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   "cell_type": "markdown",
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   "source": [
    "# Checking empty descriptions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In this example, we use `fastobo` to create a small validation script which will report empty definitions in an OBO file. We also use `requests` in order to connect to the OBO library."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import fastobo\n",
    "import requests"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`fastobo.load` takes a file-handle, which can be accessed using the `raw` property of the `Response` object returned by `requests.get`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "res = requests.get(\"http://purl.obolibrary.org/obo/ms.obo\", stream=True)\n",
    "doc = fastobo.load(res.raw)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Header\n",
    "\n",
    "Now, we can check the header for empty descriptions in definition clauses: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "for clause in doc.header:\n",
    "    if isinstance(clause, fastobo.header.SynonymTypedefClause) and not clause.description:\n",
    "        print(\"Empty description in definition of\", clause.typedef)\n",
    "    elif isinstance(clause, fastobo.header.SubsetdefClause) and not clause.description:\n",
    "        print(\"Empty description in definition of\", clause.subset)\n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note that we are using `isinstance` a lot compared to what you may be used to in other Python library: this is because `fastobo` is based on a Rust library which is strongly-typed, so that is reflected in the Python library that wraps it. We could use the strong typing to write the same snippet using type-specific callback wrapped in a `dict`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "def check_synonym_typedef(clause):\n",
    "    if not clause.description:\n",
    "        print(\"Empty description in definition of\", clause.typedef, \"in header\")\n",
    "\n",
    "def check_subsetdef(clause):\n",
    "    if not clause.description:\n",
    "        print(\"Empty description in definition of\", clause.subset, \"in header\")\n",
    "        \n",
    "CALLBACKS = {\n",
    "    fastobo.header.SynonymTypedefClause: check_synonym_typedef,\n",
    "    fastobo.header.SynonymTypedefClause: check_subsetdef,\n",
    "}\n",
    "\n",
    "for clause in doc.header:\n",
    "    callback = CALLBACKS.get(type(clause))\n",
    "    if callback is not None:\n",
    "        callback(clause)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Such a construct can be used to process all possible clauses while reducing the number of `if`/`elif` branches, in particular when many different clauses are processed at the same time."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Entities"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Checking for definitions in entity frames is straightforward: all definition clauses have a `definition` property that returns the textual definition of the entity. We can use duck-typing here to check for empty definitions:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "for frame in doc:\n",
    "    for clause in frame:\n",
    "        try:\n",
    "            if not clause.definition:\n",
    "                print(\"Empty definition of\", frame.id)\n",
    "        except AttributeError:\n",
    "            pass"
   ]
  }
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