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   "cell_type": "markdown",
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   "source": [
    "# Create a simple ISA descriptor\n",
    "\n",
    "This example creates minimal metadata for a single study ISA descriptor with no assay declared. \n",
    "\n",
    "It shows how to serialize (write) the ISA Model content to ISA-Tab and ISA-JSON formats."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# If executing the notebooks on `Google Colab`,uncomment the following command \n",
    "# and run it to install the required python libraries. Also, make the test datasets available.\n",
    "\n",
    "# !pip install -r requirements.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from isatools.model import (\n",
    "    Investigation,\n",
    "    Study,\n",
    "    OntologyAnnotation,\n",
    "    Sample,\n",
    "    Source,\n",
    "    Protocol,\n",
    "    ProtocolParameter,\n",
    "    Process\n",
    ")\n",
    "import datetime"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Study metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "investigation = Investigation()\n",
    "study = Study(filename=\"s_study.txt\")\n",
    "study.identifier = \"S1\"\n",
    "study.title = \"My Simple ISA Study\"\n",
    "study.description = \"We could alternatively use the class constructor's parameters to set some default \" \\\n",
    "          \"values at the time of creation, however we want to demonstrate how to use the \" \\\n",
    "          \"object's instance variables to set values.\"\n",
    "study.submission_date = str(datetime.datetime.today())\n",
    "study.public_release_date = str(datetime.datetime.today())\n",
    "study.sources = [Source(name=\"source1\")]\n",
    "study.samples = [Sample(name=\"sample1\")]\n",
    "study.protocols = [\n",
    "    Protocol(name=\"sample collection\"),\n",
    "    Protocol(\n",
    "        name=\"data analysis with Galaxy\",\n",
    "        uri=\"https://doi.org/10.5464/workflow.cwl\",\n",
    "        protocol_type=OntologyAnnotation(term=\"data transformation\"),\n",
    "        parameters=[\n",
    "            ProtocolParameter(parameter_name=OntologyAnnotation(term=\"genome assembly\")),\n",
    "            ProtocolParameter(parameter_name=OntologyAnnotation(term=\"cut-off value\"))\n",
    "        ]\n",
    "    ),\n",
    "    Protocol(\n",
    "        name=\"data visualization with Intermine\",\n",
    "        uri=\"https://intermine.org/10.5464/network.svg\",\n",
    "        protocol_type=OntologyAnnotation(term=\"data visualization\"),\n",
    "    )\n",
    "]\n",
    "study.process_sequence = [\n",
    "    Process(\n",
    "        executes_protocol=study.protocols[-1],\n",
    "        inputs=[study.sources[-1]],\n",
    "        outputs=[study.samples[-1]]\n",
    "    )\n",
    "]\n",
    "investigation.studies = [study]\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Let's see the object :\n",
    "investigation"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Writing to ISA-Tab"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from isatools.isatab import dumps\n",
    "print(dumps(investigation))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Writing to ISA-JSON"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import json\n",
    "from isatools.isajson import ISAJSONEncoder\n",
    "print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## About this notebook\n",
    "\n",
    "- authors: philippe.rocca-serra@oerc.ox.ac.uk, massimiliano.izzo@oerc.ox.ac.uk\n",
    "- license: CC-BY 4.0\n",
    "- support: isatools@googlegroups.com\n",
    "- issue tracker: https://github.com/ISA-tools/isa-api/issues"
   ]
  }
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