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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| #!/opt/bin/python3 | ||
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| """ | ||
| At this point we should have a directory with a JSON file with metadata, a tarball | ||
| uploaded by the user, and a status.json file. | ||
| This script does the following: | ||
| - Loads the JSON metadata file and stores it in MySQL | ||
| - Migrates the H5AD file to the proper directory | ||
| - Migrates the original tarball so it can be downloaded by users | ||
| Returns a status of these steps as JSON data like this: | ||
| result = { | ||
| "success": 1, | ||
| "metadata_loaded": 1, | ||
| "h5ad_migrated": 1, | ||
| "tarball_migrated": 1, | ||
| "message": "All steps completed successfully." | ||
| } | ||
| """ | ||
|
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| import cgi | ||
| import json | ||
| import os, sys | ||
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| lib_path = os.path.abspath(os.path.join('..', '..', 'lib')) | ||
| sys.path.append(lib_path) | ||
| import geardb | ||
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| from gear.metadata import Metadata | ||
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| user_upload_file_base = '../uploads/files' | ||
| dataset_final_dir = '../datasets' | ||
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| result = { | ||
| "success": 0, | ||
| "metadata_loaded": 0, | ||
| "h5ad_migrated": 0, | ||
| "tarball_migrated": 0, | ||
| "message": "" | ||
| } | ||
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| def main(): | ||
| print('Content-Type: application/json\n\n', flush=True) | ||
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| form = cgi.FieldStorage() | ||
| share_uid = form.getvalue('share_uid') | ||
| session_id = form.getvalue('session_id') | ||
| dataset_id = form.getvalue('dataset_uid') | ||
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| user = geardb.get_user_from_session_id(session_id) | ||
| if user is None: | ||
| result['message'] = 'User ID not found. Please log in to continue.' | ||
| print(json.dumps(result)) | ||
| sys.exit(0) | ||
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| dataset_upload_dir = os.path.join(user_upload_file_base, session_id, share_uid) | ||
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| # if the upload directory doesn't exist, we can't process the dataset | ||
| if not os.path.exists(dataset_upload_dir): | ||
| result['message'] = 'Dataset/directory not found.' | ||
| print(json.dumps(result)) | ||
| sys.exit(0) | ||
|
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| # Load the metadata | ||
| metadata_file = os.path.join(dataset_upload_dir, 'metadata.json') | ||
| if not os.path.exists(metadata_file): | ||
| result['message'] = 'Metadata file not found.' | ||
| print(json.dumps(result)) | ||
| sys.exit(0) | ||
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| with open(metadata_file, 'r') as f: | ||
| metadata = json.load(f) | ||
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| # Load the metadata into the database | ||
| metadata = Metadata(file_path=metadata_file) | ||
| try: | ||
| metadata.save_to_mysql(status='complete') | ||
| result['metadata_loaded'] = 1 | ||
| except Exception as e: | ||
| result['message'] = 'Error saving metadata to MySQL: {}'.format(str(e)) | ||
| print(json.dumps(result)) | ||
| sys.exit(0) | ||
|
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| # migrate the H5AD file | ||
| h5ad_file = os.path.join(dataset_upload_dir, f'{share_uid}.h5ad') | ||
| if not os.path.exists(h5ad_file): | ||
| result['message'] = 'H5AD file not found: {}'.format(h5ad_file) | ||
| print(json.dumps(result)) | ||
| sys.exit(0) | ||
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| h5ad_dest = os.path.join(dataset_final_dir, f'{dataset_id}.h5ad') | ||
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| try: | ||
| os.rename(h5ad_file, h5ad_dest) | ||
| result['h5ad_migrated'] = 1 | ||
| except Exception as e: | ||
| result['message'] = 'Error migrating H5AD file: {}'.format(str(e)) | ||
| print(json.dumps(result)) | ||
| sys.exit(0) | ||
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| # if we made it this far, all is well, so return success | ||
| result['success'] = 1 | ||
| result['message'] = 'All steps completed successfully.' | ||
| print(json.dumps(result)) | ||
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| if __name__ == '__main__': | ||
| main() |
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