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README.md

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  • Must be in base folder before running any command (ex. alertremake)

Manual Operation

For updating and creating databases manually

Example usage [foreground]

python3 driver_manual.py -db {DATABASE TAG} -m {MODE} -r {RESTART FROM}

Example usage [background]

nohup python3 -u driver_manual.py -db {DATABASE TAG} -m {MODE} -r {RESTART FROM} &

Arguments

Tags

  • ct [Clinical Trial Database]
  • pm [PubMed Database]
  • gnt [NIH Funded Projects Database]
  • gard [GARD Database] --has no update mode; build database in full when triggered

Modes

  • create
  • update

Restart from

Do not use this tag if you are not restarting from scratch (ct trial progress is greater than 0)

  • 4 [Database population]
  • 3 [Query generation]
  • 2 [Full trial data gathering]
  • 1 [NCTID gathering]
  • 0 [Rare disease name webscraping; from scratch]

Automatic Operation

For updating databases automatically This can be paired with the linux nohup command to run in the background

Example usage [foreground]

python3 driver_automatic.py -db {DATABASE TAG}

Example usage [background]

nohup python3 -u driver_automatic.py -db {DATABASE TAG} & This will redirect all console output to a nohup.txt in the base directory

Arguments

Tags

  • ct [Clinical Trial Database]
  • pm [PubMed Database]
  • gnt [NIH Funded Projects Database]