{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "9bdd6a77",
   "metadata": {},
   "source": [
    "\n",
    "Example for creating a COMBINE archive."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7cf211b9",
   "metadata": {
    "lines_to_next_cell": 2
   },
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "\n",
    "from pymetadata.console import console\n",
    "from pymetadata.omex import EntryFormat, ManifestEntry, Omex"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "22795a31",
   "metadata": {
    "lines_to_next_cell": 2
   },
   "source": [
    "\n",
    "Creating an empty archive and adding entry for SBML."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "be17333a",
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "\n",
    "def create_omex(omex_path: Path, results_dir: Path) -> None:\n",
    "    \"\"\"Create OMEX archive of resources.\"\"\"\n",
    "    omex = Omex()\n",
    "    omex.add_entry(\n",
    "        entry=ManifestEntry(\n",
    "            location=\"./sbml/repressilator_sbml_libsbml.xml\",\n",
    "            format=EntryFormat.SBML_L3V2,\n",
    "            master=False,\n",
    "        ),\n",
    "        entry_path=results_dir / \"repressilator_sbml_libsbml.xml\",\n",
    "    )\n",
    "\n",
    "    omex.add_entry(\n",
    "        entry=ManifestEntry(\n",
    "            location=\"./sbml/repressilator_sbml_antimony.xml\",\n",
    "            format=EntryFormat.SBML_L3V2,\n",
    "            master=False,\n",
    "        ),\n",
    "        entry_path=results_dir / \"repressilator_sbml_antimony.xml\",\n",
    "    )\n",
    "\n",
    "    omex.add_entry(\n",
    "        entry=ManifestEntry(\n",
    "            location=\"./sbml/repressilator_sbml_sbmlutils.xml\",\n",
    "            format=EntryFormat.SBML_L3V2,\n",
    "            master=False,\n",
    "        ),\n",
    "        entry_path=results_dir / \"repressilator_sbml_sbmlutils.xml\",\n",
    "    )\n",
    "\n",
    "    omex.add_entry(\n",
    "        entry=ManifestEntry(\n",
    "            location=\"./cellml/repressilator_cellml.cellml\",\n",
    "            format=EntryFormat.CELLML,\n",
    "            master=False,\n",
    "        ),\n",
    "        entry_path=results_dir / \"repressilator_cellml.cellml\",\n",
    "    )\n",
    "\n",
    "    omex.add_entry(\n",
    "        entry=ManifestEntry(\n",
    "            location=\"./biopax/repressilator_biopax.owl\",\n",
    "            format=EntryFormat.BIOPAX,\n",
    "            master=False,\n",
    "        ),\n",
    "        entry_path=results_dir / \"repressilator_biopax.owl\",\n",
    "    )\n",
    "\n",
    "    omex.add_entry(\n",
    "        entry=ManifestEntry(\n",
    "            location=\"./sbgn/repressilator_sbgn.sbgn\",\n",
    "            format=EntryFormat.SBGN,\n",
    "            master=False,\n",
    "        ),\n",
    "        entry_path=results_dir / \"repressilator_sbgn.sbgn\",\n",
    "    )\n",
    "    omex.add_entry(\n",
    "        entry=ManifestEntry(\n",
    "            location=\"./sbgn/repressilator_sbgn.png\",\n",
    "            format=EntryFormat.PNG,\n",
    "            master=False,\n",
    "        ),\n",
    "        entry_path=results_dir / \"repressilator_sbgn.png\",\n",
    "    )\n",
    "\n",
    "    omex.add_entry(\n",
    "        entry=ManifestEntry(\n",
    "            location=\"./sedml/repressilator_sedml.xml\",\n",
    "            format=EntryFormat.SEDML,\n",
    "            master=False,\n",
    "        ),\n",
    "        entry_path=results_dir / \"repressilator_sedml.xml\"\n",
    "        # FIXME: add the model relative and test\n",
    "    )\n",
    "\n",
    "    console.print(omex)\n",
    "    omex.to_omex(omex_path)\n",
    "\n",
    "\n",
    "if __name__ == \"__main__\":\n",
    "    from combine_notebooks import RESULTS_DIR\n",
    "\n",
    "    create_omex(omex_path=RESULTS_DIR / \"combine.omex\", results_dir=RESULTS_DIR)"
   ]
  }
 ],
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  "jupytext": {
   "cell_metadata_filter": "-all",
   "main_language": "python",
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