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Source code for galaxy.datatypes.upload_util

import os
from typing import (

from galaxy.datatypes import (
from galaxy.util.checkers import is_single_file_zip

[docs]class UploadProblemException(Exception): pass
[docs]class HandleUploadResponse(NamedTuple): stdout: Optional[str] ext: str datatype: data.Data is_binary: bool converted_path: Optional[str] converted_newlines: bool converted_spaces: bool
[docs]def handle_upload( registry, path: str, # dataset.path requested_ext: str, # dataset.file_type name: str, # dataset.name, tmp_prefix: Optional[str], tmp_dir: Optional[str], check_content: bool, link_data_only: bool, in_place: bool, auto_decompress: bool, convert_to_posix_lines: bool, convert_spaces_to_tabs: bool, ) -> HandleUploadResponse: stdout = None converted_path = None multi_file_zip = False # Does the first 1MB look like binary content? file_prefix = sniff.FilePrefix(path, auto_decompress=auto_decompress) is_binary = file_prefix.binary converted_newlines, converted_spaces = False, False # Decompress if needed/desired and determine/validate filetype. If a keep-compressed datatype is explicitly selected # or if autodetection is selected and the file sniffs as a keep-compressed datatype, it will not be decompressed. if not link_data_only: if auto_decompress and file_prefix.compressed_format == "zip" and not is_single_file_zip(path): multi_file_zip = True try: ( ext, converted_path, compression_type, converted_newlines, converted_spaces, ) = sniff.handle_uploaded_dataset_file_internal( file_prefix, registry, ext=requested_ext, tmp_prefix=tmp_prefix, tmp_dir=tmp_dir, in_place=in_place, check_content=check_content, uploaded_file_ext=os.path.splitext(name)[1].lower().lstrip("."), convert_to_posix_lines=convert_to_posix_lines, convert_spaces_to_tabs=convert_spaces_to_tabs, ) except sniff.InappropriateDatasetContentError as exc: raise UploadProblemException(exc) elif requested_ext == "auto": ext = sniff.guess_ext(file_prefix, registry.sniff_order) else: ext = requested_ext # The converted path will be the same as the input path if no conversion was done (or in-place conversion is used) converted_path = None if converted_path == path else converted_path # Validate datasets where the filetype was explicitly set using the filetype's sniffer (if any) if requested_ext != "auto": datatype = registry.get_datatype_by_extension(requested_ext) # Enable sniffer "validate mode" (prevents certain sniffers from disabling themselves) if check_content and hasattr(datatype, "sniff"): try: is_of_datatype = datatype.sniff(path) except Exception: is_of_datatype = False if not is_of_datatype: stdout = f"Warning: The file 'Type' was set to '{requested_ext}' but the file does not appear to be of that type" # Handle unsniffable binaries if is_binary and ext == "binary": upload_ext = os.path.splitext(name)[1].lower().lstrip(".") if registry.is_extension_unsniffable_binary(upload_ext): stdout = ( "Warning: The file's datatype cannot be determined from its contents and was guessed based on" f" its extension, to avoid this warning, manually set the file 'Type' to '{upload_ext}' when uploading" " this type of file" ) ext = upload_ext else: stdout = ( "The uploaded binary file format cannot be determined automatically, please set the file 'Type'" " manually" ) datatype = registry.get_datatype_by_extension(ext) if multi_file_zip and not getattr(datatype, "compressed", False): stdout = "ZIP file contained more than one file, only the first file was added to Galaxy." return HandleUploadResponse(stdout, ext, datatype, is_binary, converted_path, converted_newlines, converted_spaces)