mirror of
https://github.com/galaxyproject/galaxy.git
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90 lines
3.2 KiB
Python
90 lines
3.2 KiB
Python
import argparse
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import json
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import os
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import sys
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from galaxy.files import ConfiguredFileSources
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def get_file_sources(file_sources_path):
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assert os.path.exists(file_sources_path), f"file sources path [{file_sources_path}] does not exist"
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with open(file_sources_path) as f:
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file_sources_as_dict = json.load(f)
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file_sources = ConfiguredFileSources.from_dict(file_sources_as_dict)
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return file_sources
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def check_for_duplicate_name(files_to_export):
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seen = set()
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duplicates = set()
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for entry in files_to_export:
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name = entry["staging_path"]
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if name in seen:
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duplicates.add(name)
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seen.add(name)
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if duplicates:
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sys.exit(f"Duplicate export filenames given: {', '.join(duplicates)}, failing export")
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def write_if_not_exists(file_sources, target_uri, real_data_path):
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file_source_path = file_sources.get_file_source_path(target_uri)
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if os.path.exists(file_source_path.path):
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print(f'Error: File "{file_source_path.path}" already exists. Skipping.')
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return 1
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file_source = file_source_path.file_source
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file_source.write_from(file_source_path.path, real_data_path)
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def get_directory_uri(args):
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directory_uri = args.directory_uri
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if not directory_uri:
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inputs = json.load(open(args.inputs, "r"))
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directory_uri = inputs["d_uri"]
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if not directory_uri.endswith("/"):
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directory_uri = f"{directory_uri}/"
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return directory_uri
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def main(argv=None):
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if argv is None:
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argv = sys.argv[1:]
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args = _parser().parse_args(argv)
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exit_code = 0
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file_sources = get_file_sources(args.file_sources)
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directory_uri = get_directory_uri(args)
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export_metadata_files = args.export_metadata_files
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with open(args.files_to_export) as f:
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files_to_export = json.load(f)
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counter = 0
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check_for_duplicate_name(files_to_export)
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for entry in files_to_export:
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name = entry["staging_path"]
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real_data_path = entry["source_path"]
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target_uri = f"{directory_uri}{name}"
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if write_if_not_exists(file_sources, target_uri, real_data_path):
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exit_code = 1
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if export_metadata_files:
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metadata_files = entry.get("metadata_files", [])
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for metadata_file in metadata_files:
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metadata_file_uri = f"{directory_uri}{metadata_file['staging_path']}"
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if write_if_not_exists(file_sources, metadata_file_uri, metadata_file["source_path"]):
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exit_code = 1
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counter += 1
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print(f"{counter} out of {len(files_to_export)} files have been exported.\n")
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sys.exit(exit_code)
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def _parser():
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parser = argparse.ArgumentParser()
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parser.add_argument("--inputs", type=str, help="galaxy inputs")
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# post 2026.XX drop the directory-uri argument and just assume inputs always contains d_uri.
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parser.add_argument("--directory-uri", type=str, help="directory target URI")
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parser.add_argument("--file-sources", type=str, help="file sources json")
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parser.add_argument("--files-to-export", type=str, help="files to export")
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parser.add_argument("--export-metadata-files", type=bool, help="export metadata files", default=False)
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return parser
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if __name__ == "__main__":
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main()
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