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    "#  How to use `refgenconf ` to manage Refgenie assets in a pipeline\n",
    "\n",
    "Below we present an example use of `refgenconf` package. It is installed automatically with `refgenie` (or separately installable with `pip install refgenconf`). All the asset fetching functionality is impelmented in `refgenconf` package, so pipelines that just use Python API do not need to depend on `refgenie`.\n",
    "\n",
    "## Goal\n",
    "The goal of the code below is to **get a path to the refgenie-managed fasta file for a user-specified genome**. \n",
    "\n",
    "Genome FASTA is a part of `fasta` asset, accessible as a `fasta` seek key. To retrieve the path this file on the command line one would say: `refgenie seek <genome>/fasta`. For example:\n",
    "```\n",
    "refgenie seek hg38/fasta\n",
    "```\n",
    "\n",
    "## Steps\n",
    "\n",
    "First, let's set the `$REFGENIE` environmet variable. It should be set by a pipeline user or the config file path should be provided explictly, e.g. as an input to the pipeline (here shown as `user_provided_cfg_path = None` -- not provided) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "os.environ[\"REFGENIE\"] = \"./refgenie.yaml\"\n",
    "user_provided_cfg_path = None\n",
    "user_provided_genome = \"rCRSd\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, let's import components of `refgenconf` that we'll use"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "from refgenconf import RefGenConf, select_genome_config, RefgenconfError, CFG_ENV_VARS, CFG_FOLDER_KEY\n",
    "from yacman import UndefinedAliasError"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now, we can use the `select_genome_config` function to determine the preferred path to the config file. If `user_provided_cfg_path` is `None` (not specified) the `$REFGENIE` environment variable is used. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "refgenie_cfg_path = select_genome_config(filename=user_provided_cfg_path, check_exist=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The function returns `None` if none of the above point to a valid path. That's why we raise an aproppriate error below. Obviously, the name of `--rfg-config` argument depends on pipeline design. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "if not refgenie_cfg_path:\n",
    "    raise OSError(f\"Could not determine path to a refgenie genome configuration file.\"\n",
    "                  f\"Use --rfg-config argument or set '{CFG_ENV_VARS}' environment variable to provide it\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Otherwise it returns a determined path (`str`). So, we check if it exists and read the object if it does. If it does not, we can initialize the config file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "File '/Users/mstolarczyk/code/refgenie/docs_jupyter/refgenie.yaml' does not exist. Initializing refgenie genome configuration file.\n"
     ]
    }
   ],
   "source": [
    "if isinstance(refgenie_cfg_path, str) and os.path.exists(refgenie_cfg_path):\n",
    "    print(f\"Reading refgenie genome configuration file from file: {refgenie_cfg_path}\")\n",
    "    rgc = RefGenConf(filepath=refgenie_cfg_path)\n",
    "else:\n",
    "    print(f\"File '{refgenie_cfg_path}' does not exist. Initializing refgenie genome configuration file.\")\n",
    "    rgc = RefGenConf(entries={CFG_FOLDER_KEY: os.path.dirname(refgenie_cfg_path)})\n",
    "    rgc.initialize_config_file(filepath=refgenie_cfg_path)\n",
    "    rgc.subscribe(urls=\"http://rg.databio.org:82\", reset=True) # subscribe to the desired server, if needed"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally, we try to retrieve the path to out asset of interest and pull from `refgenieserver` if the retrieval fails."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Could not determine path to chrom.sizes asset, pulling\n"
     ]
    },
    {
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      "text/plain": [
       "Output()"
      ]
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     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Determined path to fasta asset: /Users/mstolarczyk/code/refgenie/docs_jupyter/alias/rCRSd/fasta/default/rCRSd.fa\n"
     ]
    }
   ],
   "source": [
    "try:\n",
    "    fasta = rgc.seek(genome_name=user_provided_genome, asset_name=\"fasta\", tag_name=\"default\",\n",
    "                                seek_key=\"fasta\")\n",
    "except (RefgenconfError, UndefinedAliasError):\n",
    "    print(\"Could not determine path to chrom.sizes asset, pulling\")\n",
    "    rgc.pull(genome=user_provided_genome, asset=\"fasta\", tag=\"default\")\n",
    "    fasta = rgc.seek(genome_name=user_provided_genome, asset_name=\"fasta\", tag_name=\"default\",\n",
    "                                seek_key=\"fasta\")\n",
    "print(f\"Determined path to fasta asset: {fasta}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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