{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "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",
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      "2\n",
      "User: andrej studen CSRF: eea88833c27f8e5eab0869f8c9c81845\n",
      "b'{\\n  \"rowsAffected\" : 1,\\n  \"queryName\" : \"clinicalDataInternational\",\\n  \"schemaName\" : \"study\",\\n  \"containerPath\" : \"/iPNUMMretro/Study\",\\n  \"rows\" : [ {\\n    \"date\" : null,\\n    \"firstITInfusionDate\" : \"2017/11/17 00:00:00\",\\n    \"gender\" : 2,\\n    \"bestResponse\" : 2,\\n    \"actionableMutation\" : 1,\\n    \"itLine\" : 2,\\n    \"SequenceNum\" : 0.0000,\\n    \"Created\" : \"2021/04/13 11:07:34\",\\n    \"lsid\" : \"urn:lsid:ijs.si:Study.Data-129:5007.NIX-LJU-D2002-IRAE-A016.0.0000\",\\n    \"itStartDate\" : \"2017/11/17 00:00:00\",\\n    \"thyroiditisGrade\" : 7,\\n    \"immunosupressionFlag\" : 2,\\n    \"PatientId\" : \"NIX-LJU-D2002-IRAE-A016\",\\n    \"colitisDate\" : null,\\n    \"pneumonitisDate\" : null,\\n    \"firstITStartDate\" : \"2017/11/17 00:00:00\",\\n    \"pneumonitisGrade\" : 7,\\n    \"dsrowid\" : 1073,\\n    \"CreatedBy\" : 1003,\\n    \"thyroiditisDate\" : null,\\n    \"itTreatmentSetting\" : 2,\\n    \"psECOGStartIT\" : \"0\",\\n    \"QCState\" : null,\\n    \"melanomaPrimaryAnatomicSite\" : null,\\n    \"itStartAge\" : \"73\",\\n    \"itType\" : null,\\n    \"sourcelsid\" : null,\\n    \"colitisGrade\" : 7,\\n    \"durationOfCurrentIT\" : null\\n  } ],\\n  \"command\" : \"update\"\\n}'\n"
     ]
    }
   ],
   "source": [
    "import csv\n",
    "import datetime\n",
    "import sys\n",
    "import os\n",
    "\n",
    "sys.path.append(os.path.join(os.path.expanduser('~'),'software','src','nixSuite','wrapper'))\n",
    "import nixWrapper\n",
    "nixWrapper.loadLibrary('labkeyInterface')\n",
    "import labkeyInterface\n",
    "net=labkeyInterface.labkeyInterface()\n",
    "fconfig=os.path.join(os.path.expanduser('~'),'.labkey','network.json')\n",
    "net.init(fconfig)\n",
    "net.getCSRF()\n",
    "import labkeyFileBrowser\n",
    "sys.path.append(os.getcwd())\n",
    "import downloadPatient\n",
    "fb=labkeyFileBrowser.labkeyFileBrowser(net)\n",
    "project='iPNUMMretro/Study'\n",
    "dataset='clinicalDataInternational'\n",
    "import labkeyDatabaseBrowser\n",
    "db=labkeyDatabaseBrowser.labkeyDB(net)\n",
    "\n",
    "cf='/home/studen/Downloads/iraeMMPilot.csv'\n",
    "rows=[]\n",
    "with open(cf,'r') as f:\n",
    "    rd=csv.DictReader(f,delimiter='\\t')\n",
    "    for r in rd:\n",
    "        rows.append(r)\n",
    "#print(rows)  \n",
    "def getDate(f):\n",
    "    return datetime.datetime.strptime(f,'%m/%d/%Y')\n",
    "\n",
    "for r in rows:\n",
    "    idFilter={'variable':'PatientId','value':r['ParticipantId'],'oper':'eq'}\n",
    "    ds=db.selectRows(project,'study',dataset,[idFilter])\n",
    "    if len(ds['rows'])==0:\n",
    "        print('No match found for {}'.format(r['ParticipantId']))\n",
    "    else:\n",
    "        qrow=ds['rows'][0]\n",
    "        \n",
    "    startItDate=getDate(r['start IT date'])\n",
    "    dob=getDate(r['date of birth'])\n",
    "    qrow['itStartAge']='{:.0f}'.format((startItDate-dob).days/365.)\n",
    "    qrow['gender']=1\n",
    "    if r['sex']=='male':\n",
    "        qrow['gender']=2\n",
    "    qrow['psECOGStartIT']=r['PS WHO']\n",
    "    qv=6\n",
    "    v=r['BRAF mut']\n",
    "    if v=='WT':\n",
    "        qv=1\n",
    "    if v.find('BRAF V600K')>-1:\n",
    "        qv=3\n",
    "    if v.find('BRAF V600E')>-1:\n",
    "        qv=2\n",
    "    qrow['actionableMutation']=qv\n",
    "    v=r['origo ']\n",
    "    qv=4\n",
    "    if v=='cutaneous':\n",
    "        qv=3\n",
    "    if v=='ocular':\n",
    "        qv=1\n",
    "        \n",
    "    \n",
    "    qrow['melanomaPrimaryMutationSite']=qv\n",
    "    qrow['itTreatmentSetting']=2 #metastaticDisease\n",
    "    qrow['itStartDate']=getDate(r['start IT date']).isoformat()\n",
    "    qrow['firstITStartDate']=getDate(r['start IT date']).isoformat()\n",
    "    \n",
    "    v=r['best response']\n",
    "    qv=5\n",
    "    if v=='CR':\n",
    "        qv=4\n",
    "    if v=='PD':\n",
    "        qv=1\n",
    "    if v=='radilogical response':\n",
    "        qv=2\n",
    "    if v=='Radiological response':\n",
    "        qv=2\n",
    "    qrow['bestResponse']=qv\n",
    "    \n",
    "    qrow['immunosupressionFlag']=2 #No\n",
    "    qrow['firstITInfusionDate']=getDate(r['start IT date']).isoformat()\n",
    "    qrow['itLine']=2 #First\n",
    "    print(qrow['bestResponse'])\n",
    "    qrow['pneumonitisGrade']=7 #G0\n",
    "    qrow['colitisGrade']=7 #G0\n",
    "    qrow['thyroditisGrade']=7 #G0\n",
    "    \n",
    "    print(db.modifyRows('update',project,'study',dataset,[qrow]))\n",
    "    \n",
    "    "
   ]
  },
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   "cell_type": "raw",
   "metadata": {},
   "source": []
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