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 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8d48ca51-ba3b-412b-b5c1-8de044c96817",
   "metadata": {},
   "outputs": [],
   "source": [
    "#load required libraries\n",
    "import sys\n",
    "import os\n",
    "import SimpleITK\n",
    "import numpy\n",
    "import matplotlib.pyplot\n",
    "import chardet\n",
    "import json\n",
    "\n",
    "#you should get nixSuite via git clone https://git0.fmf.uni-lj.si/studen/nixSuite.git\n",
    "#if you don't put it to $HOME/software/src/, you should update the path\n",
    "nixSuite=os.path.join(os.path.expanduser('~'),'software','src','nixSuite')\n",
    "sys.path.append(os.path.join(nixSuite,'wrapper'))\n",
    "import nixWrapper\n",
    "nixWrapper.loadLibrary('labkeyInterface')\n",
    "import labkeyInterface\n",
    "import labkeyDatabaseBrowser\n",
    "import labkeyFileBrowser\n",
    "\n",
    "def connectDB(server):\n",
    "    #check connectivity. This checks the configuration in $HOME/.labkey/network.json, \n",
    "    #where paths to certificates are stored\n",
    "    net=labkeyInterface.labkeyInterface()\n",
    "    fconfig=os.path.join(os.path.expanduser('~'),'.labkey','{}.json'.format(server))\n",
    "    net.init(fconfig)\n",
    "    #this reports the certificate used\n",
    "    try:\n",
    "        print('Using: {}'.format(net.connectionConfig['SSL']['user']))\n",
    "    except KeyError:\n",
    "        pass\n",
    "    #This gets a deafult CSRF code; It should report user name plus a long string of random hex numbers\n",
    "    net.getCSRF()\n",
    "    db=labkeyDatabaseBrowser.labkeyDB(net)\n",
    "    fb=labkeyFileBrowser.labkeyFileBrowser(net)\n",
    "    return db,fb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1322d7a2-b34b-43ef-8c7a-74065d41b560",
   "metadata": {},
   "outputs": [],
   "source": [
    "db,fb=connectDB('onko-nix')\n",
    "imageDir='preprocessedImages'\n",
    "idFilter={'variable':'ParticipantId','value':'1057/18','oper':'eq'}\n",
    "project='limfomiPET/Study'\n",
    "ds=db.selectRows(project,'study','Imaging1',[idFilter])\n",
    "localDir=os.path.join(os.path.expanduser('~'),'temp','limfomiPET')\n",
    "if not os.path.isdir(localDir):\n",
    "    os.mkdir(localDir)\n",
    "for r in ds['rows']:\n",
    "    print(r)\n",
    "    remotePath='/'.join([imageDir,r['patientCode'],r['visitCode'],r['ctResampled']])\n",
    "    urlPath=fb.formatPathURL(project,remotePath)\n",
    "    #print('{}'.format(fb.entryExists(urlPath)))\n",
    "    localPath=os.path.join(localDir,r['ctResampled'])\n",
    "    fb.readFileToFile(urlPath,localPath)\n",
    "    "
   ]
  }
 ],
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