{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "c5793b89",
   "metadata": {},
   "source": [
    "# Create a Genome Topology for your Agent"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ee8c352b",
   "metadata": {},
   "source": [
    "In order to create a agent you first need to create its genome. An agent's genome is very much like a genome in biology where it is an organism's complete set of genetic instructions. In this case, the genome is for an AI agent. A genome can be created manually, algorithmically, or using the Intelligent Artifacts Lab GUI (Lab). For now let's a genome that is located in the config folder named, 'demo-all.' All you need to do is upload the Genome in the Lab's Topology Creator. Moreover, a genome can be downloaded and uploaded for later use or sharing after spawning an agent (covered in the next section below). The genome file is a JavaScript Object Notation (JSON) string that can be imported as below:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "f852fe71",
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "from ia.gaius.genome_info import Genome\n",
    "import json\n",
    "\n",
    "genome_topology = '''{\"elements\":{\"nodes\":[{\"data\":{\"name\":\"P1\",\"id\":\"p7ae0a0612\",\"type\":\"primitive\",\"sources\":[\"observables\"],\"manipulatives\":[],\"always_update_frequencies\":false,\"auto_act_method\":\"none\",\"auto_act_threshold\":0.8,\"auto_learn_method\":\"none\",\"classifier\":\"CVC\",\"datastore\":\"mongodb\",\"dynamic_sequence_length\":true,\"max_sequence_length\":0,\"sort\":true,\"process_predictions\":true,\"quiescence\":3,\"search_depth\":10,\"recall_threshold\":0.1,\"smoothness\":3,\"max_predictions\":100,\"persistence\":5},\"position\":{\"x\":587,\"y\":272.5975},\"group\":\"nodes\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":false,\"classes\":\"\"},{\"data\":{\"name\":\"P2\",\"id\":\"p5b55a8399\",\"type\":\"primitive\",\"sources\":[\"m44ee0fd21\"],\"manipulatives\":[\"m44ee0fd21\"],\"always_update_frequencies\":false,\"auto_act_method\":\"none\",\"auto_act_threshold\":0.8,\"auto_learn_method\":\"none\",\"classifier\":\"CVC\",\"datastore\":\"mongodb\",\"dynamic_sequence_length\":true,\"max_sequence_length\":0,\"sort\":true,\"process_predictions\":true,\"quiescence\":3,\"search_depth\":10,\"recall_threshold\":0.1,\"smoothness\":3,\"max_predictions\":100,\"persistence\":5},\"position\":{\"x\":687,\"y\":272.5975},\"group\":\"nodes\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":false,\"classes\":\"\"},{\"data\":{\"name\":\"P3\",\"id\":\"p85643c122\",\"type\":\"primitive\",\"sources\":[\"observables\"],\"manipulatives\":[\"mb94faab95\"],\"always_update_frequencies\":false,\"auto_act_method\":\"none\",\"auto_act_threshold\":0.8,\"auto_learn_method\":\"none\",\"classifier\":\"CVC\",\"datastore\":\"mongodb\",\"dynamic_sequence_length\":true,\"max_sequence_length\":0,\"sort\":true,\"process_predictions\":true,\"quiescence\":3,\"search_depth\":10,\"recall_threshold\":0.1,\"smoothness\":3,\"max_predictions\":100,\"persistence\":5},\"position\":{\"x\":789,\"y\":271.5975},\"group\":\"nodes\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":false,\"classes\":\"\"},{\"data\":{\"displayName\":\"Multiplier\",\"mtype\":\"normal\",\"name\":\"emotiveMultiplier\",\"inputs\":[\"strings\",\"emotives\",\"vectors\"],\"outputs\":[\"strings\",\"emotives\",\"vectors\",\"predictions\"],\"description\":\"Multiplies emotive values by a configurable value.\",\"tags\":[\"emotives\",\"multiply\",\"multiplication\",\"multi\",\"value\",\"factor\"],\"category\":\"emotives\",\"genes\":{\"sources\":{\"alleles\":[],\"mutability\":0,\"value\":[\"observables\"],\"volatility\":0},\"multiplier\":{\"alleles\":[1,2,3,4,5,6,7,8,9,10],\"mutability\":0,\"value\":5,\"volatility\":0}},\"id\":\"m44ee0fd21\",\"type\":\"manipulative\",\"primitive\":\"p5b55a8399\"},\"position\":{\"x\":687,\"y\":372.5975},\"group\":\"nodes\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":false,\"classes\":\"\"},{\"data\":{\"displayName\":\"abstraction\",\"name\":\"abstraction\",\"category\":\"standard\",\"mtype\":\"output\",\"description\":\"Output manipulative to forward abstracted predictions to other Primitives. The chosen field of the predictions are forwarded as. The are also forwarded. No are forwarded.\",\"tags\":[\"abstraction\",\"name\",\"present\",\"past\",\"future\",\"missing\",\"matches\",\"extras\",\"output\",\"forward\",\"abstract\",\"emotives\",\"strings\",\"emotive\",\"classification\"],\"genes\":{\"sources\":{\"alleles\":[],\"mutability\":0,\"value\":[\"cognition-data\"],\"volatility\":0},\"primitives\":{\"alleles\":[],\"mutability\":0,\"value\":[\"pc4dff12d6\"],\"volatility\":0},\"field\":{\"alleles\":[\"name\",\"past\",\"present\",\"future\",\"missing\",\"extras\",\"matches\",\"classification\"],\"mutability\":0,\"value\":[\"name\"],\"volatility\":0}},\"id\":\"mb94faab95\",\"type\":\"manipulative\",\"primitive\":\"p85643c122\"},\"position\":{\"x\":789,\"y\":171.59750000000003},\"group\":\"nodes\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":false,\"classes\":\"\"},{\"data\":{\"name\":\"P4\",\"id\":\"pc4dff12d6\",\"type\":\"primitive\",\"sources\":[\"observables\"],\"manipulatives\":[],\"always_update_frequencies\":false,\"auto_act_method\":\"none\",\"auto_act_threshold\":0.8,\"auto_learn_method\":\"none\",\"classifier\":\"CVC\",\"datastore\":\"mongodb\",\"dynamic_sequence_length\":true,\"max_sequence_length\":0,\"sort\":true,\"process_predictions\":true,\"quiescence\":3,\"search_depth\":10,\"recall_threshold\":0.1,\"smoothness\":3,\"max_predictions\":100,\"persistence\":5},\"position\":{\"x\":788,\"y\":81.59750000000003},\"group\":\"nodes\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":false,\"classes\":\"\"}],\"edges\":[{\"data\":{\"id\":\"eb7965422f\",\"source\":\"m44ee0fd21\",\"target\":\"p5b55a8399\",\"type\":\"edge\"},\"position\":{\"x\":0,\"y\":0},\"group\":\"edges\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":true,\"classes\":\"\"},{\"data\":{\"id\":\"ec26380337\",\"source\":\"p85643c122\",\"target\":\"mb94faab95\",\"type\":\"edge\"},\"position\":{\"x\":0,\"y\":0},\"group\":\"edges\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":true,\"classes\":\"abstractionEdge\"},{\"data\":{\"id\":\"e5dd3a5044\",\"source\":\"mb94faab95\",\"target\":\"pc4dff12d6\",\"type\":\"edge\"},\"position\":{\"x\":0,\"y\":0},\"group\":\"edges\",\"removed\":false,\"selected\":false,\"selectable\":false,\"locked\":false,\"grabbable\":true,\"pannable\":true,\"classes\":\"abstractionEdge\"}]},\"style\":[{\"selector\":\"edge\",\"style\":{\"target-arrow-shape\":\"triangle\",\"curve-style\":\"straight\",\"control-point-distances\":10,\"control-point-weights\":0.1,\"width\":1,\"overlay-color\":\"#fff\"}},{\"selector\":\"edge.curved\",\"style\":{\"curve-style\":\"bezier\"}}],\"data\":{},\"zoomingEnabled\":true,\"userZoomingEnabled\":true,\"zoom\":1,\"minZoom\":1e-50,\"maxZoom\":1,\"panningEnabled\":true,\"userPanningEnabled\":true,\"pan\":{\"x\":0,\"y\":0},\"boxSelectionEnabled\":false,\"renderer\":{\"name\":\"canvas\"},\"wheelSensitivity\":0.1,\"motionBlur\":false,\"agent\":\"demo-all\",\"description\":\"tutorial\"}'''\n",
    "genome = Genome(json.loads(genome_topology))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "482958df",
   "metadata": {},
   "source": [
    "Parameter values in genomes are intended to be modified. Since the genome file is a JSON object, modifying values is easy. You can also use the Genome object class to easily find nodes and values for modification.\n",
    "\n",
    "The following example will change the `'recall_threshold'` and `'max_predictions'` of the primitive 'P1':"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "f5090ba4",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "P4:       \n",
      " ID               : pc4dff12d6       \n",
      " Recall Threshold : 0.1       \n",
      " Max Predictions  : 100\n"
     ]
    }
   ],
   "source": [
    "for p in genome.primitives.values():\n",
    "    if p['name'] == 'P1':\n",
    "        p['recall_threshold'] = 0.1\n",
    "        p['max_predictions'] = 10\n",
    "        \n",
    "print(\"%s: \\\n",
    "      \\n ID               : %s \\\n",
    "      \\n Recall Threshold : %s \\\n",
    "      \\n Max Predictions  : %s\" %(p['name'], p['id'], p['recall_threshold'], p['max_predictions']))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "61ec5b53",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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