Update process_records command to not overwrite existing files

microbiomedata / nmdc_automation

Prototype automation

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Closed mbthornton-lbl closed 1 month ago

mbthornton-lbl commented 1 month ago

This PR provides changes to 2 methods used in symbolic link creation and file re-writing for the process-records command.

assembly_file_operations: Add a check if the new file already exists, log and skip
link_data_file_paths: Add a check if the symbolic link already exists, log and skip