irAEMM/pythonScripts/linkOrthanc.py

import os
import json
import re
import sys
import datetime
import re

fhome=os.path.expanduser('~')
sys.path.insert(1,fhome+'/software/src/labkeyInterface')
import labkeyInterface
import labkeyDatabaseBrowser

fconfig=os.path.join(fhome,'.labkey','network.json')

net=labkeyInterface.labkeyInterface()
net.init(fconfig)
db=labkeyDatabaseBrowser.labkeyDB(net)


i=0
projectOrthanc='Orthanc/Database'
projectIPNU='iPNUMMretro/Study'

ds=db.selectRows(projectIPNU,'study','Imaging',[])

varList={'CT':['startswith','CT%20WB'],'PETWB':['eq','PET%20WB'],
        'PETWBUncorrected':['eq','PET%20WB%20Uncorrected'],
        'Topogram':['startswith','Topogram']}

i=0

for row in ds['rows']:

    for var in varList:
        print('Filtering for {}/{}'.format(var,varList[var][1]))
        qfilter={}
        qfilter['variable']='seriesDescription'
        qfilter['value']=varList[var][1]
        qfilter['oper']=varList[var][0]
        
        qfilter1={}
        qfilter1['variable']='PatientId'
        qfilter1['value']=row['PatientId']
        qfilter1['oper']='eq'

        #don't have dates, so I have to poll
        qfilter2={}
        qfilter2['variable']='studyDate'
        qfilter2['oper']='dateeq'
        fdate=row['date']
        fdate=re.sub(r' (.*)$','',fdate)
        fdate=re.sub(r'/',r'-',fdate)
        qfilter2['value']=fdate


        tfilter=[qfilter,qfilter1,qfilter2]
        ds1=db.selectRows(projectOrthanc,'study','Imaging',tfilter)
        print('[{}][{}][{}]: {}'.format(\
                row['PatientId'],var,fdate,len(ds1['rows'])))
        
        
        for r1 in ds1['rows']:
            print("ID: {}, DESC: {}, DATE: {}".format(\
                r1['PatientId'],r1['seriesDescription'],r1['studyDate']))
            #print("Study date {}/{}".format(row['date'],r1['studyDate']))


            
        row[var]=len(ds1['rows'])
        if len(ds1['rows'])==1:
            row[var]=ds1['rows'][0]['orthancSeries']

        if len(ds1['rows'])>1:
            if var=='CT':
                varC=[r1['orthancSeries']  for r1 in ds1['rows']\
                        if r1['seriesDescription'].find('fov')<0] 
                if len(varC)==1:
                    row[var]=varC[0]

       
    db.modifyRows('update',projectIPNU,'study','Imaging',[row])
        
print("Done")