Synaptic events fitting with user model.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Using this notebook\n",
    " \n",
    "- You have to execute this notebook by running each cell consecutively.\n",
    "- To retain any changes made, you need to save the notebook. \n",
    "\n",
    "For detailed information about the notebook interface see _Help -> User Interface Tour_ in the menu, and the [Guidebook](https://lbologna.github.io/hbp-sp6-guidebook/getting_started/getting_started.html#working-with-collabs) for working with Collabs."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from IPython.display import HTML, Javascript, display, clear_output\n",
    "from ipywidgets import widgets\n",
    "\n",
    "import re\n",
    "import os\n",
    "import pytz\n",
    "import json\n",
    "import time\n",
    "import shutil\n",
    "import tarfile\n",
    "import zipfile\n",
    "import requests\n",
    "import warnings\n",
    "import dateutil\n",
    "import subprocess\n",
    "import unicodedata\n",
    "import xml.etree.ElementTree"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "if os.path.isdir('GUIUM'):\n",
    "    shutil.rmtree('GUIUM')\n",
    "os.mkdir('GUIUM')\n",
    "os.chdir(\"GUIUM\")\n",
    "\n",
    "        \n",
    "h0=HTML('''<style>\n",
    "    .widget-label { min-width: 17ex !important;}\n",
    "</style>''')\n",
    "h0.display='none'\n",
    "\n",
    "javascript2 = \"\"\"\n",
    "<script type=\"text/Javascript\">\n",
    "document.styleSheets[0].insertRule(\".widget-listbox.form-control { width: auto }\", 1);\n",
    "document.styleSheets[0].insertRule(\".form_login > label { width: 30% }\", 1);\n",
    "document.styleSheets[0].insertRule(\".form_login > label + input { width: 70% }\", 1);\n",
    "</script>\n",
    "\"\"\"\n",
    "\n",
    "h1=HTML(javascript2)\n",
    "h1.display='none'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "subprocess.call(\"nrnivmodl\");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "if os.path.isdir('transfer'):\n",
    "    shutil.rmtree('transfer')\n",
    "os.mkdir('transfer')\n",
    "os.chdir('transfer')\n",
    "shutil.copy2(os.path.join('..','..', 'cellprop.py'), '.')\n",
    "shutil.copy2(os.path.join('..','..', 'fitness.py'), '.')\n",
    "shutil.copy2(os.path.join('..','..', 'fitting.py'), '.')\n",
    "shutil.copy2(os.path.join('..','..', 'readconffile.py'), '.')\n",
    "shutil.copy2(os.path.join('..','..', 'readexpfile.py'), '.')\n",
    "shutil.copy2(os.path.join('..','..', 'data', 'netstims.mod'), '.')\n",
    "#shutil.copy2(os.path.join('..','..', 'data', 'ProbGABAAB_EMS_GEPH_g.mod'), '.')\n",
    "\n",
    "os.chdir(\"..\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "warnings.filterwarnings('ignore') "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "file_widget=widgets.FileUpload()\n",
    "file_widget3=widgets.FileUpload()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "HE=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"Select experimental file\" \\\n",
    "style=\"color: black; background-color: white; border: none; font-weight: bold\" size=\"60\" \\\n",
    "maxlength=\"400\" disabled=\"true\" id=\"testo\" />\"\"\")\n",
    "file_widget.layout.display='none'\n",
    "file_widget.layout.display=''\n",
    "HM=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"Select mod file\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "file_widget3.layout.display='none'\n",
    "file_widget3.layout.display=''\n",
    "H1=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"name of file containing raw traces\" \\\n",
    "style=\"color: black; background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" \\\n",
    "disabled=\"true\" id=\"testo\" />\"\"\")\n",
    "T1=widgets.Text()\n",
    "T1.value=''\n",
    "T1.disabled=True\n",
    "H2=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"name of mod file\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "T2=widgets.Text()\n",
    "T2.value=''\n",
    "T2.disabled=True\n",
    "H3=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"name of parameters file\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "T3=widgets.Text()\n",
    "T3.value='parameters.txt'\n",
    "H4=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" rows=\"2\" value=\"flagdata==0 data with one time \\\n",
    "column for all currents; ==1 data with one time column for each current\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "H4=widgets.HTML(\"\"\"<textarea name=\"textarea\" rows=\"2\" disabled=\"true\" style=\"width:400px; height:40px; \\\n",
    "color: black; background-color: white; border: none; font-weight: bold; resize: none\">flagdata==0 data \\\n",
    "with one time column for all currents; ==1 data with one time column for each current</textarea>\"\"\")\n",
    "T4=widgets.Text()\n",
    "T4.value='0'\n",
    "H5=widgets.HTML(\"\"\"<textarea name=\"textarea\" rows=\"2\" disabled=\"true\" style=\"width:400px; height:40px; \\\n",
    "color: black; background-color: white; border: none; font-weight: bold; resize: none\">flagcut==0 \\\n",
    "data not cutted;\\n ==1 data cutted below 20% of max</textarea>\"\"\")\n",
    "T5=widgets.Text()\n",
    "T5.value='1'\n",
    "H6=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"number of traces\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "T6=widgets.Text()\n",
    "T6.value=''\n",
    "H7=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"PROTOCOL\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "H8=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"VCLAMP AMP\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "T7=widgets.Text()\n",
    "T7.value=''\n",
    "H9=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"REVERSAL POTENTIAL\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "T8=widgets.Text()\n",
    "T8.value=''\n",
    "H10=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"FITTING PARAMETERS INITIAL VALUES AND \\\n",
    "CONSTRAINTS\" style=\"color: black; background-color: white; border: none; font-weight: bold\" size=\"60\" \\\n",
    "maxlength=\"400\" disabled=\"true\" id=\"testo\" />\"\"\")\n",
    "H11=widgets.HTML(\"\"\"<textarea name=\"textarea\" disabled=\"true\" style=\"width:460px; height:15px; \\\n",
    "color: black; background-color: white; border: none; font-weight: bold; resize: none\">nr of params, \\\n",
    "names of params, initial values, min, max</textarea>\"\"\")\n",
    "T9=widgets.Text()\n",
    "T9.value='0'\n",
    "T9.layout.width=\"10%\"\n",
    "lists=[H1,T1,H2,T2,H3,T3,H4,T4,H5,T5,H6,T6,H7,H8,T7,H9,T8,H10,H11,T9]\n",
    "mybox = widgets.VBox(children=lists)\n",
    "names=[]\n",
    "listsB=[]\n",
    "for i in range(int(T9.value)):\n",
    "    names.append('T'+str(i+10))\n",
    "    T10=widgets.Text()\n",
    "    T10.value=str(i)\n",
    "    T10.layout.width=\"10%\"\n",
    "    T10.disabled=True\n",
    "    T11=widgets.Text()\n",
    "    T11.value=''\n",
    "    T11.layout.width=\"15%\"\n",
    "    T12=widgets.Text()\n",
    "    T12.value=''\n",
    "    T12.layout.width=\"15%\"\n",
    "    T13=widgets.Text()\n",
    "    T13.value=''\n",
    "    T13.layout.width=\"15%\"\n",
    "    T14=widgets.Text()\n",
    "    T14.value=''\n",
    "    T14.layout.width=\"15%\"\n",
    "    lists1=[T10,T11,T12,T13,T14]\n",
    "    mybox1=HBox(children=lists1)\n",
    "    listsB.append(mybox1)\n",
    "global myboxB\n",
    "myboxB=widgets.VBox(children=listsB)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def params(_):\n",
    "    if T9.value!='':\n",
    "        myboxB.layout.display='none'\n",
    "        names=[]\n",
    "        listsB=[]\n",
    "        myboxB.children=listsB\n",
    "        for i in range(int(T9.value)):\n",
    "            names.append('T'+str(i+10))\n",
    "            T10=widgets.Text()\n",
    "            T10.disabled=True\n",
    "            T10.value=str(i)\n",
    "            T10.layout.width=\"10%\"\n",
    "            T11=widgets.Text()\n",
    "            T11.value=''\n",
    "            T11.layout.width=\"15%\"\n",
    "            T12=widgets.Text()\n",
    "            T12.value=''\n",
    "            T12.layout.width=\"15%\"\n",
    "            T13=widgets.Text()\n",
    "            T13.value=''\n",
    "            T13.layout.width=\"15%\"\n",
    "            T14=widgets.Text()\n",
    "            T14.value=''\n",
    "            T14.layout.width=\"15%\"\n",
    "            lists1=[T10,T11,T12,T13,T14]\n",
    "            mybox1=widgets.HBox(children=lists1)\n",
    "            listsB.append(mybox1)\n",
    "        myboxB.children=listsB\n",
    "        myboxB.layout.display='' \n",
    "    else:\n",
    "        myboxB.layout.display='none'\n",
    "H12=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"DEPENDENCY RULES FOR PARAMETERS NOT FITTED\" \\\n",
    "style=\"color: black; background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" \\\n",
    "disabled=\"true\" id=\"testo\" />\"\"\")\n",
    "T15=widgets.Text()\n",
    "T15.value='0'\n",
    "T15.layout.width=\"10%\"\n",
    "names2=[]\n",
    "listsB2=[]\n",
    "for i in range(int(T15.value)):\n",
    "    names2.append('T'+str(i+16))\n",
    "    T16=widgets.Text()\n",
    "    T16.layout.width=\"25%\"\n",
    "    lists2=[T16]\n",
    "    mybox2=HBox(children=lists2)\n",
    "    listsB2.append(mybox2)\n",
    "global myboxB2\n",
    "myboxB2=widgets.VBox(children=listsB2)\n",
    "def dep(_):\n",
    "    if T15.value!='':\n",
    "        myboxB2.layout.display='none'\n",
    "        names2=[]\n",
    "        listsB2=[]\n",
    "        myboxB2.children=listsB2\n",
    "        for i in range(int(T15.value)):\n",
    "            names2.append('T'+str(i+16))\n",
    "            T16=Text()\n",
    "            T16.layout.width=\"25%\"\n",
    "            lists2=[T16]\n",
    "            mybox2=HBox(children=lists2)\n",
    "            listsB2.append(mybox2)\n",
    "        myboxB2.children=listsB2\n",
    "        myboxB2.layout.display=''\n",
    "    else:\n",
    "        myboxB2.layout.display='none'\n",
    "T15.observe(dep) \n",
    "H13=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"EXCLUSION RULES\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "T17=widgets.Text()\n",
    "T17.value='0'\n",
    "T17.layout.width=\"10%\"\n",
    "names3=[]\n",
    "listsB3=[]\n",
    "for i in range(int(T17.value)):\n",
    "    names2.append('T'+str(i+18))\n",
    "    T18=widgets.Text()\n",
    "    T18.layout.width=\"25%\"\n",
    "    lists3=[T18]\n",
    "    mybox3=HBox(children=lists3)\n",
    "    listsB3.append(mybox3)\n",
    "global myboxB3\n",
    "myboxB3=widgets.VBox(children=listsB3)\n",
    "def excl(_):\n",
    "    if T17.value!='':\n",
    "        myboxB3.layout.display='none'\n",
    "        names3=[]\n",
    "        listsB3=[]\n",
    "        myboxB3.children=listsB3\n",
    "        for i in range(int(T17.value)):\n",
    "            names2.append('T'+str(i+18))\n",
    "            T18=widgets.Text()\n",
    "            T18.layout.width=\"25%\"\n",
    "            T18.value=''\n",
    "            lists3=[T18]\n",
    "            mybox3=HBox(children=lists3)\n",
    "            listsB3.append(mybox3)\n",
    "        myboxB3.children=listsB3\n",
    "        myboxB3.layout.display=''\n",
    "    else:\n",
    "        myboxB3.layout.display='none'\n",
    "T17.observe(excl) \n",
    "T9.observe(params)\n",
    "H14=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"seed\" style=\"color: black; \\\n",
    "background-color: white; border: none; font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" \\\n",
    "id=\"testo\" />\"\"\")\n",
    "T19=widgets.Text()\n",
    "T19.value='1234567'\n",
    "T19.layout.width=\"25%\"\n",
    "H10.visible=False\n",
    "H11.visible=False\n",
    "T9.visible=False\n",
    "myboxB.layout.display=''\n",
    "H12.visible=False\n",
    "T15.visible=False\n",
    "myboxB2.layout.display=''\n",
    "H13.visible=False\n",
    "T17.visible=False\n",
    "myboxB3.layout.display=''\n",
    "H14.visible=False\n",
    "T19.visible=False"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def writefile(_):\n",
    "    for file in os.listdir(\".\"):\n",
    "        if file.startswith(\"config.txt\"):\n",
    "            os.remove(file)\n",
    "    with open('config.txt','w') as f:\n",
    "        f.write('//name of file containing raw traces\\n')\n",
    "        f.write(T1.value.strip()+'\\n')\n",
    "        f.write('//name of mod file\\n')\n",
    "        f.write(T2.value.strip()+'\\n')\n",
    "        f.write('//name of parameters file\\n')\n",
    "        f.write(T3.value.strip()+'\\n')\n",
    "        f.write('//flagdata==0 data with one time column for all currents;'+\\\n",
    "                ' ==1 data with one time column for each current\\n')\n",
    "        f.write(T4.value.strip()+'\\n')\n",
    "        f.write('//flagcut==0 data not cutted; ==1 data cutted below 20% of max\\n')\n",
    "        f.write(T5.value.strip()+'\\n')\n",
    "        f.write('//number of traces\\n')\n",
    "        f.write(T6.value.strip()+'\\n')\n",
    "        f.write('//PROTOCOL\\n')\n",
    "        f.write('//VCLAMP AMP\\n')\n",
    "        f.write(T7.value.strip()+'\\n')\n",
    "        f.write('//REVERSAL POTENTIAL\\n')\n",
    "        f.write(T8.value.strip()+'\\n')\n",
    "        f.write('//FITTING PARAMETERS AND INITIAL VALUES\\n')\n",
    "        f.write(T9.value.strip()+'\\n')\n",
    "        for i in range(int(T9.value.strip())):\n",
    "            f.write(myboxB.children[i].children[0].value+' '+myboxB.children[i].children[1].value+\\\n",
    "                    ' '+myboxB.children[i].children[2].value)\n",
    "            f.write('\\n')\n",
    "        f.write('//CONSTRAINTS\\n')\n",
    "        for i in range(int(T9.value.strip())):\n",
    "            f.write(myboxB.children[i].children[3].value+' '+myboxB.children[i].children[4].value)\n",
    "            f.write('\\n')\n",
    "        f.write('//DEPENDENCY RULES FOR PARAMETERS NOT FITTED\\n')\n",
    "        f.write(T15.value.strip()+'\\n')\n",
    "        for i in range(int(T15.value.strip())):\n",
    "            f.write(myboxB2.children[i].children[0].value)\n",
    "            f.write('\\n')\n",
    "        f.write('//EXCLUSION RULES\\n')\n",
    "        f.write(T17.value.strip()+'\\n')\n",
    "        for i in range(int(T17.value.strip())):\n",
    "            f.write(myboxB3.children[i].children[0].value)\n",
    "            f.write('\\n')\n",
    "        f.write('//seed\\n')\n",
    "        f.write(T19.value.strip()+'\\n')\n",
    "        f.write('\\n')\n",
    "    f.close()\n",
    "    with open(list(file_widget.value.keys())[0], \"wb\") as fp:\n",
    "        fp.write(file_widget.value[list(file_widget.value.keys())[0]]['content'])\n",
    "    with open(list(file_widget3.value.keys())[0], \"wb\") as fp2:\n",
    "        fp2.write(file_widget3.value[list(file_widget3.value.keys())[0]]['content'])\n",
    "\n",
    "def writefileifnotemptycell(_):\n",
    "    if T1.value.strip()!='' and T2.value.strip()!='' and T3.value.strip()!='' and T4.value.strip()!='' \\\n",
    "    and T5.value.strip()!='' and T6.value.strip()!='' and T7.value.strip()!='' and T8.value.strip()!='' and \\\n",
    "    T9.value.strip()!='' and T15.value.strip()!='' and T17.value.strip()!='' and T19.value.strip()!='':\n",
    "        BTC.disabled=True\n",
    "        os.chdir(\"transfer\")\n",
    "        writefile(_)\n",
    "        os.chdir(\"..\")\n",
    "        label.value = \"File generated!\"\n",
    "    else:\n",
    "        label.value = \"Please fill in the required fields!\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def fileloaded(_):\n",
    "    if len(list(file_widget.value.keys()))!=0:\n",
    "        T1.value=list(file_widget.value.keys())[0]\n",
    "    if len(list(file_widget3.value.keys()))!=0:\n",
    "        T2.value=list(file_widget3.value.keys())[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "label = widgets.Label()\n",
    "BTC=widgets.Button()\n",
    "BTC.description='Write config file'\n",
    "BTC.on_click(writefileifnotemptycell)\n",
    "HT=widgets.HTML(\"\"\"<input name=\"mioTesto\" type=\"text\" value=\"Select experimental file and mod file \\\n",
    "and write config file\" style=\"color: black; background-color: white; border: none; \\\n",
    "font-weight: bold\" size=\"60\" maxlength=\"400\" disabled=\"true\" id=\"testo\" />\"\"\")\n",
    "display(HT)\n",
    "lists=[HE,file_widget]\n",
    "myboxpage1=widgets.VBox(children=lists)\n",
    "page1=widgets.Box(children=[myboxpage1])\n",
    "lists=[HM,file_widget3]\n",
    "myboxpage2=widgets.VBox(children=lists)\n",
    "page2=widgets.Box(children=[myboxpage2])\n",
    "lists=[H1,T1,H2,T2,H6,T6,H7,H8,T7,H9,T8]\n",
    "myboxpage3=widgets.VBox(children=lists)\n",
    "page3=widgets.Box(children=[myboxpage3])\n",
    "lists=[H10,H11,T9,myboxB,H12,T15,myboxB2,H13,T17,myboxB3,H14,T19, label, BTC]\n",
    "myboxpage4=widgets.VBox(children=lists)\n",
    "page4=widgets.Box(children=[myboxpage4])\n",
    "tabs = widgets.Tab(children=[page1,page2,page3,page4])\n",
    "\n",
    "display(tabs)\n",
    "tabs.set_title(0, 'First page')\n",
    "tabs.set_title(1, 'Second page')\n",
    "tabs.set_title(2, 'Third page')\n",
    "tabs.set_title(3, 'Fourth page')\n",
    "tabs.observe(fileloaded)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "os.chdir(\"..\")\n",
    "%run \"unicore_api_Python3.ipynb\"\n",
    "file = open(\"data/img/Work-in-progress3.png\", \"rb\")\n",
    "image = file.read()\n",
    "IU = widgets.Image(value=image, format='png', width=400)\n",
    "IU.layout.display='none'\n",
    "os.chdir(\"GUIUM\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "STU=widgets.Text()\n",
    "STU.description='status'\n",
    "STU.value=''\n",
    "STU.disabled=True\n",
    "STU.layout.width='70%'\n",
    "STU.layout.display='none'\n",
    "STN=widgets.Text()\n",
    "STN.description='status'\n",
    "STN.value=''\n",
    "STN.disabled=True\n",
    "STN.layout.width='70%'\n",
    "STN.layout.display='none'\n",
    "\n",
    "def assign_file_types(filename):\n",
    "    \"\"\" assign file types based on file name and extension \"\"\"\n",
    "    fname, extension = os.path.splitext(filename)\n",
    "    if extension == '.txt':\n",
    "        filetype = 'text/plain'\n",
    "    else:\n",
    "        filetype = 'application/unknown'\n",
    "    return filetype"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def checkloginNSG(_):\n",
    "    username=username_widget.value\n",
    "    password=password_widget.value\n",
    "    KEY = 'Application_Fitting-DA5A3D2F8B9B4A5D964D4D2285A49C57'\n",
    "    headers = {'cipres-appkey' : KEY}\n",
    "    URL = 'https://nsgr.sdsc.edu:8443/cipresrest/v1/job/'+username\n",
    "    r = requests.get(URL, auth=(username, password),headers=headers,verify=False)\n",
    "    root = xml.etree.ElementTree.fromstring(r.text)\n",
    "    a=0\n",
    "    for child in root:\n",
    "        if child.tag == 'displayMessage':\n",
    "            a=1\n",
    "            msg=child.text\n",
    "    if a==0:\n",
    "        msg='Authenticated successfully'\n",
    "        msg_widget.disabled=True\n",
    "        buttonlogin.disabled=True\n",
    "        username_widget.disabled=True\n",
    "        password_widget.disabled=True\n",
    "    msg_widget.value=msg\n",
    "    msg_widget.layout.display=''\n",
    "\n",
    "username_widget = widgets.Text(description='Username:')\n",
    "username_widget.layout.width='249px'\n",
    "password_widget = widgets.Password(description='Password:')\n",
    "buttonlogin = widgets.Button()\n",
    "buttonlogin.description = 'Login NSG'\n",
    "buttonlogin.background_color='gainsboro'\n",
    "buttonlogin.border_color='black'\n",
    "buttonlogin.width='20%'\n",
    "buttonlogin.on_click(checkloginNSG)\n",
    "msg_widget = widgets.Text(layout=widgets.Layout(width='40%'))\n",
    "msg_widget.layout.display='none' "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def runNSG(_):\n",
    "    global runningUNSG\n",
    "    if msg_widget.value=='Authenticated successfully':\n",
    "        labelNSG.value = \"\"\n",
    "        RBHPC.disabled=True\n",
    "        RBM.disabled=True\n",
    "        TR.disabled=True\n",
    "        TT.disabled=True\n",
    "        TSK.disabled=True\n",
    "        ND.disabled=True\n",
    "        WT.disabled=True\n",
    "        myboxUNSG.children[0].disabled=True\n",
    "        runningUNSG=True\n",
    "        IU.layout.display=''\n",
    "        global CRA_USER, PASSWORD, KEY, URL, TOOL\n",
    "        username=username_widget.value\n",
    "        password=password_widget.value\n",
    "        CRA_USER = username\n",
    "        PASSWORD = password\n",
    "        KEY = 'Application_Fitting-DA5A3D2F8B9B4A5D964D4D2285A49C57'\n",
    "        URL = 'https://nsgr.sdsc.edu:8443/cipresrest/v1'\n",
    "        TOOL = 'NEURON_EXPANSE' \n",
    "    \n",
    "        with open(os.path.join('transfer', 'start.py'),'w') as f:\n",
    "            expf=list(file_widget.value.keys())[0]\n",
    "            conff='config.txt'\n",
    "            modf=list(file_widget3.value.keys())[0]\n",
    "            f.write('import fitting')\n",
    "            f.write('\\n')\n",
    "            if RBM.value=='all_traces':\n",
    "                f.write('fitting.fitting(\\''+conff+'\\',\\''+expf+'\\',\\''+\\\n",
    "                        modf+'\\',\\''+'True'+'\\',\\''+'False'+'\\',\\''+'False'+'\\','+'3'+')\\n')\n",
    "            else:\n",
    "                if RBM.value=='singletrace':\n",
    "                    f.write('fitting.fitting(\\''+conff+'\\',\\''+expf+'\\',\\''+\\\n",
    "                            modf+'\\',\\''+'False'+'\\',\\''+'True'+'\\',\\''+'False'+'\\',\\''+\\\n",
    "                            unicodedata.normalize('NFKD', TR.value)+'\\')\\n')\n",
    "                else:\n",
    "                    f.write('fitting.fitting(\\''+conff+'\\',\\''+expf+'\\',\\''+\\\n",
    "                            modf+'\\',\\''+'False'+'\\',\\''+'False'+'\\',\\''+'True'+'\\',\\''+\\\n",
    "                            unicodedata.normalize('NFKD', TR.value)+'\\')\\n')                      \n",
    "            f.write('\\n')\n",
    "        f.close()\n",
    "        zfName = 'transfer.zip'\n",
    "        foo = zipfile.ZipFile(zfName, 'w')\n",
    "        for root, dirs, files in os.walk('./transfer'):\n",
    "            for f in files:\n",
    "                foo.write(os.path.join(root, f))\n",
    "        foo.close()\n",
    "    \n",
    "        os.popen('pwd').read()\n",
    "        os.popen('ls -ltr').read()\n",
    "        headers = {'cipres-appkey' : KEY}\n",
    "        if TT.value=='':\n",
    "            jobname='NSG_Job'\n",
    "        else:\n",
    "            jobname=unicodedata.normalize('NFKD', TT.value)\n",
    "        nrcores=unicodedata.normalize('NFKD', TSK.value)\n",
    "        nrnodes=unicodedata.normalize('NFKD', ND.value)\n",
    "        runtime=unicodedata.normalize('NFKD', WT.value)\n",
    "        payload = {'tool' : TOOL, 'metadata.statusEmail' : 'false',\\\n",
    "                   'vparam.pythonoption_' : '1', \\\n",
    "                   'metadata.clientJobId': jobname,\\\n",
    "                   'vparam.number_cores_' : nrcores, \\\n",
    "                   'vparam.number_nodes_' : nrnodes, \\\n",
    "                   'vparam.runtime_' : float(runtime), \\\n",
    "                   'vparam.filename_': 'start.py'}\n",
    "        files = {'input.infile_' : open('transfer.zip','rb')}\n",
    "\n",
    "        r = requests.post('{}/job/{}'.format(URL, CRA_USER), auth=(CRA_USER, PASSWORD),\\\n",
    "                          data=payload, \\\n",
    "                          headers=headers, files=files,verify=False)\n",
    "    \n",
    "        root = xml.etree.ElementTree.fromstring(r.text)\n",
    "\n",
    "        global outputuri, selfuri\n",
    "        for child in root:\n",
    "            if child.tag == 'resultsUri':\n",
    "                for urlchild in child:\n",
    "                    if urlchild.tag == 'url':\n",
    "                        outputuri = urlchild.text\n",
    "            if child.tag == 'selfUri':\n",
    "                for urlchild in child:\n",
    "                    if urlchild.tag == 'url':\n",
    "                        selfuri = urlchild.text\n",
    "        myboxUNSG.children[1].layout.display=''\n",
    "    else:\n",
    "        labelNSG.value = \"You have to login to NSG before running a job!\"\n",
    "        runningUNSG=False\n",
    "        CheckSNSG.layout.display='none'\n",
    "        myboxConf.children[1].layout.display='none'\n",
    "        myboxConf.layout.display=''\n",
    "        myboxUNSG.children[0].disabled=False\n",
    "\n",
    "        \n",
    "def runNSGifconfig(_):\n",
    "    if os.path.isfile(os.path.join('transfer', 'config.txt')):\n",
    "        labelNSG.value = \"\"\n",
    "        runNSG(_)\n",
    "    else:\n",
    "        labelNSG.value = \"You have to write the config file first!\"\n",
    "\n",
    "\n",
    "def checksimnsg(CheckSNSG):\n",
    "    headers = {'cipres-appkey' : KEY}\n",
    "    r = requests.get(selfuri, auth=(CRA_USER, PASSWORD), headers=headers,verify=False)\n",
    "    root = xml.etree.ElementTree.fromstring(r.text)\n",
    "    job_submissiontime=root.find('dateSubmitted').text\n",
    "    job_name=root.find('metadata').find('entry').find('value').text\n",
    "    for child in root:\n",
    "        if child.tag == 'jobStage':\n",
    "            STN.layout.display=''\n",
    "            STN.value=job_name+' '+child.text+' '+\\\n",
    "            dateutil.parser.parse(job_submissiontime).\\\n",
    "            astimezone(pytz.timezone('CET')).strftime(\"%d/%m/%Y %H:%M:%S\")\n",
    "            jobstage=child.text\n",
    "        if child.tag == 'terminalStage':\n",
    "            jobstatus = child.text\n",
    "    if (jobstatus=='true') & (jobstage=='COMPLETED'):\n",
    "        IU.layout.display='none'\n",
    "        CheckSNSG.disabled=True\n",
    "        r = requests.get(outputuri,headers=headers, auth=(CRA_USER, PASSWORD),verify=False)\n",
    "        globaldownloadurilist = []\n",
    "        lengths = []\n",
    "        root = xml.etree.ElementTree.fromstring(r.text)\n",
    "        for child in root:\n",
    "            if child.tag == 'jobfiles':\n",
    "                for jobchild in child:\n",
    "                    if jobchild.tag == 'jobfile':\n",
    "                        for downloadchild in jobchild:\n",
    "                            if downloadchild.tag == 'downloadUri':\n",
    "                                for attchild in downloadchild:\n",
    "                                    if attchild.tag == 'url':\n",
    "                                        globaldownloadurilist.append(attchild.text)\n",
    "                            if downloadchild.tag == 'length':\n",
    "                                lengths.append(downloadchild.text)\n",
    "        r = requests.get(selfuri, auth=(CRA_USER, PASSWORD), headers=headers,verify=False)\n",
    "        root = xml.etree.ElementTree.fromstring(r.text)\n",
    "        for child in root:\n",
    "            if child.tag == 'messages':\n",
    "                for childs in child:\n",
    "                    texts=[]\n",
    "                    for childss in childs:\n",
    "                        texts.append(childss.text)\n",
    "                    if texts[1]=='SUBMITTED':\n",
    "                        subname=texts[2]\n",
    "        os.chdir(\"..\")\n",
    "        storeto_path = os.path.join('resultsNSG')\n",
    "        if not os.path.exists(storeto_path):\n",
    "            os.mkdir(storeto_path)\n",
    "        storeto = str(os.path.join(storeto_path,TT.value+'_usermodel_'+\\\n",
    "                                   dateutil.parser.parse(job_submissiontime).\\\n",
    "                                   astimezone(pytz.timezone('CET')).\\\n",
    "                                   strftime(\"%d%m%Y%H%M%S\")))\n",
    "        os.mkdir(storeto)\n",
    "        os.chdir(storeto)\n",
    "        for downloaduri in globaldownloadurilist:\n",
    "            if float(lengths[globaldownloadurilist.index(downloaduri)])<=5048000:\n",
    "                r = requests.get(downloaduri, auth=(CRA_USER, PASSWORD), headers=headers,verify=False)\n",
    "                d = r.headers['content-disposition']\n",
    "                filename_list = re.findall('filename=(.+)', d)\n",
    "                for filename in filename_list:\n",
    "                    if filename in ['output.tar.gz', 'STDOUT', 'STDERR']:\n",
    "                        with open(filename, 'wb') as fd:\n",
    "                            for chunk in r.iter_content():\n",
    "                                fd.write(chunk) \n",
    "                        if filename=='output.tar.gz':\n",
    "                            ff = tarfile.open(\"output.tar.gz\")\n",
    "                            ff.extractall('OUTPUT')\n",
    "                            ff.close()        \n",
    "                            os.remove('output.tar.gz')\n",
    "                            for filename in os.listdir(os.path.join('OUTPUT', 'transfer')):\n",
    "                                if filename.endswith(\"txt\") \\\n",
    "                                    or (filename.endswith(\"mod\") and not(filename.startswith(\"netstims\"))) \\\n",
    "                                    or filename == 'test.csv' \\\n",
    "                                    or filename == 'start.py':\n",
    "                                    shutil.copy2(os.path.join('OUTPUT', 'transfer', filename), \".\")\n",
    "                            shutil.rmtree('OUTPUT')\n",
    "        os.chdir(\"../../GUIUM\")\n",
    "        runningUNSG=False\n",
    "    else:\n",
    "        if (jobstatus=='true'):\n",
    "            labelNSG.value = \"Error submitting job!\"\n",
    "            IU.layout.display='none'\n",
    "            CheckSNSG.layout.display='none'\n",
    "            myboxConf.layout.display=''\n",
    "            runningUNSG=False\n",
    "            myboxUNSG.children[0].disabled=False"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def runmethod(change):\n",
    "    if RBM.value=='all_traces':\n",
    "        TR.value='3'\n",
    "        TR.layout.display='none'\n",
    "    else:\n",
    "        TR.value='3'\n",
    "        TR.layout.display=''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def RBHPCclick(_):\n",
    "    #clear_output()\n",
    "    myboxUM.children[0].layout.display='none'\n",
    "    RunSUNICORE.layout.display='none'        \n",
    "    CheckSUNICORE.layout.display='none'\n",
    "    STU.layout.display='none'\n",
    "    IU.layout.display='none'\n",
    "    formMNSG.layout.display=''\n",
    "    myboxUNSG.children[0].layout.display=''\n",
    "    myboxConf.children[0].layout.display=''\n",
    "    myboxConf.children[1].layout.display='none'\n",
    "    myboxConf.children[2].value='24'\n",
    "    myboxConf.children[3].value='2'\n",
    "    myboxConf.children[4].value='0.5'\n",
    "    if runningUNSG:\n",
    "        STN.layout.display=''\n",
    "        IU.layout.display=''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "RBHPC = widgets.RadioButtons(description= 'Run on:', options=['NSG'])\n",
    "display(RBHPC)\n",
    "RBM=widgets.RadioButtons(options=['all_traces','singletrace','demo'],description='run')\n",
    "display(RBM)\n",
    "RBM.observe(runmethod,names='value')\n",
    "formMNSG=widgets.VBox(children=[username_widget,password_widget,buttonlogin,msg_widget])\n",
    "display(formMNSG)\n",
    "TR = widgets.Text()\n",
    "TR.description='Trace:'\n",
    "TR.layout.display='none'\n",
    "display(TR)\n",
    "TT = widgets.Text()\n",
    "TT.description='Title:'\n",
    "WT = widgets.Text()\n",
    "WT.description='Walltime:'\n",
    "ND = widgets.Text()\n",
    "ND.description='N. of nodes:'\n",
    "TSK = widgets.Text()\n",
    "TSK.description='N. of CPUs:'\n",
    "myboxConf = widgets.VBox(children=[TT,TSK,ND,WT])\n",
    "myboxConf.children[1].value='24'\n",
    "myboxConf.children[2].value='2'\n",
    "myboxConf.children[3].value='10'\n",
    "myboxConf.layout.display=''\n",
    "display(myboxConf)\n",
    "RunSNSG = widgets.Button()\n",
    "RunSNSG.description = 'Run NSG simulation'\n",
    "RunSNSG.background_color='gainsboro'\n",
    "RunSNSG.border_color='black'\n",
    "RunSNSG.layout = widgets.Layout(width='30%')\n",
    "RunSNSG.on_click(runNSGifconfig)\n",
    "CheckSNSG = widgets.Button()\n",
    "CheckSNSG.description = 'Check NSG simulation'\n",
    "CheckSNSG.background_color='gainsboro'\n",
    "CheckSNSG.border_color='black'\n",
    "CheckSNSG.layout = widgets.Layout(width='30%')\n",
    "CheckSNSG.on_click(checksimnsg)\n",
    "buttonSNSG = [RunSNSG, CheckSNSG]\n",
    "myboxUNSG = widgets.HBox(children=buttonSNSG)\n",
    "myboxUNSG.children[1].layout.display='none'\n",
    "labelNSG = widgets.Label()\n",
    "labelNSG.value = \"\"\n",
    "display(labelNSG)\n",
    "display(STU)\n",
    "display(STN)\n",
    "display(myboxUNSG)\n",
    "display(IU)       \n",
    "runningUNSG=False\n",
    "RBHPC.on_trait_change(RBHPCclick,'value')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from IPython.display import HTML\n",
    "\n",
    "HTML('''\n",
    "<button class=\"toggle_button\" onclick=\"toggleCode(this)\">Show Code</button>\n",
    "<script>\n",
    "    function toggleCode(button) {\n",
    "        boxes = button.closest(\".jp-Notebook\").querySelectorAll(\".jp-Cell-inputWrapper\");\n",
    "        if (boxes[0].style.display == \"none\") {\n",
    "            boxes.forEach(box => box.style.display = '');\n",
    "            button.innerHTML = \"Hide Code\";\n",
    "        } else {\n",
    "            boxes.forEach(box => box.style.display = 'none');\n",
    "            button.innerHTML = \"Show Code\";\n",
    "        }\n",
    "    }\n",
    "    document.querySelectorAll(\".jp-Cell-inputWrapper\").forEach(box => box.style.display = 'none');\n",
    "</script>\n",
    "''')"
   ]
  }
 ],
 "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": "3.6.9"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}