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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## BioModels\n",
    "\n",
    "In this tutorial, we will attempt to import models from [BioModels](https://www.ebi.ac.uk/biomodels) into your account on [Cell Collective](https://cellcollective.org).\n",
    "\n",
    "Begin by importing the ccapi module into your workspace."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ccapi"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now, let’s try creating a client object in order to interact with services provided by [Cell Collective](https://cellcollective.org)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "client = ccapi.Client()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Authenticate your client using a ***password flow type authentication*** scheme.\n",
    "\n",
    "**NOTE**: *Before you can authenticate using ccapi, you must first register an application of the appropriate type on [Cell Collective](https://cellcollective.org). If you do not require a user context, it is read only.*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "client.auth(email = \"test@cellcollective.org\", password = \"test\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's import the **[Hamey2017 - Blood stem cell regulatory network](https://www.ebi.ac.uk/biomodels/MODEL1610060000)** from BioModels into Cell Collective.\n",
    "\n",
    "You can use the `read_id` routine from `ccapi.services.biomodels` to import a model into [Cell Collective](https://cellcollective.org) using a [BioModels](https://www.ebi.ac.uk/biomodels) identifier."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from ccapi.services.biomodels import read_id"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Pass a valid `client` object and a valid BioModels ID."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'read_id' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-1-a3f54c5170fc>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mread_id\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mclient\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"e_coli_core\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msave\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0mmodel\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'read_id' is not defined"
     ]
    }
   ],
   "source": [
    "model = read_id(client, \"e_coli_core\", save = True)\n",
    "model"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can view details about this model by accessing the default version."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This can also be viewed on the UI."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "![]()"
   ]
  }
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