irAEMM/pythonScripts/listOrthanc.py

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


fhome=os.path.expanduser('~')

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


def getValue(filename,tags):
    #extract value of tags (list of tags) from dcmdump-ed file
    #supply tags without braces ie. 0002,0008
    #rows is a list of lines from file
    with open(filename,"r") as f:
        out=f.read()
        lst=out.split('\n')
        for tag in tags.keys():
            tags[tag]=loadDicom.getTagValue(lst,tag)
    return True


net=labkeyInterface.labkeyInterface()
net.init(fhome+'/.labkey/network.json')

db=labkeyDatabaseBrowser.labkeyDB(net)

#by default uses .labkey/Remote.json configuration


dicomBase='/data/dicom/database/dicom'
project='IPNUMMretro/Study'
schema='study'
outputList='imageList'

ds=db.selectRows(project,schema,'Imaging',{})

dicomProject='Test/Transfer'
dicomDataset='Imaging'


for row in ds['rows']:
    print("ID: {}".format(row['PatientId']))
    nfilter=[{'variable':'PatientId','value':row['PatientId'],'oper':'eq'}]
    ds1=db.selectRows(dicomProject,'study',dicomDataset,nfilter)
    for fi in ds1['rows']:
        fdir=os.path.join(dicomBase,fi['Study'],fi['Series'])
        #print("Instance: {} ".format(fdir))
        files=os.listdir(fdir)
        for f in files:
            tfile=os.path.join(fdir,f)
            print("{}".format(tfile))
            #add files to orthanc via PACS
            #outText=subprocess.check_output([storescu,peer,port,tfile])
            oRow={'PatientId':row['PatientId'],'Series':fi['Series'],'Study':fi['Study'],'file':f,'statusFlag':'AVAILABLE'}
            ds2=db.selectRows(project,'lists',outputList,[{'variable':'file','value':f,'oper':'eq'}])
            if len(ds2['rows']):
                continue
            db.modifyRows('insert',project,'lists',outputList,[oRow])

   
print("Done")
quit()