get_nbib_dataset.ipynb

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   "source": [
    "import os\n",
    "import io\n",
    "import sys\n",
    "import glob\n",
    "import zipfile\n",
    "import requests\n",
    "from datetime import datetime\n",
    "\n",
    "def simple_bool(message):\n",
    "    choose = input(message+\" (y/n): \").lower()\n",
    "    your_bool = choose in [\"y\", \"yes\",\"yea\",\"sure\"]\n",
    "    return your_bool\n",
    "\n",
    "def get_and_extract(file, dir = os.getcwd(), ext = '.zip'):\n",
    "    url='https://zenodo.org/record/8205724/files/'+file+'.zip?download=1'\n",
    "    zip_file_name = file+ext\n",
    "    extracted_folder_name = dir\n",
    "    # Download the ZIP file\n",
    "    response = requests.get(url)\n",
    "    if response.status_code == 200:\n",
    "        # Extract the ZIP contents\n",
    "        with io.BytesIO(response.content) as zip_buffer:\n",
    "            with zipfile.ZipFile(zip_buffer, 'r') as zip_ref:\n",
    "                zip_ref.extractall(extracted_folder_name)\n",
    "        print(f\"ZIP file '{zip_file_name}' extracted to '{extracted_folder_name}' successfully.\")\n",
    "    else:\n",
    "        print(\"Failed to download the ZIP file.\")\n",
    "\n",
    "if simple_bool('Download nbib-data from Zenodo?\\n (careful! 5GB unpacked, download and extraction time estimated 8-9 minutes)'):\n",
    "    timea = datetime.now()\n",
    "    get_and_extract('nbib_data')\n",
    "    print('Download and extraction time ',datetime.now()-timea)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "\n",
    "#set source dataset:-----------------------\n",
    "db_tag = 'pcg'\n",
    "db_name = 'grpm_db_' + db_tag\n",
    "db_path = 'grpm_dataset/'+db_name\n",
    "\n",
    "time1 = datetime.now()\n",
    "#import gene-fullnbib\n",
    "dummy_nbib = pd.read_csv(db_path+'/complete_nbibtable.csv', index_col=0)\n",
    "dummy_nbib['pubmed_id'] = dummy_nbib['pubmed_id'].astype(str)\n",
    "time2 = datetime.now()\n",
    "print('time import nbib: ', time2-time1)\n",
    "print(dummy_nbib.memory_usage().sum() / 1024 / 1024, 'MB')\n",
    "\n",
    "display(dummy_nbib)"
   ],
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    "collapsed": false
   }
  }
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