irAEMM/pythonScripts/modifyDataset.py

#a script to modify a patient from list. Current implementation deletes 
#all data for patients identified by study regulatory number from study

#basic python
import os
import subprocess
import re
import datetime
import sys
import json


def main(parameterFile):
    fhome=os.path.expanduser('~')

    with open(os.path.join(fhome,".labkey","setup.json")) as f:
        setup=json.load(f)

    sys.path.insert(0,setup["paths"]["nixWrapper"])
    import nixWrapper

    nixWrapper.loadLibrary("labkeyInterface")

    import labkeyInterface
    import labkeyDatabaseBrowser
    import labkeyFileBrowser


    net=labkeyInterface.labkeyInterface()
    net.init(os.path.join(fhome,'.labkey','network.json'))

    db=labkeyDatabaseBrowser.labkeyDB(net)

    #by default uses .labkey/Remote.json configuration
    with open(parameterFile) as f:
        pars=json.load(f)


    project=pars['project']
    schema=pars['schema']
    query=pars['query']
    

    #study section ################



#select patients enroled under regulatory number
    
    ds=db.selectRows(project,schema,query,[])

    for r in ds['rows']:
        r['View']='[VIEW]'
        db.modifyRows('update',project,schema,query,[r])

    print("Done")

if __name__ == '__main__':
    main(sys.argv[1])