{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "8d48ca51-ba3b-412b-b5c1-8de044c96817",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loadLibrary\n",
      "remoteSourcesURL https://git0.fmf.uni-lj.si/studen/nixSuite/raw/master/remoteResources/resources.json\n",
      "{'labkeyInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}, 'irAEMM': {'url': 'https://git0.fmf.uni-lj.si/studen/iraemm/archive/master.zip', 'branch': 'master', 'modules': ['iraemmBrowser']}, 'SlicerLabkeyExtension': {'url': 'https://git0.fmf.uni-lj.si/studen/SlicerLabkeyExtension/archive/SlicerExtensionIndex.zip', 'branch': 'SlicerExtensionIndex', 'modules': ['labkeyBrowser']}, 'limfomiPET': {'url': 'https://git0.fmf.uni-lj.si/studen/limfomiPET/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser', 'segmentationBrowser']}, 'parseConfig': {'url': 'https://git0.fmf.uni-lj.si/studen/parseConfig/archive/master.zip', 'branch': 'master', 'modules': []}, 'orthancInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}, 'dynamicSPECT': {'url': 'https://git0.fmf.uni-lj.si/studen/dynamicSPECT/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser']}}\n",
      "{'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}\n",
      "File  /home/studen/temp/labkeyInterface.zip: True\n"
     ]
    }
   ],
   "source": [
    "#load required libraries\n",
    "import sys\n",
    "import os\n",
    "import chardet\n",
    "import json\n",
    "\n",
    "#you should get nixWrapper using an appropriate env\n",
    "#more details https://git0.fmf.uni-lj.si/studen/nixWrapper\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": 4,
   "id": "1322d7a2-b34b-43ef-8c7a-74065d41b560",
   "metadata": {},
   "outputs": [],
   "source": [
    "def readFiles():\n",
    "    db,fb=connectDB('labkey-public')\n",
    "    return\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"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "ca7a6974-8526-4039-9b8b-e5ee11e8eaed",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "User: andrej studen CSRF: 6c0eabd844a84d6713f144ede8aa881c\n"
     ]
    }
   ],
   "source": [
    "readFiles()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e68e3f81-285e-46a7-a072-4c1b0a6618e2",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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