Source code for immuneML.presentation.html.Util

import logging
import os
import shutil
from enum import Enum
from pathlib import Path
import numpy as np

from immuneML.reports.ReportOutput import ReportOutput
from immuneML.reports.ReportResult import ReportResult
from immuneML.util.PathBuilder import PathBuilder

[docs]class Util:
[docs] @staticmethod def to_dict_recursive(obj, base_path: Path): if not hasattr(obj, "__dict__"): if (isinstance(obj, Path) or isinstance(obj, str)) and os.path.isfile(obj): obj_abs_path = os.path.abspath(obj) base_abs_path = os.path.abspath(str(base_path)) res_path = os.path.relpath(obj_abs_path, base_abs_path) return res_path elif hasattr(obj, "name"): return elif isinstance(obj, list): return [Util.to_dict_recursive(element, base_path) for element in obj] else: return obj if obj is not None else "" elif isinstance(obj, Enum): return str(obj) else: vars_obj = vars(obj) result = { attribute_name: Util.to_dict_recursive(vars_obj[attribute_name], base_path) for attribute_name in vars_obj.keys() } if isinstance(obj, ReportOutput): path = getattr(obj, "path") if path is not None: result['is_download_link'] = True result['download_link'] = os.path.relpath(path=getattr(obj, "path"), start=base_path) result['file_name'] = getattr(obj, "name") if any([ext == path.suffix for ext in ['.svg', '.jpg', '.png']]): result['is_embed'] = False else: result['is_embed'] = True else: result['is_download_link'] = False return result
[docs] @staticmethod def get_css_content(css_path: Path): with"rb") as file: content = return content
[docs] @staticmethod def make_downloadable_zip(base_path: Path, path_to_zip: Path, filename: str = "") -> str: if filename == "": filename = "_".join(Path(os.path.relpath(str(path_to_zip), str(base_path)).replace(".", "")).parts) / "zip") zip_file_path = shutil.make_archive(base_name=base_path / f"zip/{filename}", format="zip", root_dir=str(path_to_zip)) return zip_file_path
[docs] @staticmethod def get_full_specs_path(base_path) -> str: specs_path = list(base_path.glob("../**/full*.yaml")) if len(specs_path) == 1: path_str = os.path.relpath(specs_path[0], base_path) else: path_str = "" return path_str
[docs] @staticmethod def get_table_string_from_csv_string(csv_string: str, separator: str = ",", has_header: bool = True) -> str: table_string = "<table>\n" for index, line in enumerate(csv_string.splitlines()): if index == 0 and has_header: table_string += "<thead>\n" table_string += "<tr>\n" for col in line.split(separator): table_string += f"<td>{col}</td>\n" table_string += "</tr>\n" if index == 0 and has_header: table_string += "</thead>\n" table_string += "</table>\n" return table_string
[docs] @staticmethod def get_table_string_from_csv(csv_path: Path, separator: str = ",", has_header: bool = True) -> str: with"r") as file: table_string = Util.get_table_string_from_csv_string( return table_string
[docs] @staticmethod def update_report_paths(report_result: ReportResult, path: Path) -> ReportResult: for attribute in vars(report_result): attribute_value = getattr(report_result, attribute) if isinstance(attribute_value, list): for output in attribute_value: if isinstance(output, ReportOutput): new_filename = "_".join([part for part in Path(os.path.relpath(path=str(output.path), start=str(path))).parts if part != ".."]) new_path = path / new_filename if output.path != new_path: shutil.copyfile(src=str(output.path), dst=new_path) output.path = new_path else: logging.warning(f"HTML util: one of the report outputs was not returned properly from the report {}, " f"and it will not be moved to HTML output folder.") return report_result