{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "308becec-d420-4754-badf-7ce9914bade5",
   "metadata": {},
   "source": [
    "# KBase Workspace"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "afbaad60-3c4d-476d-89bb-9b4f6eb1ca53",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cobrakbase 0.2.8\n"
     ]
    }
   ],
   "source": [
    "import cobrakbase"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a0c9a8fc-7855-4dcf-8ff5-74837dfeb57a",
   "metadata": {},
   "source": [
    "## Initialize KBase client with a valid token"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3c8738d1-a7f0-4296-892c-41257d3d67bc",
   "metadata": {},
   "outputs": [],
   "source": [
    "kbase = cobrakbase.KBaseAPI() # or kbase = cobrakbase.KBaseAPI(YOUR_LOGIN_TOKEN)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ebe2b75f-7d34-460c-8c4f-de57b7e76eb0",
   "metadata": {},
   "outputs": [],
   "source": [
    "ws = \"filipeliu:narrative_1561151919387\""
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7c64f6bc-656e-45ad-8356-4a423499f351",
   "metadata": {},
   "source": [
    "#### Get Object\n",
    "get_object returns raw dict object"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "a064f6ad-2e1e-482b-bd6e-ea0a73fc9d12",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "__VERSION__ <class 'int'>\n",
      "biochemistry_ref <class 'str'>\n",
      "biomasses <class 'list'>\n",
      "compartments <class 'list'>\n",
      "compcompounds <class 'list'>\n",
      "complexes <class 'list'>\n",
      "compounds <class 'list'>\n",
      "domain <class 'str'>\n",
      "id <class 'str'>\n",
      "name <class 'str'>\n",
      "pathways <class 'list'>\n",
      "reactions <class 'list'>\n",
      "roles <class 'list'>\n",
      "subsystems <class 'list'>\n",
      "type <class 'str'>\n"
     ]
    }
   ],
   "source": [
    "data = kbase.get_object('GramNegModelTemplateV2', 'NewKBaseModelTemplates')\n",
    "for k in data:\n",
    "    print(k, type(data[k]))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "303659ad-2591-4cf9-ad45-b2e42ca53e69",
   "metadata": {},
   "source": [
    "get_from_ws returns ModelSEEDpy datatypes (e.g., Model, Genome, Media, Template)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "d8c518e4-6241-4644-92c9-642dc63b4e5f",
   "metadata": {},
   "outputs": [],
   "source": [
    "template = kbase.get_from_ws('GramNegModelTemplateV2', 'NewKBaseModelTemplates')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "657ee707-e88a-4b48-ab63-d3448a4e241d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>ID</strong></td>\n",
       "                <td>GramNegative.modeltemplate</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x07f8e8fb4c730</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of metabolites</strong></td>\n",
       "                <td>6359</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of species</strong></td>\n",
       "                <td>6884</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of reactions</strong></td>\n",
       "                <td>8656</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of roles</strong></td>\n",
       "                <td>20572</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of complexes</strong></td>\n",
       "                <td>9764</td>\n",
       "            </tr>\n",
       "          </table>"
      ],
      "text/plain": [
       "<cobrakbase.core.kbasefba.newmodeltemplate.NewModelTemplate at 0x7f8e8fb4c730>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "template"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "8f458ab0-a68c-4564-8179-753815eb468d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Reaction identifier</strong></td><td>rxn00001_c</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Name</strong></td><td>diphosphate phosphohydrolase</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x07f8e84198820</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Stoichiometry</strong></td>\n",
       "                <td>\n",
       "                    <p style='text-align:right'>cpd00001_c + cpd00012_c --> 2 cpd00009_c + cpd00067_c</p>\n",
       "                    <p style='text-align:right'>H2O + PPi --> 2 Phosphate + H+</p>\n",
       "                </td>\n",
       "            </tr><tr>\n",
       "                <td><strong>GPR</strong></td><td>cpx01835 or cpx01834 or cpx34574 or cpx52693 or cpx01833</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Lower bound</strong></td><td>0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Upper bound</strong></td><td>1000</td>\n",
       "            </tr>\n",
       "        </table>\n",
       "        "
      ],
      "text/plain": [
       "<NewModelTemplateReaction rxn00001_c at 0x7f8e84198820>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "template.reactions.rxn00001_c"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c56f1fc5-4f7c-4b52-9623-11d4a6cf95dd",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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