ecell4-datasource.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import sys"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ecell4 import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ecell4.database import sbml"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "biomodels = sbml.BioModelsDataSource"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "mid = 'BIOMD0000000005'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "invalid null reference in method 'SBMLReader_readSBMLFromString', argument 2 of type 'std::string const &'",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-6-2bd4e2fcd831>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0my0\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdict\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mbiomodels\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mmid\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0minitial_amounts\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;32m/usr/local/lib/python2.7/dist-packages/ecell4/database/sbml.py\u001b[0m in \u001b[0;36m__init__\u001b[1;34m(self, mid, cache)\u001b[0m\n\u001b[0;32m     83\u001b[0m             \u001b[0mxml\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mXML\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mmid\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     84\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 85\u001b[1;33m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread_from_string\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mxml\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;32m/usr/local/lib/python2.7/dist-packages/ecell4/database/sbml.py\u001b[0m in \u001b[0;36mread_from_string\u001b[1;34m(self, xml)\u001b[0m\n\u001b[0;32m     17\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     18\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0mread_from_string\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mxml\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 19\u001b[1;33m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdata\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mlibsbml\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSBMLReader\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mreadSBMLFromString\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mxml\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     20\u001b[0m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmodel\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgetModel\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     21\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/usr/local/lib/python2.7/dist-packages/libsbml/__init__.pyc\u001b[0m in \u001b[0;36mreadSBMLFromString\u001b[1;34m(self, xml)\u001b[0m\n\u001b[0;32m   2077\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   2078\u001b[0m         \"\"\"\n\u001b[1;32m-> 2079\u001b[1;33m         \u001b[1;32mreturn\u001b[0m \u001b[0m_libsbml\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSBMLReader_readSBMLFromString\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mxml\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   2080\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   2081\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mValueError\u001b[0m: invalid null reference in method 'SBMLReader_readSBMLFromString', argument 2 of type 'std::string const &'"
     ]
    }
   ],
   "source": [
    "y0 = dict(biomodels(mid).initial_amounts())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}