def _create_empty_widget(self, ) -> QWidget:
toolbar = QToolBar(self)
toolbar.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
spacer_begin = QWidget(toolbar)
spacer_begin.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Preferred)
spacer_end = QWidget(toolbar)
spacer_end.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Preferred)
toolbar.addWidget(spacer_begin)
toolbar.addAction(self._action_new)
toolbar.addAction(self._action_open)
toolbar.addWidget(spacer_end)
return toolbar
class VqlEditorWidget(plugin.PluginWidget):
"""Exposed class to manage VQL/SQL queries from the mainwindow"""
LOCATION = plugin.FOOTER_LOCATION
ENABLE = True
def __init__(self, parent=None):
super().__init__(parent)
self.setWindowTitle(self.tr("VQL Editor"))
# Top toolbar
self.top_bar = QToolBar()
self.top_bar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.run_action = self.top_bar.addAction(FIcon(0xF040A),
self.tr("Run"), self.run_vql)
self.run_action.setShortcuts(
[Qt.CTRL + Qt.Key_R, QKeySequence.Refresh])
self.run_action.setToolTip(
self.tr("Run VQL query (%s)" %
self.run_action.shortcut().toString()))
# Syntax highlighter and autocompletion
self.text_edit = CodeEdit()
# Error handling
self.log_edit = QLabel()
self.log_edit.setMinimumHeight(40)
self.log_edit.setStyleSheet(
"QWidget{{background-color:'{}'; color:'{}'}}".format(
style.WARNING_BACKGROUND_COLOR, style.WARNING_TEXT_COLOR))
self.log_edit.hide()
self.log_edit.setFrameStyle(QFrame.StyledPanel | QFrame.Raised)
main_layout = QVBoxLayout()
main_layout.addWidget(self.top_bar)
main_layout.addWidget(self.text_edit)
main_layout.addWidget(self.log_edit)
main_layout.setContentsMargins(0, 0, 0, 0)
main_layout.setSpacing(0)
self.setLayout(main_layout)
def on_open_project(self, conn: sqlite3.Connection):
"""overrided from PluginWidget : Do not call this methods
Args:
conn (sqlite3.Connection): sqlite3 connection
"""
self.conn = conn
self._fill_completer()
self.on_refresh()
def on_refresh(self):
"""overrided from PluginWidget"""
vql_query = build_vql_query(
self.mainwindow.state.fields,
self.mainwindow.state.source,
self.mainwindow.state.filters,
self.mainwindow.state.group_by,
self.mainwindow.state.having,
)
self.set_vql(vql_query)
def set_vql(self, text: str):
"""Set vql source code without executed
Args:
text (str): VQL query
"""
self.text_edit.blockSignals(True)
self.text_edit.setPlainText(text)
self.text_edit.blockSignals(False)
def _fill_completer(self):
"""Create Completer with his model
Fill the model with the SQL keywords and database fields
"""
# preload samples , selection and wordset
samples = [i["name"] for i in sql.get_samples(self.conn)]
selections = [i["name"] for i in sql.get_selections(self.conn)]
wordsets = [i["name"] for i in sql.get_wordsets(self.conn)]
# keywords = []
self.text_edit.completer.model.clear()
self.text_edit.completer.model.beginResetModel()
# register keywords
for keyword in self.text_edit.syntax.sql_keywords:
self.text_edit.completer.model.add_item(keyword, "VQL keywords",
FIcon(0xF0169), "#f6ecf0")
for selection in selections:
self.text_edit.completer.model.add_item(selection, "Source table",
FIcon(0xF04EB), "#f6ecf0")
for wordset in wordsets:
self.text_edit.completer.model.add_item(f"WORDSET['{wordset}']",
"WORDSET", FIcon(0xF04EB),
"#f6ecf0")
for field in sql.get_fields(self.conn):
name = field["name"]
description = "<b>{}</b> ({}) from {} <br/><br/> {}".format(
field["name"], field["type"], field["category"],
field["description"])
color = style.FIELD_TYPE.get(field["type"], "str")["color"]
icon = FIcon(
style.FIELD_TYPE.get(field["type"], "str")["icon"], "white")
if field["category"] == "variants" or field[
"category"] == "annotations":
self.text_edit.completer.model.add_item(
name, description, icon, color)
if field["category"] == "samples":
# Overwrite name
for sample in samples:
name = "sample['{}'].{}".format(sample, field["name"])
description = "<b>{}</b> ({}) from {} {} <br/><br/> {}".format(
field["name"],
field["type"],
field["category"],
sample,
field["description"],
)
self.text_edit.completer.model.add_item(
name, description, icon, color)
self.text_edit.completer.model.endResetModel()
# if field["category"] == "samples":
# for sample in samples:
# keywords.append("sample['{}'].{}".format(sample, field["name"]))
# else:
# keywords.append(field["name"])
def check_vql(self) -> bool:
"""Check VQL statement; return True if OK, False when an error occurs
Notes:
This function also sets the error message to the bottom of the view.
Returns:
bool: Status of VQL query (True if valid, False otherwise).
"""
try:
self.log_edit.hide()
_ = [i for i in vql.parse_vql(self.text_edit.toPlainText())]
except (TextXSyntaxError, VQLSyntaxError) as e:
# Show the error message on the ui
# Available attributes: e.message, e.line, e.col
self.set_message("%s: %s, col: %d" %
(e.__class__.__name__, e.message, e.col))
return False
return True
def run_vql(self):
"""Execute VQL code
Suported commands and the plugins that need to be refreshed in consequence:
- select_cmd: main ui (all plugins in fact)
- count_cmd: *not supported*
- drop_cmd: selections & wordsets
- create_cmd: selections
- set_cmd: selections
- bed_cmd: selections
- show_cmd: *not supported*
- import_cmd: wordsets
"""
# Check VQL syntax first
if not self.check_vql():
return
for cmd in vql.parse_vql(self.text_edit.toPlainText()):
LOGGER.debug("VQL command %s", cmd)
cmd_type = cmd["cmd"]
# If command is a select kind
if cmd_type == "select_cmd":
# => Command will be executed in different widgets (variant_view)
# /!\ VQL Editor will not check SQL validity of the command
# columns from variant table
self.mainwindow.state.fields = cmd["fields"]
# name of the variant selection
self.mainwindow.state.source = cmd["source"]
self.mainwindow.state.filters = cmd["filters"]
self.mainwindow.state.group_by = cmd["group_by"]
self.mainwindow.state.having = cmd["having"]
# Refresh all plugins
self.mainwindow.refresh_plugins(sender=self)
continue
try:
# Check SQL validity of selections related commands
command.create_command_from_obj(self.conn, cmd)()
except (sqlite3.DatabaseError, VQLSyntaxError) as e:
# Display errors in VQL editor
self.set_message(str(e))
LOGGER.exception(e)
continue
# Selections related commands
if cmd_type in ("create_cmd", "set_cmd", "bed_cmd"):
# refresh source editor plugin for selections
self.mainwindow.refresh_plugin("source_editor")
continue
if cmd_type == "drop_cmd":
# refresh source editor plugin for selections
self.mainwindow.refresh_plugin("source_editor")
# refresh wordset plugin
self.mainwindow.refresh_plugin("word_set")
if cmd_type == "import_cmd":
# refresh wordset plugin
self.mainwindow.refresh_plugin("word_set")
def set_message(self, message: str):
"""Show message error at the bottom of the view
Args:
message (str): Error message
"""
if self.log_edit.isHidden():
self.log_edit.show()
icon_64 = FIcon(0xF0027, style.WARNING_TEXT_COLOR).to_base64(18, 18)
self.log_edit.setText("""<div height=100%>
<img src="data:image/png;base64,{}" align="left"/>
<span> {} </span>
</div>""".format(icon_64, message))
