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AoU EHR Submission Validator

Validate submissions for the All of Us EHR data

Requirements

  • Python >=3.6 (download from here and install)
  • pip (download get-pip.py and run python get-pip.py)

Installation / Configuration

  • Install requirements by running

     pip install -r requirements.txt

Running

  • Update _settings.py and rename it to settings.py
  • Create a folder and place all the EHR submission files to be validated into it
  • Set the "csv_dir" parameter in settings.py to the full path of the folder created above
  • Ensure the resources folder is also downloaded and is located in the same place as omop_file_validator.py
  • Execute the following at the command line:
python omop_file_validator.py [-h] [-r RESTRICT]

Evaluate OMOP files for formatting issues before AoU submission.

optional arguments:
  -h, --help            show this help message and exit
  -r RESTRICT, --restrict RESTRICT
                        Number of rows to restrict for validation per file. e.g. --restrict 1000 for only validating
                        the first 1000 lines

Validation logic

  • File names must follow naming convention {table}.csv
  • Files must be in CSV format (comma-delimited) as specified by rfc4180
  • Column names and types must follow the conventions in resources/omop