fsp.ipynb

{
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Search Term: fibrosis\n",
      "Search Term ' fibrosis ' found in the following cases on https://digital.pathology.johnshopkins.edu/repos/451\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Description</th>\n",
       "      <th>Diagnosis</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Week136:Case3</td>\n",
       "      <td>Focal nodular hyperplasia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>Week342:Case1</td>\n",
       "      <td>Hyalinizing granuloma</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>Week378:Case1</td>\n",
       "      <td>HypertrophyReplacement fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>Week3:Case6</td>\n",
       "      <td>Malignant mesothelioma</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>Week73:Case2</td>\n",
       "      <td>Sinonasal polyps of cystic fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>5</td>\n",
       "      <td>Week444:Case5</td>\n",
       "      <td>fibrosing non-specific interstitial pneumonia patternInterstitial fibrosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>6</td>\n",
       "      <td>Week254:Case3</td>\n",
       "      <td>UIPUsual interstitial pneumonitis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>7</td>\n",
       "      <td>Week18:Case3</td>\n",
       "      <td>folded lung syndromeRound atelectasis</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     Description                                                                    Diagnosis\n",
       "0  Week136:Case3   Focal nodular hyperplasia                                                 \n",
       "1  Week342:Case1   Hyalinizing granuloma                                                     \n",
       "2  Week378:Case1   HypertrophyReplacement fibrosis                                           \n",
       "3  Week3:Case6     Malignant mesothelioma                                                    \n",
       "4  Week73:Case2    Sinonasal polyps of cystic fibrosis                                       \n",
       "5  Week444:Case5   fibrosing non-specific interstitial pneumonia patternInterstitial fibrosis\n",
       "6  Week254:Case3   UIPUsual interstitial pneumonitis                                         \n",
       "7  Week18:Case3    folded lung syndromeRound atelectasis                                     "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "###### INPUT A SEARCH TERM For CASES IN SP UNKNOWNS: https://digital.pathology.johnshopkins.edu/repos/451 #########\n",
    "txt = input(\"Search Term: \")\n",
    "\n",
    "import json\n",
    "import re\n",
    "import pandas as pd\n",
    "\n",
    "filename = 'thisfile.csv'\n",
    "\n",
    "commands = {}\n",
    "with open(filename) as fh:\n",
    "    for line in fh:\n",
    "        #print(line)\n",
    "        if bool(re.search(\":\", line)):\n",
    "            command,desc= line.rsplit(':',1);\n",
    "            command=command.replace(\" \",\"\")\n",
    "            desc=desc.replace(\",\\n\",\"\")\n",
    "            commands[command] = desc\n",
    "\n",
    "#print(commands)\n",
    "\n",
    "from googleapiclient.discovery import build\n",
    "import pprint\n",
    "\n",
    "my_api_key = \"AIzaSyDSWjeCe5YDjpMyUo1ASvPs_YCiezla55U\"\n",
    "my_cse_id = \"012186595233664989134:ueeop7vueol\"\n",
    "\n",
    "def google_search(search_term, api_key, cse_id, **kwargs):\n",
    "    service = build(\"customsearch\", \"v1\", developerKey=api_key)\n",
    "    res = service.cse().list(q=search_term, cx=cse_id, **kwargs).execute()\n",
    "    return res['items']\n",
    "\n",
    "results = google_search(\n",
    "    txt, my_api_key, my_cse_id, num=10)\n",
    "#for result in results:\n",
    "    #pprint.pprint(result)\n",
    "\n",
    "    \n",
    "    \n",
    "\n",
    "rr=[r[\"htmlTitle\"] for r in results]\n",
    "#print(rr)\n",
    "\n",
    "spc = {}\n",
    "\n",
    "for line in rr:\n",
    "    #print(line)\n",
    "    if bool(re.search(\"|\", line)):\n",
    "        #print(line)\n",
    "        command,desc= line.split('|',1);\n",
    "        command=command.replace(\" \",\"\")\n",
    "        spc[command] = desc\n",
    "\n",
    "#print(spc)\n",
    "\n",
    "ss=set(commands.keys()).intersection(set(spc.keys()))\n",
    "\n",
    "#for val in ss: \n",
    "    #print(val,commands[val]) \n",
    "\n",
    "dfObj=pd.DataFrame(columns = ['Description' , 'Diagnosis'])\n",
    "for val in ss: \n",
    "    dfObj = dfObj.append({'Description' : val, 'Diagnosis' : commands[val]},ignore_index=True )\n",
    "\n",
    "print(\"Search Term\", \"'\",txt,\"'\", \"found in the following cases on https://digital.pathology.johnshopkins.edu/repos/451\")\n",
    "pd.set_option('display.max_colwidth', -1)\n",
    "dfObj"
   ]
  }
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