class OWSql(OWWidget): name = "SQL Table" id = "orange.widgets.data.sql" description = "Load data set from SQL." icon = "icons/SQLTable.svg" priority = 30 category = "Data" keywords = ["data", "file", "load", "read", "SQL"] class Outputs: data = Output("Data", Table, doc="Attribute-valued data set read from the input file.") settings_version = 2 want_main_area = False resizing_enabled = False host = Setting(None) port = Setting(None) database = Setting(None) schema = Setting(None) username = "" password = "" table = Setting(None) sql = Setting("") guess_values = Setting(True) download = Setting(False) materialize = Setting(False) materialize_table_name = Setting("") class Information(OWWidget.Information): data_sampled = Msg("Data description was generated from a sample.") class Error(OWWidget.Error): connection = Msg("{}") no_backends = Msg("Please install a backend to use this widget") missing_extension = Msg("Database is missing extension{}: {}") def __init__(self): super().__init__() self.backend = None self.data_desc_table = None self.database_desc = None vbox = gui.vBox(self.controlArea, "Server", addSpace=True) box = gui.vBox(vbox) self.backends = BackendModel(Backend.available_backends()) self.backendcombo = QComboBox(box) if len(self.backends): self.backendcombo.setModel(self.backends) else: self.Error.no_backends() box.setEnabled(False) box.layout().addWidget(self.backendcombo) self.servertext = QLineEdit(box) self.servertext.setPlaceholderText('Server') self.servertext.setToolTip('Server') self.servertext.editingFinished.connect(self._load_credentials) if self.host: self.servertext.setText(self.host if not self.port else '{}:{}'.format(self.host, self.port)) box.layout().addWidget(self.servertext) self.databasetext = QLineEdit(box) self.databasetext.setPlaceholderText('Database[/Schema]') self.databasetext.setToolTip('Database or optionally Database/Schema') if self.database: self.databasetext.setText( self.database if not self.schema else '{}/{}'.format(self.database, self.schema)) box.layout().addWidget(self.databasetext) self.usernametext = QLineEdit(box) self.usernametext.setPlaceholderText('Username') self.usernametext.setToolTip('Username') box.layout().addWidget(self.usernametext) self.passwordtext = QLineEdit(box) self.passwordtext.setPlaceholderText('Password') self.passwordtext.setToolTip('Password') self.passwordtext.setEchoMode(QLineEdit.Password) box.layout().addWidget(self.passwordtext) self._load_credentials() self.tables = TableModel() tables = gui.hBox(box) self.tablecombo = QComboBox( minimumContentsLength=35, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength ) self.tablecombo.setModel(self.tables) self.tablecombo.setToolTip('table') tables.layout().addWidget(self.tablecombo) self.connect() index = self.tablecombo.findText(str(self.table)) if index != -1: self.tablecombo.setCurrentIndex(index) # set up the callback to select_table in case of selection change self.tablecombo.activated[int].connect(self.select_table) self.connectbutton = gui.button( tables, self, '↻', callback=self.connect) self.connectbutton.setSizePolicy( QSizePolicy.Fixed, QSizePolicy.Fixed) tables.layout().addWidget(self.connectbutton) self.custom_sql = gui.vBox(box) self.custom_sql.setVisible(False) self.sqltext = QTextEdit(self.custom_sql) self.sqltext.setPlainText(self.sql) self.custom_sql.layout().addWidget(self.sqltext) mt = gui.hBox(self.custom_sql) cb = gui.checkBox(mt, self, 'materialize', 'Materialize to table ') cb.setToolTip('Save results of the query in a table') le = gui.lineEdit(mt, self, 'materialize_table_name') le.setToolTip('Save results of the query in a table') self.executebtn = gui.button( self.custom_sql, self, 'Execute', callback=self.open_table) box.layout().addWidget(self.custom_sql) gui.checkBox(box, self, "guess_values", "Auto-discover categorical variables", callback=self.open_table) gui.checkBox(box, self, "download", "Download data to local memory", callback=self.open_table) gui.rubber(self.buttonsArea) QTimer.singleShot(0, self.select_table) def _load_credentials(self): self._parse_host_port() cm = self._credential_manager(self.host, self.port) self.username = cm.username self.password = cm.password if self.username: self.usernametext.setText(self.username) if self.password: self.passwordtext.setText(self.password) def _save_credentials(self): cm = self._credential_manager(self.host, self.port) cm.username = self.username or '' cm.password = self.password or '' def _credential_manager(self, host, port): return CredentialManager("SQL Table: {}:{}".format(host, port)) def error(self, id=0, text=""): super().error(id, text) err_style = 'QLineEdit {border: 2px solid red;}' if 'server' in text or 'host' in text: self.servertext.setStyleSheet(err_style) else: self.servertext.setStyleSheet('') if 'role' in text: self.usernametext.setStyleSheet(err_style) else: self.usernametext.setStyleSheet('') if 'database' in text: self.databasetext.setStyleSheet(err_style) else: self.databasetext.setStyleSheet('') def _parse_host_port(self): hostport = self.servertext.text().split(':') self.host = hostport[0] self.port = hostport[1] if len(hostport) == 2 else None def connect(self): self._parse_host_port() self.database, _, self.schema = self.databasetext.text().partition('/') self.username = self.usernametext.text() or None self.password = self.passwordtext.text() or None try: if self.backendcombo.currentIndex() < 0: return backend = self.backends[self.backendcombo.currentIndex()] self.backend = backend(dict( host=self.host, port=self.port, database=self.database, user=self.username, password=self.password )) self.Error.connection.clear() self._save_credentials() self.database_desc = OrderedDict(( ("Host", self.host), ("Port", self.port), ("Database", self.database), ("User name", self.username) )) self.refresh_tables() except BackendError as err: error = str(err).split('\n')[0] self.Error.connection(error) self.database_desc = self.data_desc_table = None self.tablecombo.clear() def refresh_tables(self): self.tables.clear() self.Error.missing_extension.clear() if self.backend is None: self.data_desc_table = None return self.tables.append("Select a table") self.tables.append("Custom SQL") self.tables.extend(self.backend.list_tables(self.schema)) # Called on tablecombo selection change: def select_table(self): curIdx = self.tablecombo.currentIndex() if self.tablecombo.itemText(curIdx) != "Custom SQL": self.custom_sql.setVisible(False) return self.open_table() else: self.custom_sql.setVisible(True) self.data_desc_table = None self.database_desc["Table"] = "(None)" self.table = None if len(str(self.sql)) > 14: return self.open_table() #self.Error.missing_extension( # 's' if len(missing) > 1 else '', # ', '.join(missing), # shown=missing) def open_table(self): table = self.get_table() self.data_desc_table = table self.Outputs.data.send(table) def get_table(self): curIdx = self.tablecombo.currentIndex() if curIdx <= 0: if self.database_desc: self.database_desc["Table"] = "(None)" self.data_desc_table = None return if self.tablecombo.itemText(curIdx) != "Custom SQL": self.table = self.tables[self.tablecombo.currentIndex()] self.database_desc["Table"] = self.table if "Query" in self.database_desc: del self.database_desc["Query"] what = self.table else: what = self.sql = self.sqltext.toPlainText() self.table = "Custom SQL" if self.materialize: import psycopg2 if not self.materialize_table_name: self.Error.connection( "Specify a table name to materialize the query") return try: with self.backend.execute_sql_query("DROP TABLE IF EXISTS " + self.materialize_table_name): pass with self.backend.execute_sql_query("CREATE TABLE " + self.materialize_table_name + " AS " + self.sql): pass with self.backend.execute_sql_query("ANALYZE " + self.materialize_table_name): pass except (psycopg2.ProgrammingError, BackendError) as ex: self.Error.connection(str(ex)) return try: table = SqlTable(dict(host=self.host, port=self.port, database=self.database, user=self.username, password=self.password), what, backend=type(self.backend), inspect_values=False) except BackendError as ex: self.Error.connection(str(ex)) return self.Error.connection.clear() sample = False if table.approx_len() > LARGE_TABLE and self.guess_values: confirm = QMessageBox(self) confirm.setIcon(QMessageBox.Warning) confirm.setText("Attribute discovery might take " "a long time on large tables.\n" "Do you want to auto discover attributes?") confirm.addButton("Yes", QMessageBox.YesRole) no_button = confirm.addButton("No", QMessageBox.NoRole) sample_button = confirm.addButton("Yes, on a sample", QMessageBox.YesRole) confirm.exec() if confirm.clickedButton() == no_button: self.guess_values = False elif confirm.clickedButton() == sample_button: sample = True self.Information.clear() if self.guess_values: QApplication.setOverrideCursor(QCursor(Qt.WaitCursor)) if sample: s = table.sample_time(1) domain = s.get_domain(inspect_values=True) self.Information.data_sampled() else: domain = table.get_domain(inspect_values=True) QApplication.restoreOverrideCursor() table.domain = domain if self.download: if table.approx_len() > MAX_DL_LIMIT: QMessageBox.warning( self, 'Warning', "Data is too big to download.\n" "Consider using the Data Sampler widget to download " "a sample instead.") self.download = False elif table.approx_len() > AUTO_DL_LIMIT: confirm = QMessageBox.question( self, 'Question', "Data appears to be big. Do you really " "want to download it to local memory?", QMessageBox.Yes | QMessageBox.No, QMessageBox.No) if confirm == QMessageBox.No: self.download = False if self.download: table.download_data(MAX_DL_LIMIT) table = Table(table) return table def send_report(self): if not self.database_desc: self.report_paragraph("No database connection.") return self.report_items("Database", self.database_desc) if self.data_desc_table: self.report_items("Data", report.describe_data(self.data_desc_table)) @classmethod def migrate_settings(cls, settings, version): if version < 2: # Until Orange version 3.4.4 username and password had been stored # in Settings. cm = cls._credential_manager(settings["host"], settings["port"]) cm.username = settings["username"] cm.password = settings["password"]
class SchemeInfoEdit(QWidget): """Scheme info editor widget. """ def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.scheme = None self.__setupUi() def __setupUi(self): layout = QFormLayout() layout.setRowWrapPolicy(QFormLayout.WrapAllRows) layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow) self.name_edit = LineEdit(self) self.name_edit.setPlaceholderText(self.tr("untitled")) self.name_edit.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed) self.desc_edit = QTextEdit(self) self.desc_edit.setTabChangesFocus(True) layout.addRow(self.tr("Title"), self.name_edit) layout.addRow(self.tr("Description"), self.desc_edit) self.__schemeIsUntitled = True self.setLayout(layout) def setScheme(self, scheme): """Set the scheme to display/edit """ self.scheme = scheme if not scheme.title: self.name_edit.setText(self.tr("untitled")) self.name_edit.selectAll() self.__schemeIsUntitled = True else: self.name_edit.setText(scheme.title) self.__schemeIsUntitled = False self.desc_edit.setPlainText(scheme.description or "") def commit(self): """Commit the current contents of the editor widgets back to the scheme. """ if self.__schemeIsUntitled and \ self.name_edit.text() == self.tr("untitled"): # 'untitled' text was not changed name = "" else: name = self.name_edit.text().strip() description = self.desc_edit.toPlainText().strip() self.scheme.title = name self.scheme.description = description def paintEvent(self, event): return StyledWidget_paintEvent(self, event) def title(self): return self.name_edit.text().strip() def description(self): return self.desc_edit.toPlainText().strip()
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 OWSql(OWWidget): name = "SQL Table" id = "orange.widgets.data.sql" description = "Load data set from SQL." icon = "icons/SQLTable.svg" priority = 10 category = "Data" keywords = ["data", "file", "load", "read"] class Outputs: data = Output( "Data", Table, doc="Attribute-valued data set read from the input file.") settings_version = 2 want_main_area = False resizing_enabled = False host = Setting(None) port = Setting(None) database = Setting(None) schema = Setting(None) username = "" password = "" table = Setting(None) sql = Setting("") guess_values = Setting(True) download = Setting(False) materialize = Setting(False) materialize_table_name = Setting("") class Information(OWWidget.Information): data_sampled = Msg("Data description was generated from a sample.") class Error(OWWidget.Error): connection = Msg("{}") no_backends = Msg("Please install a backend to use this widget") missing_extension = Msg("Database is missing extension{}: {}") def __init__(self): super().__init__() self.backend = None self.data_desc_table = None self.database_desc = None vbox = gui.vBox(self.controlArea, "Server", addSpace=True) box = gui.vBox(vbox) self.backendmodel = BackendModel(Backend.available_backends()) self.backendcombo = QComboBox(box) if len(self.backendmodel): self.backendcombo.setModel(self.backendmodel) else: self.Error.no_backends() box.setEnabled(False) box.layout().addWidget(self.backendcombo) self.servertext = QLineEdit(box) self.servertext.setPlaceholderText('Server') self.servertext.setToolTip('Server') self.servertext.editingFinished.connect(self._load_credentials) if self.host: self.servertext.setText(self.host if not self.port else '{}:{}'. format(self.host, self.port)) box.layout().addWidget(self.servertext) self.databasetext = QLineEdit(box) self.databasetext.setPlaceholderText('Database[/Schema]') self.databasetext.setToolTip('Database or optionally Database/Schema') if self.database: self.databasetext.setText( self.database if not self.schema else '{}/{}'. format(self.database, self.schema)) box.layout().addWidget(self.databasetext) self.usernametext = QLineEdit(box) self.usernametext.setPlaceholderText('Username') self.usernametext.setToolTip('Username') box.layout().addWidget(self.usernametext) self.passwordtext = QLineEdit(box) self.passwordtext.setPlaceholderText('Password') self.passwordtext.setToolTip('Password') self.passwordtext.setEchoMode(QLineEdit.Password) box.layout().addWidget(self.passwordtext) self._load_credentials() tables = gui.hBox(box) self.tablemodel = TableModel() self.tablecombo = QComboBox( minimumContentsLength=35, sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLength) self.tablecombo.setModel(self.tablemodel) self.tablecombo.setToolTip('table') tables.layout().addWidget(self.tablecombo) self.tablecombo.activated[int].connect(self.select_table) self.connectbutton = gui.button(tables, self, '↻', callback=self.connect) self.connectbutton.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed) tables.layout().addWidget(self.connectbutton) self.custom_sql = gui.vBox(box) self.custom_sql.setVisible(False) self.sqltext = QTextEdit(self.custom_sql) self.sqltext.setPlainText(self.sql) self.custom_sql.layout().addWidget(self.sqltext) mt = gui.hBox(self.custom_sql) cb = gui.checkBox(mt, self, 'materialize', 'Materialize to table ') cb.setToolTip('Save results of the query in a table') le = gui.lineEdit(mt, self, 'materialize_table_name') le.setToolTip('Save results of the query in a table') self.executebtn = gui.button(self.custom_sql, self, 'Execute', callback=self.open_table) box.layout().addWidget(self.custom_sql) gui.checkBox(box, self, "guess_values", "Auto-discover categorical variables", callback=self.open_table) gui.checkBox(box, self, "download", "Download data to local memory", callback=self.open_table) gui.rubber(self.buttonsArea) QTimer.singleShot(0, self.connect) def _load_credentials(self): self._parse_host_port() cm = self._credential_manager(self.host, self.port) self.username = cm.username self.password = cm.password if self.username: self.usernametext.setText(self.username) if self.password: self.passwordtext.setText(self.password) def _save_credentials(self): cm = self._credential_manager(self.host, self.port) cm.username = self.username cm.password = self.password def _credential_manager(self, host, port): return CredentialManager("SQL Table: {}:{}".format(host, port)) def error(self, id=0, text=""): super().error(id, text) err_style = 'QLineEdit {border: 2px solid red;}' if 'server' in text or 'host' in text: self.servertext.setStyleSheet(err_style) else: self.servertext.setStyleSheet('') if 'role' in text: self.usernametext.setStyleSheet(err_style) else: self.usernametext.setStyleSheet('') if 'database' in text: self.databasetext.setStyleSheet(err_style) else: self.databasetext.setStyleSheet('') def _parse_host_port(self): hostport = self.servertext.text().split(':') self.host = hostport[0] self.port = hostport[1] if len(hostport) == 2 else None def connect(self): self._parse_host_port() self.database, _, self.schema = self.databasetext.text().partition('/') self.username = self.usernametext.text() or None self.password = self.passwordtext.text() or None try: if self.backendcombo.currentIndex() < 0: return backend = self.backendmodel[self.backendcombo.currentIndex()] self.backend = backend( dict(host=self.host, port=self.port, database=self.database, user=self.username, password=self.password)) self.Error.connection.clear() self._save_credentials() self.database_desc = OrderedDict( (("Host", self.host), ("Port", self.port), ("Database", self.database), ("User name", self.username))) self.refresh_tables() self.select_table() except BackendError as err: error = str(err).split('\n')[0] self.Error.connection(error) self.database_desc = self.data_desc_table = None self.tablecombo.clear() def refresh_tables(self): self.tablemodel.clear() self.Error.missing_extension.clear() if self.backend is None: self.data_desc_table = None return self.tablemodel.append("Select a table") self.tablemodel.extend(self.backend.list_tables(self.schema)) self.tablemodel.append("Custom SQL") def select_table(self): curIdx = self.tablecombo.currentIndex() if self.tablecombo.itemText(curIdx) != "Custom SQL": self.custom_sql.setVisible(False) return self.open_table() else: self.custom_sql.setVisible(True) self.data_desc_table = None self.database_desc["Table"] = "(None)" self.table = None #self.Error.missing_extension( # 's' if len(missing) > 1 else '', # ', '.join(missing), # shown=missing) def open_table(self): table = self.get_table() self.data_desc_table = table self.Outputs.data.send(table) def get_table(self): if self.tablecombo.currentIndex() <= 0: if self.database_desc: self.database_desc["Table"] = "(None)" self.data_desc_table = None return if self.tablecombo.currentIndex() < self.tablecombo.count() - 1: self.table = self.tablemodel[self.tablecombo.currentIndex()] self.database_desc["Table"] = self.table if "Query" in self.database_desc: del self.database_desc["Query"] else: self.sql = self.table = self.sqltext.toPlainText() if self.materialize: import psycopg2 if not self.materialize_table_name: self.Error.connection( "Specify a table name to materialize the query") return try: with self.backend.execute_sql_query( "DROP TABLE IF EXISTS " + self.materialize_table_name): pass with self.backend.execute_sql_query( "CREATE TABLE " + self.materialize_table_name + " AS " + self.table): pass with self.backend.execute_sql_query( "ANALYZE " + self.materialize_table_name): pass self.table = self.materialize_table_name except (psycopg2.ProgrammingError, BackendError) as ex: self.Error.connection(str(ex)) return try: table = SqlTable(dict(host=self.host, port=self.port, database=self.database, user=self.username, password=self.password), self.table, backend=type(self.backend), inspect_values=False) except BackendError as ex: self.Error.connection(str(ex)) return self.Error.connection.clear() sample = False if table.approx_len() > LARGE_TABLE and self.guess_values: confirm = QMessageBox(self) confirm.setIcon(QMessageBox.Warning) confirm.setText("Attribute discovery might take " "a long time on large tables.\n" "Do you want to auto discover attributes?") confirm.addButton("Yes", QMessageBox.YesRole) no_button = confirm.addButton("No", QMessageBox.NoRole) sample_button = confirm.addButton("Yes, on a sample", QMessageBox.YesRole) confirm.exec() if confirm.clickedButton() == no_button: self.guess_values = False elif confirm.clickedButton() == sample_button: sample = True self.Information.clear() if self.guess_values: QApplication.setOverrideCursor(QCursor(Qt.WaitCursor)) if sample: s = table.sample_time(1) domain = s.get_domain(inspect_values=True) self.Information.data_sampled() else: domain = table.get_domain(inspect_values=True) QApplication.restoreOverrideCursor() table.domain = domain if self.download: if table.approx_len() > MAX_DL_LIMIT: QMessageBox.warning( self, 'Warning', "Data is too big to download.\n" "Consider using the Data Sampler widget to download " "a sample instead.") self.download = False elif table.approx_len() > AUTO_DL_LIMIT: confirm = QMessageBox.question( self, 'Question', "Data appears to be big. Do you really " "want to download it to local memory?", QMessageBox.Yes | QMessageBox.No, QMessageBox.No) if confirm == QMessageBox.No: self.download = False if self.download: table.download_data(MAX_DL_LIMIT) table = Table(table) return table def send_report(self): if not self.database_desc: self.report_paragraph("No database connection.") return self.report_items("Database", self.database_desc) if self.data_desc_table: self.report_items("Data", report.describe_data(self.data_desc_table)) @classmethod def migrate_settings(cls, settings, version): if version < 2: # Until Orange version 3.4.4 username and password had been stored # in Settings. cm = cls._credential_manager(settings["host"], settings["port"]) cm.username = settings["username"] cm.password = settings["password"]
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=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) 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 SchemeInfoEdit(QWidget): """Scheme info editor widget. """ def __init__(self, *args, **kwargs): QWidget.__init__(self, *args, **kwargs) self.scheme = None self.__setupUi() def __setupUi(self): layout = QFormLayout() layout.setRowWrapPolicy(QFormLayout.WrapAllRows) layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow) self.name_edit = LineEdit(self) self.name_edit.setPlaceholderText(self.tr("untitled")) self.name_edit.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed) self.desc_edit = QTextEdit(self) self.desc_edit.setTabChangesFocus(True) layout.addRow(self.tr("标题"), self.name_edit) layout.addRow(self.tr("描述"), self.desc_edit) self.__schemeIsUntitled = True self.setLayout(layout) def setScheme(self, scheme): """Set the scheme to display/edit """ self.scheme = scheme if not scheme.title: self.name_edit.setText(self.tr("untitled")) self.name_edit.selectAll() self.__schemeIsUntitled = True else: self.name_edit.setText(scheme.title) self.__schemeIsUntitled = False self.desc_edit.setPlainText(scheme.description or "") def commit(self): """Commit the current contents of the editor widgets back to the scheme. """ if self.__schemeIsUntitled and \ self.name_edit.text() == self.tr("untitled"): # 'untitled' text was not changed name = "" else: name = str(self.name_edit.text()).strip() description = str(self.desc_edit.toPlainText()).strip() self.scheme.title = name self.scheme.description = description def paintEvent(self, event): return StyledWidget_paintEvent(self, event) def title(self): return str(self.name_edit.text()).strip() def description(self): return str(self.desc_edit.toPlainText()).strip()