def exportToPdf(self):
data = self.textContent.toPlainText()
if not data: return
dir = QDir()
docsPath = '{}/Documents'.format(dir.homePath())
if not dir.exists(docsPath):
docsPath = '{}/Documentos'.format(dir.homePath())
#Regresa una tupla (filename, filter)
filename = QFileDialog.getSaveFileName(self, 'Exportar a pdf',
docsPath, 'Archivo pdf *.pdf')
if not filename: return
filename = filename[0]
if not '.pdf' in filename: filename += '.pdf'
printer = QPrinter(QPrinter.HighResolution)
printer.setPaperSize(QPrinter.Letter)
printer.setPageMargins(2, 2, 2, 2, QPrinter.Millimeter)
printer.setCreator('Notepad')
printer.setPrintProgram('Notepad')
printer.setOutputFormat(QPrinter.PdfFormat)
printer.setOutputFileName(filename)
self.textContent.print_(printer)
self.showMessage('Pdf guardado: {}'.format(filename))
def saveFileAs(self):
dir = QDir()
docsPath = '{}/Documents'.format(dir.homePath())
if not dir.exists(docsPath):
docsPath = '{}/Documentos'.format(dir.homePath())
#Regresa una tupla (filename, filter)
filename = QFileDialog.getSaveFileName(self, 'Guardar como', docsPath,
self.fileFilter)
if not filename: return
if self.filename:
windowTitle = self.windowTitle().split('-')[0]
self.setWindowTitle('{} - {}'.format(windowTitle, filename[0]))
else:
self.setWindowTitle('{} - {}'.format(self.windowTitle(),
filename[0]))
self.filename = filename[0]
file = QFile(self.filename)
if not file.open(QIODevice.WriteOnly): return
data = self.textContent.toPlainText()
stream = QTextStream(file)
stream.setCodec('UTF-8')
stream << data
file.flush()
file.close()
self.showMessage('Archivo guardado')
def _browse(self):
"""Open a dialog box to set the data file
The file is opened and we show an alert if annotations are detected.
"""
# Reload last directory used
app_settings = QSettings()
last_directory = app_settings.value("last_directory", QDir.homePath())
filepath, filetype = QFileDialog.getOpenFileName(
self,
self.tr("Open a file"),
last_directory,
self.tr(
"VCF file (*.vcf *.vcf.gz);; CSV file (*.csv *.tsv *.txt)"),
)
if filepath:
# Display and save directory
self.file_path_edit.setText(filepath)
app_settings.setValue("last_directory", os.path.dirname(filepath))
if "vcf" in filepath:
# TODO: detect annotations on other tyes of files...
annotation_type = detect_vcf_annotation(filepath)
if annotation_type:
text = self.tr(
"<b>%s annotations detected!</b>") % annotation_type
else:
text = self.tr(
"<b>No annotation data has been detected!</b>")
self.anotation_detect_label.setText(text)
def on_import_clicked(self):
"""Slot called when import PED file is clicked
We open PED file (ped, tfam) to get the their samples that will
be associated to the current samples of the project.
"""
# Reload last directory used
app_settings = QSettings()
last_directory = app_settings.value("last_directory", QDir.homePath())
filepath, filetype = QFileDialog.getOpenFileName(
self,
self.tr("Open PED file"),
last_directory,
self.tr("PED files (*.ped *.tfam)"),
)
if not filepath:
return
LOGGER.info("vcf samples: %s", self.vcf_samples)
# Get samples of individual_ids that are already on the VCF file
self.view.samples = [
# samples argument is empty dict since its not
sample for sample in PedReader(filepath, dict())
if sample[1] in self.vcf_samples
]
def __openEntries(self):
didRemoveRows = False
if self.tableWidget.rowCount() > 0:
messageBox = QMessageBox()
messageBox.setWindowTitle("Clear current entries?")
messageBox.setText(
"Opening a record will delete the current entries. Continue?")
messageBox.setStandardButtons(QMessageBox.Ok | QMessageBox.Cancel)
result = messageBox.exec_()
if result == QMessageBox.Ok:
didRemoveRows = True
model = self.tableWidget.model() # type: QAbstractItemModel
for i in range(self.tableWidget.rowCount()):
model.removeRow(i)
if self.tableWidget.rowCount() == 0 or didRemoveRows:
fileName = QFileDialog.getOpenFileName(self.mainWindow,
"Open Entry",
QDir.homePath(),
"CSV Files(*.csv *.txt)")
if fileName[0]:
with open(fileName[0]) as csvfile:
reader = csv.reader(csvfile, delimiter=",")
for row in reader:
self.tableWidget.insertRow(self.tableWidget.rowCount())
model = self.tableWidget.model()
for j in range(self.tableWidget.columnCount()):
model.setData(
model.index(self.tableWidget.rowCount() - 1,
j), row[j])
def openFile(self):
fileName, _ = QFileDialog.getOpenFileName(self, "Open Movie",
QDir.homePath())
if fileName != '':
self.mediaPlayer.setMedia(
QMediaContent(QUrl.fromLocalFile(fileName)))
self.playButton.setEnabled(True)
def go_home(self, checked=False):
"""Slot for the 'Home' button. Scrolls the treeview to show and select the user's home directory."""
self.ui.comboBox_current_path.setCurrentIndex(-1)
home_index = self.file_model.index(QDir.homePath())
self.ui.treeView_file_system.collapseAll()
self.ui.treeView_file_system.setCurrentIndex(home_index)
self.ui.treeView_file_system.expand(home_index)
self.ui.treeView_file_system.scrollTo(home_index, hint=QAbstractItemView.PositionAtTop)
def getConfigFileDir(self):
# Get the home directory path
homePath = QDir.homePath()
if homePath is not None:
if homePath[-1] != '/':
homePath += '/'
debugMessage("HOMEDIR: {}".format(homePath))
return homePath
def add_module(self):
module_full_name = QFileDialog.getOpenFileName(self, 'Выберите модуль',
QDir.homePath(),
'*.module')[0]
if module_full_name != '':
idx = module_full_name.rfind('/')
if idx != -1:
module_short_name = module_full_name[idx + 1:]
self.check_module(module_full_name, module_short_name)
def open(self):
list, _ = QFileDialog.getOpenFileNames(self, 'Open File',
QDir.homePath())
for path in list:
if path[-3:] == 'm3u':
self.load(path)
else:
self.add_item(path)
def openFile(self):
fileName, _ = QFileDialog.getOpenFileName(
self, "Open Movie",
QDir.homePath() + "/Videos",
"Media (*.webm *.mp4 *.ts *.avi *.mpeg *.mpg *.mkv *.VOB *.m4v *.3gp *.mp3 *.m4a *.wav *.ogg *.flac *.m3u *.m3u8)"
)
if fileName != '':
self.loadFilm(fileName)
print("File loaded")
def newNotebook(self):
name, ok = QInputDialog.getText(
self, "Notebook name",
"How would you like your notebook to be named?")
if ok:
storagePath = QDir.homePath() + "/.config/wikinotebook/" + name
nb = self.nbManager.createNewNotebook(name, storagePath)
self.switchNotebook(nb.name)
def __init__(self, label: str, button_label: str):
super().__init__(QFileDialog())
self.__label = label
self.__button_label = button_label
self._default_path = QDir.homePath()
self.__value_changed_callbacks = []
self.__line_edit = None
self.__button = None
def change_video(self, row):
dialog = QFileDialog(self, caption="Open Video", directory=QDir.homePath())
dialog.setFileMode(QFileDialog.ExistingFile)
dialog.setViewMode(QFileDialog.Detail)
if dialog.exec_():
video_name = self.list_model.item(row, 0)
videos = self.list_model.item(row, 2)
v = dialog.selectedFiles()[0]
video_name.setText(pathlib.Path(v).name)
videos.setText(v)
def change_question(self, row):
dialog = QFileDialog(self, caption="Open Question", directory=QDir.homePath())
dialog.setFileMode(QFileDialog.ExistingFile)
dialog.setViewMode(QFileDialog.Detail)
if dialog.exec_():
questions_name = self.list_model.item(row, 1)
questions = self.list_model.item(row, 3)
q = dialog.selectedFiles()[0]
questions_name.setText(pathlib.Path(q).name)
questions.setText(q)
def add_questions(self):
dialog = QFileDialog(self, caption="Open Questions", directory=QDir.homePath())
dialog.setFileMode(QFileDialog.ExistingFiles)
dialog.setViewMode(QFileDialog.Detail)
if dialog.exec_():
question_names = dialog.selectedFiles()
for question in question_names:
last = self.find_last_row('question')
if last == -1:
self.add_item(question=question)
else:
self.edit_item(index=last, question=question)
def add_videos(self):
dialog = QFileDialog(self, caption="Open Video", directory=QDir.homePath())
dialog.setFileMode(QFileDialog.ExistingFiles)
dialog.setViewMode(QFileDialog.Detail)
if dialog.exec_():
video_names = dialog.selectedFiles()
for video in video_names:
last = self.find_last_row('video')
if last == -1:
self.add_item(video=video)
else:
self.edit_item(index=last, video=video)
def getFilePath(self, caption="find", filters=""):
result = {}
result["error"] = True
result["name"] = ""
result["fullname"] = ""
#"Buscar Imagen Nueva",
#tr("Imagenes (*.png *.xpm *.jpg *.gif *.jpeg *.bmp *ppm)")
namefile = QFileDialog.getOpenFileName(None, caption, QDir.homePath(),
filters)
if namefile[0] != "":
result["error"] = False
result["name"] = QFileInfo(namefile[0]).fileName()
result["fullname"] = namefile[0]
return result
def openFile(self):
dir = QDir()
docsPath = '{}/Documents'.format(dir.homePath())
if not dir.exists(docsPath):
docsPath = '{}/Documentos'.format(dir.homePath())
#Regresa una tupla (filename, filter)
filename = QFileDialog.getOpenFileName(self, 'Abrir', docsPath,
self.fileFilter)
if not filename: return
self.filename = filename[0]
file = QFile(self.filename)
if not file.open(QIODevice.ReadOnly): return
data = file.readAll()
file.close()
self.textContent.clear()
self.textContent.setText(str(data, encoding='utf-8'))
self.setWindowTitle('{} - {}'.format(self.windowTitle(),
self.filename))
def open_directory(self):
directory_url = QFileDialog.getExistingDirectory(
self, '0Open directory', QDir.homePath())
dir = QDir(directory_url)
filters = [
'*.mp4', '*.m4v', '*.mov', '*.mpg', '*.mpeg', '*.mp3', '*.m4a',
'*.wmv', '*.wav', '*.aiff'
]
dir.setNameFilters(filters)
file_list = dir.entryList()
path = dir.absolutePath() + '/'
for file in file_list:
self.add_item(path + file)
def export_as_csv(self):
"""Export variants into CSV file"""
# Reload last directory used
last_directory = self.app_settings.value("last_directory",
QDir.homePath())
filepath, _ = QFileDialog.getSaveFileName(self,
self.tr("Save project"),
last_directory,
self.tr("(*.csv)"))
if filepath:
with open(filepath, "w") as file:
writer = CsvWriter(file)
writer.save(self.conn)
def on_load_file(self):
"""Allow to automatically add words from a file
See Also:
:meth:`load_file`
"""
# Reload last directory used
last_directory = QSettings().value("last_directory", QDir.homePath())
filepath, _ = QFileDialog.getOpenFileName(self,
self.tr("Open Word set"),
last_directory,
self.tr("Text file (*.txt)"))
if filepath:
self.load_file(filepath)
def load_config(self):
"""Loads EnigmaAPI settings from a config file and refershes GUI"""
dialog = QFileDialog(self)
filename = dialog.getOpenFileName(self, "Load settings",
QDir.homePath(),
"Enigma config (*.json)")[0]
if filename:
try:
self.__enigma_api.load_from(filename)
logging.info('Successfully loaded config from file "%s"',
filename)
except (FileNotFoundError, JSONDecodeError) as error:
QMessageBox.critical(
self,
"Load config",
"Error retrieving data from "
"selected file!\nError message:\n\n %s" % repr(error),
)
logging.error('Failed to load config from file "%s"',
filename,
exc_info=True)
return
except Exception as error:
QMessageBox.critical(
self,
"Load config",
"Following error occured during "
"applying loaded settings:\n%s" % repr(error),
)
logging.error(
"Unable to load config from file, keeping old settings...",
exc_info=True,
)
return
# Refresh gui after loading setings
self.__rotors.generate_rotors()
self.__input_textbox.blockSignals(True)
self.refresh_gui()
self.__input_textbox.blockSignals(False)
self.__rotors.set_positions()
logging.info('Checkpoint set to "%s"',
str(self.__enigma_api.positions()))
self.__enigma_api.set_checkpoint()
else:
logging.info("No load file selected...")
def video_directory(self):
dialog = QFileDialog(self, caption="Open Video Directory", directory=QDir.homePath())
dialog.setFileMode(QFileDialog.Directory)
dialog.setViewMode(QFileDialog.Detail)
if dialog.exec_():
dir_names = dialog.selectedFiles()
dir_path = pathlib.Path(dir_names[0])
files = []
for ext in self.vtype_s:
files.extend(dir_path.glob(ext))
for video in files:
last = self.find_last_row('video')
if last == -1:
self.add_item(video=str(video))
else:
self.edit_item(index=last, video=str(video))
def openProjectBtnHandler(self):
""" Handler invoked when the "Open" button is pressed.
It causes the plugin to open a file open dialog and then subsequently
opening the, by the user, selected file.
"""
lastPath = self.openFilePath
dflPath = lastPath if lastPath != "" else QDir.homePath()
filename = QFileDialog.getOpenFileName(
self, self.tr("Open BCF File"), dflPath,
self.tr("BCF Files (*.bcf *.bcfzip)"))
if filename[0] != "":
model.openProjectBtnHandler(filename[0])
self.openFilePath = filename[0]
self.projectOpened.emit()
def export_message(self):
"""Opens a dialog to get the save location, exports current Enigma
settings and encrypted message to the file"""
dialog = QFileDialog(self)
filename = dialog.getSaveFileName(self, "Save Enigma message",
QDir.homePath(), "*.txt")[0]
if filename and not findall(r"\.txt$", filename):
filename += ".txt"
logging.info(
".txt file extension for save file not found, adding...")
if filename:
logging.info('Exporing message to "%s"...', filename)
with open(filename, "w") as file:
message = "\n".join(wrap(self.__output_textbox.text(), 29))
file.write("%s\n%s\n" % (str(self.__enigma_api), message))
def export_ped(self):
"""Export samples into PED/PLINK file"""
# Reload last directory used
last_directory = self.app_settings.value("last_directory",
QDir.homePath())
# noinspection PyCallByClass
filepath, _ = QFileDialog.getSaveFileName(self,
self.tr("Save project"),
last_directory, "(*.tfam)")
if filepath:
filepath = filepath if filepath.endswith(
".tfam") else filepath + ".tfam"
with open(filepath, "w") as file:
writer = PedWriter(file)
writer.save(self.conn)
def save_config(self):
"""Collects data from EnigmaAPI and saves it to selected filename"""
dialog = QFileDialog(self)
dialog.setDefaultSuffix("json")
filename = dialog.getSaveFileName(self, "Save settings",
QDir.homePath(),
"Enigma config (*.json)")[0]
# To prevent from saving files without a file extension...
if filename and not findall(r"\.json$", filename.lower()):
filename += ".json"
logging.info(
".json file extension for save file not found, adding...")
if filename:
self.__enigma_api.save_to(filename)
else:
logging.info("No save file selected...")
def __init__(self):
super().__init__()
self.setTitle(self.tr("Project creation"))
self.setSubTitle(
self.tr(
"This wizard will guide you to create a cutevariant project."))
# Reload last directory used
app_settings = QSettings()
self.last_directory = app_settings.value("last_directory",
QDir.homePath())
self.project_name_edit = QLineEdit()
self.project_path_edit = QLineEdit()
self.project_path_edit.setText(self.last_directory)
self.browse_button = QPushButton(self.tr("Browse"))
self.reference = QComboBox()
# Unused for now
self.reference.hide()
self.reference.addItem("hg19")
self.registerField("project_name", self.project_name_edit, "text")
self.registerField("project_path", self.project_path_edit, "text")
self.registerField("reference", self.reference, "currentText")
v_layout = QFormLayout()
browse_layout = QHBoxLayout()
browse_layout.addWidget(self.project_path_edit)
browse_layout.addWidget(self.browse_button)
browse_layout.setContentsMargins(0, 0, 0, 0)
v_layout.addRow(self.tr("Reference genom"), self.reference)
v_layout.addRow(self.tr("Project Name"), self.project_name_edit)
v_layout.addRow(self.tr("Create in"), browse_layout)
self.setLayout(v_layout)
self.browse_button.clicked.connect(self._browse)
self.project_path_edit.textChanged.connect(self.completeChanged)
self.project_name_edit.textChanged.connect(self.completeChanged)
def open_project(self):
"""Slot to open an already existing project from a QFileDialog"""
# Reload last directory used
last_directory = self.app_settings.value("last_directory",
QDir.homePath())
filepath, _ = QFileDialog.getOpenFileName(
self,
self.tr("Open project"),
last_directory,
self.tr("Cutevariant project (*.db)"),
)
if filepath:
try:
self.open(filepath)
except Exception as e:
self.status_bar.showMessage(e.__class__.__name__ + ": " +
str(e))
raise