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   "source": [
    "# Author Search Demo\n",
    "\n",
    "![pdbj](https://pdbj.org/content/default.svg)\n",
    "\n",
    "AuthorSearch shows how to query PDB structures by metadata. This example queries the name fields in the audit_author and citation_author categories.\n",
    "\n",
    "\n",
    "## References\n",
    "\n",
    "Each category represents a table and fields represent database columns, see:\n",
    "[Available tables and columns](https://pdbj.org/mine-rdb-docs)\n",
    "\n",
    "Data are provided through: \n",
    "[Mine 2 SQL](https://pdbj.org/help/mine2-sql)\n",
    "\n",
    "Queries can be designed with the interactive\n",
    "[PDBj Mine 2 query service](https://pdbj.org/mine/sql)\n",
    "\n",
    "\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext\n",
    "from mmtfPyspark.webfilters import PdbjMineSearch\n",
    "from mmtfPyspark.io import mmtfReader"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark Context"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                  .setAppName(\"AuthorSearchDemo\")\n",
    "sc = SparkContext(conf = conf)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Query to find PDB structures for Doudna, J.A. as a deposition (audit) author or as an author in the primary PDB citation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "sqlQuery = \"SELECT pdbid from audit_author \" \\\n",
    "                + \"WHERE name LIKE 'Doudna%J.A.%' \" \\\n",
    "                + \"UNION \" \\\n",
    "                + \"SELECT pdbid from citation_author \" \\\n",
    "                + \"WHERE citation_id = 'primary' AND name LIKE 'Doudna%J.A.%'\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## Read PDB and filter by author"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of entries matching query: 90\n"
     ]
    }
   ],
   "source": [
    "path = \"../../resources/mmtf_reduced_sample/\"\n",
    "\n",
    "pdb = mmtfReader.read_sequence_file(path, sc) \\\n",
    "                .filter(PdbjMineSearch(sqlQuery))\n",
    "\n",
    "print(f\"Number of entries matching query: {pdb.count()}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Terminate Spark Context"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
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