omop_create_dataset_mini.ipynb

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      "[INFO] adding /home/paulroujansky/git/DataForGood/batch4_diafoirus_fleming to sys.path\n"
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    "    # Add private path to 'batch4_diafoirus_fleming'\n",
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   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import pickle as pkl\n",
    "\n",
    "from fleming_lib.dataset import create_dataset\n",
    "from fleming_lib.tools import connect_to_omop"
   ]
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   "source": [
    "# Open a connection to OMOP\n",
    "conn = connect_to_omop()"
   ]
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     "text": [
      "Batch 1/1 - Done                                                                                     [21 s      ]\n"
     ]
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   "source": [
    "# Define list of patients\n",
    "list_patients = [62063368, 62063384, 62063393]\n",
    "\n",
    "# Create dataset\n",
    "dataset = create_dataset(conn, list_patients=list_patients, n_patients_per_batch=10, verbose=True)"
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   "source": [
    "# Save dataset\n",
    "fname = 'dataset_omop'\n",
    "# - to CSV:\n",
    "dataset.to_csv(fname + '.csv', sep='\\t', encoding='utf-8', index=False)\n",
    "# - to Pickle:\n",
    "pkl.dump(dataset, open(fname + '.pkl', 'wb'))"
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