solidipes.utils package

Submodules

• solidipes.utils.cloud module
  • add_global_mount_info()
  • check_process_return()
  • connect_to_postgres()
  • convert_cloud_to_cloud()
  • convert_local_to_cloud()
  • get_existing_mount_info()
  • get_mount_id()
  • list_mounts()
  • mount()
  • mount_all()
  • mount_nfs_with_mount_command()
  • mount_s3_juicefs()
  • mount_s3_juicefs_psql()
  • mount_s3_juicefs_sqlite3()
  • mount_s3fs()
  • mount_smb_with_mount_command()
  • mount_sshfs()
  • mount_with_mount_command()
  • remove_keys_from_info()
  • rsync()
  • unmount()
  • unmount_all()
  • wait_mount()
  • write_temp_passwd_file()
• solidipes.utils.config module
• solidipes.utils.git_infos module
  • GitInfos
    • GitInfos._set_gitlab_uri()
• solidipes.utils.metadata module
• solidipes.utils.solidipes_logging module
  • FormatterShell
    • FormatterShell.MESSAGE_COLORS
    • FormatterShell.PREFIX_COLORS
    • FormatterShell.format()
  • getLogger()
  • invalidPrint()
• solidipes.utils.utils module
  • _get_config_path()
  • add_completed_stage()
  • bcolors
    • bcolors.BLACK
    • bcolors.BLINK
    • bcolors.BLUE
    • bcolors.BOLD
    • bcolors.BRIGHT_BLACK
    • bcolors.BRIGHT_BLUE
    • bcolors.BRIGHT_CYAN
    • bcolors.BRIGHT_GREEN
    • bcolors.BRIGHT_MAGENTA
    • bcolors.BRIGHT_RED
    • bcolors.BRIGHT_WHITE
    • bcolors.BRIGHT_YELLOW
    • bcolors.CYAN
    • bcolors.GREEN
    • bcolors.MAGENTA
    • bcolors.RED
    • bcolors.RESET
    • bcolors.UNDERLINE
    • bcolors.WHITE
    • bcolors.YELLOW
  • dict_to_pretty_str()
  • find_config_directory()
  • generate_readme()
  • get_cloud_dir_path()
  • get_cloud_info()
  • get_completed_stages()
  • get_config()
  • get_config_path()
  • get_git_repository()
  • get_git_root()
  • get_ignore()
  • get_mimes()
  • get_mimes_path()
  • get_path_relative_to_root()
  • get_path_relative_to_workdir()
  • get_readme_path()
  • get_solidipes_directory()
  • get_study_description_path()
  • get_study_log_path()
  • get_study_metadata()
  • get_study_metadata_path()
  • get_study_root_path()
  • get_user_solidipes_directory()
  • get_zenodo_infos()
  • include_metadata_description()
  • init_git_repository()
  • is_stage_completed()
  • load_yaml()
  • populate_metadata_mandatory_fields()
  • remove_completed_stage()
  • rename_file()
  • save_yaml()
  • separate_metadata_description()
  • set_cloud_info()
  • set_config()
  • set_ignore()
  • set_mimes()
  • set_study_metadata()
  • set_zenodo_infos()
  • transform_data_containers_to_dict()
  • transform_dict_to_data_containers()
• solidipes.utils.zenodo_utils module
  • ZenodoException
  • _download_zenodo_licenses()
  • check_response()
  • clean_deposition()
  • create_deposition()
  • download_file()
  • download_files()
  • get_access_token()
  • get_existing_deposition_identifier()
  • get_existing_deposition_infos()
  • get_host_and_id()
  • save_deposition_identifier()
  • upload_archive()
  • upload_deposition_metadata()

Module contents

exception solidipes.utils.ZenodoException

Bases: ValueError

solidipes.utils.add_completed_stage(stage)

class solidipes.utils.bcolors

Bases: object

BLACK = '\x1b[30m'

BLINK = '\x1b[5m'

BLUE = '\x1b[34m'

BOLD = '\x1b[1m'

BRIGHT_BLACK = '\x1b[90m'

BRIGHT_BLUE = '\x1b[94m'

BRIGHT_CYAN = '\x1b[96m'

BRIGHT_GREEN = '\x1b[92m'

BRIGHT_MAGENTA = '\x1b[95m'

BRIGHT_RED = '\x1b[91m'

BRIGHT_WHITE = '\x1b[97m'

BRIGHT_YELLOW = '\x1b[93m'

CYAN = '\x1b[36m'

GREEN = '\x1b[32m'

MAGENTA = '\x1b[35m'

RED = '\x1b[31m'

RESET = '\x1b[0m'

UNDERLINE = '\x1b[4m'

WHITE = '\x1b[37m'

YELLOW = '\x1b[33m'

solidipes.utils.check_response(response, expected_status_code, task_description)

solidipes.utils.download_files(record, destination, progressbar=False)

solidipes.utils.generate_readme(*args, with_title=True, **kwargs)

solidipes.utils.get_cloud_info(*args, **kwargs)

solidipes.utils.get_completed_stages()

solidipes.utils.get_git_repository(initial_path='')

solidipes.utils.get_git_root(initial_path='')

solidipes.utils.get_host_and_id(identifier)

Extract Zenodo host and study ID from string identifier

URL has one of the following forms: - https://zenodo.org/record/1234567#xxx - https://zenodo.org/deposit/1234567#xxx - https://sandbox.zenodo.org/record/1234567#xxx - https://sandbox.zenodo.org/deposit/1234567#xxx - https://doi.org/10.5281/zenodo.1234567

DOI has the form 10.5281/zenodo.1234567

Parameters:

identifier (str) – URL or DOI of the study to download

Returns:

Zenodo host and study ID

host: “zenodo.org” or “sandbox.zenodo.org”

Return type:

(str, str)

solidipes.utils.get_ignore(*args, **kwargs) → set[str]

solidipes.utils.get_mimes(*args, **kwargs)

solidipes.utils.get_path_relative_to_root(path)

Express path relative to study root

solidipes.utils.get_readme_path(*args, **kwargs)

solidipes.utils.get_study_description_path(*args, **kwargs)

solidipes.utils.get_study_log_path()

solidipes.utils.get_study_metadata(*args, md_to_html=False, **kwargs)

solidipes.utils.get_study_metadata_path(*args, **kwargs)

solidipes.utils.get_study_root_path(initial_path='', **kwargs)

solidipes.utils.include_metadata_description(metadata, generate_readme=False, use_readme=False, md_to_html=False, **kwargs)

Update metadata description field with DESCRIPTION.md file

solidipes.utils.is_stage_completed(stage)

solidipes.utils.list_mounts(only_mounted=False)

Get config expressed relative to working directory, with mount status

solidipes.utils.mount_all(headless=False, allow_root=False)

Mount all mounts that are not already mounted

solidipes.utils.mount_s3fs(path, mount_info=None)

solidipes.utils.remove_completed_stage(stage)

solidipes.utils.rename_file(old_name, new_name)

solidipes.utils.set_cloud_info(config, *args, **kwargs)

solidipes.utils.set_ignore(config: set[str], *args, **kwargs)

solidipes.utils.set_mimes(config, *args, **kwargs)

solidipes.utils.set_study_metadata(config, *args, html_to_md=False, **kwargs)

solidipes.utils.unmount(path, headless=False)