def populate_widget(self):
settings = Settings()
# Update prefix
prefix = settings.value("DB_NEW_REACT_PREFIX", DB_NEW_REACT_PREFIX)
self.lineEdit_prefix.setText(prefix)
# Update checkbox
name_setting = settings.value("DB_GET_REACT_NAME", DB_GET_REACT_NAME)
self.checkBox_use_name.setChecked(convert_to_bool(name_setting))
def store_settings(self):
settings = Settings()
settings.setValue("DB_NEW_MET_PREFIX", self.lineEdit_prefix.text())
settings.setValue("DB_GET_MET_NAME",
self.checkBox_use_name.isChecked())
settings.setValue("DB_GET_FL_AND_CH",
self.checkBox_use_formula.isChecked())
settings.sync()
def populate_widget(self):
settings = Settings()
# Update prefix
prefix = settings.value("DB_NEW_MET_PREFIX", DB_NEW_MET_PREFIX)
self.lineEdit_prefix.setText(prefix)
# Update checkbox
name_setting = settings.value("DB_GET_MET_NAME", DB_GET_MET_NAME)
self.checkBox_use_name.setChecked(convert_to_bool(name_setting))
formula_charge_setting = settings.value("DB_GET_FL_AND_CH",
DB_GET_FL_AND_CH)
self.checkBox_use_formula.setChecked(
convert_to_bool(formula_charge_setting))
def __init__(self, parent):
QDialog.__init__(self, parent)
self.setupUi(self)
# Setup the email field with current value
self.settings = Settings()
self.eMailLineEdit.setText(self.settings.value("Email"))
self.eMailLineEdit.setValidator(
QRegExpValidator(QRegExp(r"[^@\s]+@[^@\s]+\.[^@\s.]+$")))
# Setup database path
self.label_database_path.setText(
self.settings.value("DATABASE_PATH", DB_PATH))
self.pushButton_change_path.clicked.connect(self.change_database_path)
# Setup debug checkbox with current state
if LOGGER.isEnabledFor(logging.DEBUG):
self.debugModeCheckBox.setChecked(True)
def retrieve_data(self):
settings = Settings()
email = settings.value("Email")
tool = quote(settings.applicationName())
if not email:
self.error.emit(
"NCBI requests users of their webservice to identify themselves with an email adress! \n\nPlease set your email in the settings to download data from ncbi!"
)
self.finished.emit()
return
try:
self.information = get_pubmed_information(pmid=self.pmid,
email=email,
tool=tool)
except URLError:
self.error.emit(
"There appears to be a problem with your internet connection!")
except (ValueError, TypeError) as e:
self.error.emit(repr(e))
self.finished.emit()
def load_knowns(self):
settings = Settings()
last_path = settings.value(
"LastPath") or QStandardPaths.DesktopLocation or None
filename, filters = QFileDialog.getOpenFileName(
self, self.tr("Open known publications"), last_path,
self.tr("Text file (*.txt)"))
if filename:
with open(filename, "r") as open_file:
try:
self.known_ids = dict(
(line.strip("\n").split("\t")) for line in open_file)
self.known_id_path = filename
if self.found_ids:
self.update_display(self.current_index, "right")
except ValueError:
self.error_dialog.showMessage("Wrong file format!")
return
for reference in self.parent().model.references.values():
if reference.pmid:
self.known_ids[reference.pmid] = "Already in model!"
def __init__(self, mainwindow):
QDialog.__init__(self, mainwindow)
self.setupUi(self)
self.error_dialog = QErrorMessage(self)
self.found_ids = []
self.known_ids = {}
self.known_id_path = None
self.current_index = 0
self.count = 0
self.pmid_thread = QtCore.QThread(self)
self.pmid_worker = RetrievePubmedData()
self.pmid_worker.moveToThread(self.pmid_thread)
self.pmid_thread.started.connect(self.pmid_worker.retrieve_data)
self.pmid_worker.error.connect(self.error_dialog.showMessage)
self.pmid_worker.finished.connect(self.pmid_thread.quit)
self.pmid_worker.finished.connect(self.update_info_from_online)
# Search parameters
settings = Settings()
self.email = settings.value("Email")
self.tool = quote(settings.applicationName())
# Connect slots
self.webView.loadProgress.connect(self.progressBar.setValue)
# Adjust window settings
self.setWindowFlags(QtCore.Qt.Window)
#self.webView.page().setLinkDelegationPolicy(QWebEnginePage.DelegateExternalLinks)
self.webView.setContentsMargins(0, 0, 0, 0)
self.buttonPrevious.setVisible(False)
self.buttonNext.setVisible(False)
self.resultsBox.layout().setContentsMargins(9, 0, 9, 9)
self.resultsBox.hide()
self.adjustSize()
self.load_knowns()
def get_database_path():
settings = Settings()
return settings.value("DATABASE_PATH", DB_PATH)
def store_database_path(database_path):
settings = Settings()
settings.setValue("DATABASE_PATH", database_path)
settings.sync()
def restore_view_state(self):
with Settings(group=self.__class__.__name__) as settings:
restore_state(self.dataView.horizontalHeader(), settings.value("TableHeader"))
def save_view_state(self):
with Settings(group=self.__class__.__name__) as settings:
settings.setValue("TableHeader", self.dataView.horizontalHeader().saveState())
def version_is_ignored(self):
return Settings().value("IgnoreVersion") == self.latest_version
def ignore_version(self):
if self.checkBox.isChecked():
Settings().setValue("IgnoreVersion", self.latest_version)
class EditSettingsDialog(QDialog, Ui_EditSettingsDialog):
def __init__(self, parent):
QDialog.__init__(self, parent)
self.setupUi(self)
# Setup the email field with current value
self.settings = Settings()
self.eMailLineEdit.setText(self.settings.value("Email"))
self.eMailLineEdit.setValidator(
QRegExpValidator(QRegExp(r"[^@\s]+@[^@\s]+\.[^@\s.]+$")))
# Setup database path
self.label_database_path.setText(
self.settings.value("DATABASE_PATH", DB_PATH))
self.pushButton_change_path.clicked.connect(self.change_database_path)
# Setup debug checkbox with current state
if LOGGER.isEnabledFor(logging.DEBUG):
self.debugModeCheckBox.setChecked(True)
@pyqtSlot()
def toggle_ok_button(self):
""" Check that the current E-mail adresse is valid or empty in order
to enable the OK button """
self.buttonBox.button(QDialogButtonBox.Ok).setEnabled(
self.eMailLineEdit.hasAcceptableInput()
or not self.eMailLineEdit.text())
@pyqtSlot()
def change_database_path(self):
current_path = self.settings.value("DATABASE_PATH", DB_PATH)
filename, filter = QFileDialog.getSaveFileName(
self, self.tr("Change location"), current_path,
self.tr("Database (*.db)"))
if filename:
self.label_database_path.setText(filename)
@pyqtSlot()
def save_settings(self):
""" Save the currently entered E-mail """
# Set logger to debug mode
if self.debugModeCheckBox.isChecked() and not LOGGER.isEnabledFor(
logging.DEBUG):
logging.disable(logging.NOTSET)
LOGGER.info("DEBUG MODE ON")
log_package_versions()
# Switch debug mode off
elif not self.debugModeCheckBox.isChecked() and LOGGER.isEnabledFor(
logging.DEBUG):
logging.disable(logging.DEBUG)
LOGGER.info("DEBUG MODE OFF")
# Save settings
if self.settings.value("Email") != self.eMailLineEdit.text():
self.settings.setValue("Email", self.eMailLineEdit.text())
if self.settings.value(
"DATABASE_PATH") != self.label_database_path.text():
self.settings.setValue("DATABASE_PATH",
self.label_database_path.text())
self.settings.sync()
