class FileWidget(QWidget):
on_open = pyqtSignal(str)
# TODO consider removing directory_aliases since it is not used any more
def __init__(self,
dialog_title='',
dialog_format='',
start_dir=os.path.expanduser('~/'),
icon_size=(12, 20),
minimal_width=200,
browse_label='Browse',
on_open=None,
reload_button=True,
reload_label='Reload',
recent_files=None,
directory_aliases=None,
allow_empty=True,
empty_file_label='(none)'):
""" Creates a widget with a button for file loading and
an optional combo box for recent files and reload buttons.
Args:
dialog_title (str): The title of the dialog.
dialog_format (str): Formats for the dialog.
start_dir (str): A directory to start from.
icon_size (int, int): The size of buttons' icons.
on_open (callable): A callback function that accepts filepath as the only argument.
reload_button (bool): Whether to show reload button.
reload_label (str): The text displayed on the reload button.
recent_files (List[str]): List of recent files.
directory_aliases (dict): An {alias: dir} dictionary for fast directories' access.
allow_empty (bool): Whether empty path is allowed.
"""
super().__init__()
self.dialog_title = dialog_title
self.dialog_format = dialog_format
self.start_dir = start_dir
# Recent files should also contain `empty_file_label` so
# when (none) is selected this is stored in settings.
self.recent_files = recent_files if recent_files is not None else []
self.directory_aliases = directory_aliases or {}
self.allow_empty = allow_empty
self.empty_file_label = empty_file_label
if self.empty_file_label not in self.recent_files \
and (self.allow_empty or not self.recent_files):
self.recent_files.append(self.empty_file_label)
self.check_existence()
self.on_open.connect(on_open)
layout = QHBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
if recent_files is not None:
self.file_combo = QComboBox()
self.file_combo.setMinimumWidth(minimal_width)
self.file_combo.activated[int].connect(self.select)
self.update_combo()
layout.addWidget(self.file_combo)
self.browse_button = QPushButton(browse_label)
self.browse_button.setFocusPolicy(Qt.NoFocus)
self.browse_button.clicked.connect(self.browse)
self.browse_button.setIcon(self.style().standardIcon(
QStyle.SP_DirOpenIcon))
self.browse_button.setIconSize(QSize(*icon_size))
self.browse_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
layout.addWidget(self.browse_button)
if reload_button:
self.reload_button = QPushButton(reload_label)
self.reload_button.setFocusPolicy(Qt.NoFocus)
self.reload_button.clicked.connect(self.reload)
self.reload_button.setIcon(self.style().standardIcon(
QStyle.SP_BrowserReload))
self.reload_button.setSizePolicy(QSizePolicy.Fixed,
QSizePolicy.Fixed)
self.reload_button.setIconSize(QSize(*icon_size))
layout.addWidget(self.reload_button)
def browse(self, start_dir=None):
start_dir = start_dir or self.start_dir
path, _ = QFileDialog().getOpenFileName(self, self.dialog_title,
start_dir, self.dialog_format)
if path and self.recent_files is not None:
if path in self.recent_files:
self.recent_files.remove(path)
self.recent_files.insert(0, path)
self.update_combo()
if path:
self.open_file(path)
def select(self, n):
name = self.file_combo.currentText()
if name == self.empty_file_label:
del self.recent_files[n]
self.recent_files.insert(0, self.empty_file_label)
self.update_combo()
self.open_file(self.empty_file_label)
elif name in self.directory_aliases:
self.browse(self.directory_aliases[name])
elif n < len(self.recent_files):
name = self.recent_files[n]
del self.recent_files[n]
self.recent_files.insert(0, name)
self.update_combo()
self.open_file(self.recent_files[0])
def update_combo(self):
""" Sync combo values to the changes in self.recent_files. """
if self.recent_files is not None:
self.file_combo.clear()
for i, file in enumerate(self.recent_files):
# remove (none) when we have some files and allow_empty=False
if file == self.empty_file_label and \
not self.allow_empty and len(self.recent_files) > 1:
del self.recent_files[i]
else:
self.file_combo.addItem(os.path.split(file)[1])
for alias in self.directory_aliases.keys():
self.file_combo.addItem(alias)
def reload(self):
if self.recent_files:
self.select(0)
def check_existence(self):
if self.recent_files:
to_remove = []
for file in self.recent_files:
doc_path = os.path.join(get_sample_corpora_dir(), file)
exists = any(os.path.exists(f) for f in [file, doc_path])
if file != self.empty_file_label and not exists:
to_remove.append(file)
for file in to_remove:
self.recent_files.remove(file)
def open_file(self, path):
self.on_open.emit(path if path != self.empty_file_label else '')
def get_selected_filename(self):
if self.recent_files:
return self.recent_files[0]
else:
return self.empty_file_label
class OWPubmed(OWWidget):
name = 'Pubmed'
description = 'Fetch data from Pubmed.'
icon = 'icons/Pubmed.svg'
priority = 140
outputs = [(Output.CORPUS, Corpus)]
want_main_area = False
resizing_enabled = False
QT_DATE_FORMAT = 'yyyy-MM-dd'
PY_DATE_FORMAT = '%Y-%m-%d'
MIN_DATE = date(1800, 1, 1)
# Settings.
recent_emails = Setting([])
author = Setting('')
pub_date_from = Setting('')
pub_date_to = Setting('')
recent_keywords = Setting([])
last_advanced_query = Setting('')
num_records = Setting(1000)
# Text includes checkboxes.
includes_authors = Setting(True)
includes_title = Setting(True)
includes_mesh = Setting(True)
includes_abstract = Setting(True)
includes_url = Setting(True)
class Warning(OWWidget.Warning):
no_query = Msg('Please specify the keywords for this query.')
class Error(OWWidget.Error):
api_error = Msg('API error: {}.')
def __init__(self):
super().__init__()
self.output_corpus = None
self.pubmed_api = None
self.progress = None
self.email_is_valid = False
self.record_count = 0
self.download_running = False
# To hold all the controls. Makes access easier.
self.pubmed_controls = []
h_box = gui.hBox(self.controlArea)
label = gui.label(h_box, self, 'Email:')
label.setMaximumSize(label.sizeHint())
# Drop-down for recent emails.
self.email_combo = QComboBox(h_box)
self.email_combo.setMinimumWidth(150)
self.email_combo.setEditable(True)
self.email_combo.lineEdit().textChanged.connect(self.sync_email)
h_box.layout().addWidget(self.email_combo)
self.email_combo.activated[int].connect(self.select_email)
# RECORD SEARCH
self.search_tabs = gui.tabWidget(self.controlArea)
# --- Regular search ---
regular_search_box = gui.widgetBox(self.controlArea, addSpace=True)
# Author
self.author_input = gui.lineEdit(regular_search_box,
self,
'author',
'Author:',
orientation=Qt.Horizontal)
self.pubmed_controls.append(self.author_input)
h_box = gui.hBox(regular_search_box)
year_box = gui.widgetBox(h_box, orientation=Qt.Horizontal)
min_date = QDate.fromString(
self.MIN_DATE.strftime(self.PY_DATE_FORMAT), self.QT_DATE_FORMAT)
if not self.pub_date_from:
self.pub_date_from = self.MIN_DATE.strftime(self.PY_DATE_FORMAT)
if not self.pub_date_to:
self.pub_date_to = date.today().strftime(self.PY_DATE_FORMAT)
self.date_from = QDateEdit(QDate.fromString(self.pub_date_from,
self.QT_DATE_FORMAT),
displayFormat=self.QT_DATE_FORMAT,
minimumDate=min_date,
calendarPopup=True)
self.date_to = QDateEdit(QDate.fromString(self.pub_date_to,
self.QT_DATE_FORMAT),
displayFormat=self.QT_DATE_FORMAT,
minimumDate=min_date,
calendarPopup=True)
self.date_from.dateChanged.connect(lambda date: setattr(
self, 'pub_date_from', date.toString(self.QT_DATE_FORMAT)))
self.date_to.dateChanged.connect(lambda date: setattr(
self, 'pub_date_to', date.toString(self.QT_DATE_FORMAT)))
self.pubmed_controls.append(self.date_from)
self.pubmed_controls.append(self.date_to)
gui.label(year_box, self, 'From:')
year_box.layout().addWidget(self.date_from)
gui.label(year_box, self, 'to:')
year_box.layout().addWidget(self.date_to)
# Keywords.
h_box = gui.hBox(regular_search_box)
label = gui.label(h_box, self, 'Query:')
label.setMaximumSize(label.sizeHint())
self.keyword_combo = QComboBox(h_box)
self.keyword_combo.setMinimumWidth(150)
self.keyword_combo.setEditable(True)
h_box.layout().addWidget(self.keyword_combo)
self.keyword_combo.activated[int].connect(self.select_keywords)
self.pubmed_controls.append(self.keyword_combo)
tab_height = regular_search_box.sizeHint()
regular_search_box.setMaximumSize(tab_height)
# --- Advanced search ---
advanced_search_box = gui.widgetBox(self.controlArea, addSpace=True)
# Advanced search query.
h_box = gui.hBox(advanced_search_box)
self.advanced_query_input = QTextEdit(h_box)
h_box.layout().addWidget(self.advanced_query_input)
self.advanced_query_input.setMaximumSize(tab_height)
self.pubmed_controls.append(self.advanced_query_input)
gui.createTabPage(self.search_tabs, 'Regular search',
regular_search_box)
gui.createTabPage(self.search_tabs, 'Advanced search',
advanced_search_box)
# Search info label.
self.search_info_label = gui.label(self.controlArea, self,
'Number of records found: /')
# Search for records button.
self.run_search_button = gui.button(
self.controlArea,
self,
'Find records',
callback=self.run_search,
tooltip='Performs a search for articles that fit the '
'specified parameters.')
self.pubmed_controls.append(self.run_search_button)
h_line = QFrame()
h_line.setFrameShape(QFrame.HLine)
h_line.setFrameShadow(QFrame.Sunken)
self.controlArea.layout().addWidget(h_line)
# RECORD RETRIEVAL
# Text includes box.
text_includes_box = gui.widgetBox(self.controlArea,
'Text includes',
addSpace=True)
self.authors_checkbox = gui.checkBox(text_includes_box, self,
'includes_authors', 'Authors')
self.title_checkbox = gui.checkBox(text_includes_box, self,
'includes_title', 'Article title')
self.mesh_checkbox = gui.checkBox(text_includes_box, self,
'includes_mesh', 'Mesh headings')
self.abstract_checkbox = gui.checkBox(text_includes_box, self,
'includes_abstract', 'Abstract')
self.url_checkbox = gui.checkBox(text_includes_box, self,
'includes_url', 'URL')
self.pubmed_controls.append(self.authors_checkbox)
self.pubmed_controls.append(self.title_checkbox)
self.pubmed_controls.append(self.mesh_checkbox)
self.pubmed_controls.append(self.abstract_checkbox)
self.pubmed_controls.append(self.url_checkbox)
# Num. records.
h_box = gui.hBox(self.controlArea)
label = gui.label(h_box, self, 'Retrieve')
label.setMaximumSize(label.sizeHint())
self.num_records_input = gui.spin(h_box,
self,
'num_records',
minv=1,
maxv=10000)
self.max_records_label = gui.label(h_box, self, 'records from /.')
self.max_records_label.setMaximumSize(
self.max_records_label.sizeHint())
self.pubmed_controls.append(self.num_records_input)
# Download articles.
# Search for records button.
self.retrieve_records_button = gui.button(
self.controlArea,
self,
'Retrieve records',
callback=self.retrieve_records,
tooltip='Retrieves the specified documents.')
self.pubmed_controls.append(self.retrieve_records_button)
# Num. retrieved records info label.
self.retrieval_info_label = gui.label(
self.controlArea, self, 'Number of records retrieved: /')
# Load the most recent emails.
self.set_email_list()
# Load the most recent queries.
self.set_keyword_list()
# Check the email and enable controls accordingly.
if self.recent_emails:
email = self.recent_emails[0]
self.email_is_valid = validate_email(email)
self.enable_controls()
def sync_email(self):
email = self.email_combo.currentText()
self.email_is_valid = validate_email(email)
self.enable_controls()
def enable_controls(self):
# Enable/disable controls accordingly.
for control in self.pubmed_controls:
control.setEnabled(self.email_is_valid)
if self.pubmed_api is None or self.pubmed_api.search_record_count == 0:
self.retrieve_records_button.setEnabled(False)
if not self.email_is_valid:
self.email_combo.setFocus()
def run_search(self):
self.Error.clear()
self.Warning.clear()
self.run_search_button.setEnabled(False)
self.retrieve_records_button.setEnabled(False)
# Add the email to history.
email = self.email_combo.currentText()
if email not in self.recent_emails:
self.recent_emails.insert(0, email)
# Check if the PubMed object is present.
if self.pubmed_api is None:
self.pubmed_api = Pubmed(
email=email,
progress_callback=self.api_progress_callback,
error_callback=self.api_error_callback,
)
if self.search_tabs.currentIndex() == 0:
# Get query parameters.
terms = self.keyword_combo.currentText().split()
authors = self.author_input.text().split()
error = self.pubmed_api._search_for_records(
terms, authors, self.pub_date_from, self.pub_date_to)
if error is not None:
self.Error.api_error(str(error))
return
if self.keyword_combo.currentText() not in self.recent_keywords:
self.recent_keywords.insert(0,
self.keyword_combo.currentText())
else:
query = self.advanced_query_input.toPlainText()
if not query:
self.Warning.no_query()
self.run_search_button.setEnabled(True)
self.retrieve_records_button.setEnabled(True)
return
error = self.pubmed_api._search_for_records(advanced_query=query)
if error is not None:
self.Error.api_error(str(error))
return
self.last_advanced_query = query
self.enable_controls()
self.update_search_info()
def retrieve_records(self):
self.Warning.clear()
self.Error.clear()
if self.pubmed_api is None:
return
if self.download_running:
self.download_running = False
self.run_search_button.setEnabled(True)
self.retrieve_records_button.setText('Retrieve records')
self.pubmed_api.stop_retrieving()
return
self.download_running = True
self.run_search_button.setEnabled(False)
self.output_corpus = None # Clear the old records.
# Change the button label.
self.retrieve_records_button.setText('Stop retrieving')
# Text fields.
text_includes_params = [
self.includes_authors,
self.includes_title,
self.includes_mesh,
self.includes_abstract,
self.includes_url,
True, # Publication date field; included always.
]
required_text_fields = [
field for field_name, field in zip(
text_includes_params, PUBMED_TEXT_FIELDS) if field_name
]
batch_size = min(Pubmed.MAX_BATCH_SIZE, self.num_records) + 1
with self.progressBar(self.num_records / batch_size) as progress:
self.progress = progress
self.output_corpus = self.pubmed_api._retrieve_records(
self.num_records, required_text_fields)
self.retrieve_records_button.setText('Retrieve records')
self.download_running = False
self.send(Output.CORPUS, self.output_corpus)
self.update_retrieval_info()
self.run_search_button.setEnabled(True)
def api_progress_callback(self, start_at=None):
if start_at is not None:
self.progress.count = start_at
else:
self.progress.advance()
def api_error_callback(self, error):
self.Error.api_error(str(error))
if self.progress is not None:
self.progress.finish()
def update_search_info(self):
max_records_count = min(self.pubmed_api.MAX_RECORDS,
self.pubmed_api.search_record_count)
self.search_info_label.setText(
'Number of retrievable records for '
'this search query: {} '.format(max_records_count))
self.max_records_label.setText(
'records from {}.'.format(max_records_count))
self.max_records_label.setMaximumSize(
self.max_records_label.sizeHint())
self.num_records_input.setMaximum(max_records_count)
self.retrieve_records_button.setFocus()
def update_retrieval_info(self):
document_count = 0
if self.output_corpus is not None:
document_count = len(self.output_corpus)
self.retrieval_info_label.setText(
'Number of records retrieved: {} '.format(document_count))
self.retrieval_info_label.setMaximumSize(
self.retrieval_info_label.sizeHint())
def select_email(self, n):
if n < len(self.recent_emails):
email = self.recent_emails[n]
del self.recent_emails[n]
self.recent_emails.insert(0, email)
if len(self.recent_emails) > 0:
self.set_email_list()
def set_email_list(self):
self.email_combo.clear()
for email in self.recent_emails:
self.email_combo.addItem(email)
def select_keywords(self, n):
if n < len(self.recent_keywords):
keywords = self.recent_keywords[n]
del self.recent_keywords[n]
self.recent_keywords.insert(0, keywords)
if len(self.recent_keywords) > 0:
self.set_keyword_list()
def set_keyword_list(self):
self.keyword_combo.clear()
if not self.recent_keywords:
# Sample queries.
self.recent_keywords.append('orchid')
self.recent_keywords.append('hypertension')
self.recent_keywords.append('blood pressure')
self.recent_keywords.append('radiology')
for keywords in self.recent_keywords:
self.keyword_combo.addItem(keywords)
def open_calendar(self, widget):
cal_dlg = CalendarDialog(self, 'Date picker')
if cal_dlg.exec_():
widget.setText(cal_dlg.picked_date)
def send_report(self):
if not self.pubmed_api:
return
max_records_count = min(self.pubmed_api.MAX_RECORDS,
self.pubmed_api.search_record_count)
if self.search_tabs.currentIndex() == 0:
terms = self.keyword_combo.currentText()
authors = self.author_input.text()
self.report_items(
(('Query', terms if terms else None),
('Authors', authors if authors else None),
('Date', 'from {} to {}'.format(self.pub_date_from,
self.pub_date_to)),
('Number of records retrieved', '{}/{}'.format(
len(self.output_corpus) if self.output_corpus else 0,
max_records_count))))
else:
query = self.advanced_query_input.toPlainText()
self.report_items(
(('Query', query if query else None),
('Number of records retrieved', '{}/{}'.format(
len(self.output_corpus) if self.output_corpus else 0,
max_records_count))))
class FileLoader(QWidget):
activated = pyqtSignal()
file_loaded = pyqtSignal()
def __init__(self):
super().__init__()
self.recent_paths = []
self.file_combo = QComboBox()
self.file_combo.setMinimumWidth(80)
self.file_combo.activated.connect(self._activate)
self.browse_btn = QPushButton("...")
icon = self.style().standardIcon(QStyle.SP_DirOpenIcon)
self.browse_btn.setIcon(icon)
self.browse_btn.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Fixed)
self.browse_btn.clicked.connect(self.browse)
self.load_btn = QPushButton("")
icon = self.style().standardIcon(QStyle.SP_BrowserReload)
self.load_btn.setIcon(icon)
self.load_btn.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Fixed)
self.load_btn.setAutoDefault(True)
self.load_btn.clicked.connect(self.file_loaded)
def browse(self):
start_file = self.last_path() or os.path.expanduser("~/")
formats = ["Text files (*.txt)", "All files (*)"]
file_name, _ = QFileDialog.getOpenFileName(None, "Open...", start_file,
";;".join(formats),
formats[0])
if not file_name:
return
self.add_path(file_name)
self._activate()
def _activate(self):
self.activated.emit()
self.file_loaded.emit()
def set_current_file(self, path: str):
if path:
self.add_path(path)
self.file_combo.setCurrentText(path)
else:
self.file_combo.setCurrentText("(none)")
def get_current_file(self) -> Optional[RecentPath]:
index = self.file_combo.currentIndex()
if index >= len(self.recent_paths) or index < 0:
return None
path = self.recent_paths[index]
return path if isinstance(path, RecentPath) else None
def add_path(self, filename: str):
recent = RecentPath.create(filename, [])
if recent in self.recent_paths:
self.recent_paths.remove(recent)
self.recent_paths.insert(0, recent)
self.set_file_list()
def set_file_list(self):
self.file_combo.clear()
for i, recent in enumerate(self.recent_paths):
self.file_combo.addItem(recent.basename)
self.file_combo.model().item(i).setToolTip(recent.abspath)
if not os.path.exists(recent.abspath):
self.file_combo.setItemData(i, QBrush(Qt.red),
Qt.TextColorRole)
self.file_combo.addItem(_DEFAULT_NONE)
def last_path(self) -> Optional[str]:
return self.recent_paths[0].abspath if self.recent_paths else None
class FileWidget(QWidget):
on_open = pyqtSignal(str)
def __init__(self,
dialog_title='',
dialog_format='',
start_dir=os.path.expanduser('~/'),
icon_size=(12, 20),
minimal_width=200,
browse_label='Browse',
on_open=None,
reload_button=True,
reload_label='Reload',
recent_files=None,
directory_aliases=None,
allow_empty=True,
empty_file_label='(none)'):
""" Creates a widget with a button for file loading and
an optional combo box for recent files and reload buttons.
Args:
dialog_title (str): The title of the dialog.
dialog_format (str): Formats for the dialog.
start_dir (str): A directory to start from.
icon_size (int, int): The size of buttons' icons.
on_open (callable): A callback function that accepts filepath as the only argument.
reload_button (bool): Whether to show reload button.
reload_label (str): The text displayed on the reload button.
recent_files (List[str]): List of recent files.
directory_aliases (dict): An {alias: dir} dictionary for fast directories' access.
allow_empty (bool): Whether empty path is allowed.
"""
super().__init__()
self.dialog_title = dialog_title
self.dialog_format = dialog_format
self.start_dir = start_dir
self.recent_files = recent_files
self.directory_aliases = directory_aliases or {}
self.check_existence()
self.on_open.connect(on_open)
self.allow_empty = allow_empty
self.empty_file_label = empty_file_label
layout = QHBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
if recent_files is not None:
self.file_combo = QComboBox()
self.file_combo.setMinimumWidth(minimal_width)
self.file_combo.activated[int].connect(self.select)
self.update_combo()
layout.addWidget(self.file_combo)
self.browse_button = QPushButton(browse_label)
self.browse_button.setFocusPolicy(Qt.NoFocus)
self.browse_button.clicked.connect(self.browse)
self.browse_button.setIcon(self.style().standardIcon(
QStyle.SP_DirOpenIcon))
self.browse_button.setIconSize(QSize(*icon_size))
self.browse_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
layout.addWidget(self.browse_button)
if reload_button:
self.reload_button = QPushButton(reload_label)
self.reload_button.setFocusPolicy(Qt.NoFocus)
self.reload_button.clicked.connect(self.reload)
self.reload_button.setIcon(self.style().standardIcon(
QStyle.SP_BrowserReload))
self.reload_button.setSizePolicy(QSizePolicy.Fixed,
QSizePolicy.Fixed)
self.reload_button.setIconSize(QSize(*icon_size))
layout.addWidget(self.reload_button)
def browse(self, start_dir=None):
start_dir = start_dir or self.start_dir
path, _ = QFileDialog().getOpenFileName(self, self.dialog_title,
start_dir, self.dialog_format)
if path and self.recent_files is not None:
if path in self.recent_files:
self.recent_files.remove(path)
self.recent_files.insert(0, path)
self.update_combo()
self.open_file(path)
def select(self, n):
name = self.file_combo.currentText()
if n < len(self.recent_files):
name = self.recent_files[n]
del self.recent_files[n]
self.recent_files.insert(0, name)
self.open_file(self.recent_files[0])
self.update_combo()
elif name == self.empty_file_label:
self.open_file(self.empty_file_label)
elif name in self.directory_aliases:
self.browse(self.directory_aliases[name])
def update_combo(self):
if self.recent_files is not None:
self.file_combo.clear()
for file in self.recent_files:
self.file_combo.addItem(os.path.split(file)[1])
if self.allow_empty or not self.recent_files:
self.file_combo.addItem(self.empty_file_label)
for alias in self.directory_aliases.keys():
self.file_combo.addItem(alias)
def reload(self):
if self.recent_files:
self.select(0)
def check_existence(self):
if self.recent_files:
to_remove = [
file for file in self.recent_files if not os.path.exists(file)
]
for file in to_remove:
self.recent_files.remove(file)
def open_file(self, path):
try:
self.on_open.emit(path if path != self.empty_file_label else '')
except (OSError, IOError):
self.loading_error_signal.emit('Could not open "{}".'.format(path))
class FileWidget(QWidget):
on_open = pyqtSignal(str)
def __init__(self, dialog_title='', dialog_format='',
start_dir=os.path.expanduser('~/'),
icon_size=(12, 20), minimal_width=200,
browse_label='Browse', on_open=None,
reload_button=True, reload_label='Reload',
recent_files=None, directory_aliases=None,
allow_empty=True, empty_file_label='(none)'):
""" Creates a widget with a button for file loading and
an optional combo box for recent files and reload buttons.
Args:
dialog_title (str): The title of the dialog.
dialog_format (str): Formats for the dialog.
start_dir (str): A directory to start from.
icon_size (int, int): The size of buttons' icons.
on_open (callable): A callback function that accepts filepath as the only argument.
reload_button (bool): Whether to show reload button.
reload_label (str): The text displayed on the reload button.
recent_files (List[str]): List of recent files.
directory_aliases (dict): An {alias: dir} dictionary for fast directories' access.
allow_empty (bool): Whether empty path is allowed.
"""
super().__init__()
self.dialog_title = dialog_title
self.dialog_format = dialog_format
self.start_dir = start_dir
self.recent_files = recent_files
self.directory_aliases = directory_aliases or {}
self.check_existence()
self.on_open.connect(on_open)
self.allow_empty = allow_empty
self.empty_file_label = empty_file_label
layout = QHBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
if recent_files is not None:
self.file_combo = QComboBox()
self.file_combo.setMinimumWidth(minimal_width)
self.file_combo.activated[int].connect(self.select)
self.update_combo()
layout.addWidget(self.file_combo)
self.browse_button = QPushButton(browse_label)
self.browse_button.setFocusPolicy(Qt.NoFocus)
self.browse_button.clicked.connect(self.browse)
self.browse_button.setIcon(self.style()
.standardIcon(QStyle.SP_DirOpenIcon))
self.browse_button.setIconSize(QSize(*icon_size))
self.browse_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
layout.addWidget(self.browse_button)
if reload_button:
self.reload_button = QPushButton(reload_label)
self.reload_button.setFocusPolicy(Qt.NoFocus)
self.reload_button.clicked.connect(self.reload)
self.reload_button.setIcon(self.style()
.standardIcon(QStyle.SP_BrowserReload))
self.reload_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
self.reload_button.setIconSize(QSize(*icon_size))
layout.addWidget(self.reload_button)
def browse(self, start_dir=None):
start_dir = start_dir or self.start_dir
path, _ = QFileDialog().getOpenFileName(self, self.dialog_title,
start_dir, self.dialog_format)
if path and self.recent_files is not None:
if path in self.recent_files:
self.recent_files.remove(path)
self.recent_files.insert(0, path)
self.update_combo()
self.open_file(path)
def select(self, n):
name = self.file_combo.currentText()
if n < len(self.recent_files):
name = self.recent_files[n]
del self.recent_files[n]
self.recent_files.insert(0, name)
self.open_file(self.recent_files[0])
self.update_combo()
elif name == self.empty_file_label:
self.open_file(self.empty_file_label)
elif name in self.directory_aliases:
self.browse(self.directory_aliases[name])
def update_combo(self):
if self.recent_files is not None:
self.file_combo.clear()
for file in self.recent_files:
self.file_combo.addItem(os.path.split(file)[1])
if self.allow_empty or not self.recent_files:
self.file_combo.addItem(self.empty_file_label)
for alias in self.directory_aliases.keys():
self.file_combo.addItem(alias)
def reload(self):
if self.recent_files:
self.select(0)
def check_existence(self):
if self.recent_files:
to_remove = [
file for file in self.recent_files if not os.path.exists(file)
]
for file in to_remove:
self.recent_files.remove(file)
def open_file(self, path):
try:
self.on_open.emit(path if path != self.empty_file_label else '')
except (OSError, IOError):
self.loading_error_signal.emit('Could not open "{}".'
.format(path))
class OWPubmed(OWWidget):
name = 'Pubmed'
description = 'Fetch data from Pubmed.'
icon = 'icons/Pubmed.svg'
priority = 20
outputs = [(Output.CORPUS, Corpus)]
want_main_area = False
resizing_enabled = False
QT_DATE_FORMAT = 'yyyy-MM-dd'
PY_DATE_FORMAT = '%Y-%m-%d'
MIN_DATE = date(1800, 1, 1)
# Settings.
recent_emails = Setting([])
author = Setting('')
pub_date_from = Setting('')
pub_date_to = Setting('')
recent_keywords = Setting([])
last_advanced_query = Setting('')
num_records = Setting(1000)
# Text includes checkboxes.
includes_authors = Setting(True)
includes_title = Setting(True)
includes_mesh = Setting(True)
includes_abstract = Setting(True)
includes_url = Setting(True)
class Warning(OWWidget.Warning):
no_query = Msg('Please specify the keywords for this query.')
class Error(OWWidget.Error):
api_error = Msg('API error: {}.')
def __init__(self):
super().__init__()
self.output_corpus = None
self.pubmed_api = None
self.progress = None
self.email_is_valid = False
self.record_count = 0
self.download_running = False
# To hold all the controls. Makes access easier.
self.pubmed_controls = []
h_box = gui.hBox(self.controlArea)
label = gui.label(h_box, self, 'Email:')
label.setMaximumSize(label.sizeHint())
# Drop-down for recent emails.
self.email_combo = QComboBox(h_box)
self.email_combo.setMinimumWidth(150)
self.email_combo.setEditable(True)
self.email_combo.lineEdit().textChanged.connect(self.sync_email)
h_box.layout().addWidget(self.email_combo)
self.email_combo.activated[int].connect(self.select_email)
# RECORD SEARCH
self.search_tabs = gui.tabWidget(self.controlArea)
# --- Regular search ---
regular_search_box = gui.widgetBox(self.controlArea, addSpace=True)
# Author
self.author_input = gui.lineEdit(regular_search_box, self, 'author',
'Author:', orientation=Qt.Horizontal)
self.pubmed_controls.append(self.author_input)
h_box = gui.hBox(regular_search_box)
year_box = gui.widgetBox(h_box, orientation=Qt.Horizontal)
min_date = QDate.fromString(
self.MIN_DATE.strftime(self.PY_DATE_FORMAT),
self.QT_DATE_FORMAT
)
if not self.pub_date_from:
self.pub_date_from = self.MIN_DATE.strftime(self.PY_DATE_FORMAT)
if not self.pub_date_to:
self.pub_date_to = date.today().strftime(self.PY_DATE_FORMAT)
self.date_from = QDateEdit(
QDate.fromString(self.pub_date_from, self.QT_DATE_FORMAT),
displayFormat=self.QT_DATE_FORMAT,
minimumDate=min_date,
calendarPopup=True
)
self.date_to = QDateEdit(
QDate.fromString(self.pub_date_to, self.QT_DATE_FORMAT),
displayFormat=self.QT_DATE_FORMAT,
minimumDate=min_date,
calendarPopup=True
)
self.date_from.dateChanged.connect(
lambda date: setattr(self, 'pub_date_from',
date.toString(self.QT_DATE_FORMAT)))
self.date_to.dateChanged.connect(
lambda date: setattr(self, 'pub_date_to',
date.toString(self.QT_DATE_FORMAT)))
self.pubmed_controls.append(self.date_from)
self.pubmed_controls.append(self.date_to)
gui.label(year_box, self, 'From:')
year_box.layout().addWidget(self.date_from)
gui.label(year_box, self, 'to:')
year_box.layout().addWidget(self.date_to)
# Keywords.
h_box = gui.hBox(regular_search_box)
label = gui.label(h_box, self, 'Query:')
label.setMaximumSize(label.sizeHint())
self.keyword_combo = QComboBox(h_box)
self.keyword_combo.setMinimumWidth(150)
self.keyword_combo.setEditable(True)
h_box.layout().addWidget(self.keyword_combo)
self.keyword_combo.activated[int].connect(self.select_keywords)
self.pubmed_controls.append(self.keyword_combo)
tab_height = regular_search_box.sizeHint()
regular_search_box.setMaximumSize(tab_height)
# --- Advanced search ---
advanced_search_box = gui.widgetBox(self.controlArea, addSpace=True)
# Advanced search query.
h_box = gui.hBox(advanced_search_box)
self.advanced_query_input = QTextEdit(h_box)
h_box.layout().addWidget(self.advanced_query_input)
self.advanced_query_input.setMaximumSize(tab_height)
self.pubmed_controls.append(self.advanced_query_input)
gui.createTabPage(self.search_tabs, 'Regular search',
regular_search_box)
gui.createTabPage(self.search_tabs, 'Advanced search',
advanced_search_box)
# Search info label.
self.search_info_label = gui.label(
self.controlArea, self,
'Number of records found: /')
# Search for records button.
self.run_search_button = gui.button(
self.controlArea,
self,
'Find records',
callback=self.run_search,
tooltip='Performs a search for articles that fit the '
'specified parameters.')
self.pubmed_controls.append(self.run_search_button)
h_line = QFrame()
h_line.setFrameShape(QFrame.HLine)
h_line.setFrameShadow(QFrame.Sunken)
self.controlArea.layout().addWidget(h_line)
# RECORD RETRIEVAL
# Text includes box.
text_includes_box = gui.widgetBox(self.controlArea,
'Text includes', addSpace=True)
self.authors_checkbox = gui.checkBox(text_includes_box, self,
'includes_authors', 'Authors')
self.title_checkbox = gui.checkBox(text_includes_box, self,
'includes_title', 'Article title')
self.mesh_checkbox = gui.checkBox(text_includes_box, self,
'includes_mesh', 'Mesh headings')
self.abstract_checkbox = gui.checkBox(text_includes_box, self,
'includes_abstract', 'Abstract')
self.url_checkbox = gui.checkBox(text_includes_box, self,
'includes_url', 'URL')
self.pubmed_controls.append(self.authors_checkbox)
self.pubmed_controls.append(self.title_checkbox)
self.pubmed_controls.append(self.mesh_checkbox)
self.pubmed_controls.append(self.abstract_checkbox)
self.pubmed_controls.append(self.url_checkbox)
# Num. records.
h_box = gui.hBox(self.controlArea)
label = gui.label(h_box, self, 'Retrieve')
label.setMaximumSize(label.sizeHint())
self.num_records_input = gui.spin(h_box, self, 'num_records',
minv=1, maxv=100000)
self.max_records_label = gui.label(h_box, self, 'records from /.')
self.max_records_label.setMaximumSize(self.max_records_label
.sizeHint())
self.pubmed_controls.append(self.num_records_input)
# Download articles.
# Search for records button.
self.retrieve_records_button = gui.button(
self.controlArea,
self,
'Retrieve records',
callback=self.retrieve_records,
tooltip='Retrieves the specified documents.')
self.pubmed_controls.append(self.retrieve_records_button)
# Num. retrieved records info label.
self.retrieval_info_label = gui.label(
self.controlArea,
self,
'Number of records retrieved: /')
# Load the most recent emails.
self.set_email_list()
# Load the most recent queries.
self.set_keyword_list()
# Check the email and enable controls accordingly.
if self.recent_emails:
email = self.recent_emails[0]
self.email_is_valid = validate_email(email)
self.enable_controls()
def sync_email(self):
email = self.email_combo.currentText()
self.email_is_valid = validate_email(email)
self.enable_controls()
def enable_controls(self):
# Enable/disable controls accordingly.
for control in self.pubmed_controls:
control.setEnabled(self.email_is_valid)
if self.pubmed_api is None or self.pubmed_api.search_record_count == 0:
self.retrieve_records_button.setEnabled(False)
if not self.email_is_valid:
self.email_combo.setFocus()
def run_search(self):
self.Error.clear()
self.Warning.clear()
self.run_search_button.setEnabled(False)
self.retrieve_records_button.setEnabled(False)
# Add the email to history.
email = self.email_combo.currentText()
if email not in self.recent_emails:
self.recent_emails.insert(0, email)
# Check if the PubMed object is present.
if self.pubmed_api is None:
self.pubmed_api = Pubmed(
email=email,
progress_callback=self.api_progress_callback,
error_callback=self.api_error_callback,
)
if self.search_tabs.currentIndex() == 0:
# Get query parameters.
terms = self.keyword_combo.currentText().split()
authors = self.author_input.text().split()
error = self.pubmed_api._search_for_records(
terms, authors, self.pub_date_from, self.pub_date_to
)
if error is not None:
self.Error.api_error(str(error))
return
if self.keyword_combo.currentText() not in self.recent_keywords:
self.recent_keywords.insert(
0,
self.keyword_combo.currentText()
)
else:
query = self.advanced_query_input.toPlainText()
if not query:
self.Warning.no_query()
self.run_search_button.setEnabled(True)
self.retrieve_records_button.setEnabled(True)
return
error = self.pubmed_api._search_for_records(advanced_query=query)
if error is not None:
self.Error.api_error(str(error))
return
self.last_advanced_query = query
self.enable_controls()
self.update_search_info()
def retrieve_records(self):
self.Warning.clear()
self.Error.clear()
if self.pubmed_api is None:
return
if self.download_running:
self.download_running = False
self.run_search_button.setEnabled(True)
self.retrieve_records_button.setText('Retrieve records')
self.pubmed_api.stop_retrieving()
return
self.download_running = True
self.run_search_button.setEnabled(False)
self.output_corpus = None # Clear the old records.
# Change the button label.
self.retrieve_records_button.setText('Stop retrieving')
# Text fields.
text_includes_params = [
self.includes_authors,
self.includes_title,
self.includes_mesh,
self.includes_abstract,
self.includes_url,
True, # Publication date field; included always.
]
required_text_fields = [
field
for field_name, field
in zip(text_includes_params, PUBMED_TEXT_FIELDS)
if field_name
]
batch_size = min(Pubmed.MAX_BATCH_SIZE, self.num_records) + 1
with self.progressBar(self.num_records/batch_size) as progress:
self.progress = progress
self.output_corpus = self.pubmed_api._retrieve_records(
self.num_records,
required_text_fields
)
self.retrieve_records_button.setText('Retrieve records')
self.download_running = False
self.send(Output.CORPUS, self.output_corpus)
self.update_retrieval_info()
self.run_search_button.setEnabled(True)
def api_progress_callback(self, start_at=None):
if start_at is not None:
self.progress.count = start_at
else:
self.progress.advance()
def api_error_callback(self, error):
self.Error.api_error(str(error))
if self.progress is not None:
self.progress.finish()
def update_search_info(self):
max_records_count = min(
self.pubmed_api.MAX_RECORDS,
self.pubmed_api.search_record_count
)
self.search_info_label.setText(
'Number of retrievable records for '
'this search query: {} '.format(max_records_count)
)
self.max_records_label.setText(
'records from {}.'.format(max_records_count)
)
self.max_records_label.setMaximumSize(self.max_records_label
.sizeHint())
self.num_records_input.setMaximum(max_records_count)
self.retrieve_records_button.setFocus()
def update_retrieval_info(self):
document_count = 0
if self.output_corpus is not None:
document_count = len(self.output_corpus)
self.retrieval_info_label.setText(
'Number of records retrieved: {} '.format(document_count)
)
self.retrieval_info_label.setMaximumSize(
self.retrieval_info_label.sizeHint()
)
def select_email(self, n):
if n < len(self.recent_emails):
email = self.recent_emails[n]
del self.recent_emails[n]
self.recent_emails.insert(0, email)
if len(self.recent_emails) > 0:
self.set_email_list()
def set_email_list(self):
self.email_combo.clear()
for email in self.recent_emails:
self.email_combo.addItem(email)
def select_keywords(self, n):
if n < len(self.recent_keywords):
keywords = self.recent_keywords[n]
del self.recent_keywords[n]
self.recent_keywords.insert(0, keywords)
if len(self.recent_keywords) > 0:
self.set_keyword_list()
def set_keyword_list(self):
self.keyword_combo.clear()
if not self.recent_keywords:
# Sample queries.
self.recent_keywords.append('orchid')
self.recent_keywords.append('hypertension')
self.recent_keywords.append('blood pressure')
self.recent_keywords.append('radiology')
for keywords in self.recent_keywords:
self.keyword_combo.addItem(keywords)
def open_calendar(self, widget):
cal_dlg = CalendarDialog(self, 'Date picker')
if cal_dlg.exec_():
widget.setText(cal_dlg.picked_date)
class FileWidget(QWidget):
on_open = pyqtSignal(str)
# TODO consider removing directory_aliases since it is not used any more
def __init__(self, dialog_title='', dialog_format='',
start_dir=os.path.expanduser('~/'),
icon_size=(12, 20), minimal_width=200,
browse_label='Browse', on_open=None,
reload_button=True, reload_label='Reload',
recent_files=None, directory_aliases=None,
allow_empty=True, empty_file_label='(none)'):
""" Creates a widget with a button for file loading and
an optional combo box for recent files and reload buttons.
Args:
dialog_title (str): The title of the dialog.
dialog_format (str): Formats for the dialog.
start_dir (str): A directory to start from.
icon_size (int, int): The size of buttons' icons.
on_open (callable): A callback function that accepts filepath as the only argument.
reload_button (bool): Whether to show reload button.
reload_label (str): The text displayed on the reload button.
recent_files (List[str]): List of recent files.
directory_aliases (dict): An {alias: dir} dictionary for fast directories' access.
allow_empty (bool): Whether empty path is allowed.
"""
super().__init__()
self.dialog_title = dialog_title
self.dialog_format = dialog_format
self.start_dir = start_dir
# Recent files should also contain `empty_file_label` so
# when (none) is selected this is stored in settings.
self.recent_files = recent_files if recent_files is not None else []
self.directory_aliases = directory_aliases or {}
self.allow_empty = allow_empty
self.empty_file_label = empty_file_label
if self.empty_file_label not in self.recent_files \
and (self.allow_empty or not self.recent_files):
self.recent_files.append(self.empty_file_label)
self.check_existence()
self.on_open.connect(on_open)
layout = QHBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
if recent_files is not None:
self.file_combo = QComboBox()
self.file_combo.setMinimumWidth(minimal_width)
self.file_combo.activated[int].connect(self.select)
self.update_combo()
layout.addWidget(self.file_combo)
self.browse_button = QPushButton(browse_label)
self.browse_button.setFocusPolicy(Qt.NoFocus)
self.browse_button.clicked.connect(self.browse)
self.browse_button.setIcon(self.style()
.standardIcon(QStyle.SP_DirOpenIcon))
self.browse_button.setIconSize(QSize(*icon_size))
self.browse_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
layout.addWidget(self.browse_button)
if reload_button:
self.reload_button = QPushButton(reload_label)
self.reload_button.setFocusPolicy(Qt.NoFocus)
self.reload_button.clicked.connect(self.reload)
self.reload_button.setIcon(self.style()
.standardIcon(QStyle.SP_BrowserReload))
self.reload_button.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
self.reload_button.setIconSize(QSize(*icon_size))
layout.addWidget(self.reload_button)
def browse(self, start_dir=None):
start_dir = start_dir or self.start_dir
path, _ = QFileDialog().getOpenFileName(self, self.dialog_title,
start_dir, self.dialog_format)
if path and self.recent_files is not None:
if path in self.recent_files:
self.recent_files.remove(path)
self.recent_files.insert(0, path)
self.update_combo()
if path:
self.open_file(path)
def select(self, n):
name = self.file_combo.currentText()
if name == self.empty_file_label:
del self.recent_files[n]
self.recent_files.insert(0, self.empty_file_label)
self.update_combo()
self.open_file(self.empty_file_label)
elif name in self.directory_aliases:
self.browse(self.directory_aliases[name])
elif n < len(self.recent_files):
name = self.recent_files[n]
del self.recent_files[n]
self.recent_files.insert(0, name)
self.update_combo()
self.open_file(self.recent_files[0])
def update_combo(self):
""" Sync combo values to the changes in self.recent_files. """
if self.recent_files is not None:
self.file_combo.clear()
for i, file in enumerate(self.recent_files):
# remove (none) when we have some files and allow_empty=False
if file == self.empty_file_label and \
not self.allow_empty and len(self.recent_files) > 1:
del self.recent_files[i]
else:
self.file_combo.addItem(os.path.split(file)[1])
for alias in self.directory_aliases.keys():
self.file_combo.addItem(alias)
def reload(self):
if self.recent_files:
self.select(0)
def check_existence(self):
if self.recent_files:
to_remove = []
for file in self.recent_files:
doc_path = os.path.join(get_sample_corpora_dir(), file)
exists = any(os.path.exists(f) for f in [file, doc_path])
if file != self.empty_file_label and not exists:
to_remove.append(file)
for file in to_remove:
self.recent_files.remove(file)
def open_file(self, path):
self.on_open.emit(path if path != self.empty_file_label else '')
def get_selected_filename(self):
if self.recent_files:
return self.recent_files[0]
else:
return self.empty_file_label