example_gui.ipynb

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       "  var docs_json = {\"bdb78db8-cd03-4e82-b8e3-5d0a2431b8cc\":{\"version\":\"3.1.1\",\"title\":\"Bokeh Application\",\"defs\":[{\"type\":\"model\",\"name\":\"ReactiveHTML1\"},{\"type\":\"model\",\"name\":\"FlexBox1\",\"properties\":[{\"name\":\"align_content\",\"kind\":\"Any\",\"default\":\"flex-start\"},{\"name\":\"align_items\",\"kind\":\"Any\",\"default\":\"flex-start\"},{\"name\":\"flex_direction\",\"kind\":\"Any\",\"default\":\"row\"},{\"name\":\"flex_wrap\",\"kind\":\"Any\",\"default\":\"wrap\"},{\"name\":\"justify_content\",\"kind\":\"Any\",\"default\":\"flex-start\"}]},{\"type\":\"model\",\"name\":\"FloatPanel1\",\"properties\":[{\"name\":\"config\",\"kind\":\"Any\",\"default\":{\"type\":\"map\"}},{\"name\":\"contained\",\"kind\":\"Any\",\"default\":true},{\"name\":\"position\",\"kind\":\"Any\",\"default\":\"right-top\"},{\"name\":\"offsetx\",\"kind\":\"Any\",\"default\":null},{\"name\":\"offsety\",\"kind\":\"Any\",\"default\":null},{\"name\":\"theme\",\"kind\":\"Any\",\"default\":\"primary\"},{\"name\":\"status\",\"kind\":\"Any\",\"default\":\"normalized\"}]},{\"type\":\"model\",\"name\":\"GridStack1\",\"properties\":[{\"name\":\"mode\",\"kind\":\"Any\",\"default\":\"warn\"},{\"name\":\"ncols\",\"kind\":\"Any\",\"default\":null},{\"name\":\"nrows\",\"kind\":\"Any\",\"default\":null},{\"name\":\"allow_resize\",\"kind\":\"Any\",\"default\":true},{\"name\":\"allow_drag\",\"kind\":\"Any\",\"default\":true},{\"name\":\"state\",\"kind\":\"Any\",\"default\":[]}]},{\"type\":\"model\",\"name\":\"drag1\",\"properties\":[{\"name\":\"slider_width\",\"kind\":\"Any\",\"default\":5},{\"name\":\"slider_color\",\"kind\":\"Any\",\"default\":\"black\"},{\"name\":\"value\",\"kind\":\"Any\",\"default\":50}]},{\"type\":\"model\",\"name\":\"click1\",\"properties\":[{\"name\":\"terminal_output\",\"kind\":\"Any\",\"default\":\"\"},{\"name\":\"debug_name\",\"kind\":\"Any\",\"default\":\"\"},{\"name\":\"clears\",\"kind\":\"Any\",\"default\":0}]},{\"type\":\"model\",\"name\":\"FastWrapper1\",\"properties\":[{\"name\":\"object\",\"kind\":\"Any\",\"default\":null},{\"name\":\"style\",\"kind\":\"Any\",\"default\":null}]},{\"type\":\"model\",\"name\":\"NotificationAreaBase1\",\"properties\":[{\"name\":\"position\",\"kind\":\"Any\",\"default\":\"bottom-right\"},{\"name\":\"_clear\",\"kind\":\"Any\",\"default\":0}]},{\"type\":\"model\",\"name\":\"NotificationArea1\",\"properties\":[{\"name\":\"notifications\",\"kind\":\"Any\",\"default\":[]},{\"name\":\"position\",\"kind\":\"Any\",\"default\":\"bottom-right\"},{\"name\":\"_clear\",\"kind\":\"Any\",\"default\":0},{\"name\":\"types\",\"kind\":\"Any\",\"default\":[{\"type\":\"map\",\"entries\":[[\"type\",\"warning\"],[\"background\",\"#ffc107\"],[\"icon\",{\"type\":\"map\",\"entries\":[[\"className\",\"fas fa-exclamation-triangle\"],[\"tagName\",\"i\"],[\"color\",\"white\"]]}]]},{\"type\":\"map\",\"entries\":[[\"type\",\"info\"],[\"background\",\"#007bff\"],[\"icon\",{\"type\":\"map\",\"entries\":[[\"className\",\"fas fa-info-circle\"],[\"tagName\",\"i\"],[\"color\",\"white\"]]}]]}]}]},{\"type\":\"model\",\"name\":\"Notification\",\"properties\":[{\"name\":\"background\",\"kind\":\"Any\",\"default\":null},{\"name\":\"duration\",\"kind\":\"Any\",\"default\":3000},{\"name\":\"icon\",\"kind\":\"Any\",\"default\":null},{\"name\":\"message\",\"kind\":\"Any\",\"default\":\"\"},{\"name\":\"notification_type\",\"kind\":\"Any\",\"default\":null},{\"name\":\"_destroyed\",\"kind\":\"Any\",\"default\":false}]},{\"type\":\"model\",\"name\":\"TemplateActions1\",\"properties\":[{\"name\":\"open_modal\",\"kind\":\"Any\",\"default\":0},{\"name\":\"close_modal\",\"kind\":\"Any\",\"default\":0}]},{\"type\":\"model\",\"name\":\"BootstrapTemplateActions1\",\"properties\":[{\"name\":\"open_modal\",\"kind\":\"Any\",\"default\":0},{\"name\":\"close_modal\",\"kind\":\"Any\",\"default\":0}]},{\"type\":\"model\",\"name\":\"MaterialTemplateActions1\",\"properties\":[{\"name\":\"open_modal\",\"kind\":\"Any\",\"default\":0},{\"name\":\"close_modal\",\"kind\":\"Any\",\"default\":0}]}],\"roots\":[{\"type\":\"object\",\"name\":\"panel.models.browser.BrowserInfo\",\"id\":\"80455c79-8d94-43da-a70e-29148b014577\"},{\"type\":\"object\",\"name\":\"panel.models.comm_manager.CommManager\",\"id\":\"a8ed8671-5d69-4fad-9496-7475e3c90c59\",\"attributes\":{\"plot_id\":\"80455c79-8d94-43da-a70e-29148b014577\",\"comm_id\":\"de626b29e50840b894ba98dcfdcfac1a\",\"client_comm_id\":\"61907a6f3ed24b6b89e3e32141ab9df0\"}}],\"callbacks\":{\"type\":\"map\"}}};\n",
       "  var render_items = [{\"docid\":\"bdb78db8-cd03-4e82-b8e3-5d0a2431b8cc\",\"roots\":{\"80455c79-8d94-43da-a70e-29148b014577\":\"a39c3b0e-7521-44b1-b799-071848882e96\"},\"root_ids\":[\"80455c79-8d94-43da-a70e-29148b014577\"]}];\n",
       "  var docs = Object.values(docs_json)\n",
       "  if (!docs) {\n",
       "    return\n",
       "  }\n",
       "  const py_version = docs[0].version.replace('rc', '-rc.').replace('.dev', '-dev.')\n",
       "  const is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1\n",
       "  function embed_document(root) {\n",
       "    var Bokeh = get_bokeh(root)\n",
       "    Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "    for (const render_item of render_items) {\n",
       "      for (const root_id of render_item.root_ids) {\n",
       "\tconst id_el = document.getElementById(root_id)\n",
       "\tif (id_el.children.length && (id_el.children[0].className === 'bk-root')) {\n",
       "\t  const root_el = id_el.children[0]\n",
       "\t  root_el.id = root_el.id + '-rendered'\n",
       "\t}\n",
       "      }\n",
       "    }\n",
       "  }\n",
       "  function get_bokeh(root) {\n",
       "    if (root.Bokeh === undefined) {\n",
       "      return null\n",
       "    } else if (root.Bokeh.version !== py_version && !is_dev) {\n",
       "      if (root.Bokeh.versions === undefined || !root.Bokeh.versions.has(py_version)) {\n",
       "\treturn null\n",
       "      }\n",
       "      return root.Bokeh.versions.get(py_version);\n",
       "    } else if (root.Bokeh.version === py_version) {\n",
       "      return root.Bokeh\n",
       "    }\n",
       "    return null\n",
       "  }\n",
       "  function is_loaded(root) {\n",
       "    var Bokeh = get_bokeh(root)\n",
       "    return (Bokeh != null && Bokeh.Panel !== undefined)\n",
       "  }\n",
       "  if (is_loaded(root)) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    var attempts = 0;\n",
       "    var timer = setInterval(function(root) {\n",
       "      if (is_loaded(root)) {\n",
       "        clearInterval(timer);\n",
       "        embed_document(root);\n",
       "      } else if (document.readyState == \"complete\") {\n",
       "        attempts++;\n",
       "        if (attempts > 200) {\n",
       "          clearInterval(timer);\n",
       "\t  var Bokeh = get_bokeh(root)\n",
       "\t  if (Bokeh == null || Bokeh.Panel == null) {\n",
       "            console.warn(\"Panel: ERROR: Unable to run Panel code because Bokeh or Panel library is missing\");\n",
       "\t  } else {\n",
       "\t    console.warn(\"Panel: WARNING: Attempting to render but not all required libraries could be resolved.\")\n",
       "\t    embed_document(root)\n",
       "\t  }\n",
       "        }\n",
       "      }\n",
       "    }, 25, root)\n",
       "  }\n",
       "})(window);</script>"
      ]
     },
     "metadata": {
      "application/vnd.holoviews_exec.v0+json": {
       "id": "80455c79-8d94-43da-a70e-29148b014577"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "import numpy as np\n",
    "import ipywidgets as widgets\n",
    "from ipywidgets import HBox, VBox, Layout, HTML\n",
    "from IPython.display import display, IFrame\n",
    "from pyscal_rdf.structure import StructureGraph\n",
    "\n",
    "import pyscal_rdf_gui.plot as pgp\n",
    "import pyscal_rdf_gui.create as pgc\n",
    "from pyscal_rdf_gui.create_structure import CreateStructure\n",
    "from pyscal_rdf_gui.create_gb import CreateGB\n",
    "from pyscal_rdf_gui.create_vacancy import CreateVacancy\n",
    "from pyscal_rdf_gui.read_structure import ReadStructure\n",
    "from pyscal_rdf_gui.write_structure import WriteStructure\n",
    "from pyscal_rdf_gui.sparql_query import SparqlQuery\n",
    "from pyscal_rdf_gui.auto_query import AutoQuery\n",
    "from pyscal_rdf_gui.ontology import Ontology\n",
    "from pyscal_rdf_gui.properties import dataprops\n",
    "\n",
    "from pyscal3.grain_boundary import GrainBoundary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3fe68808-5c22-43ce-b88a-44c75f06a463",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "from pyscal_rdf_gui.image_elements import image_widget"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "f053512d-e8ad-4ff5-a761-1d6b33836061",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "0a8a9ae65f184490baddd28e71d8d58f",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HTML(value='\\n<img src=\"https://datashare.mpcdf.mpg.de/index.php/apps/files_sharing/ajax/publicpreview.php?x=1…"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "image_widget"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "23a9c3cd-8d9e-43e9-b384-2934639c7a34",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#this has to be created first to enable status changes\n",
    "gb = CreateGB()\n",
    "vac = CreateVacancy()\n",
    "species = None"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "5710f2a4-d149-4d06-b739-5f19a5b62496",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#Create a general element viewer\n",
    "atom_viewer = pgc.output()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "d5aad460-1f54-4e05-b835-0e2ea134a927",
   "metadata": {},
   "outputs": [],
   "source": [
    "#Structure creation widgets\n",
    "st = CreateStructure(theme=\"teal\")\n",
    "\n",
    "def create_structure(b=None):\n",
    "    \"\"\"\n",
    "    Function to create structure\n",
    "    \"\"\"\n",
    "    structure = st.dropdown.value\n",
    "    add_to_graph = st.checkbox.value\n",
    "    rep = st.repetition_box.value\n",
    "    lattice_parameter = st.lattice_parameter_box.value\n",
    "    if structure in [\"l12\", \"b2\"]:\n",
    "        element = [st.element_box.value, st.element_box_2.value]\n",
    "    else:\n",
    "        element = st.element_box.value\n",
    "    global sys\n",
    "    sys = g.create_structure(structure, \n",
    "                             lattice_constant=lattice_parameter,\n",
    "                             repetitions=[rep, rep, rep],\n",
    "                             add_to_graph=add_to_graph,\n",
    "                             element=element,\n",
    "                             names=True)\n",
    "    global species\n",
    "    species = element\n",
    "    pgp.system(sys, atom_viewer)\n",
    "    create_count_text()\n",
    "    return sys\n",
    "\n",
    "def update_element_fields(change):\n",
    "    if st.dropdown.value in [\"l12\", \"b2\"]:\n",
    "        st.element_box_2.disabled = False\n",
    "    else:\n",
    "        st.element_box_2.disabled = True\n",
    "    \n",
    "st.dropdown.observe(update_element_fields)\n",
    "\n",
    "@st.run_button.on_click\n",
    "def structure_plot_on_click(b):\n",
    "    sys = create_structure()\n",
    "    #turn on gb creation\n",
    "    gb.run_button.disabled = False\n",
    "    vac.run_button.disabled = False"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "1894efae-c026-422d-933f-a97d156c2830",
   "metadata": {},
   "outputs": [],
   "source": [
    "defect_dropdown = pgc.dropdown('Add defect', ['None', 'grain boundary', \n",
    "                            'vacancy'], \n",
    "                              value='None')\n",
    "\n",
    "defect_text = \"Add a defect\"\n",
    "defect_header = pgc.header(defect_text, theme=\"teal\")\n",
    "output_defect = pgc.output()\n",
    "\n",
    "def show_defect_menu(change):\n",
    "    if defect_dropdown.value == \"grain boundary\":\n",
    "        output_defect.clear_output()        \n",
    "        with output_defect:\n",
    "            display(gb.panel)\n",
    "    elif defect_dropdown.value == \"vacancy\":\n",
    "        output_defect.clear_output()        \n",
    "        with output_defect:\n",
    "            display(vac.panel)\n",
    "        \n",
    "\n",
    "defect_dropdown.observe(show_defect_menu)\n",
    "\n",
    "defect_panel = VBox(children=[defect_header,\n",
    "                             defect_dropdown,\n",
    "                             output_defect])\n",
    "\n",
    "@gb.sigma_button.on_click\n",
    "def show_sigmas(b):\n",
    "    axis_box = [int(x) for x in gb.axis_box.value.split()]\n",
    "    gbc = GrainBoundary()\n",
    "    gbc.axis = axis_box\n",
    "    gbc.limit = 10\n",
    "    sigmas = gbc.get_possible_sigma()[1:]\n",
    "    gb.sigma_dropdown = pgc.dropdown(\"Sigma\",\n",
    "                                 sigmas,)\n",
    "    #gb.widget_list.append(sigma_dropdown)\n",
    "    gb.sigma_hb = HBox(children=[gb.sigma_dropdown, gb.gb_plane_button])\n",
    "    output_defect.clear_output()        \n",
    "    with output_defect:\n",
    "        vbox = VBox(children=[gb.panel, gb.sigma_hb])\n",
    "        display(vbox)      \n",
    "\n",
    "#now using sigma, we need to create a dropdown of possible Gb planes\n",
    "@gb.gb_plane_button.on_click\n",
    "def show_gb_planes(b):\n",
    "    axis_box = [int(x) for x in gb.axis_box.value.split()]\n",
    "    gbc = GrainBoundary()\n",
    "    gbc.axis = axis_box\n",
    "    gbc.limit = 10\n",
    "    gbc.gb_index_limit = 3\n",
    "    gbc.sigma = gb.sigma_dropdown.value\n",
    "    _ = gbc.calculate_theta()\n",
    "    planes, _, _, _ = gbc.calculate_possible_gb_planes()\n",
    "    planes = [\" \".join(np.array(plane).astype(str)) for plane in planes]\n",
    "    gb.gb_plane_dropdown = pgc.dropdown(\"GB Plane\",\n",
    "                                    planes,)\n",
    "    gb.gb_plane_hb = VBox(children=[gb.rep_box,\n",
    "                                    HBox(children=[gb.gb_plane_dropdown, gb.run_button])])\n",
    "    output_defect.clear_output()        \n",
    "    with output_defect:\n",
    "        vbox = VBox(children=[gb.panel, gb.sigma_hb, gb.gb_plane_hb])\n",
    "        display(vbox)    \n",
    "    \n",
    "\n",
    "@gb.run_button.on_click\n",
    "def gb_plot_on_click(b):\n",
    "    #turn on gb creation\n",
    "    #convert to arrays\n",
    "    axis_box = [int(x) for x in gb.axis_box.value.split()]\n",
    "    gb_plane_box = [int(x) for x in gb.gb_plane_box.value.split()]\n",
    "    global sys\n",
    "    sys = g.create_grain_boundary(axis_box, gb.sigma_dropdown.value, \n",
    "                            gb_plane_box, element=species,\n",
    "                            repetitions=[int(x) for x in gb.rep_box.value.split()],\n",
    "                            lattice_constant=sys.atoms._lattice_constant,\n",
    "                            names=True)\n",
    "    pgp.system(sys, atom_viewer)\n",
    "    gb.run_button.disabled = True\n",
    "    output_defect.clear_output()\n",
    "    defect_dropdown.value = \"None\"\n",
    "    create_count_text()\n",
    "    return sys\n",
    "\n",
    "@vac.run_button.on_click\n",
    "def vac_plot_on_click(b):\n",
    "    global sys\n",
    "    g.add_structure_to_graph(sys)\n",
    "    value_type = vac.vacancy_dropdown.value\n",
    "    value = float(vac.vacancy_box.value)\n",
    "    if value_type == \"concentration\":\n",
    "        if (value >= 1) or (value <= 0):\n",
    "            output_defect.clear_output()\n",
    "            with output_defect:\n",
    "                print(\"Vacancy concentration should be between 0-1\")\n",
    "        else:\n",
    "            number = int(value*sys.natoms)\n",
    "            if number < 1:\n",
    "                output_defect.clear_output()\n",
    "                with output_defect:\n",
    "                    print(\"At least one atom should be deleted\")\n",
    "    else:\n",
    "        if (value <=0) or (value >= sys.natoms):\n",
    "            output_defect.clear_output()\n",
    "            with output_defect:\n",
    "                print(f'Atom number should be between 1-{sys.natoms-1}')\n",
    "        else:\n",
    "            number = value\n",
    "    #choose randomly \n",
    "    tbd = np.random.randint(sys.natoms, size=int(number))\n",
    "    sys.delete(indices=list(tbd))\n",
    "    c = (number/sys.natoms)\n",
    "    g.add_vacancy(c)\n",
    "    pgp.system(sys, atom_viewer)\n",
    "    vac.run_button.disabled = True\n",
    "    output_defect.clear_output()\n",
    "    defect_dropdown.value = \"None\"\n",
    "    create_count_text()\n",
    "    return sys    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "57f33e90-cebe-4511-bd74-38eb423efb0f",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#Read structure widgets\n",
    "rs = ReadStructure(theme=\"teal\")\n",
    "\n",
    "def read_structure(b=None):\n",
    "    #write file\n",
    "    with open(\"temp\", \"wb\") as fout:\n",
    "        fout.write(rs.upload.value[0]['content'])\n",
    "    global sys\n",
    "    sys = g.read_structure(\"temp\", \n",
    "                           format=rs.dropdown.value)\n",
    "    pgp.system(sys, atom_viewer)\n",
    "    create_count_text()\n",
    "    return sys    \n",
    "    \n",
    "@rs.run_button.on_click\n",
    "def process_file_on_click(b):\n",
    "    sys = read_structure()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "2c9b3619-2694-4975-be8f-2008f4d8dbfd",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#write structure widgets\n",
    "ws = WriteStructure(theme=\"teal\")\n",
    "\n",
    "def write_structure(b=None):\n",
    "    outfile = f'out.{ws.dropdown.value}'\n",
    "    if ws.dropdown.value in ['turtle', 'json-ld', 'xml', 'n3']:\n",
    "        sg = g.get_sample(g.sample)\n",
    "        sg.write(outfile, format=ws.dropdown.value)\n",
    "    else:\n",
    "        sys.to_file(outfile, format=ws.dropdown.value)\n",
    "\n",
    "@ws.run_button.on_click\n",
    "def write_file_on_click(b):\n",
    "    write_structure()\n",
    "    ws.output.clear_output()\n",
    "    with ws.output:\n",
    "        display(pgc.download(f'out.{ws.dropdown.value}'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "026dde3b-48d2-4f83-981f-57a7b85a641f",
   "metadata": {},
   "outputs": [],
   "source": [
    "#Creation panel\n",
    "creation_panel = VBox(children=[\n",
    "                      st.panel,\n",
    "                      defect_panel,\n",
    "                      rs.panel])\n",
    "\n",
    "\n",
    "vis_label = pgc.header(\"Visualise structure\", theme=\"teal\")\n",
    "vis_structure_panel = VBox(children=[vis_label,\n",
    "                      atom_viewer,\n",
    "                      ws.panel,\n",
    "                      ])\n",
    "\n",
    "creation_tab = HBox(children=[creation_panel, \n",
    "                              vis_structure_panel])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "d7fe9b83-d218-4828-9986-24e56e9d3e36",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#Widgets for querying\n",
    "sq = SparqlQuery()\n",
    "\n",
    "@sq.run_button.on_click\n",
    "def query_plot_on_click(b):\n",
    "    run_query()\n",
    "    \n",
    "def run_query(b=None):\n",
    "    query = sq.query_box.value\n",
    "    res = g.graph.query(query)\n",
    "    sq.output.clear_output()\n",
    "    with sq.output:\n",
    "        for r in res:\n",
    "            print(r[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "8e255db1-ed91-460d-82ed-810278407b0f",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#Ontology visualisation widgets\n",
    "on = Ontology()\n",
    "on.output.clear_output()\n",
    "with on.output:\n",
    "    display(IFrame(src=\"https://service.tib.eu/webvowl/#iri=http://purls.helmholtz-metadaten.de/cmso/\", width='100%', height='500px'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "1ed3b9f0-ed87-46e3-af1e-58375832dacd",
   "metadata": {},
   "outputs": [],
   "source": [
    "wso = WriteStructure(theme=\"teal\")\n",
    "\n",
    "def write_structure_onto(b=None):\n",
    "    outfile = f'out.{ws.dropdown.value}'\n",
    "    if ws.dropdown.value in ['turtle', 'json-ld', 'xml', 'n3']:\n",
    "        sg = g.get_sample(g.sample)\n",
    "        sg.write(outfile, format=ws.dropdown.value)\n",
    "    else:\n",
    "        sys.to_file(outfile, format=ws.dropdown.value)\n",
    "        \n",
    "@wso.run_button.on_click\n",
    "def write_file_on_click(b):\n",
    "    write_structure_onto()\n",
    "    wso.output.clear_output()\n",
    "    with wso.output:\n",
    "        display(pgc.download(f'out.{wso.dropdown.value}'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "ecf1bcc2-78fc-486f-abc1-3a1b104fad01",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#Automated query code\n",
    "aq = AutoQuery()\n",
    "\n",
    "def update_compare_output(change):\n",
    "    aq.compare_output.clear_output()\n",
    "    if aq.property_dropdown.value in dataprops.keys():\n",
    "        with aq.compare_output:\n",
    "            display(aq.compare_options)\n",
    "\n",
    "with aq.compare_output:\n",
    "    display(aq.compare_options)\n",
    "    \n",
    "aq.property_dropdown.observe(update_compare_output)\n",
    "\n",
    "def update_input_fields(change):\n",
    "    aq.input_output.clear_output()\n",
    "    if aq.compare_options.value == \" equal to \":\n",
    "        equal_inp = HBox(children=[aq.input_field_1])\n",
    "        with aq.input_output:\n",
    "            display(equal_inp)\n",
    "    elif aq.compare_options.value == \" in between \":\n",
    "        equal_inp = HBox(children=[aq.input_field_1, \n",
    "                                   pgc.text(\"and\"), \n",
    "                                   aq.input_field_2])\n",
    "        with aq.input_output:\n",
    "            display(equal_inp)\n",
    "    elif aq.compare_options.value == \" equal to either \":\n",
    "        equal_inp = HBox(children=[aq.input_field_1, \n",
    "                                   pgc.text(\"or\"), \n",
    "                                   aq.input_field_2])\n",
    "        with aq.input_output:\n",
    "            display(equal_inp)\n",
    "\n",
    "with aq.input_output:\n",
    "    display(HBox(children=[aq.input_field_1]))\n",
    "    \n",
    "aq.compare_options.observe(update_input_fields)\n",
    "\n",
    "def convert_to_datatype(value, dtype):\n",
    "    if dtype == \"string\":\n",
    "        return str(value)\n",
    "    elif dtype == \"integer\":\n",
    "        return int(value)\n",
    "    else:\n",
    "        return float(value)\n",
    "    \n",
    "@aq.run_button.on_click\n",
    "def run_query_on_click(b):\n",
    "    run_auto_query()\n",
    "    \n",
    "def run_auto_query(b=None):\n",
    "    #if it is equal to\n",
    "    dtype = dataprops[aq.property_dropdown.value][\"dtype\"]\n",
    "    if aq.compare_options.value == \" equal to \":\n",
    "        value = convert_to_datatype(aq.input_field_1.value, dtype)\n",
    "    elif aq.compare_options.value == \" in between \":\n",
    "        value = [convert_to_datatype(aq.input_field_1.value, dtype),\n",
    "                 convert_to_datatype(aq.input_field_2.value, dtype)]\n",
    "    else:\n",
    "        value = [convert_to_datatype(aq.input_field_1.value, \"string\"),\n",
    "                 convert_to_datatype(aq.input_field_2.value, \"string\")]\n",
    "    \n",
    "    results = g.query_sample(dataprops[aq.property_dropdown.value][\"onto\"],\n",
    "              value, \n",
    "              return_query=False)\n",
    "    results = [r[0] for r in results]\n",
    "    global result_dropdown\n",
    "    result_dropdown = pgc.dropdown(\"Samples\", results)\n",
    "    disp = HBox(children=[result_dropdown,\n",
    "                         aq.plot_structure_button,\n",
    "                         aq.visualise_graph_button,\n",
    "                         aq.inspect_button,\n",
    "                         wso.dropdown,\n",
    "                         wso.run_button,\n",
    "                         wso.output])\n",
    "    aq.result_output.clear_output()\n",
    "    with aq.result_output:\n",
    "        display(disp)\n",
    "        \n",
    "@aq.show_button.on_click\n",
    "def run_show_on_click(b):\n",
    "    run_auto_query_show()\n",
    "    \n",
    "def run_auto_query_show(b=None):\n",
    "    #if it is equal to\n",
    "    dtype = dataprops[aq.property_dropdown.value][\"dtype\"]\n",
    "    if aq.compare_options.value == \" equal to \":\n",
    "        value = convert_to_datatype(aq.input_field_1.value, dtype)\n",
    "    elif aq.compare_options.value == \" in between \":\n",
    "        value = [convert_to_datatype(aq.input_field_1.value, dtype),\n",
    "                 convert_to_datatype(aq.input_field_2.value, dtype)]\n",
    "    else:\n",
    "        value = [convert_to_datatype(aq.input_field_1.value, \"string\"),\n",
    "                 convert_to_datatype(aq.input_field_2.value, \"string\")]\n",
    "    \n",
    "    results, query = g.query_sample(dataprops[aq.property_dropdown.value][\"onto\"],\n",
    "              value, \n",
    "              return_query=True)\n",
    "    aq.result_output.clear_output()\n",
    "    with aq.result_output:\n",
    "        display(query)\n",
    "\n",
    "\n",
    "\n",
    "@aq.plot_structure_button.on_click\n",
    "def plot_structure_on_click(b):\n",
    "    run_plot_structure()\n",
    "\n",
    "def run_plot_structure(b=None):\n",
    "    #get sys from sample\n",
    "    sys = g.get_system_from_sample(result_dropdown.value) \n",
    "    pgp.system(sys, aq.result_plotter)\n",
    "    \n",
    "@aq.visualise_graph_button.on_click\n",
    "def visualise_graph_on_click(b):\n",
    "    run_visualise_graph()\n",
    "\n",
    "def run_visualise_graph(b=None):\n",
    "    #get sys from sample\n",
    "    sgraph, na = g.get_sample(result_dropdown.value, \n",
    "                              no_atoms=True)\n",
    "    aq.result_plotter.clear_output()\n",
    "    dot = sgraph.visualise(backend=\"graphviz\")\n",
    "    with aq.result_plotter:\n",
    "        display(dot)\n",
    "\n",
    "@aq.inspect_button.on_click\n",
    "def inspect_graph_on_click(b):\n",
    "    run_inspect_graph()\n",
    "\n",
    "def run_inspect_graph(b=None):\n",
    "    #get sys from sample\n",
    "    inspectinfo = g.inspect_sample(sample=result_dropdown.value)\n",
    "    aq.result_plotter.clear_output()\n",
    "    with aq.result_plotter:\n",
    "        display(print(inspectinfo))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "fa99d883-1515-4a90-a90e-fc50bb18dc22",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#Create a structure graph\n",
    "#g = StructureGraph(store='SQLAlchemy', store_file='project.db')\n",
    "g = StructureGraph(graph_file='projectdata.ttl')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "e523d8ee-fdcc-4acd-8a21-5d11d64c4e0d",
   "metadata": {},
   "outputs": [],
   "source": [
    "#widget to show number of samples\n",
    "#this has to come after the main graph is created\n",
    "count_output = pgc.output()\n",
    "\n",
    "def create_count_text():\n",
    "    text = \"Database has %d samples\"%g.n_samples\n",
    "    onto_label = pgc.text(text)\n",
    "    count_output.clear_output()\n",
    "    with count_output:\n",
    "        display(onto_label)\n",
    "\n",
    "create_count_text()    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "19ed64e2-c20b-41f4-b626-4c04b304f077",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "authors_panel = widgets.HTML(\"\"\"\n",
    "<b><font color='#006064'>IUC17: Ontologies for defects in crystals</b><br>\n",
    "<font color='#006064'> TA-OMS: Abril Guzmán, Volker Hofmann, Stefan Sandfeld <br> TA-WSD: Sarath Menon, Tilmann Hickel <br>\n",
    "<b><font color='#006064'> Resources </b><br>\n",
    "<a href=\\\"https://github.com/Materials-Data-Science-and-Informatics/cmso-ontology\\\">CMSO Ontology</a> <br> \n",
    "<a href=\\\"https://github.com/pyscal/pyscal_rdf\\\">pyscal-rdf</a>\n",
    "             \"\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "4db6616c-87f3-4062-82cd-f1e01a549f3a",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "image_panel = widgets.HTML(\"\"\"\n",
    "<img src=\"https://datashare.mpcdf.mpg.de/index.php/apps/files_sharing/ajax/publicpreview.php?x=1920&y=619&a=true&file=Demo.png&t=qjr8s9QYEBE2gnb&scalingup=0\" width=\"25%\" align=\"justify\">\n",
    "<table table style='table-layout:fixed;width:100%' border=\"0\">\n",
    "  <th style='width: 65%;'> </th>\n",
    "<tr>\n",
    "  <td>\n",
    "    <img src=\"https://www.mpie.de/4475264/original-1609193623.jpg?t=eyJ3aWR0aCI6MTIwMCwiaGVpZ2h0IjpudWxsLCJmaXQiOm51bGwsIm9ial9pZCI6NDQ3NTI2NH0%3D--73876e3c61ca1ef4ba1ca8817030fbd88c980e0b\" width=\"25%\">\n",
    "    &nbsp;<img src=\"https://www.fz-juelich.de/de/ias/bilder/ias-9-emblem-5-3.png/@@images/image/teaser\" width=\"12%\">\n",
    "    &nbsp;&nbsp;<img src=\"https://upload.wikimedia.org/wikipedia/de/thumb/8/8b/J%C3%BClich_fz_logo.svg/1200px-J%C3%BClich_fz_logo.svg.png\" width=\"15%\">\n",
    "    &nbsp;&nbsp;&nbsp;&nbsp;<img src=\"https://www.nfdi.de/wp-content/uploads/2022/03/Logo_NFDI-MatWerk-1000px.png\" width=\"10%\">\n",
    "  </td>\n",
    "</tr>\n",
    "</table>\n",
    "\"\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "66f8ddad-d974-479e-a245-6515b46dab76",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "extra_panel = VBox(children=[authors_panel, image_panel])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "d7abf947-17a4-4308-a69d-32fdc5bba567",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "89fab4260c554f5caa555130557b2348",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(Tab(children=(HBox(children=(VBox(children=(VBox(children=(HTML(value=\"<b><font color='#006064'…"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#final tab arrangement\n",
    "tab = widgets.Tab(children=[creation_tab,\n",
    "                            aq.panel,\n",
    "                            sq.panel,\n",
    "                            on.panel,\n",
    "                            extra_panel])\n",
    "tab.set_title(0, 'Structure Creation')\n",
    "tab.set_title(1, 'Automated Query')\n",
    "tab.set_title(2, 'SPARQL Query')\n",
    "tab.set_title(3, 'Ontology')\n",
    "tab.set_title(4, 'About')\n",
    "\n",
    "\n",
    "main = widgets.VBox(children=[tab,\n",
    "                             count_output])\n",
    "main"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6fa30f2e-cedd-416a-a69f-5e2aca7efcff",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ff1763c0-2d6b-45c7-a73a-bbf969f648e0",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d195926e-84d7-44b8-a638-62066f25a646",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "73b84280-b24f-4a36-8baf-91b25fbddb0a",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3e9fc22b-839d-4d82-a493-beb63b3887c2",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ddceee79-9667-4022-a07c-d73df18506ad",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1b385547-9616-4a3e-bcfe-13473a15a181",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "645335ed-75a1-4399-a89a-fcd04a22a5a9",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f3699683-9fe6-4565-9860-fb536ea14c50",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "701c1765-6f74-4454-bd28-1dd80110b409",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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