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()
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)
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, 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 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 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()
