ethos-viral-analysis.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Unknown option: '-forcemake'\n",
      "Possible solutions: --forcemake\n",
      "\n",
      "Generic values (AMISearchTool)\n",
      "================================\n",
      "-v to see generic values\n",
      "oldstyle            true\n",
      "\n",
      "Specific values (AMISearchTool)\n",
      "================================\n",
      "oldstyle             true\n",
      "strip numbers        false\n",
      "wordCountRange       (20,1000000)\n",
      "wordLengthRange      (1,20)\n",
      "\n",
      "dictionaryList       [country, sars_covid_2]\n",
      "dictionaryTop        null\n",
      "dictionarySuffix     [xml]\n",
      "\n",
      "0    [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool  - old style search command); change\n",
      "0 [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool  - old style search command); change\n",
      "cProject: ethos-viral\n",
      "legacy cmd> word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt\n",
      "legacy cmd> search(country)\n",
      "legacy cmd> search(sars_covid_2)\n"
     ]
    },
    {
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     "output_type": "stream",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n",
      "create data tables\n",
      "rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr"
     ]
    }
   ],
   "source": [
    "!ami-search -p ethos-viral -forcemake --dictionary=country --dictionary=sars_covid_2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"100%\"\n",
       "            height=\"300px\"\n",
       "            src=\"ethos-viral/full.dataTables.html\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7f8264394a20>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from IPython.display import IFrame,display\n",
    "\n",
    "display(IFrame(src=\"ethos-viral/full.dataTables.html\", width=\"100%\", height=\"300px\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"90%\"\n",
       "            height=\"350px\"\n",
       "            src=\"ethos-viral/__cooccurrence/allPlots.svg\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x7f826433d400>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "display(IFrame(src=\"ethos-viral/__cooccurrence/allPlots.svg\", width=\"90%\", height=\"350px\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}