.delete_entity_from_db(conn,'vistrail', vt_id) db.services.io.close_db_connection(conn) return 1 except Exception, e: self.server_logger.info("Error: %s"%str(e)) if conn: db.services.io.close_db_connection(conn) return "FAILURE: %s" %str(e)
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def remove_vt_from_db(self, host, port, db_name, user, vt_id): """remove_vt_from_db(host:str, port:int, db_name:str, user:str, vt_id:int) -> 0 or 1 Remove a vistrail from the repository """ config = {} config['host'] = host config['port'] = int(port) config['db'] = db_name config['user'] = db_write_user config['passwd'] = db_write_pass try: conn = db.services.io.open_db_connection(config) db.services.io.delete_entity_from_db(conn,'vistrail', vt_id) db.services.io.close_db_connection(conn) return 1 except Exception, e: self.server_logger.info("Error: %s"%str(e)) if conn: db.services.io.close_db_connection(conn) return "FAILURE: %s" %str(e)
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def get_runnable_workflows(self, host, port, db_name, vt_id): print "get_runnable_workflows" try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_runnable_workflows(self, host, port, db_name, vt_id): print "get_runnable_workflows" try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_wf_datasets(self, host, port, db_name, vt_id, version): print 'get workflow datasets' self.server_logger.info("Request: get_wf_datasets(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_wf_datasets(self, host, port, db_name, vt_id, version): print 'get workflow datasets' self.server_logger.info("Request: get_wf_datasets(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
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def run_from_db(self, host, port, db_name, vt_id, path_to_figures, version=None, vt_tag='', parameters=''):
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def run_from_db(self, host, port, db_name, vt_id, path_to_figures, version=None, vt_tag='', parameters=''):
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def get_tag_version(self, host, port, db_name, vt_id, vt_tag): self.server_logger.info("Request: get_tag_version(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, vt_tag)) version = -1 try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_tag_version(self, host, port, db_name, vt_id, vt_tag): self.server_logger.info("Request: get_tag_version(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, vt_tag)) version = -1 try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_vt_xml(self, host, port, db_name, vt_id): self.server_logger.info("Request: get_vt_xml(%s,%s,%s,%s)"%(host, port, db_name, vt_id)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_vt_xml(self, host, port, db_name, vt_id): self.server_logger.info("Request: get_vt_xml(%s,%s,%s,%s)"%(host, port, db_name, vt_id)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_wf_xml(self, host, port, db_name, vt_id, version): self.server_logger.info("Request: get_wf_xml(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_wf_xml(self, host, port, db_name, vt_id, version): self.server_logger.info("Request: get_wf_xml(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_wf_xml(self, host, port, db_name, vt_id, version): self.server_logger.info("Request: get_wf_xml(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_wf_xml(self, host, port, db_name, vt_id, version): self.server_logger.info("Request: get_wf_xml(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_vt_zip(self, host, port, db_name, vt_id): """get_vt_zip(host:str, port: str, db_name: str, vt_id:str) -> str Returns a .vt file encoded as base64 string """ self.server_logger.info("Request: get_vt_zip(%s,%s,%s,%s)"%(host, port, db_name, vt_id)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None) save_bundle = locator.load() #create temporary file (fd, name) = tempfile.mkstemp(prefix='vt_tmp', suffix='.vt') os.close(fd) fileLocator = FileLocator(name) fileLocator.save(save_bundle) contents = open(name).read() result = base64.b64encode(contents) os.unlink(name) self.server_logger.info("SUCCESS!") return result except Exception, e: self.server_logger.info("Error: %s"%str(e)) return "FAILURE: %s" %str(e)
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def get_vt_zip(self, host, port, db_name, vt_id): """get_vt_zip(host:str, port: str, db_name: str, vt_id:str) -> str Returns a .vt file encoded as base64 string """ self.server_logger.info("Request: get_vt_zip(%s,%s,%s,%s)"%(host, port, db_name, vt_id)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None) save_bundle = locator.load() #create temporary file (fd, name) = tempfile.mkstemp(prefix='vt_tmp', suffix='.vt') os.close(fd) fileLocator = FileLocator(name) fileLocator.save(save_bundle) contents = open(name).read() result = base64.b64encode(contents) os.unlink(name) self.server_logger.info("SUCCESS!") return result except Exception, e: self.server_logger.info("Error: %s"%str(e)) return "FAILURE: %s" %str(e)
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def get_wf_vt_zip(self, host, port, db_name, vt_id, version): """get_wf_vt_zip(host:str, port:str, db_name:str, vt_id:str, version:str) -> str Returns a vt file containing the single workflow defined by version encoded as base64 string """ self.server_logger.info("Request: get_wf_vt_zip(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None) (v, _ , _) = io.load_vistrail(locator) p = v.getPipeline(long(version)) if p: vistrail = Vistrail() action_list = [] for module in p.module_list: action_list.append(('add', module)) for connection in p.connection_list: action_list.append(('add', connection)) action = core.db.action.create_action(action_list) vistrail.add_action(action, 0L) vistrail.addTag("Imported workflow", action.id) pipxmlstr = io.serialize(vistrail) result = base64.b64encode(pipxmlstr) else: result = "Error: Pipeline was not materialized" self.server_logger.info(result) except Exception, e: result = "Error: %s"%str(e) self.server_logger.info(result) return result
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def get_wf_vt_zip(self, host, port, db_name, vt_id, version): """get_wf_vt_zip(host:str, port:str, db_name:str, vt_id:str, version:str) -> str Returns a vt file containing the single workflow defined by version encoded as base64 string """ self.server_logger.info("Request: get_wf_vt_zip(%s,%s,%s,%s,%s)"%(host, port, db_name, vt_id, version)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None) (v, _ , _) = io.load_vistrail(locator) p = v.getPipeline(long(version)) if p: vistrail = Vistrail() action_list = [] for module in p.module_list: action_list.append(('add', module)) for connection in p.connection_list: action_list.append(('add', connection)) action = core.db.action.create_action(action_list) vistrail.add_action(action, 0L) vistrail.addTag("Imported workflow", action.id) pipxmlstr = io.serialize(vistrail) result = base64.b64encode(pipxmlstr) else: result = "Error: Pipeline was not materialized" self.server_logger.info(result) except Exception, e: result = "Error: %s"%str(e) self.server_logger.info(result) return result
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def get_db_vt_list(self, host, port, db_name): self.server_logger.info("Request: get_db_vistrail_list(%s,%s,%s)"%(host, port, db_name)) config = {} config['host'] = host config['port'] = int(port) config['db'] = db_name config['user'] = 'vtserver' config['passwd'] = '' try: rows = io.get_db_vistrail_list(config) return rows except Exception, e: self.server_logger.info("Error: %s"%str(e)) return "FAILURE: %s" %str(e)
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def get_db_vt_list(self, host, port, db_name): self.server_logger.info("Request: get_db_vistrail_list(%s,%s,%s)"%(host, port, db_name)) config = {} config['host'] = host config['port'] = int(port) config['db'] = db_name config['user'] = db_read_user config['passwd'] = db_read_pass try: rows = io.get_db_vistrail_list(config) return rows except Exception, e: self.server_logger.info("Error: %s"%str(e)) return "FAILURE: %s" %str(e)
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def get_db_vt_list_xml(self, host, port, db_name): self.server_logger.info("Request: get_db_vistrail_list(%s,%s,%s)"%(host, port, db_name)) config = {} config['host'] = host config['port'] = int(port) config['db'] = db_name config['user'] = 'vtserver' config['passwd'] = '' try: rows = io.get_db_vistrail_list(config) result = '<vistrails>' for (id, name, mod_time) in rows: result += '<vistrail id="%s" name="%s" mod_time="%s" />'%(id,name,mod_time) result += '</vistrails>' return result except Exception, e: self.server_logger.info("Error: %s"%str(e)) return "FAILURE: %s" %str(e)
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def get_db_vt_list_xml(self, host, port, db_name): self.server_logger.info("Request: get_db_vistrail_list(%s,%s,%s)"%(host, port, db_name)) config = {} config['host'] = host config['port'] = int(port) config['db'] = db_name config['user'] = db_read_user config['passwd'] = db_read_pass try: rows = io.get_db_vistrail_list(config) result = '<vistrails>' for (id, name, mod_time) in rows: result += '<vistrail id="%s" name="%s" mod_time="%s" />'%(id,name,mod_time) result += '</vistrails>' return result except Exception, e: self.server_logger.info("Error: %s"%str(e)) return "FAILURE: %s" %str(e)
| 477,297
|
def get_vt_tagged_versions(self, host, port, db_name, vt_id): self.server_logger.info("Request: get_vt_tagged_versions(%s,%s,%s,%s)"%(host, port, db_name, vt_id)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user='vtserver', passwd='', obj_id=int(vt_id), obj_type=None, connection_id=None)
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def get_vt_tagged_versions(self, host, port, db_name, vt_id): self.server_logger.info("Request: get_vt_tagged_versions(%s,%s,%s,%s)"%(host, port, db_name, vt_id)) try: locator = DBLocator(host=host, port=int(port), database=db_name, user=db_read_user, passwd=db_read_pass, obj_id=int(vt_id), obj_type=None, connection_id=None)
| 477,298
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def check_dependencies(self): """ determines if current VisTrail will be supported by the repository's VisTrail server """
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def check_dependencies(self): """ determines if current VisTrail will be supported by the repository's VisTrail server """
| 477,299
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