Migrations: Update notebook to omit Mongo credentials from commands when authentication disabled

[eecavanna]

In migrate_10_8_0_to_11_0_0.ipynb, there is a cell that contains the following:

# Dump all collections from the "origin" database.
shell_command = f"""
  {mongodump} \
      --host='{cfg.origin_mongo_host}' \
      --port='{cfg.origin_mongo_port}' \
      --username='{cfg.origin_mongo_username}' \
      --password='{cfg.origin_mongo_password}' \
      --authenticationDatabase='admin' \
      --db='nmdc' \
      --gzip \
      --out='{cfg.origin_dump_folder_path}'
"""
completed_process = subprocess.run(shell_command, shell=True)
print(f"\nReturn code: {completed_process.returncode}")

Task

When the Mongo server does not have authentication enabled, omit the --username, --password, and --authenticationDatabase options from the command.

Do the same for similar cells.

[eecavanna]

I'm going to defer this until after the Berkeley schema roll out.

[eecavanna]

Here's a snippet that has the effect I want, although it infers the authentication enabled-ness from the value of the username configuration parameter (as opposed to getting an explicit indicator of authentication enabled-ness, assuming such a thing exists):

cli_options_for_authentication = f"""
      --username='{cfg.origin_mongo_username}' \
      --password='{cfg.origin_mongo_password}' \
      --authenticationDatabase='admin'
""" if cfg.origin_mongo_username not in ["", None] else ""

# Load the transformed collections into the origin server, replacing any same-named ones that are there.
shell_command = f"""
  {mongorestore} \
      --host='{cfg.origin_mongo_host}' \
      --port='{cfg.origin_mongo_port}' \
      {cli_options_for_authentication} \
      --gzip \
      --verbose \
      --dir='{cfg.transformer_dump_folder_path}' \
      --drop \
      --preserveUUID \
      --stopOnError
"""