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| #!/usr/bin/env python3 | |
| import argparse | |
| import logging | |
| import os | |
| import os.path as op | |
| import resgen as rg | |
| import sys | |
| def main(): | |
| parser = argparse.ArgumentParser( | |
| description=""" | |
| python sync_folder.py project-name folder [folder2] ... | |
| Sync a directory with a resgen project. Tries to automatically | |
| infer filetypes and datatypes from filenames. Resgen username | |
| and password should be in the RG_USER and RG_PASSWORD environment | |
| variables. Requires `resgen-python>=0.2.3` and `higlass-python>=0.4.0`. | |
| """ | |
| ) | |
| parser.add_argument("project_name") | |
| parser.add_argument("target_dirs", nargs="+") | |
| # parser.add_argument('-o', '--options', default='yo', | |
| # help="Some option", type='str') | |
| # parser.add_argument('-u', '--useless', action='store_true', | |
| # help='Another useless option') | |
| args = parser.parse_args() | |
| logging.basicConfig(level=logging.INFO) | |
| logger = logging.getLogger(__name__) | |
| username = os.environ["RG_USER"] | |
| password = os.environ["RG_PASSWORD"] | |
| project_name = args.project_name | |
| logger.debug(f"connecting {username}/{password}") | |
| rgc = rg.connect(username, password) | |
| logger.debug(f"creating project {project_name}") | |
| project = rgc.find_or_create_project(project_name) | |
| target_dirs = args.target_dirs | |
| if not args.target_dirs: | |
| target_dirs = ["."] | |
| added = 0 | |
| filenames = set() | |
| # add files | |
| for target_dir in target_dirs: | |
| for file in os.listdir(target_dir): | |
| if file in filenames: | |
| logger.error(f"Filename {file} appears twice in the directory tree") | |
| filenames.add(file) | |
| logger.info(f"Syncing {file}") | |
| filepath = op.join(target_dir, file) | |
| logger.debug(f"Syncing: {filepath}") | |
| project.sync_dataset(filepath) | |
| added += 1 | |
| deleted = 0 | |
| dsets = project.list_datasets() | |
| for dset in dsets: | |
| filename = op.split(dset.datafile)[1] | |
| if filename not in filenames: | |
| logger.info(f"Deleting dataset with filename {filename}") | |
| project.delete_dataset(dset.uuid) | |
| logger.info(f"Finished, synced {added} files, deleted {deleted} files") | |
| if __name__ == "__main__": | |
| main() |
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