bgc_rtqc.py

import sys
from datetime import datetime
import contextlib

from medsrtqc.vms import read_vms_profiles, write_vms_profiles
from medsrtqc.qc.check import preTestCheck

with open(f'bgc_logs/{datetime.utcnow().strftime("%Y%m%d_%H%M")}_log.log', 'w') as log_file:
    with contextlib.redirect_stderr(log_file):

        # read from command line
        input_file = sys.argv[1]
        try:
            profs = read_vms_profiles(input_file,  ver='win')
            ver = 'win'
        except:
            try:
                profs = read_vms_profiles(input_file, ver='vms')
                ver = 'vms'
            except:
                raise IOError('Could not read file with either VMS or Windows encoding')

        # run tests on appropriate bgc variables
        check = preTestCheck()
        all_tests = []
        for p in profs:
            # which tests to do based on variables in profile
            tests = check.run(p)
            # add FLUA if appropriate, and QCP/QCF variables if they don't exist
            tests = p.prepare(tests)
            all_tests.append(tests)
            for t in tests:
                t.run(p)

        # only export a file if we actually did anything to it
        if len(all_tests) > 0:
            # export profiles with altered flags, CHLA_ADJUSTED likely populated
            output_file = input_file.replace('.', '_output.')
            f = open(output_file, 'wb')
            write_vms_profiles(profs, f, ver=ver)
            f.close()