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Source code for galaxy.managers.tool_data

from pathlib import Path
from typing import (

from galaxy import exceptions
from galaxy.app import StructuredApp
from galaxy.tools.data import (
from galaxy.tools.data._schema import (

[docs]class ToolDataManager: """ Interface/service object for interacting with tool data. """
[docs] def __init__(self, app: StructuredApp): self._app = app
@property def data_tables(self) -> Dict[str, TabularToolDataTable]: return self._app.tool_data_tables.data_tables
[docs] def index(self) -> ToolDataEntryList: """Return all tool data tables.""" data_tables = [table.to_dict() for table in self.data_tables.values()] return ToolDataEntryList.parse_obj(data_tables)
[docs] def show(self, table_name: str) -> ToolDataDetails: """Get details of a given data table""" data_table = self._data_table(table_name) element_view = data_table.to_dict(view='element') return ToolDataDetails.parse_obj(element_view)
[docs] def show_field(self, table_name: str, field_name: str) -> ToolDataField: """Get information about a partiular field in a tool data table""" field = self._data_table_field(table_name, field_name) return ToolDataField.parse_obj(field.to_dict())
[docs] def reload(self, table_name: str) -> ToolDataDetails: """Reloads a tool data table.""" data_table = self._data_table(table_name) data_table.reload_from_files() return self._reload_data_table(table_name)
[docs] def get_field_file_path(self, table_name: str, field_name: str, file_name: str) -> Path: """Get the absolute path to a given file name in the table field""" field_value = self._data_table_field(table_name, field_name) base_dir = Path(field_value.get_base_dir()) full_path = base_dir / file_name if str(full_path) not in field_value.get_files(): raise exceptions.ObjectNotFound("No such path in data table field.") return full_path.absolute()
[docs] def delete(self, table_name: str, values: Optional[str] = None) -> ToolDataDetails: """Removes an item from a data table""" data_table = self._data_table(table_name) if not values: raise exceptions.RequestParameterInvalidException("Invalid values for data table item specified.") split_values = values.split("\t") if len(split_values) != len(data_table.get_column_name_list()): raise exceptions.RequestParameterInvalidException(f"Invalid data table item ( {values} ) specified. Wrong number of columns ({len(split_values)} given, {len(data_table.get_column_name_list())} required).") data_table.remove_entry(split_values) return self._reload_data_table(table_name)
def _data_table(self, table_name: str) -> TabularToolDataTable: try: return self.data_tables[table_name] except KeyError: raise exceptions.ObjectNotFound(f"No such data table {table_name}") def _data_table_field(self, table_name: str, field_name: str) -> TabularToolDataField: out = self._data_table(table_name).get_field(field_name) if out is None: raise exceptions.ObjectNotFound(f"No such field {field_name} in data table {table_name}.") return out def _reload_data_table(self, name: str) -> ToolDataDetails: self._app.queue_worker.send_control_task( 'reload_tool_data_tables', noop_self=True, kwargs={'table_name': name} ) return self.show(name)