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    "### Requirements\n",
    "\n",
    "- Installed git. More on how to use and install git can be found [here][git]. \n",
    "- A zip of the certificate. Particularly, you'll need the crt and key files.\n",
    "- A labkey access configuration file. A sample for [linux][linuxConfig] or [Windows][windowsConfig]. The file paths point to locations of extracted files from certificate zip on your disk.\n",
    "\n",
    "[git]: https://git-scm.com/\n",
    "[linuxConfig]: https://git0.fmf.uni-lj.si/studen/labkeyInterface/src/master/network-config-sample.json\n",
    "[windowsConfig]: https://git0.fmf.uni-lj.si/studen/labkeyInterface/src/master/network-config-sample.json"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "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']}, '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': []}}\n"
     ]
    }
   ],
   "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"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using: /home/studen/.labkey/astuden/astuden.crt\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
      "  warnings.warn(\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "User: andrej studen CSRF: fef6cf98248ecf46dcbb51d171424039\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'fef6cf98248ecf46dcbb51d171424039'"
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     "execution_count": 3,
     "metadata": {},
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    }
   ],
   "source": [
    "#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','network.json')\n",
    "net.init(fconfig)\n",
    "#this reports the certificate used\n",
    "print('Using: {}'.format(net.connectionConfig['SSL']['user']))\n",
    "#This gets a deafult CSRF code; It should report user name plus a long string of random hex numbers\n",
    "net.getCSRF()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "db=labkeyDatabaseBrowser.labkeyDB(net)\n",
    "fb=labkeyFileBrowser.labkeyFileBrowser(net)\n",
    "#select a project\n",
    "project='EUtopia/Study'\n",
    "dataset='Imaging'\n",
    "idFilter={'variable':'ParticipantId','value':'VUB_PA3','oper':'eq'}\n",
    "#empty filter\n",
    "#qFilter=[]\n",
    "#qFilter can be a list of filters used in conjugation (logical AND)\n",
    "qFilter=[idFilter]\n",
    "ds=db.selectRows(project,'study',dataset,qFilter)\n",
    "rows=ds['rows']\n",
    "for row in rows:\n",
    "    #row as a dictionary\n",
    "    print(row)\n",
    "    #update row\n",
    "    #depending on field type adjust newValue\n",
    "    row['field']='newValue'\n",
    "    #print the new row\n",
    "    print(row)\n",
    "    #change the value of the field in database \n",
    "    #if field is not in database, it will NOT be added and no changes will occur\n",
    "    #db.modifyRows('update',project,'study',dataset,[row])    \n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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