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Source code for galaxy.tool_util.toolbox.views.sources

import logging
import os
from typing import Dict, List

import yaml

from galaxy.util import config_directories_from_setting
from .definitions import StaticToolBoxView

log = logging.getLogger(__name__)

EXTENSIONS = [".yml", ".yaml", ".json"]

[docs]class StaticToolBoxViewSources: view_directories: List[str] view_dicts: List[Dict]
[docs] def __init__(self, view_directories=None, view_dicts=None): self.view_directories = config_directories_from_setting(view_directories) or [] self.view_dicts = view_dicts or []
[docs] def get_definitions(self) -> List[StaticToolBoxView]: view_definitions = [] for view_dict in self.view_dicts: view_definitions.append(StaticToolBoxView.from_dict(view_dict)) for view_directory in self.view_directories: if not os.path.exists(view_directory): log.warning(f"Failed to find toolbox view directory {view_directory}") for filename in os.listdir(view_directory): if not looks_like_view_source_filename(filename): continue view_path = os.path.join(view_directory, filename) with open(view_path) as f: view_dict = yaml.safe_load(f) if "id" not in view_dict: file_id = os.path.splitext(filename)[0] view_dict["id"] = file_id view_definitions.append(StaticToolBoxView.from_dict(view_dict)) return view_definitions
[docs]def looks_like_view_source_filename(filename: str) -> bool: for ext in EXTENSIONS: if filename.endswith(ext): return True return False