def configure(self):
d = ConfigureDialog(self._state)
d.setModal(True)
if d.exec_():
self.serialize(self._location)
self._state = d.getState()
# When a PMR location is given we need to translate that into a
# local path for passing into the ImageSourceData class
local_dir = self._state.location()
pmr_location = self._state.pmrLocation()
if pmr_location and not len(local_dir):
# Get login details:
local_dir = os.path.join(self._location, self._state.identifier())
if not os.path.exists(local_dir):
os.mkdir(local_dir)
self._state.setLocation(local_dir)
d.setState(self._state)
if pmr_location and os.path.exists(local_dir):
pmr_tool = PMRTool()
pmr_tool.cloneWorkspace(pmr_location, local_dir)
self._configured = d.validate()
if self._configuredObserver is not None:
self._configuredObserver()
def test_make_session_no_access(self):
pmr_info = PMR()
tool = PMRTool(pmr_info)
session = tool.make_session()
self.assertFalse(isinstance(session, OAuth1Session))
# Make sure this really is a requests.Session
self.assertTrue(isinstance(session, Session))
class SearchWidget(QtWidgets.QWidget):
def __init__(self, parent=None):
super(SearchWidget, self).__init__(parent)
self._ui = Ui_SearchWidget()
self._ui.setupUi(self)
pmr_info = PMR()
self._pmrTool = PMRTool(pmr_info)
self._annotationTool = AnnotationTool()
self._makeConnections()
def setPMRInfo(self, info):
self._pmrTool.set_info(info)
def setUseExternalGit(self, use_external_git):
self._pmrTool.set_use_external_git(use_external_git)
def _makeConnections(self):
self._ui.searchButton.clicked.connect(self._searchClicked)
self._ui.searchResultsListWidget.itemClicked.connect(self._itemClicked)
def _itemClicked(self, item):
data = item.data(QtCore.Qt.UserRole)
if 'target' in data:
self._ui.targetEdit.setText(data['target'])
@handle_runtime_error
@set_wait_cursor
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 = QtWidgets.QListWidgetItem(r['title'], self._ui.searchResultsListWidget)
else:
item = QtWidgets.QListWidgetItem(r['target'], self._ui.searchResultsListWidget)
item.setData(QtCore.Qt.UserRole, r)
except PMRToolError as e:
message = convertExceptionToMessage(e)
logger.warning('PMR Tool exception raised')
logger.warning('Reason: {0}'.format(message))
def getSelectedWorkspace(self):
items = self._ui.searchResultsListWidget.selectedItems()
for item in items:
return item.data(QtCore.Qt.UserRole)
def _updateFromPMR(self):
m = self._main_window.model().workflowManager()
om = self._main_window.model().optionsManager()
pmr_info = PMR()
pmr_tool = PMRTool(pmr_info, use_external_git=om.getOption(USE_EXTERNAL_GIT))
pmr_tool.pullFromRemote(m.location())
def configure(self):
d = ConfigureDialog(self._state, QtGui.QApplication.activeWindow().currentWidget())
d.setWorkflowLocation(self._location)
d.setModal(True)
if d.exec_():
self._state = d.getState()
# When a PMR location is given we need to translate that into a
# local path for passing into the ImageSourceData class
local_dir = self._state.location()
pmr_location = self._state.pmrLocation()
if pmr_location and not len(local_dir):
# Get login details:
local_dir = self._location
if not os.path.exists(local_dir):
os.mkdir(local_dir)
self._state.setLocation(local_dir)
d.setState(self._state)
if pmr_location and os.path.exists(local_dir):
pmr_info = PMR()
pmr_tool = PMRTool(pmr_info)
pmr_tool.cloneWorkspace(pmr_location, local_dir)
self._configured = d.validate()
if self._configuredObserver is not None:
self._configuredObserver()
def test_make_session_with_access(self):
tool = PMRTool()
info = PMRInfo()
info.update_token('test', 'token')
session = tool.make_session()
self.assertTrue(isinstance(session, OAuth1Session))
info.update_token('', '')
def __init__(self, use_external_git, parent=None):
super(PMRWorkflowWidget, self).__init__(parent)
self._ui = Ui_PMRWorkflowWidget()
self._ui.setupUi(self)
pmr_info = PMR()
self._pmrTool = PMRTool(pmr_info, use_external_git)
self._termLookUpLimit = 32
self._timer = QtCore.QTimer()
self._timer.setInterval(500)
self._busy_waiting = False
self._ontological_search = False
word_list = ['pending ...']
self._list_model = OWLTermsListModel(word_list)
# self._client = Client(site=pmr_target, use_default_headers=True)
self._makeConnections()
self._ui.comboBoxSearch.clear()
self._ui.comboBoxSearch.addItems(search_domains)
self._updateUi()
def test_make_session_with_access(self):
pmr_info = PMR()
tool = PMRTool(pmr_info)
info = PMR()
info.update_token('test', 'token')
session = tool.make_session()
self.assertTrue(isinstance(session, OAuth1Session))
info.update_token('', '')
def _cloneFromPMR(self, workspace_url, workflowDir):
om = self._main_window.model().optionsManager()
pmr_info = PMR()
pmr_tool = PMRTool(pmr_info, use_external_git=om.getOption(USE_EXTERNAL_GIT))
pmr_tool.cloneWorkspace(
remote_workspace_url=workspace_url,
local_workspace_dir=workflowDir,
)
def commitChanges(self, workflowDir):
om = self._main_window.model().optionsManager()
pmr_info = PMR()
pmr_tool = PMRTool(pmr_info, use_external_git=om.getOption(USE_EXTERNAL_GIT))
if not pmr_tool.hasDVCS(workflowDir):
# nothing to commit.
return True
return self._commitChanges(workflowDir, 'Workflow saved.')
def __init__(self, parent=None):
super(SearchWidget, self).__init__(parent)
self._ui = Ui_SearchWidget()
self._ui.setupUi(self)
pmr_info = PMR()
self._pmrTool = PMRTool(pmr_info)
self._annotationTool = AnnotationTool()
self._makeConnections()
def _setIndexerFile(self, workflow_dir):
pmr_tool = PMRTool()
if not pmr_tool.hasDVCS(workflow_dir):
return
try:
pmr_tool.addFileToIndexer(workflow_dir, DEFAULT_WORKFLOW_ANNOTATION_FILENAME)
# pmr_tool.commitFiles(local_workspace_dir, message, files)
except ClientRuntimeError:
# handler will deal with this.
raise
def __init__(self, external_git, parent=None):
super(PMRRegisterDialog, self).__init__(parent)
self._ui = Ui_RegisterDialog()
self._ui.setupUi(self)
pmr_info = PMR()
self._pmr_tool = PMRTool(pmr_info, external_git)
self._makeConnections()
self._updateUi()
def make_tool(self, endpoints=None):
if endpoints is None:
endpoints = self.endpoints
def make_session(pmr_info=None):
session = TestSession()
for url, adapter in endpoints:
session.mount(url, adapter)
return session
tool = PMRTool()
tool.make_session = make_session
return tool
def __init__(self, parent=None):
QtGui.QDialog.__init__(self, parent)
self._ui = Ui_PMRSearchDialog()
self._ui.setupUi(self)
pmr_info = PMR()
self._pmrTool = PMRTool(pmr_info)
self._annotationTool = AnnotationTool()
self._makeConnections()
self._updateUi()
def __init__(self, parent=None):
super(SettingsWidget, self).__init__(parent)
self._ui = Ui_SettingsWidget()
self._ui.setupUi(self)
self._pmr_tool = PMRTool()
self._model = QtGui.QStandardItemModel()
self._updateModel()
self._ui.hostListView.setModel(self._model)
self._updateUi()
self._makeConnections()
def _setIndexerFile(self, workflow_dir):
om = self._main_window.model().optionsManager()
pmr_info = PMR()
pmr_tool = PMRTool(pmr_info, use_external_git=om.getOption(USE_EXTERNAL_GIT))
if not pmr_tool.hasDVCS(workflow_dir):
return
try:
pmr_tool.addFileToIndexer(workflow_dir, DEFAULT_WORKFLOW_ANNOTATION_FILENAME)
# pmr_tool.commitFiles(local_workspace_dir, message, files)
except ClientRuntimeError:
# handler will deal with this.
raise
def __init__(self, use_external_git, parent=None):
super(PMRDialog, self).__init__(parent)
self._ui = Ui_PMRDialog()
self._ui.setupUi(self)
self._ui.searchWidget.setUseExternalGit(use_external_git)
self._ui.settingsWidget.setUseExternalGit(use_external_git)
pmr_info = PMR()
self._pmr_tool = PMRTool(pmr_info, use_external_git)
self._makeConnections()
self._updateUi()
def make_tool(self, endpoints=None):
if endpoints is None:
endpoints = self.endpoints
def make_session(pmr_info=None):
session = TestSession()
for url, adapter in endpoints:
session.mount(url, adapter)
return session
pmr_info = PMR()
tool = PMRTool(pmr_info)
tool.make_session = make_session
return tool
def test_hasAccess(self):
# update tokens using another instance
info = PMRInfo()
t = PMRTool()
# Fresh token should have no access
self.assertFalse(t.hasAccess())
info.update_token('test', 'token')
# Now it's true
self.assertTrue(t.hasAccess())
# revoke access again.
info.update_token('', '')
# Now it's false again.
self.assertFalse(t.hasAccess())
def __init__(self, parent=None):
'''
Constructor
'''
super(PMRWorkflowWidget, self).__init__(parent)
self._ui = Ui_PMRWorkflowWidget()
self._ui.setupUi(self)
self._pmrTool = PMRTool()
self._termLookUpLimit = 32
self._timer = QtCore.QTimer()
self._timer.setInterval(500)
self._busy_waiting = False
self._ontological_search = False
word_list = ['pending ...']
self._list_model = OWLTermsListModel(word_list)
# self._client = Client(site=pmr_target, use_default_headers=True)
self._makeConnections()
self._ui.comboBoxSearch.clear()
self._ui.comboBoxSearch.addItems(search_domains)
self._updateUi()
def test_hasAccess(self):
# update tokens using another instance
info = PMR()
t = PMRTool(info)
# Fresh token should have no access
self.assertFalse(t.hasAccess())
info.update_token('test', 'token')
# Now it's true
self.assertTrue(t.hasAccess())
# revoke access again.
info.update_token('', '')
# Now it's false again.
self.assertFalse(t.hasAccess())
def _importFromPMR(self, workspace_url, workflowDir):
pmr_tool = PMRTool()
pmr_tool.cloneWorkspace(
remote_workspace_url=workspace_url,
local_workspace_dir=workflowDir,
)
logger.info('Analyze first before attempting load ...')
try:
m = self._mainWindow.model().workflowManager()
m.load(workflowDir)
m.setPreviousLocation(workflowDir)
self._graphicsScene.updateModel()
self._updateUi()
except:
self.close()
raise
def commitChanges(self, workflowDir):
pmr_tool = PMRTool()
if not pmr_tool.hasDVCS(workflowDir):
# nothing to commit.
return True
dlg = PMRHgCommitDialog(self)
dlg.setModal(True)
if dlg.exec_() == QtGui.QDialog.Rejected:
return False
action = dlg.action()
if action == QtGui.QDialogButtonBox.Ok:
return True
elif action == QtGui.QDialogButtonBox.Save:
return self._commitChanges(workflowDir, dlg.comment(), commit_local=True)
return self._commitChanges(workflowDir, dlg.comment())
class PMRDialog(QtGui.QDialog):
def __init__(self, use_external_git, parent=None):
super(PMRDialog, self).__init__(parent)
self._ui = Ui_PMRDialog()
self._ui.setupUi(self)
self._ui.searchWidget.setUseExternalGit(use_external_git)
self._ui.settingsWidget.setUseExternalGit(use_external_git)
pmr_info = PMR()
self._pmr_tool = PMRTool(pmr_info, use_external_git)
self._makeConnections()
self._updateUi()
def accept(self, *args, **kwargs):
self._ui.settingsWidget.transferModel()
return QtGui.QDialog.accept(self, *args, **kwargs)
def _updateUi(self):
pmr_info = PMR()
self._pmr_tool.set_info(pmr_info)
if self._pmr_tool.isActive():
if self._pmr_tool.hasAccess():
self._ui.loginStackedWidget.setCurrentIndex(1)
else:
self._ui.loginStackedWidget.setCurrentIndex(0)
else:
self._ui.loginStackedWidget.setCurrentIndex(2)
def _makeConnections(self):
self._ui.registerLabel.linkActivated.connect(self.register)
self._ui.deregisterLabel.linkActivated.connect(self.deregister)
self._ui.settingsWidget.hostChanged.connect(self._hostChanged)
def _hostChanged(self, index):
self._updateUi()
def register(self, link):
if link != 'mapclient.register':
return
dlg = AuthoriseApplicationDialog(self)
dlg.setModal(True)
dlg.exec_()
self._updateUi()
def deregister(self):
pmr_info = PMR()
self._pmr_tool.set_info(pmr_info)
self._pmr_tool.deregister()
self._updateUi()
def _commitChanges(self, workflowDir, comment, commit_local=False):
committed_changes = False
pmr_tool = PMRTool()
try:
pmr_tool.commitFiles(workflowDir, comment,
[workflowDir + '/%s' % (DEFAULT_WORKFLOW_PROJECT_FILENAME),
workflowDir + '/%s' % (DEFAULT_WORKFLOW_ANNOTATION_FILENAME)]) # XXX make/use file tracker
if not commit_local:
pmr_tool.pushToRemote(workflowDir)
committed_changes = True
except ClientRuntimeError:
# handler will deal with this.
raise
except Exception:
logger.exception('Error')
raise ClientRuntimeError(
'Error Saving', 'The commit to PMR did not succeed')
return committed_changes
def _createNewWorkflow(self, workflow_dir, pmr):
m = self._main_window.model().workflowManager()
om = self._main_window.model().optionsManager()
m.new(workflow_dir)
m.setPreviousLocation(workflow_dir)
if pmr:
pmr_info = PMR()
pmr_tool = PMRTool(pmr_info, use_external_git=om.getOption(USE_EXTERNAL_GIT))
if pmr_tool.hasAccess():
dir_name = os.path.basename(workflow_dir)
try:
repourl = pmr_tool.addWorkspace('Workflow: ' + dir_name, None)
pmr_tool.linkWorkspaceDirToUrl(workflow_dir, repourl)
except HTTPError as e:
logger.exception('Error creating new')
self.close()
raise ClientRuntimeError(
'Error Creating New', e)
else:
raise ClientRuntimeError('Error Creating New', "Client doesn't have access to PMR")
self._undoStack.clear()
self._ui.graphicsView.setLocation(workflow_dir)
self._graphicsScene.updateModel()
self._update_ui()
def _commitChanges(self, workflowDir, comment, commit_local=False):
committed_changes = False
om = self._main_window.model().optionsManager()
pmr_info = PMR()
pmr_tool = PMRTool(pmr_info, use_external_git=om.getOption(USE_EXTERNAL_GIT))
try:
workflow_files = [workflowDir + '/%s' % (DEFAULT_WORKFLOW_PROJECT_FILENAME),
workflowDir + '/%s' % (DEFAULT_WORKFLOW_ANNOTATION_FILENAME)]
for f in os.listdir(workflowDir):
if f.endswith(".conf"):
full_filename = os.path.join(workflowDir, f)
if full_filename not in workflow_files:
workflow_files.append(full_filename)
pmr_tool.commitFiles(workflowDir, comment, workflow_files)
# [workflowDir + '/%s' % (DEFAULT_WORKFLOW_PROJECT_FILENAME),
# workflowDir + '/%s' % (DEFAULT_WORKFLOW_ANNOTATION_FILENAME)]) # XXX make/use file tracker
if not commit_local:
pmr_tool.pushToRemote(workflowDir)
committed_changes = True
except ClientRuntimeError:
# handler will deal with this.
raise
except Exception:
logger.exception('Error')
raise ClientRuntimeError(
'Error Saving', 'The commit to PMR did not succeed')
return committed_changes
class PMRRegisterDialog(QtGui.QDialog):
def __init__(self, external_git, parent=None):
super(PMRRegisterDialog, self).__init__(parent)
self._ui = Ui_RegisterDialog()
self._ui.setupUi(self)
pmr_info = PMR()
self._pmr_tool = PMRTool(pmr_info, external_git)
self._makeConnections()
self._updateUi()
def _updateUi(self):
pmr_info = PMR()
self._pmr_tool.set_info(pmr_info)
if self._pmr_tool.isActive():
self._ui.pushButtonRegister.setEnabled(True)
if self._pmr_tool.hasAccess():
self._ui.stackedWidgetRegister.setCurrentIndex(1)
else:
self._ui.stackedWidgetRegister.setCurrentIndex(0)
else:
self._ui.pushButtonRegister.setEnabled(False)
self._ui.stackedWidgetRegister.setCurrentIndex(0)
def _makeConnections(self):
self._ui.pushButtonRegister.clicked.connect(self._register)
self._ui.pushButtonDeregister.clicked.connect(self._deregister)
self._ui.settingsWidget.hostChanged.connect(self._hostChanged)
def _register(self):
dlg = AuthoriseApplicationDialog(self)
dlg.setModal(True)
dlg.exec_()
self._updateUi()
def _deregister(self):
pmr_info = PMR()
self._pmr_tool.set_info(pmr_info)
self._pmr_tool.deregister()
self._updateUi()
def _hostChanged(self, index):
self._updateUi()
def accept(self, *args, **kwargs):
self._ui.settingsWidget.transferModel()
return QtGui.QDialog.accept(self, *args, **kwargs)
def __init__(self, parent=None):
"""
Constructor
"""
QtGui.QDialog.__init__(self, parent)
self._ui = Ui_PMRSearchDialog()
self._ui.setupUi(self)
self._pmrTool = PMRTool()
self._annotationTool = AnnotationTool()
self._makeConnections()
self._updateUi()
def _createNewWorkflow(self, workflowDir, pmr):
m = self._mainWindow.model().workflowManager()
m.new(workflowDir)
m.setPreviousLocation(workflowDir)
if pmr:
pmr_tool = PMRTool()
if pmr_tool.hasAccess():
dir_name = os.path.basename(workflowDir)
try:
repourl = pmr_tool.addWorkspace('Workflow: ' + dir_name, None)
pmr_tool.linkWorkspaceDirToUrl(workflowDir, repourl)
except HTTPError as e:
logger.exception('Error creating new')
self.close()
raise ClientRuntimeError(
'Error Creating New', e.message)
else:
raise ClientRuntimeError('Error Creating New', "Client doesn't have access to PMR")
self._undoStack.clear()
self._ui.graphicsView.setLocation(workflowDir)
self._graphicsScene.updateModel()
self._updateUi()
class PMRSearchDialog(QtGui.QDialog):
"""
Dialog for managing interaction with PMR.
"""
def __init__(self, parent=None):
QtGui.QDialog.__init__(self, parent)
self._ui = Ui_PMRSearchDialog()
self._ui.setupUi(self)
pmr_info = PMR()
self._pmrTool = PMRTool(pmr_info)
self._annotationTool = AnnotationTool()
self._makeConnections()
self._updateUi()
def _updateUi(self):
if self._pmrTool.hasAccess():
self._ui.loginStackedWidget.setCurrentIndex(1)
else:
self._ui.loginStackedWidget.setCurrentIndex(0)
def _makeConnections(self):
self._ui.searchButton.clicked.connect(self._searchClicked)
self._ui.registerLabel.linkActivated.connect(self.register)
self._ui.deregisterLabel.linkActivated.connect(self.deregister)
@handle_runtime_error
@set_wait_cursor
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 getSelectedWorkspace(self):
items = self._ui.searchResultsListWidget.selectedItems()
for item in items:
return item.data(QtCore.Qt.UserRole)
def register(self, link):
if link != 'mapclient.register':
return
dlg = AuthoriseApplicationDialog(self)
dlg.setModal(True)
dlg.exec_()
self._updateUi()
def deregister(self):
self._pmrTool.deregister()
self._updateUi()
class PMRWorkflowWidget(QtGui.QWidget):
"""
A Widget for importing and exporting to and from PMR.
"""
def __init__(self, use_external_git, parent=None):
super(PMRWorkflowWidget, self).__init__(parent)
self._ui = Ui_PMRWorkflowWidget()
self._ui.setupUi(self)
pmr_info = PMR()
self._pmrTool = PMRTool(pmr_info, use_external_git)
self._termLookUpLimit = 32
self._timer = QtCore.QTimer()
self._timer.setInterval(500)
self._busy_waiting = False
self._ontological_search = False
word_list = ['pending ...']
self._list_model = OWLTermsListModel(word_list)
# self._client = Client(site=pmr_target, use_default_headers=True)
self._makeConnections()
self._ui.comboBoxSearch.clear()
self._ui.comboBoxSearch.addItems(search_domains)
self._updateUi()
def _updateUi(self):
if self._pmrTool.hasAccess():
self._ui.labelLink.setText('<a href="mapclient.deregister">deregister</a>')
else:
self._ui.labelLink.setText('<a href="mapclient.register">register</a>')
def _makeConnections(self):
self._ui.pushButtonSearch.clicked.connect(self._searchClicked)
self._ui.pushButtonImport.clicked.connect(self._importClicked)
self._ui.pushButtonExport.clicked.connect(self._exportClicked)
self._ui.labelLink.linkActivated.connect(self._linkActivated)
self._ui.listWidgetResults.itemClicked.connect(self._searchResultClicked)
self._ui.lineEditSearch.textEdited.connect(self._searchTextEdited)
self._timer.timeout.connect(self._queryRepository)
self._ui.comboBoxSearch.currentIndexChanged.connect(self._searchTypeChanged)
def _initialiseCompleter(self):
completer = QtGui.QCompleter(self._ui.lineEditSearch)
completer.setCompletionMode(QtGui.QCompleter.UnfilteredPopupCompletion)
completer.setCaseSensitivity(QtCore.Qt.CaseInsensitive)
completer.setModel(self._list_model)
completer.setCompletionColumn(0)
completer.setCompletionRole(QtCore.Qt.DisplayRole)
return completer
def _searchTypeChanged(self, index):
text = self._ui.comboBoxSearch.currentText()
if text == ontological_search_string:
self._ontological_search = True
completer = self._initialiseCompleter()
self._ui.lineEditSearch.setCompleter(completer)
else:
self._ontological_search = False
self._ui.lineEditSearch.setCompleter(None)
def _searchTextEdited(self, new_text):
if self._ontological_search and len(new_text) and not self._busy_waiting:
if self._timer.isActive():
QtGui.QApplication.restoreOverrideCursor()
QtGui.QApplication.setOverrideCursor(QtCore.Qt.WaitCursor)
self._timer.start()
def _queryRepository(self):
self._timer.stop()
self._busy_waiting = True
search_text = self._ui.lineEditSearch.text()
pmr_target = general.PMR().host()
target = pmr_target + '/pmr2_ricordo/owlterms' + '/%s/%d' % (search_text, self._termLookUpLimit)
client = Client(site=pmr_target, use_default_headers=True)
state = client(target=target) # , data=json.dumps({'actions': {'search': 1}, 'fields': {'simple_query': 'femur'}})) # , endpoint='ricordo', data='femur')
response = state.value()
descriptions = ['%s [%s]' % (line[0], line[1].split('#')[-1]) for line in response['results']]
self._list_model.removeRows(0, self._list_model.rowCount())
self._list_model.insertRows(0, len(descriptions), descriptions)
self._busy_waiting = False
def _searchResultClicked(self, item):
r = item.data(QtCore.Qt.UserRole)
if 'source' in r:
self._ui.lineEditWorkspace.setText(r['source'])
elif 'href' in r:
self._ui.lineEditWorkspace.setText(r['href'])
def _linkActivated(self, link):
if link == 'mapclient.register':
dlg = AuthoriseApplicationDialog(self)
dlg.setModal(True)
dlg.exec_()
self._updateUi()
elif link == 'mapclient.deregister':
self._pmrTool.deregister()
self._updateUi()
def _searchClicked(self):
self._doSearch(self._ui.comboBoxSearch.currentText())
def _importClicked(self):
pass
def _exportClicked(self):
pass
def setSearchDomain(self, domain=['all', ]):
self._domain = []
if type(domain) is not list:
domain = [domain]
if len(domain) and domain[0] == 'all':
domain = search_domains
for subdomain in domain:
if subdomain in search_domains:
self._domain.append(subdomain)
if len(self._domain):
self._ui.comboBoxSearch.clear()
for subdomain in self._domain:
self._ui.comboBoxSearch.addItem(subdomain)
def setExport(self, visible=True):
if visible:
self._ui.pushButtonExport.show()
else:
self._ui.pushButtonExport.hide()
def setImport(self, visible=True):
if visible:
self._ui.pushButtonImport.show()
else:
self._ui.pushButtonImport.hide()
def workspaceUrl(self):
return self._ui.lineEditWorkspace.text()
def setWorkspaceUrl(self, url):
self._ui.lineEditWorkspace.setText(url)
@handle_runtime_error
@set_wait_cursor
def _doSearch(self, search_type):
# Set pmrlib to go
self._ui.listWidgetResults.clear()
# fix up known terms to be full blown uri
search_text = self._ui.lineEditSearch.text()
if True:
search_text = self._ui.lineEditSearch.text()
label_re = re.compile('\[([\w_\d]+)\]')
re_result = label_re.search(search_text)
if re_result:
search_text = re_result.group(1)
# search_terms = search_text.split()
# for term in search_terms:
# rdfterm = self._annotationTool.rdfFormOfTerm(term)
# if rdfterm:
# search_text = search_text + ' ' + rdfterm[1:-1]
results = self._pmrTool.search(search_text, search_type)
if search_type == workflow_search_string:
results_list = results['results']
for r in results_list:
item = QtGui.QListWidgetItem(r['obj']['title'], self._ui.listWidgetResults)
item.setData(QtCore.Qt.UserRole, r)
elif search_type == ontological_search_string:
if type(results) is dict:
return
for r in results:
label = r['label']
for sr in r['items']:
item = QtGui.QListWidgetItem(sr['title'] + ' [%s, %s]' % (sr['value'], label), self._ui.listWidgetResults)
tool_tip = 'Workspace title: %s, Ontological term: %s, Target: %s' % (sr['title'], label, sr['href'])
item.setToolTip(tool_tip)
item.setData(QtCore.Qt.UserRole, sr)
else:
for r in results:
if 'title' in r and r['title']:
item = QtGui.QListWidgetItem(r['title'], self._ui.listWidgetResults)
else:
item = QtGui.QListWidgetItem(r['target'], self._ui.listWidgetResults)
item.setData(QtCore.Qt.UserRole, r)
class SettingsWidget(QtGui.QWidget):
hostChanged = QtCore.Signal(int)
def __init__(self, parent=None):
super(SettingsWidget, self).__init__(parent)
self._ui = Ui_SettingsWidget()
self._ui.setupUi(self)
self._pmr_tool = PMRTool()
self._model = QtGui.QStandardItemModel()
self._updateModel()
self._ui.hostListView.setModel(self._model)
self._updateUi()
self._makeConnections()
def _makeConnections(self):
self._ui.addPushButton.clicked.connect(self._addClicked)
self._ui.removePushButton.clicked.connect(self._removeClicked)
self._ui.hostListView.clicked.connect(
self._updateUi
) # We are making clicking to be synonymous with selecting, OK I think for single selection mode
self._ui.hostListView.addAction(self._ui.actionAddHost)
self._ui.actionAddHost.triggered.connect(self._addClicked)
self._model.itemChanged.connect(self._hostChanged)
def _updateUi(self):
self._ui.removePushButton.setEnabled(
len(self._ui.hostListView.selectedIndexes()))
def _updateModel(self):
pmr_info = PMR()
for instance in pmr_info.hosts():
self.addHost(instance, instance == pmr_info.activeHost())
def setUseExternalGit(self, use_external_git):
self._pmr_tool.set_use_external_git(use_external_git)
def transferModel(self):
"""
Transfer the current status of the model into the PMR
information object.
"""
pmr_info = PMR()
hosts = pmr_info.hosts()
host_names_remove = [name for name in hosts]
host_names_new = []
active_host = None
index = 0
current_item = self._model.item(index)
while current_item:
current_host = current_item.text()
if current_host in host_names_remove:
host_names_remove.remove(current_host)
else:
host_names_new.append(current_host)
if current_item.checkState() == QtCore.Qt.Checked:
active_host = current_host
index += 1
current_item = self._model.item(index)
pmr_info.setActiveHost(active_host)
for host in host_names_remove:
pmr_info.removeHost(host)
for host in host_names_new:
pmr_info.addHost(host)
def _addClicked(self):
dlg = AddHostDialog(self)
dlg.setModal(True)
if dlg.exec_():
self.addHost(dlg.getHost())
def _removeClicked(self):
indexes = self._ui.hostListView.selectedIndexes()
rm_index = indexes.pop()
item = self._model.itemFromIndex(rm_index)
pmr_info = PMR()
pmr_info.removeHost(item.text())
self._model.removeRow(rm_index.row())
# item = self._model.takeItem(rm_index.row())
def _whichHostChecked(self):
index = 0
current_item = self._model.item(index)
while current_item:
if current_item.checkState():
return index
index += 1
current_item = self._model.item(index)
return -1
def _hostChanged(self, item):
pmr_info = PMR()
if not item.checkState():
pmr_info.setActiveHost(None)
self.hostChanged.emit(item.row())
return
index = 0
current_item = self._model.item(index)
self.blockSignals(True)
while current_item:
if current_item.checkState() and (current_item.row() !=
item.row()):
current_item.setCheckState(QtCore.Qt.Unchecked)
index += 1
current_item = self._model.item(index)
self.blockSignals(False)
pmr_info.setActiveHost(item.text())
self.hostChanged.emit(item.row())
@handle_runtime_error
@set_wait_cursor
def addHost(self, host, active=False):
try:
# Look for duplicates
host_item = QtGui.QStandardItem(host)
same_items = self._model.findItems(host)
if len(same_items):
raise Exception('Host "{0}" already exists'.format(host))
if self._pmr_tool.isValidHost(host):
host_item.setCheckable(True)
host_item.setCheckState(
QtCore.Qt.Checked if active else QtCore.Qt.Unchecked)
self._model.appendRow(host_item)
except Exception as e:
raise ClientRuntimeError('Error Adding Host', str(e))
class PMRWorkflowWidget(QtGui.QWidget):
'''
A Widget for importing and exporting to and from PMR.
'''
def __init__(self, parent=None):
'''
Constructor
'''
super(PMRWorkflowWidget, self).__init__(parent)
self._ui = Ui_PMRWorkflowWidget()
self._ui.setupUi(self)
self._pmrTool = PMRTool()
self._termLookUpLimit = 32
self._timer = QtCore.QTimer()
self._timer.setInterval(500)
self._busy_waiting = False
self._ontological_search = False
word_list = ['pending ...']
self._list_model = OWLTermsListModel(word_list)
# self._client = Client(site=pmr_target, use_default_headers=True)
self._makeConnections()
self._ui.comboBoxSearch.clear()
self._ui.comboBoxSearch.addItems(search_domains)
self._updateUi()
def _updateUi(self):
if self._pmrTool.hasAccess():
self._ui.labelLink.setText('<a href="mapclient.deregister">deregister</a>')
else:
self._ui.labelLink.setText('<a href="mapclient.register">register</a>')
def _makeConnections(self):
self._ui.pushButtonSearch.clicked.connect(self._searchClicked)
self._ui.pushButtonImport.clicked.connect(self._importClicked)
self._ui.pushButtonExport.clicked.connect(self._exportClicked)
self._ui.labelLink.linkActivated.connect(self._linkActivated)
self._ui.listWidgetResults.itemClicked.connect(self._searchResultClicked)
self._ui.lineEditSearch.textEdited.connect(self._searchTextEdited)
self._timer.timeout.connect(self._queryRepository)
self._ui.comboBoxSearch.currentIndexChanged.connect(self._searchTypeChanged)
def _initialiseCompleter(self):
completer = QtGui.QCompleter(self._ui.lineEditSearch)
completer.setCompletionMode(QtGui.QCompleter.UnfilteredPopupCompletion)
completer.setCaseSensitivity(QtCore.Qt.CaseInsensitive)
completer.setModel(self._list_model)
completer.setCompletionColumn(0)
completer.setCompletionRole(QtCore.Qt.DisplayRole)
return completer
def _searchTypeChanged(self, index):
text = self._ui.comboBoxSearch.currentText()
if text == ontological_search_string:
self._ontological_search = True
completer = self._initialiseCompleter()
self._ui.lineEditSearch.setCompleter(completer)
else:
self._ontological_search = False
self._ui.lineEditSearch.setCompleter(None)
def _searchTextEdited(self, new_text):
if self._ontological_search and len(new_text) and not self._busy_waiting:
if self._timer.isActive():
QtGui.QApplication.restoreOverrideCursor()
QtGui.QApplication.setOverrideCursor(QtCore.Qt.WaitCursor)
self._timer.start()
def _queryRepository(self):
self._timer.stop()
self._busy_waiting = True
search_text = self._ui.lineEditSearch.text()
pmr_target = info.PMRInfo().ipaddress
target = pmr_target + '/pmr2_ricordo/owlterms' + '/%s/%d' % (search_text, self._termLookUpLimit)
client = Client(site=pmr_target, use_default_headers=True)
state = client(target=target) # , data=json.dumps({'actions': {'search': 1}, 'fields': {'simple_query': 'femur'}})) # , endpoint='ricordo', data='femur')
response = state.value()
descriptions = ['%s [%s]' % (line[0], line[1].split('#')[-1]) for line in response['results']]
self._list_model.removeRows(0, self._list_model.rowCount())
self._list_model.insertRows(0, len(descriptions), descriptions)
self._busy_waiting = False
QtGui.QApplication.restoreOverrideCursor()
def _searchResultClicked(self, item):
r = item.data(QtCore.Qt.UserRole)
if 'source' in r:
self._ui.lineEditWorkspace.setText(r['source'])
elif 'href' in r:
self._ui.lineEditWorkspace.setText(r['href'])
def _linkActivated(self, link):
if link == 'mapclient.register':
dlg = AuthoriseApplicationDialog(self)
dlg.setModal(True)
dlg.exec_()
self._updateUi()
elif link == 'mapclient.deregister':
self._pmrTool.deregister()
self._updateUi()
def _searchClicked(self):
self._doSearch(self._ui.comboBoxSearch.currentText())
def _importClicked(self):
pass
def _exportClicked(self):
pass
def setSearchDomain(self, domain=['all', ]):
self._domain = []
if type(domain) is not list:
domain = [domain]
if len(domain) and domain[0] == 'all':
domain = search_domains
for subdomain in domain:
if subdomain in search_domains:
self._domain.append(subdomain)
if len(self._domain):
self._ui.comboBoxSearch.clear()
for subdomain in self._domain:
self._ui.comboBoxSearch.addItem(subdomain)
def setExport(self, visible=True):
if visible:
self._ui.pushButtonExport.show()
else:
self._ui.pushButtonExport.hide()
def setImport(self, visible=True):
if visible:
self._ui.pushButtonImport.show()
else:
self._ui.pushButtonImport.hide()
def workspaceUrl(self):
return self._ui.lineEditWorkspace.text()
def setWorkspaceUrl(self, url):
self._ui.lineEditWorkspace.setText(url)
@handle_runtime_error
@set_wait_cursor
def _doSearch(self, search_type):
# Set pmrlib to go
self._ui.listWidgetResults.clear()
# fix up known terms to be full blown uri
search_text = self._ui.lineEditSearch.text()
if True:
search_text = self._ui.lineEditSearch.text()
label_re = re.compile('\[([\w_\d]+)\]')
re_result = label_re.search(search_text)
if re_result:
search_text = re_result.group(1)
# search_terms = search_text.split()
# for term in search_terms:
# rdfterm = self._annotationTool.rdfFormOfTerm(term)
# if rdfterm:
# search_text = search_text + ' ' + rdfterm[1:-1]
results = self._pmrTool.search(search_text, search_type)
if search_type == workflow_search_string:
results_list = results['results']
for r in results_list:
item = QtGui.QListWidgetItem(r['obj']['title'], self._ui.listWidgetResults)
item.setData(QtCore.Qt.UserRole, r)
elif search_type == ontological_search_string:
if type(results) is dict:
return
for r in results:
label = r['label']
for sr in r['items']:
item = QtGui.QListWidgetItem(sr['title'] + ' [%s, %s]' % (sr['value'], label), self._ui.listWidgetResults)
tool_tip = 'Workspace title: %s, Ontological term: %s, Target: %s' % (sr['title'], label, sr['href'])
item.setToolTip(tool_tip)
item.setData(QtCore.Qt.UserRole, sr)
else:
for r in results:
if 'title' in r and r['title']:
item = QtGui.QListWidgetItem(r['title'], self._ui.listWidgetResults)
else:
item = QtGui.QListWidgetItem(r['target'], self._ui.listWidgetResults)
item.setData(QtCore.Qt.UserRole, r)
class PMRSearchDialog(QtGui.QDialog):
"""
Dialog for managing interaction with PMR.
"""
def __init__(self, parent=None):
"""
Constructor
"""
QtGui.QDialog.__init__(self, parent)
self._ui = Ui_PMRSearchDialog()
self._ui.setupUi(self)
self._pmrTool = PMRTool()
self._annotationTool = AnnotationTool()
self._makeConnections()
self._updateUi()
def _updateUi(self):
if self._pmrTool.hasAccess():
self._ui.loginStackedWidget.setCurrentIndex(1)
else:
self._ui.loginStackedWidget.setCurrentIndex(0)
def _makeConnections(self):
self._ui.searchButton.clicked.connect(self._searchClicked)
self._ui.registerLabel.linkActivated.connect(self.register)
self._ui.deregisterLabel.linkActivated.connect(self.deregister)
@handle_runtime_error
@set_wait_cursor
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]
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)
def getSelectedWorkspace(self):
items = self._ui.searchResultsListWidget.selectedItems()
for item in items:
return item.data(QtCore.Qt.UserRole)
def register(self, link):
if link != "mapclient.register":
return
dlg = AuthoriseApplicationDialog(self)
dlg.setModal(True)
dlg.exec_()
self._updateUi()
def deregister(self):
self._pmrTool.deregister()
self._updateUi()
def test_make_session_no_access(self):
tool = PMRTool()
session = tool.make_session()
self.assertFalse(isinstance(session, OAuth1Session))
# Make sure this really is a requests.Session
self.assertTrue(isinstance(session, Session))