Graph_tool_to_ERODE.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "# Credits\n",
    "__This notebook has been adapted from__\n",
    "- https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions#googles-colaboratory"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "kDn_lVxg3Z2G"
   },
   "source": [
    "# Installing graph-tool (https://graph-tool.skewed.de)\n",
    "\n",
    "---\n",
    "\n",
    "\n",
    "To import a library that's not in Colaboratory by default, you can use `!apt-get install`.\n",
    "\n",
    "But since graph-tool is not in the official repository, we need to add it to the list."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "GQ18Kd5F3uKe",
    "outputId": "379c8deb-7a09-4d45-cfc9-afc1e694dfdc"
   },
   "outputs": [],
   "source": [
    "!echo \"deb http://downloads.skewed.de/apt bionic main\" >> /etc/apt/sources.list\n",
    "!apt-key adv --keyserver keyserver.ubuntu.com --recv-key 612DEFB798507F25\n",
    "!apt-get update\n",
    "!apt-get install python3-graph-tool python3-matplotlib python3-cairo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "pr-ut3scRrok",
    "outputId": "650030c1-9b2a-49cb-871a-42cbf2ec9de9"
   },
   "outputs": [],
   "source": [
    "#python3-cairo from Ubuntu's reposity is linked with a different python version; we need to improvise\n",
    "!apt purge python3-cairo\n",
    "!apt install libcairo2-dev pkg-config python3-dev\n",
    "!pip install --force-reinstall pycairo\n",
    "!pip install zstandard"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "LZBU2HvQqJAw"
   },
   "source": [
    "# Repository of weighted graphs: https://networks.skewed.de/?tags=Weighted"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "-Hk9usv9pUBZ",
    "outputId": "cbc1290b-66b6-401f-9869-4269699e3add"
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import graph_tool.all as gt\n",
    "from google.colab import files\n",
    "\n",
    "from google.colab import drive\n",
    "\n",
    "import os.path\n",
    "from os import path\n",
    "\n",
    "def export_all_weightedGraphs_erodeCSV(model_names,download_file,store_on_gdrive,path_g_drive=\"weightedGraphs/\",prefix_to_weight=dict()):\n",
    "   #Exports in ERODE CSV format all weighted graphs in the list model_names. \n",
    "   #The CSV file is either stored on google drive, or downloaded, as required by the parameters (Google drive has precedence on downloading)\n",
    "   #If the google drive option is chosen, the files will be stored in folder weightedGraphs, or different paths provided in parameter path_g_drive\n",
    "   #  This should be a relative path to a folder (ending with a slash). E.g., if you pass \"weightedGraphs/\", we will store files in it in MyDrive/weightedGraphs/\n",
    "\n",
    "\n",
    "  print('Processing and exporting models')\n",
    "  print(\"\",model_names)\n",
    "\n",
    "  #Prepare gdrive\n",
    "  gdrive_path=\"/content/drive/MyDrive/\"+path_g_drive\n",
    "  if store_on_gdrive:\n",
    "    drive.mount('/content/drive')\n",
    "    if not path.exists(gdrive_path):\n",
    "      os.mkdir(gdrive_path)\n",
    "    if not path.exists(gdrive_path+\"/csv/\"):\n",
    "      os.mkdir(gdrive_path+\"/csv/\")\n",
    "\n",
    "  #Export required weighted graps\n",
    "  for model_name in model_names:\n",
    "    weight_name='weight'\n",
    "    for key in prefix_to_weight:\n",
    "      if model_name.startswith(key):\n",
    "        weight_name=prefix_to_weight[key]\n",
    "        break\n",
    "    export_weightedGraph_erodeCSV(model_name,download_file,store_on_gdrive,gdrive_path,weight_name)\n",
    "\n",
    "  #Close gdrive\n",
    "  if store_on_gdrive:\n",
    "    drive.flush_and_unmount()\n",
    "\n",
    "  print('All computations completed')\n",
    "\n",
    "def export_weightedGraph_erodeCSV(model_name,download_file,store_on_gdrive,gdrive_path,weight_name):\n",
    "  #load model\n",
    "  print(\"PROCESSING:\",model_name,\"...\")\n",
    "\n",
    "  g = gt.collection.ns[model_name]\n",
    "\n",
    "  if not(weight_name in g.edge_properties):\n",
    "    print(\" MODEL DROPPED BECAUSE NOT WEIGHTED\")\n",
    "    return\n",
    "  add_rev= not g.is_directed()\n",
    "    \n",
    "  max_nodes=200\n",
    "  n_nodes=g.num_vertices()\n",
    "  if n_nodes > max_nodes:\n",
    "    print(\" MODEL DROPPED BECAUSE IT HAS MORE THAN\",max_nodes,\"NODES\")\n",
    "    return        \n",
    "    \n",
    "  #n_nodes=len(g.get_edges())\n",
    "  #if add_rev:\n",
    "  #      n_edges=n_edges*2\n",
    "  #if n_edges > max_edges:\n",
    "  #  print(\" MODEL DROPPED BECAUSE IT HAS MORE THAN\",max_edges,\"EDGES\")\n",
    "  #  return        \n",
    "\n",
    "  model_name = model_name.replace(\"/\",\"_\")\n",
    "  model_name = model_name.replace(\" \",\"_\")\n",
    "  model_name = model_name.replace(\"-\",\"_\")\n",
    "  model_name = model_name.replace(\"(\",\"_\")\n",
    "  model_name = model_name.replace(\")\",\"_\")\n",
    "\n",
    "  #store unweighted edges in a dataframe, and add weights\n",
    "  df = pd.DataFrame(data=g.get_edges(), columns=[\"source\", \"target\"])\n",
    "  df[\"source\"]=df[\"source\"]+1\n",
    "  df[\"target\"]=df[\"target\"]+1\n",
    "  \n",
    "  if weight_name in g.edge_properties:\n",
    "    df['weight']=g.edge_properties[weight_name].get_array()\n",
    "  else:\n",
    "    df['weight']=np.ones(len(df))\n",
    "    print(\"BEWARE:\",model_name,\"DOES NOT HAVE WEIGHTS.\\n WE SET ALL WEIGHTS TO ONE!\")\n",
    "    model_name=model_name+\"_defaultWeights\"\n",
    "\n",
    "\n",
    "  #add_rev_str= str(add_rev)\n",
    "  if add_rev:\n",
    "      df_rev = df[[\"target\",\"source\",'weight']]\n",
    "      df_rev.columns = [\"source\", \"target\",'weight']\n",
    "      df=pd.concat([df,df_rev])\n",
    "      df.reset_index(drop=True, inplace=True)\n",
    "      add_rev=False\n",
    "      \n",
    "\n",
    "  #n_nodes=g.num_vertices()\n",
    "  df0 = pd.DataFrame([[n_nodes,n_nodes,n_nodes]], columns=[\"source\", \"target\",'weight'])\n",
    "  df=pd.concat([df0, df])\n",
    "  df.reset_index(drop=True, inplace=True)\n",
    "  #print(df)\n",
    "\n",
    "  dfB = pd.DataFrame(data=np.zeros(n_nodes), columns=[\"B\"])\n",
    "\n",
    "    \n",
    "  #compute file name of csv file\n",
    "  csv_file_name=\"csv/\"+model_name+'A.csv'\n",
    "  csv_file_nameB=\"csv/\"+model_name+'B.csv'\n",
    "  erode_file_name=\"import_\"+model_name+'.ode'\n",
    "    \n",
    "  if store_on_gdrive:\n",
    "    csv_file_name  =gdrive_path+\"csv/\"+model_name+'A.csv'\n",
    "    csv_file_nameB =gdrive_path+\"csv/\"+model_name+'B.csv'\n",
    "    erode_file_name=gdrive_path+\"import_\"+model_name+'.ode'\n",
    "    \n",
    "  \n",
    "\n",
    "  print(\"  \",\"Graph processed, and data structure created\")\n",
    "\n",
    "  #create csv file and download if required\n",
    "  df.to_csv( csv_file_name ,index=False,header=False)\n",
    "  dfB.to_csv(csv_file_nameB,index=False,header=False)\n",
    "\n",
    "  # Create ERODE file to import the CSV ones\n",
    "  with open(erode_file_name, 'w') as fp:\n",
    "    fp.write('begin model import_'+model_name+\"\\n\")\n",
    "    fp.write(' importAffineSystem(fileIn=\"csv/'+model_name+'A.csv\", BFile=\"csv/'+model_name+'B.csv\", ICFile=\"csv/'+model_name+'B.csv\", addReverseEdges=false)\\n')\n",
    "    #fp.write(' write(fileOut=\"ODE/'+model_name+'._ode\",format=ODE)\\n')\n",
    "    #fp.write(' reduceBE(reducedFile=\"BE/'+model_name+'_BE._ode\", csvFile=\"BE.csv\")\\n')\n",
    "    #fp.write(' reduceFE(reducedFile=\"FE/'+model_name+'_FE._ode\", csvFile=\"FE.csv\")\\n')\n",
    "    fp.write(' write(fileOut=\"EULER_ODE/'+model_name+'.ode\",format=EULER)\\n')\n",
    "    #fp.write(' reduceRndFME(aggregationFunction=TIMES,reducedFile=\"RndFME_user/'+model_name+'_RndFME_user._ode\", csvFile=\"RndTIMES_USER.csv,prePartition=USER\")\\n')\n",
    "    fp.write('end model\\n')\n",
    "    \n",
    "  \n",
    "  if download_file and not store_on_gdrive:\n",
    "    files.download(csv_file_name)\n",
    "    files.download(csv_file_nameB)\n",
    "    files.download(erode_file_name)\n",
    "\n",
    "  print(\"  \",\"All files exported\")\n",
    "\n",
    "    \n",
    "  \n",
    "#Choose the models to consider\n",
    "# Just https://networks.skewed.de/net/blumenau_drug\n",
    "#model_names=[\"blumenau_drug\"]\n",
    "#model_names=[\"cattle\"]\n",
    "#model_names=[\"blumenau_drug\",\"cattle\",\"train_terrorists\"]\n",
    "\n",
    "#All weighted networks on 21/07/2022 from smallest number of nodes to largest#\n",
    "# Taken from https://networks.skewed.de/?tags=Weighted after clicking on 'Nodes'\n",
    "model_names=[\n",
    "             \"packet_delays\",\"ambassador/1985_1989\",\"ambassador/1990_1994\",\"ambassador/1995_1999\",\"ambassador/2000\",\"ambassador/2001\",\"ambassador/2002\",\"ambassador/2003\",\"ambassador/2004\",\"ambassador/2005\",\"ambassador/2006\",\"ambassador/2007\",\"ambassador/KINSHIP\",\"ambassador/OPERATION_ID\",\"ambassador/TIE_EXTINGUISH\",\"ambassador/TIE_YEAR\",\n",
    "             \"rhesus_monkey\",\"kangaroo\",\n",
    "             \"sp_baboons/observational\",\"sp_baboons/sensor\",\"bison\",\"cattle\",\"moreno_sheep\",\"college_freshmen\",\"hens\",\n",
    "             \"freshmen/t0\",\"freshmen/t2\",\"freshmen/t3\",\"freshmen/t5\",\"freshmen/t6\",\n",
    "             \"windsurfers\",\"macaques\",\"train_terrorists\",\"highschool\",\"blumenau_drug\",\"lesmis\",\"baseball/player-player\",\"baseball/user-provider\",\"sp_office\",\"game_thrones\",\n",
    "             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    "             \"plant_pol_vazquez/Llao Llao\",\"plant_pol_vazquez/Cerro Lopez\",\"plant_pol_vazquez/Safariland\",\"plant_pol_vazquez/Arroyo Goye\",\"plant_pol_vazquez/Mascardi (nc)\",\"plant_pol_vazquez/Mascardi (c)\",\"plant_pol_vazquez/Quetrihue (nc)\",\"plant_pol_vazquez/Quetrihue (c)\",\"plant_pol_vazquez/All sites pooled\",\n",
    "             \"dom/Adcock_2015a\",\"dom/Adcock_2015b\",\"dom/Alados_1992a\",\"dom/Alados_1992b\",\"dom/Alados_1992c\",\"dom/Alados_1992d\",\"dom/Alados_1992e\",\"dom/Allee_1954\",\"dom/Anderson_2016a\",\"dom/Anderson_2016d\",\"dom/Appleby_1983\",\"dom/Archie_2006a\",\"dom/Archie_2006b\",\"dom/Archie_2006c\",\"dom/Archie_2006d\",\"dom/Archie_2006e\",\"dom/Archie_2006f\",\"dom/Archie_2006g\",\"dom/Archie_2006h\",\"dom/Archie_2006i\",\"dom/Arlet_2015f\",\"dom/Barette_1986\",\"dom/Bennett_1939\",\"dom/BergstromFedigan_2010b\",\"dom/BergstromFedigan_2010c\",\"dom/Berman_2004a\",\"dom/Berman_2004b\",\"dom/Berman_2004c\",\"dom/Blatrix_2004b\",\"dom/Blatrix_2004c\",\"dom/Blatrix_2004d\",\"dom/Blatrix_2004e\",\"dom/Bonanni_2007a\",\"dom/Bonanni_2007b\",\"dom/Bonanni_2007c\",\"dom/Bonanni_2017a\",\"dom/Bonanni_2017b\",\"dom/Bonanni_2017c\",\"dom/Bonanni_2017d\",\"dom/Bromley_1991\",\"dom/Cafazzo_2010a\",\"dom/Cafazzo_2010b\",\"dom/Cheney_1977\",\"dom/Cheney_1977b\",\"dom/CluttonBrock_1976\",\"dom/Collias_1950a\",\"dom/Collias_1950b\",\"dom/Collias_1950c\",\"dom/Collias_1951a\",\"dom/Collias_1951b\",\"dom/Collias_1951c\",\"dom/Correa_2013a\",\"dom/Correa_2013d\",\"dom/Cote_2000\",\"dom/Cote_2000b\",\"dom/Cote_2000c\",\"dom/Cote_2000d\",\"dom/Cui_2014\",\"dom/David_2003a\",\"dom/David_2003b\",\"dom/DeLaFuente_2019\",\"dom/DeLaO_2019a\",\"dom/DeLaO_2019b\",\"dom/DeLaO_2019c\",\"dom/DeLaO_2019d\",\"dom/deVries_2006\",\"dom/deWaal_1977a\",\"dom/deWaal_1977b\",\"dom/deWaal_1985\",\"dom/Diniz_2019\",\"dom/Douglis_1948a\",\"dom/Douglis_1948b\",\"dom/Dubosq2013a\",\"dom/Dubosq2013b\",\"dom/Dubosq2013c\",\"dom/Dubosq2013d\",\"dom/Dubosq2013e\",\"dom/Dubosq2013f\",\"dom/Ellard_1989\",\"dom/Essler_2016a\",\"dom/Essler_2016c\",\"dom/Essler_2016d\",\"dom/Fairbanks_1994a\",\"dom/Fairbanks_1994b\",\"dom/Fairbanks_1994c\",\"dom/Fairbanks_1994d\",\"dom/Fairbanks_1994e\",\"dom/Farentinos_1972a\",\"dom/Farentinos_1972b\",\"dom/Farentinos_1972c\",\"dom/Farentinos_1972d\",\"dom/Farentinos_1972e\",\"dom/Farentinos_1972f\",\"dom/Foerster_2016a\",\"dom/Foerster_2016b\",\"dom/Fournier_1995\",\"dom/Fournier_1995b\",\"dom/Frank_1986a\",\"dom/Frank_1986b\",\"dom/Franz_2015a\",\"dom/Franz_2015b\",\"dom/Franz_2015c\",\"dom/Franz_2015d\",\"dom/Franz_2015e\",\"dom/Funkhouser_2018a\",\"dom/Funkhouser_2018b\",\"dom/Harcourt_1979\",\"dom/Harcourt_1989\",\"dom/Hartzler_1970\",\"dom/Hass_1991\",\"dom/Hass_1991b\",\"dom/Hass_1991c\",\"dom/Hausfater_1975a\",\"dom/Hausfater_1975b\",\"dom/Hausfater_1975c\",\"dom/Hausfater_1982a\",\"dom/Hausfater_1982b\",\"dom/Hayaki_1989a\",\"dom/Hayaki_1989b\",\"dom/Heitor_2006\",\"dom/HeitorVicente_2010\",\"dom/Hewitt_2009a\",\"dom/Hewitt_2009b\",\"dom/Hewitt_2009c\",\"dom/Hewitt_2009d\",\"dom/Hirotani_1994\",\"dom/Hirsch_2007a\",\"dom/Hirsch_2007b\",\"dom/Hirsch_2007c\",\"dom/Hirsch_2007d\",\"dom/Hobson_2015a\",\"dom/Hobson_2015b\",\"dom/Holekamp_1991\",\"dom/Holekamp_1993a\",\"dom/Holekamp_1993b\",\"dom/Isbell_1998a\",\"dom/Isbell_1998b\",\"dom/Ito_1993a\",\"dom/Ito_1993b\",\"dom/Ito_1993c\",\"dom/Izar_2006\",\"dom/IzawaWatanabe_2011\",\"dom/Jenks_1995a\",\"dom/Jenks_1995b\",\"dom/Johnson_2017\",\"dom/Jones_1980a\",\"dom/Jones_1980b\",\"dom/Kaufmann_1974\",\"dom/Kikkawa_1980\",\"dom/Koenig_2004\",\"dom/Kohda_1991\",\"dom/Kolodziejczyk_2005\",\"dom/Korstjens_2002\",\"dom/Koutnik_1981\",\"dom/Koutnik_1981b\",\"dom/Kurvers_2009\",\"dom/Lahti_1994a\",\"dom/Lahti_1994b\",\"dom/Langbein_2004a\",\"dom/Langbein_2004b\",\"dom/Langbein_2004c\",\"dom/Langbein_2004d\",\"dom/Langley_2018\",\"dom/Lee_1979a\",\"dom/Lee_1979b\",\"dom/Lee_2017a\",\"dom/Lee_2017b\",\"dom/Lee_2017c\",\"dom/Lee_2017d\",\"dom/Lee_2017e\",\"dom/Lee_2017f\",\"dom/Lee_2018a\",\"dom/Lee_2018b\",\"dom/Lee_2018c\",\"dom/Lee_2018d\",\"dom/Lee_2018e\",\"dom/Lee_2019a\",\"dom/Lee_2019b\",\"dom/Lee_2019c\",\"dom/Lee_2019d\",\"dom/Lee_2019e\",\"dom/Lott_1979\",\"dom/Lott_1987\",\"dom/Lu_2008a\",\"dom/Lu_2008b\",\"dom/Malherbe_2007\",\"dom/Marler_1955\",\"dom/Masure_1934\",\"dom/Masure_1934a\",\"dom/Masure_1934b\",\"dom/Mather_1985\",\"dom/Matsuda_2012\",\"dom/McCune_2019a\",\"dom/McCune_2019c\",\"dom/McCune_2019d\",\"dom/McCune_2019e\",\"dom/McCune_2019f\",\"dom/McDougall_2010\",\"dom/McMahan_1984\",\"dom/Miller_2010a\",\"dom/Miller_2010b\",\"dom/Miller_2010c\",\"dom/Moller_1987a\",\"dom/Moller_1987b\",\"dom/Moller_1987c\",\"dom/Monnin_1999\",\"dom/Moore_1978a\",\"dom/Moore_1978b\",\"dom/Murray_2007\",\"dom/Mwamende_2009a\",\"dom/Mwamende_2009b\",\"dom/Myrberg_1972\",\"dom/Myrberg_1974\",\"dom/Nakano_1994\",\"dom/Nakano_1995\",\"dom/Natoli_1991\",\"dom/Nelissen_1985a\",\"dom/Nelissen_1985b\",\"dom/NewtonFisher_2004a\",\"dom/NewtonFisher_2004b\",\"dom/Norscia_2015a\",\"dom/Norscia_2015b\",\"dom/Norscia_2015c\",\"dom/Norscia_2015d\",\"dom/Norscia_2015e\",\"dom/Norscia_2015f\",\"dom/Norscia_2015g\",\"dom/Norscia_2015h\",\"dom/Norscia_2015i\",\"dom/Norscia_2015j\",\"dom/Ortius_1995\",\"dom/Oshea_1976\",\"dom/Owens_1996\",\"dom/Painter_2018\",\"dom/Paoli_2006\",\"dom/Pardi_1948a\",\"dom/Pardi_1948b\",\"dom/Parsons_1980a\",\"dom/Parsons_1980b\",\"dom/Patterson_1977\",\"dom/Payne_2003\",\"dom/Poisbleau_2005a\",\"dom/Poisbleau_2005b\",\"dom/Poisbleau_2005c\",\"dom/Poisbleau_2006a\",\"dom/Poisbleau_2006b\",\"dom/Post_1992\",\"dom/Prieto_1978\",\"dom/Reason_1988\",\"dom/Richter_2009\",\"dom/RizaldiWatanabe_2010a\",\"dom/RizaldiWatanabe_2010b\",\"dom/Robbins_2008\",\"dom/Roell_1978\",\"dom/Rossler_2017\",\"dom/Rovero_1999a\",\"dom/Rovero_1999b\",\"dom/Russell_1970a\",\"dom/Russell_1970b\",\"dom/Rutberg_1986a\",\"dom/Rutberg_1986b\",\"dom/Samuels_1987\",\"dom/Samuels_1987b\",\"dom/Sandel_2017a\",\"dom/Sandel_2017b\",\"dom/SatohOhkawara_2008a\",\"dom/SatohOhkawara_2008b\",\"dom/SatohOhkawara_2008c\",\"dom/ScheinFohrman_1955\",\"dom/SchjelderupEbbe_1922a\",\"dom/SchjelderupEbbe_1922b\",\"dom/ScottLockhard_1999a\",\"dom/ScottLockhard_1999b\",\"dom/Seibert_2001\",\"dom/Setchell_2005a\",\"dom/Setchell_2005b\",\"dom/SetiaVanSchaik_2007\",\"dom/Seyfarth_1976a\",\"dom/Seyfarth_1976b\",\"dom/Seyfarth_1976c\",\"dom/Seyfarth_1976d\",\"dom/Seyfarth_1976e\",\"dom/Seyfarth_1976f\",\"dom/Sharpe_2013a\",\"dom/Sharpe_2013b\",\"dom/Sharpe_2013c\",\"dom/Sharpe_2013d\",\"dom/Shimoji_2014a\",\"dom/Shimoji_2014b\",\"dom/Shimoji_2014c\",\"dom/Shoemaker_1939\",\"dom/Silk_2019a\",\"dom/Slotow_1993\",\"dom/Smith_1976\",\"dom/Smith_2011a\",\"dom/Solberg_1997a\",\"dom/Solberg_1997b\",\"dom/Solberg_1997c\",\"dom/SomersNel_1998a\",\"dom/SomersNel_1998b\",\"dom/SomersNel_1998c\",\"dom/Stamps_1978\",\"dom/Sterck_1997\",\"dom/Strauss_2019a\",\"dom/Strauss_2019b\",\"dom/Strauss_2019c\",\"dom/Strauss_2019d\",\"dom/StrayerCummins_1980\",\"dom/StrayerCummins_1980b\",\"dom/StrayerCummins_1980c\",\"dom/StrayerCummins_1980d\",\"dom/Struhsaker_1967a\",\"dom/Struhsaker_1967b\",\"dom/Sullivan_1982\",\"dom/Surbeck_2011\",\"dom/SurbeckHohmann_2013b\",\"dom/Tamm_1977\",\"dom/Tamura_1988\",\"dom/Tarvin_1997\",\"dom/Thompson_1960a\",\"dom/Thompson_1960b\",\"dom/Thompson_1960c\",\"dom/Thompson_1960d\",\"dom/Thompson_1960e\",\"dom/Thompson_1993a\",\"dom/Thompson_1993b\",\"dom/Tilson_1984\",\"dom/Tong_2020a\",\"dom/Tong_2020b\",\"dom/Tong_2020c\",\"dom/Tong_2020d\",\"dom/Tong_2020e\",\"dom/Tong_2020f\",\"dom/Tong_2020g\",\"dom/Tong_2020h\",\"dom/Tong_2020i\",\"dom/Tong_2020j\",\"dom/Torr_1996a\",\"dom/Torr_1996b\",\"dom/Torr_1996c\",\"dom/Trebouet_2019a\",\"dom/Trebouet_2019b\",\"dom/Trebouet_2019c\",\"dom/Trebouet_2019d\",\"dom/Trunzer_1999\",\"dom/Utt_2008a\",\"dom/ValLaillet_2008a\",\"dom/ValLaillet_2008b\",\"dom/ValLaillet_2008c\",\"dom/ValLaillet_2008d\",\"dom/ValLaillet_2008e\",\"dom/ValLaillet_2008f\",\"dom/VanDessel_2018a\",\"dom/VanDessel_2018b\",\"dom/VanDierendonck_1995\",\"dom/VanHooffWensing_1987\",\"dom/Varley_1966\",\"dom/Varley_1966b\",\"dom/Vervaecke_2000\",\"dom/Vervaecke_2010a\",\"dom/Vervaecke_2010b\",\"dom/Vervaecke_2010c\",\"dom/Vervaecke_2010d\",\"dom/Vilette_2020\",\"dom/Waterhouse_1976a\",\"dom/Waterhouse_1976b\",\"dom/Waterhouse_1976c\",\"dom/Watson_1970a\",\"dom/Watson_1970b\",\"dom/Watt_1986a\",\"dom/Watt_1986b\",\"dom/Watt_1986c\",\"dom/Watt_1986d\",\"dom/Watt_1986e\",\"dom/Watt_1986f\",\"dom/Watts_1985\",\"dom/Watts_1994a\",\"dom/Watts_1994b\",\"dom/Watts_1994c\",\"dom/Wells_1979\",\"dom/WestEberhard_1986\",\"dom/White_2007a\",\"dom/White_2007b\",\"dom/White_2007c\",\"dom/Wikberg_2013a\",\"dom/Wikberg_2013b\",\"dom/Wikberg_2013c\",\"dom/Wikberg_2013d\",\"dom/Wikberg_2013e\",\"dom/Wikberg_2013f\",\"dom/Williams_1972\",\"dom/Williamson_2016a\",\"dom/Williamson_2016b\",\"dom/Williamson_2016c\",\"dom/Williamson_2016d\",\"dom/Williamson_2016e\",\"dom/Williamson_2016f\",\"dom/Williamson_2016g\",\"dom/Williamson_2016h\",\"dom/Williamson_2016i\",\"dom/Williamson_2016j\",\"dom/Williamson_2016k\",\"dom/Williamson_2017a\",\"dom/Williamson_2017b\",\"dom/Williamson_2017c\",\"dom/Williamson_2017d\",\"dom/Williamson_2017e\",\"dom/Williamson_2017f\",\"dom/Williamson_2017g\",\"dom/Williamson_2017h\",\"dom/Williamson_2017i\",\"dom/Williamson_2017j\",\"dom/Williamson_2017k\",\"dom/Williamson_2017l\",\"dom/Williamson_2017m\",\"dom/Williamson_2017n\",\"dom/Williamson_2017o\",\"dom/Williamson_2019a\",\"dom/Williamson_2019b\",\"dom/Williamson_2019c\",\"dom/Williamson_2019d\",\"dom/Williamson_2019e\",\"dom/Williamson_2019f\",\"dom/Williamson_2019g\",\"dom/Williamson_2019h\",\"dom/Wittemeyer_2007\",\"dom/Wittig_2003\",\"dom/Yasukawa_1983a\",\"dom/Yasukawa_1983b\",\"dom/Yasukawa_1983c\",\"dom/Yasukawa_1983d\",\"dom/Yasukawa_1983e\",\"dom/Yasukawa_1983f\",\"dom/Yasukawa_1983g\",\"dom/Yasukawa_1983h\",\"dom/Zine_2000\",\n",
    "             \"cintestinalis\",\n",
    "             \"faculty_hiring/computer_science\",\"faculty_hiring/business\",\"faculty_hiring/history\",\n",
    "             \"fao_trade\",\"residence_hall\",\"un_migrations\",\"sp_primary_school\",\"celegansneural\",\n",
    "             \"sp_high_school/proximity\",\"sp_high_school/diaries\",\"sp_high_school/survey\",\"sp_high_school/facebook\",\n",
    "             \"london_transport\",\n",
    "             \"sp_colocation/Thiers13\",\"sp_colocation/SFHH\",\"sp_colocation/LyonSchool\",\"sp_colocation/LH10\",\"sp_colocation/InVS15\",\"sp_colocation/InVS13\",\n",
    "             \"webkb/webkb_wisconsin_link1\",\"webkb/webkb_wisconsin_cocite\",\"webkb/webkb_washington_link1\",\"webkb/webkb_washington_cocite\",\"webkb/webkb_cornell_link1\",\"webkb/webkb_cornell_cocite\",\"webkb/webkb_texas_link1\",\"webkb/webkb_texas_cocite\",\n",
    "            \"celegans_2019/male_chemical\",\"celegans_2019/male_gap_junction\",\"celegans_2019/hermaphrodite_chemical\",\"celegans_2019/hermaphrodite_gap_junction\",\"celegans_2019/male_chemical_synapse\",\"celegans_2019/male_gap_junction_synapse\",\"celegans_2019/hermaphrodite_chemical_synapse\",\"celegans_2019/hermaphrodite_gap_junction_synapse\",\"celegans_2019/male_chemical_corrected\",\"celegans_2019/male_gap_junction_corrected\",\"celegans_2019/hermaphrodite_chemical_corrected\",\"celegans_2019/hermaphrodite_gap_junction_corrected\",\n",
    "            #\"messal_shale\", #DOES NOT WORK\n",
    "             \"plant_pol_kato\",\n",
    "             \"copenhagen/sms\",\"copenhagen/fb_friends\",\"copenhagen/calls\",\"copenhagen/bt\",\n",
    "            \"product_space/HS\",\"product_space/SITC\",\n",
    "            \"unicodelang\",\n",
    "            \"budapest_connectome/all_20k\",\"budapest_connectome/all_200k\",\"budapest_connectome/all_1m\",\"budapest_connectome/female_20k\",\"budapest_connectome/female_200k\",\"budapest_connectome/female_1m\",\"budapest_connectome/male_20k\",\"budapest_connectome/male_200k\",\"budapest_connectome/male_1m\",\n",
    "            \"new_zealand_collab\",\"netscience\",\"bible_nouns\",\n",
    "            # \"add_health/comm1\",\"add_health/comm2\",\"add_health/comm3\",\"add_health/comm4\",#there are about 100 graphs. we consider only 4. BUT IT DOES NOT WORK: files offline\n",
    "            \"openflights\",\"bitcoin_alpha\",\"bitcoin_trust\",\"advogato\",\"foldoc\",\n",
    "            \"physics_collab/pierreAuger\",\"physics_collab/arXiv\",\n",
    "            \"escorts\",\"fly_hemibrain\",\n",
    "            \"arxiv_collab/cond-mat-1999\",\"arxiv_collab/cond-mat-2003\",\"arxiv_collab/cond-mat-2005\",\"arxiv_collab/astro-ph-1999\",\"arxiv_collab/hep-th-1999\",\n",
    "            \"us_agencies/alabama\",\"us_agencies/alaska\",\"us_agencies/arizona\",\"us_agencies/arkansas\",\"us_agencies/california\",\"us_agencies/colorado\",\"us_agencies/connecticut\",\"us_agencies/delaware\",\"us_agencies/florida\",\"us_agencies/georgia\",\"us_agencies/hawaii\",\"us_agencies/idaho\",\"us_agencies/illinois\",\"us_agencies/indiana\",\"us_agencies/iowa\",\"us_agencies/kansas\",\"us_agencies/kentucky\",\"us_agencies/louisiana\",\"us_agencies/maine\",\"us_agencies/maryland\",\"us_agencies/massachusetts\",\"us_agencies/michigan\",\"us_agencies/minnesota\",\"us_agencies/mississippi\",\"us_agencies/missouri\",\"us_agencies/montana\",\"us_agencies/nebraska\",\"us_agencies/nevada\",\"us_agencies/newhampshire\",\"us_agencies/newjersey\",\"us_agencies/newmexico\",\"us_agencies/newyork\",\"us_agencies/northcarolina\",\"us_agencies/northdakota\",\"us_agencies/ohio\",\"us_agencies/oklahoma\",\"us_agencies/oregon\",\"us_agencies/pennsylvania\",\"us_agencies/rhodeisland\",\"us_agencies/southcarolina\",\"us_agencies/southdakota\",\"us_agencies/tennessee\",\"us_agencies/texas\",\"us_agencies/utah\",\"us_agencies/vermont\",\"us_agencies/virginia\",\"us_agencies/washington\",\"us_agencies/westvirginia\",\"us_agencies/wisconsin\",\"us_agencies/wyoming\",\"us_agencies/aggregate\",\n",
    "           \"eu_procurements_alt/AT_2008\",\"eu_procurements_alt/AT_2009\",\"eu_procurements_alt/AT_2010\",\"eu_procurements_alt/AT_2011\",\"eu_procurements_alt/AT_2012\",\"eu_procurements_alt/AT_2013\",\"eu_procurements_alt/AT_2014\",\"eu_procurements_alt/AT_2015\",\"eu_procurements_alt/AT_2016\",\"eu_procurements_alt/BE_2008\",\"eu_procurements_alt/BE_2009\",\"eu_procurements_alt/BE_2010\",\"eu_procurements_alt/BE_2011\",\"eu_procurements_alt/BE_2012\",\"eu_procurements_alt/BE_2013\",\"eu_procurements_alt/BE_2014\",\"eu_procurements_alt/BE_2015\",\"eu_procurements_alt/BE_2016\",\"eu_procurements_alt/BG_2008\",\"eu_procurements_alt/BG_2009\",\"eu_procurements_alt/BG_2010\",\"eu_procurements_alt/BG_2011\",\"eu_procurements_alt/BG_2012\",\"eu_procurements_alt/BG_2013\",\"eu_procurements_alt/BG_2014\",\"eu_procurements_alt/BG_2015\",\"eu_procurements_alt/BG_2016\",\"eu_procurements_alt/CY_2008\",\"eu_procurements_alt/CY_2009\",\"eu_procurements_alt/CY_2010\",\"eu_procurements_alt/CY_2011\",\"eu_procurements_alt/CY_2012\",\"eu_procurements_alt/CY_2013\",\"eu_procurements_alt/CY_2014\",\"eu_procurements_alt/CY_2015\",\"eu_procurements_alt/CY_2016\",\"eu_procurements_alt/CZ_2008\",\"eu_procurements_alt/CZ_2009\",\"eu_procurements_alt/CZ_2010\",\"eu_procurements_alt/CZ_2011\",\"eu_procurements_alt/CZ_2012\",\"eu_procurements_alt/CZ_2013\",\"eu_procurements_alt/CZ_2014\",\"eu_procurements_alt/CZ_2015\",\"eu_procurements_alt/CZ_2016\",\"eu_procurements_alt/DE_2008\",\"eu_procurements_alt/DE_2009\",\"eu_procurements_alt/DE_2010\",\"eu_procurements_alt/DE_2011\",\"eu_procurements_alt/DE_2012\",\"eu_procurements_alt/DE_2013\",\"eu_procurements_alt/DE_2014\",\"eu_procurements_alt/DE_2015\",\"eu_procurements_alt/DE_2016\",\"eu_procurements_alt/DK_2008\",\"eu_procurements_alt/DK_2009\",\"eu_procurements_alt/DK_2010\",\"eu_procurements_alt/DK_2011\",\"eu_procurements_alt/DK_2012\",\"eu_procurements_alt/DK_2013\",\"eu_procurements_alt/DK_2014\",\"eu_procurements_alt/DK_2015\",\"eu_procurements_alt/DK_2016\",\"eu_procurements_alt/EE_2008\",\"eu_procurements_alt/EE_2009\",\"eu_procurements_alt/EE_2010\",\"eu_procurements_alt/EE_2011\",\"eu_procurements_alt/EE_2012\",\"eu_procurements_alt/EE_2013\",\"eu_procurements_alt/EE_2014\",\"eu_procurements_alt/EE_2015\",\"eu_procurements_alt/EE_2016\",\"eu_procurements_alt/ES_2008\",\"eu_procurements_alt/ES_2009\",\"eu_procurements_alt/ES_2010\",\"eu_procurements_alt/ES_2011\",\"eu_procurements_alt/ES_2012\",\"eu_procurements_alt/ES_2013\",\"eu_procurements_alt/ES_2014\",\"eu_procurements_alt/ES_2015\",\"eu_procurements_alt/ES_2016\",\"eu_procurements_alt/FI_2008\",\"eu_procurements_alt/FI_2009\",\"eu_procurements_alt/FI_2010\",\"eu_procurements_alt/FI_2011\",\"eu_procurements_alt/FI_2012\",\"eu_procurements_alt/FI_2013\",\"eu_procurements_alt/FI_2014\",\"eu_procurements_alt/FI_2015\",\"eu_procurements_alt/FI_2016\",\"eu_procurements_alt/FR_2008\",\"eu_procurements_alt/FR_2009\",\"eu_procurements_alt/FR_2010\",\"eu_procurements_alt/FR_2011\",\"eu_procurements_alt/FR_2012\",\"eu_procurements_alt/FR_2013\",\"eu_procurements_alt/FR_2014\",\"eu_procurements_alt/FR_2015\",\"eu_procurements_alt/FR_2016\",\"eu_procurements_alt/GR_2008\",\"eu_procurements_alt/GR_2009\",\"eu_procurements_alt/GR_2010\",\"eu_procurements_alt/GR_2011\",\"eu_procurements_alt/GR_2012\",\"eu_procurements_alt/GR_2013\",\"eu_procurements_alt/GR_2014\",\"eu_procurements_alt/GR_2015\",\"eu_procurements_alt/GR_2016\",\"eu_procurements_alt/HU_2008\",\"eu_procurements_alt/HU_2009\",\"eu_procurements_alt/HU_2010\",\"eu_procurements_alt/HU_2011\",\"eu_procurements_alt/HU_2012\",\"eu_procurements_alt/HU_2013\",\"eu_procurements_alt/HU_2014\",\"eu_procurements_alt/HU_2015\",\"eu_procurements_alt/HU_2016\",\"eu_procurements_alt/IE_2008\",\"eu_procurements_alt/IE_2009\",\"eu_procurements_alt/IE_2010\",\"eu_procurements_alt/IE_2011\",\"eu_procurements_alt/IE_2012\",\"eu_procurements_alt/IE_2013\",\"eu_procurements_alt/IE_2014\",\"eu_procurements_alt/IE_2015\",\"eu_procurements_alt/IE_2016\",\"eu_procurements_alt/IT_2008\",\"eu_procurements_alt/IT_2009\",\"eu_procurements_alt/IT_2010\",\"eu_procurements_alt/IT_2011\",\"eu_procurements_alt/IT_2012\",\"eu_procurements_alt/IT_2013\",\"eu_procurements_alt/IT_2014\",\"eu_procurements_alt/IT_2015\",\"eu_procurements_alt/IT_2016\",\"eu_procurements_alt/LT_2008\",\"eu_procurements_alt/LT_2009\",\"eu_procurements_alt/LT_2010\",\"eu_procurements_alt/LT_2011\",\"eu_procurements_alt/LT_2012\",\"eu_procurements_alt/LT_2013\",\"eu_procurements_alt/LT_2014\",\"eu_procurements_alt/LT_2015\",\"eu_procurements_alt/LT_2016\",\"eu_procurements_alt/LV_2008\",\"eu_procurements_alt/LV_2009\",\"eu_procurements_alt/LV_2010\",\"eu_procurements_alt/LV_2011\",\"eu_procurements_alt/LV_2012\",\"eu_procurements_alt/LV_2013\",\"eu_procurements_alt/LV_2014\",\"eu_procurements_alt/LV_2015\",\"eu_procurements_alt/LV_2016\",\"eu_procurements_alt/NL_2008\",\"eu_procurements_alt/NL_2009\",\"eu_procurements_alt/NL_2010\",\"eu_procurements_alt/NL_2011\",\"eu_procurements_alt/NL_2012\",\"eu_procurements_alt/NL_2013\",\"eu_procurements_alt/NL_2014\",\"eu_procurements_alt/NL_2015\",\"eu_procurements_alt/NL_2016\",\"eu_procurements_alt/NO_2008\",\"eu_procurements_alt/NO_2009\",\"eu_procurements_alt/NO_2010\",\"eu_procurements_alt/NO_2011\",\"eu_procurements_alt/NO_2012\",\"eu_procurements_alt/NO_2013\",\"eu_procurements_alt/NO_2014\",\"eu_procurements_alt/NO_2015\",\"eu_procurements_alt/NO_2016\",\"eu_procurements_alt/PL_2008\",\"eu_procurements_alt/PL_2009\",\"eu_procurements_alt/PL_2010\",\"eu_procurements_alt/PL_2011\",\"eu_procurements_alt/PL_2012\",\"eu_procurements_alt/PL_2013\",\"eu_procurements_alt/PL_2014\",\"eu_procurements_alt/PL_2015\",\"eu_procurements_alt/PL_2016\",\"eu_procurements_alt/PT_2008\",\"eu_procurements_alt/PT_2009\",\"eu_procurements_alt/PT_2010\",\"eu_procurements_alt/PT_2011\",\"eu_procurements_alt/PT_2012\",\"eu_procurements_alt/PT_2013\",\"eu_procurements_alt/PT_2014\",\"eu_procurements_alt/PT_2015\",\"eu_procurements_alt/PT_2016\",\"eu_procurements_alt/RO_2008\",\"eu_procurements_alt/RO_2009\",\"eu_procurements_alt/RO_2010\",\"eu_procurements_alt/RO_2011\",\"eu_procurements_alt/RO_2012\",\"eu_procurements_alt/RO_2013\",\"eu_procurements_alt/RO_2014\",\"eu_procurements_alt/RO_2015\",\"eu_procurements_alt/RO_2016\",\"eu_procurements_alt/SE_2008\",\"eu_procurements_alt/SE_2009\",\"eu_procurements_alt/SE_2010\",\"eu_procurements_alt/SE_2011\",\"eu_procurements_alt/SE_2012\",\"eu_procurements_alt/SE_2013\",\"eu_procurements_alt/SE_2014\",\"eu_procurements_alt/SE_2015\",\"eu_procurements_alt/SE_2016\",\"eu_procurements_alt/SI_2008\",\"eu_procurements_alt/SI_2009\",\"eu_procurements_alt/SI_2010\",\"eu_procurements_alt/SI_2011\",\"eu_procurements_alt/SI_2012\",\"eu_procurements_alt/SI_2013\",\"eu_procurements_alt/SI_2014\",\"eu_procurements_alt/SI_2015\",\"eu_procurements_alt/SI_2016\",\"eu_procurements_alt/SK_2008\",\"eu_procurements_alt/SK_2009\",\"eu_procurements_alt/SK_2010\",\"eu_procurements_alt/SK_2011\",\"eu_procurements_alt/SK_2012\",\"eu_procurements_alt/SK_2013\",\"eu_procurements_alt/SK_2014\",\"eu_procurements_alt/SK_2015\",\"eu_procurements_alt/SK_2016\",\"eu_procurements_alt/UK_2008\",\"eu_procurements_alt/UK_2009\",\"eu_procurements_alt/UK_2010\",\"eu_procurements_alt/UK_2011\",\"eu_procurements_alt/UK_2012\",\"eu_procurements_alt/UK_2013\",\"eu_procurements_alt/UK_2014\",\"eu_procurements_alt/UK_2015\",\"eu_procurements_alt/UK_2016\",\n",
    "            \"jester\",\"libimseti\",\"wiki_article_words\",\"bookcrossing\",\n",
    "            \"twitter_higgs/social\",\"twitter_higgs/retweet\",\"twitter_higgs/reply\",\"twitter_higgs/mention\",\"twitter_higgs/activity\",\n",
    "            \"eu_procurements\"  ,\"epinions\",\n",
    "            #\"yahoo_song\", #DOES NOT WORK ON COLAB: TOO MUCH RAM\n",
    "             \"mag_history_coauthor/max-25-bip\",\"mag_history_coauthor/max-25-proj\",\"mag_history_coauthor/full-bip\",\"mag_history_coauthor/full-proj\",\n",
    "             \"mag_geology_coauthor/max-25-bip\",\"mag_geology_coauthor/max-25-proj\",\"mag_geology_coauthor/full-bip\",\"mag_geology_coauthor/full-proj\",\n",
    "             \"amazon_ratings\"#,\n",
    "             #\"dblp_simplices/max-25-bip\",\"dblp_simplices/max-25-proj\",\"dblp_simplices/full-bip\",\"dblp_simplices/full-proj\",\n",
    "             #\"bag_of_words/enron\",\"bag_of_words/kos\",\"bag_of_words/nips\",\"bag_of_words/nytimes\", #\"bag_of_words/pubmed\", TOO BIG\n",
    "             #\"microsoft_concept\"\n",
    "]\n",
    "\n",
    "#Unfortunately, not all models classified as weighted have weights. We handle these cases setting deafult weight 1\n",
    "#model_names=[\"hens\"] # DOES NOT HAVE WEIGHTS! The default '1' will be set to all edges\n",
    "\n",
    "prefix_to_weight={'eu_procurements_alt/':'pctSingleBid','arxiv_collab/':'value','bag_of_words/':'count',\n",
    "                  'budapest_connectome/':'occurences','celegans_2019':'connectivity',\n",
    "                  'us_agencies/':'link_counts','plant_pol_vazquez':'count'}\n",
    "\n",
    "#Set flags on where to store the obtained CSV files\n",
    "download_file=False\n",
    "store_on_gdrive=True\n",
    "path_g_drive=\"weightedGraphs/\"\n",
    "export_all_weightedGraphs_erodeCSV(model_names,download_file,store_on_gdrive,path_g_drive,prefix_to_weight)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# If interested in drawing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# from graph_tool.all import *\n",
    "# g = collection.data[\"celegansneural\"]\n",
    "# state = minimize_nested_blockmodel_dl(g)\n",
    "# state = minimize_nested_blockmodel_dl(g)\n",
    "# state.draw()"
   ]
  }
 ],
 "metadata": {
  "colab": {
   "collapsed_sections": [],
   "name": "Graph_tool_to_ERODE",
   "provenance": []
  },
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.9.10"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}