{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Resolving Strategies\n",
    "\n",
    "* Example on how to use resolving strategies\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-09-23T18:50:20.068658Z",
     "start_time": "2019-09-23T18:50:19.054054Z"
    }
   },
   "outputs": [],
   "source": [
    "import os\n",
    "import json\n",
    "\n",
    "from kgforge.core import KnowledgeGraphForge\n",
    "from kgforge.specializations.resources import Dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      " ········\n"
     ]
    }
   ],
   "source": [
    "import getpass\n",
    "TOKEN = getpass.getpass()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "BUCKET = \"dke/kgforge\"\n",
    "forge = KnowledgeGraphForge(\"../use-cases/prod-forge-nexus.yml\",\n",
    " bucket=BUCKET,\n",
    " token=TOKEN\n",
    " )"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### List available resolvers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'agent': {'agents': {'bucket': 'bbp/agents', 'filters': None}},\n",
       " 'ontology': {'terms': {'bucket': 'neurosciencegraph/datamodels',\n",
       "   'filters': None},\n",
       "  'CellType': {'bucket': 'neurosciencegraph/datamodels',\n",
       "   'filters': {'subClassOf*.id': 'BrainCellType'}},\n",
       "  'BrainRegion': {'bucket': 'neurosciencegraph/datamodels',\n",
       "   'filters': {'subClassOf*.id': 'BrainRegion'}},\n",
       "  'Species': {'bucket': 'neurosciencegraph/datamodels',\n",
       "   'filters': {'has_rank.id': 'http://purl.obolibrary.org/obo/NCBITaxon_species'}},\n",
       "  'Strain': {'bucket': 'neurosciencegraph/datamodels',\n",
       "   'filters': {'has_rank.id': 'http://purl.obolibrary.org/obo/NCBITaxon_strain'}}}}"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "forge.resolvers(output='dict')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "case_insensitive = forge.resolve('Pv+', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "exact = forge.resolve('PV+', scope='ontology', strategy='EXACT_MATCH')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "assert case_insensitive == exact"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Try with a similar string, but other characters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "similar = forge.resolve('pv-', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "similar1 = forge.resolve('pv:', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "assert similar is None\n",
    "assert similar1 is None"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Combine spaces and other characters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    id: https://bbp.epfl.ch/ontologies/core/ttypes/229_L6_IT_CTX\n",
      "    type: Class\n",
      "    label: 229_L6 IT CTX\n",
      "    subClassOf:\n",
      "    [\n",
      "        https://bbp.epfl.ch/ontologies/core/ttypes/L4_5_6_IT_Car3\n",
      "        https://bbp.epfl.ch/ontologies/core/celltypes/NeuronTranscriptomicType\n",
      "    ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "print(forge.resolve('229_l6 it ctx', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    id: https://bbp.epfl.ch/ontologies/core/ttypes/264_L5_6_NP_CTX\n",
      "    type: Class\n",
      "    label: 264_L5/6 NP CTX\n",
      "    subClassOf:\n",
      "    [\n",
      "        https://bbp.epfl.ch/ontologies/core/ttypes/L5_6_NP_CTX\n",
      "        https://bbp.epfl.ch/ontologies/core/celltypes/NeuronTranscriptomicType\n",
      "    ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "print(forge.resolve('264_L5/6 np CTX', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH'))"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Resolve from a specific ontology\n",
    "This is particularly useful when two entities have a similar acronym like the example below, where there is a brain region called BAC, and a electrical cell type labelled bAC.\n",
    "\n",
    "Without any specification, it will return the first result in the list of matches (no priority or ranking)."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### List available ontologies to resolve from"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['terms', 'CellType', 'BrainRegion', 'Species', 'Strain']"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(forge.resolvers(output='dict')['ontology'].keys()) # terms is for resolving accross all ontologies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    id: http://uri.interlex.org/base/ilx_0738199\n",
      "    type: Class\n",
      "    label: bAC\n",
      "    notation: bAC\n",
      "    prefLabel: Burst accommodating electrical type\n",
      "    subClassOf:\n",
      "    [\n",
      "        nsg:EType\n",
      "        bmo:NeuronElectricalType\n",
      "    ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "from kgforge.core.commons.strategies import ResolvingStrategy\n",
    "\n",
    "print(forge.resolve(\"bAC\", scope=\"ontology\", target=\"terms\", \n",
    "                    strategy=ResolvingStrategy.EXACT_CASE_INSENSITIVE_MATCH))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    id: http://uri.interlex.org/base/ilx_0738199\n",
      "    type: Class\n",
      "    label: bAC\n",
      "    notation: bAC\n",
      "    prefLabel: Burst accommodating electrical type\n",
      "    subClassOf:\n",
      "    [\n",
      "        nsg:EType\n",
      "        bmo:NeuronElectricalType\n",
      "    ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "print(forge.resolve(\"bAC\", scope=\"ontology\", target=\"CellType\", strategy=\"EXACT_CASE_INSENSITIVE_MATCH\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    id: http://api.brain-map.org/api/v2/data/Structure/287\n",
      "    type: Class\n",
      "    label: Bed nucleus of the anterior commissure\n",
      "    isDefinedBy: http://bbp.epfl.ch/neurosciencegraph/ontologies/core/brainregion\n",
      "    notation: BAC\n",
      "    prefLabel: Bed nucleus of the anterior commissure\n",
      "    subClassOf: nsg:BrainRegion\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "print(forge.resolve(\"bAC\", scope=\"ontology\", target=\"BrainRegion\", strategy=\"EXACT_CASE_INSENSITIVE_MATCH\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    id: http://purl.obolibrary.org/obo/NCBITaxon_10116\n",
      "    type: Class\n",
      "    label: Rattus norvegicus\n",
      "    altLabel: rat\n",
      "    atlasRelease:\n",
      "    {\n",
      "        id: https://bbp.epfl.ch/neurosciencegraph/data/4906ab85-694f-469d-962f-c0174e901885\n",
      "    }\n",
      "    subClassOf:\n",
      "    [\n",
      "        nsg:Species\n",
      "        NCBITaxon:10114\n",
      "    ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "print(forge.resolve(\"rat\", scope=\"ontology\", target=\"Species\", strategy=\"EXACT_CASE_INSENSITIVE_MATCH\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    id: http://www.ebi.ac.uk/efo/EFO_0001342\n",
      "    type: Class\n",
      "    label: Wistar\n",
      "    altLabel:\n",
      "    [\n",
      "        Rats, Wistar\n",
      "        Wistar rat\n",
      "        Wistar rats\n",
      "    ]\n",
      "    atlasRelease:\n",
      "    {\n",
      "        id: https://bbp.epfl.ch/neurosciencegraph/data/4906ab85-694f-469d-962f-c0174e901885\n",
      "    }\n",
      "    subClassOf: NCBITaxon:10116\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "print(forge.resolve(\"Wistar\", scope=\"ontology\", target=\"Strain\", strategy=\"EXACT_CASE_INSENSITIVE_MATCH\"))"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Ensuring one label"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "resource = forge.resolve(\"AOB_MC\", scope=\"ontology\", target=\"terms\", strategy=\"EXACT_MATCH\")\n",
    "assert isinstance(resource.label, str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "excitatory = forge.resolve(\"exc\", scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH')\n",
    "assert isinstance(excitatory.label, str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    id: https://neuroshapes.org/ExcitatoryNeuron\n",
      "    type: Class\n",
      "    label: Excitatory Neuron\n",
      "    notation: Exc\n",
      "    prefLabel: Excitatory Neuron\n",
      "    subClassOf: bmo:NeurotransmitterType\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "print(excitatory)"
   ]
  }
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