ibridges.data_operations.upload

ibridges.data_operations.upload(local_path, irods_path, overwrite=False, on_error='fail', resc_name='', copy_empty_folders=True, options=None, dry_run=False, metadata=None, progress_bar=True)

Upload a local directory or file to iRODS.

Parameters:

  • local_path (Union[str, Path]) – Absolute path to the directory to upload

  • irods_path (IrodsPath) – Absolute irods destination path

  • overwrite (bool) – If data object or collection already exists on iRODS, overwrite

  • on_error (str) – When a transfer of a file fails, by default the whole transfer will stop and print the error message(fail). By setting ‘on-error’ to ‘warn’, those errors will be turned into warnings and the transfer continues with the next file. Setting ‘on-error’ to ‘skip’ will omit any message and simply proceed.

  • resc_name (str) – Name of the resource to which data is uploaded, by default the server will decide

  • copy_empty_folders (bool) – Create respective iRODS collection for empty folders. Default: True.

  • options (Optional[dict]) – Python-irodsclient options found in irods.keywords. The following keywords will be ignored since they are set by iBridges: FORCE_FLAG_KW, RESC_NAME_KW, NUM_THREADS_KW, REG_CHKSUM_KW, VERIFY_CHKSUM_KW.

  • dry_run (bool) – Whether to do a dry run before uploading the files/folders.

  • metadata (Union[None, str, Path, dict]) – If not None, it should point to a file that contains the metadata for the upload.

  • progress_bar (bool) – Whether to display a progress bar.

Return type:

Operations

Returns:

Operations object that can be used to execute the upload in case of a dry-run.

Raises:

  • FileNotFoundError: – If the local_path is not a valid filename of directory.

  • DataObjectExistsError: – If the data object to be uploaded already exists without using overwrite==True.

  • PermissionError: – If the iRODS server does not allow the collection or data object to be created.

Examples

>>> ipath = IrodsPath(session, "~/some_col")
>>> # Below will create a collection with "~/some_col/dir".
>>> upload(Path("dir"), ipath)

>>> # Same, but now data objects that exist will be overwritten.
>>> upload(Path("dir"), ipath, overwrite=True)

>>> # Perform the upload in two steps with a dry-run
>>> ops = upload(Path("some_file.txt"), ipath, dry_run=True)  # Does not upload
>>> ops.print_summary()  # Check if this is what you want here.
>>> ops.execute()  # Performs the upload