def _searchClicked(self):
# Set pmrlib to go
self._ui.searchResultsListWidget.clear()
# fix up known terms to be full blown uri
search_text = self._ui.searchLineEdit.text()
search_terms = search_text.split()
for term in search_terms:
rdfterm = self._annotationTool.rdfFormOfTerm(term)
if rdfterm:
search_text = search_text + ' ' + rdfterm[1:-1]
try:
results = self._pmrTool.search(search_text)
for r in results:
if 'title' in r and r['title']:
item = QtGui.QListWidgetItem(
r['title'], self._ui.searchResultsListWidget)
else:
item = QtGui.QListWidgetItem(
r['target'], self._ui.searchResultsListWidget)
item.setData(QtCore.Qt.UserRole, r)
except PMRToolError as e:
message = convertExceptionToMessage(e)
logger.warn('PMR Tool exception raised')
logger.warn('Reason: {0}'.format(message))
def execute(self):
self._current += 1
if self._current >= len(self._topological_order):
self._current = -1
if callable(self._finished_callback):
self._finished_callback()
else:
# Form input requirements
current_node = self._topological_order[self._current]
if current_node in self._reverse_dependency_graph:
connections = []
for node in self._reverse_dependency_graph[current_node]:
# Find connection information and extract outputs from steps
new_connections = self._connections_for_nodes(
node, current_node)
connections.extend(
[c for c in new_connections if c not in connections])
if len(new_connections) == 0:
logger.critical(
'Connection in workflow not found, something has gone horribly wrong'
)
raise WorkflowError(
'Connection in workflow not found, something has gone horribly wrong'
)
for connection in connections:
# Alternative indexing based on index of port based on type.
# But don't use this as it is not what is documented.
# source_step = connection.source()._step
# destination_step = current_node._step
# source_ports = [port for port in source_step._ports if port.hasProvides()]
# destination_ports = [port for port in destination_step._ports if port.hasUses()]
# source_data_index = source_ports.index(source_step._ports[connection.sourceIndex()])
# destination_data_index = destination_ports.index(destination_step._ports[connection.destinationIndex()])
# dataIn = source_step.getPortData(source_data_index)
# destination_step.setPortData(destination_data_index, dataIn)
dataIn = connection.source().getStep().getPortData(
connection.sourceIndex())
current_node.getStep().setPortData(
connection.destinationIndex(), dataIn)
try:
current_node.getStep().execute()
except Exception as e:
self._current = -1
log_message = 'Exception caught while executing the workflow: ' + convertExceptionToMessage(
e)
exc_type, exc_value, exc_traceback = sys.exc_info()
redirect_output = FileTypeObject()
traceback.print_exception(exc_type,
exc_value,
exc_traceback,
file=redirect_output)
raise WorkflowError(log_message + '\n\n' +
''.join(redirect_output.messages))
def run(self):
python_dir = self._virt_env_dir + '\Scripts\python.exe'
pip_dir = self._virt_env_dir + '\Scripts\pip.exe'
logs_dir = self._virt_env_dir[:-13] + '\logs'
self._ui.label.setText('Searching for packages in pip index...')
self._ui.progressBar.setMaximum(len(self._packages_to_install))
found_packages = []
not_found_packages = []
for package in self._packages_to_install:
self._ui.label.setText('Searching for "' + package +
'" package...')
try:
output = subprocess.check_output(
[python_dir, pip_dir, 'search', package], shell=True)
found_packages += [package]
except Exception as e:
not_found_packages += [package]
self._ui.progressBar.setValue(self._ui.progressBar.value() + 1)
self._ui.progressBar.reset()
self._ui.progressBar.setMaximum(20 * len(found_packages))
unsuccessful_installs = {}
for package in found_packages:
self.count += 1
self._ui.label.setText('Installing "' + package + '" package...')
for i in range(0, 10):
time.sleep((random.randrange(0, 100) / 1000))
self._ui.progressBar.setValue(self._ui.progressBar.value() +
1.5)
try:
with open(
logs_dir + 'package_install_report_' + package +
'.log', 'w') as file_out:
subprocess.check_call(
[python_dir, pip_dir, 'install', package],
shell=True,
stdout=file_out,
stderr=file_out)
except Exception as e:
unsuccessful_installs[package] = convertExceptionToMessage(e)
logger.warning('"' + package +
'" dependency could not be installed.')
logger.warning('Reason: ' + unsuccessful_installs[package])
for i in range(0, 5):
time.sleep(0.004)
self._ui.progressBar.setValue(self._ui.progressBar.value() + 1)
while self._ui.progressBar.value() < self._ui.progressBar.maximum():
time.sleep(0.004)
self._ui.progressBar.setValue(self._ui.progressBar.value() + 1)
return unsuccessful_installs
def cancelInstallation(self):
for i in range(0, self.count - 1):
try:
subprocess.check_call([
self._virt_env_dir + '\Scripts\python.exe',
self._virt_env_dir + '\Scripts\pip.exe', 'uninstall',
self._packages_to_install
],
shell=True)
except Exception as e:
message = convertExceptionToMessage(e)
logger.info('Could not uninstall "' +
self._packages_to_install[i] + '" package.')
logger.info('Reason: ' + message)