Issues #5, #6, and #7. Also made the export of object graph faster by…

… saving a history of objects. Instead of always calling openBIS for the objects. One may check inside the dictionary if it is already there.
nanotech-empa · Dec 13, 2024 · 18ac957 · 18ac957
1 parent 11295fa
commit 18ac957
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diff --git a/Notebooks/Metadata_Schemas_LinkML/materialMLinfo.yaml b/Notebooks/Metadata_Schemas_LinkML/materialMLinfo.yaml
@@ -103,7 +103,8 @@ classes:
       openbis_code: AM
       openbis_label: Atomistic Model
     slots:
-     - structure
+     - volume
+     - cell
      - dimensionality
      - atoms_positions
      - periodic_boundary_conditions
@@ -1770,6 +1771,22 @@ types:
 # slots are first-class entities in the metamodel
 # declaring them here allows them to be reused elsewhere
 slots:
+  cell:
+    description: Cell
+    range: object
+    multivalued: false
+    slot_uri:
+    annotations:
+      openbis_type: JSON
+      openbis_label: Cell
+  volume:
+    description: Volume
+    range: double
+    multivalued: false
+    slot_uri:
+    annotations:
+      openbis_type: REAL
+      openbis_label: Volume
   filepath_executable:
     description: Filepath executable
     range: string

diff --git a/Notebooks/connection_to_openbis/.create_molecule-0.ipynb b/Notebooks/connection_to_openbis/.create_molecule-0.ipynb
@@ -0,0 +1,240 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from IPython.display import display\n",
+    "import ipywidgets as ipw\n",
+    "import widgets\n",
+    "import utils\n",
+    "import os\n",
+    "import rdkit\n",
+    "from rdkit.Chem import AllChem, Draw, rdMolDescriptors\n",
+    "import io\n",
+    "from pathlib import Path"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "CONFIG = utils.read_json(\"config.json\")\n",
+    "CONFIG_ELN = utils.get_aiidalab_eln_config()\n",
+    "# CONFIG_ELN = utils.read_json(\"eln_config.json\")\n",
+    "OPENBIS_SESSION, SESSION_DATA = utils.connect_openbis(CONFIG_ELN[\"url\"], CONFIG_ELN[\"token\"])\n",
+    "\n",
+    "molecule_widgets = widgets.ObjectPropertiesWidgets(\"Molecule\")\n",
+    "\n",
+    "molecule_structure = ipw.Image(\n",
+    "    value=utils.read_file(CONFIG[\"default_image_filepath\"]), format='jpg', \n",
+    "    width='420px', height='450px', layout=ipw.Layout(border='solid 1px #cccccc')\n",
+    ")\n",
+    "\n",
+    "molecule_cdxml_file = ipw.FileUpload(multiple = False, accept = '.cdxml')\n",
+    "\n",
+    "molecule_support_files = ipw.FileUpload(multiple = True)\n",
+    "\n",
+    "increase_buttons_size = utils.HTML(data = ''.join(CONFIG[\"save_home_buttons_settings\"]))\n",
+    "create_button = utils.Button(\n",
+    "    description = '', disabled = False, button_style = '', tooltip = 'Save', \n",
+    "    icon = 'save', layout = ipw.Layout(width = '100px', height = '50px')\n",
+    ")\n",
+    "quit_button = utils.Button(\n",
+    "    description = '', disabled = False, button_style = '', \n",
+    "    tooltip = 'Main menu', icon = 'home', layout = ipw.Layout(width = '100px', height = '50px')\n",
+    ")\n",
+    "save_close_buttons_hbox = ipw.HBox([create_button, quit_button])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def close_notebook(b):\n",
+    "    display(utils.Javascript(data = 'window.location.replace(\"home.ipynb\")'))\n",
+    "\n",
+    "def load_molecule_structure(change):\n",
+    "    for filename in molecule_cdxml_file.value:\n",
+    "        file_info = molecule_cdxml_file.value[filename]\n",
+    "        utils.save_file(file_info['content'], \"structures/structure.cdxml\")\n",
+    "        \n",
+    "    cdxml_molecule = utils.read_file(\"structures/structure.cdxml\")\n",
+    "    molecules = rdkit.Chem.MolsFromCDXML(cdxml_molecule)\n",
+    "    \n",
+    "    if len(molecules) == 1:\n",
+    "        mol = molecules[0] # Get first molecule\n",
+    "        mol_chemical_formula = rdMolDescriptors.CalcMolFormula(mol) # Sum Formula\n",
+    "        mol_smiles = rdkit.Chem.MolToSmiles(mol) # Canonical Smiles\n",
+    "        chem_mol = rdkit.Chem.MolFromSmiles(mol_smiles)\n",
+    "        \n",
+    "        if chem_mol is not None:\n",
+    "            AllChem.Compute2DCoords(chem_mol) # Add coords to the atoms in the molecule\n",
+    "            img = Draw.MolToImage(chem_mol)\n",
+    "            buffer = io.BytesIO()\n",
+    "            img.save(buffer, format=\"PNG\")\n",
+    "            molecule_structure.value = buffer.getvalue()\n",
+    "            img.save(\"structures/structure.png\")\n",
+    "        else:\n",
+    "            print(f\"Cannot generate molecule image.\")\n",
+    "            \n",
+    "        molecule_widgets.properties_widgets[\"sum_formula\"].value = mol_chemical_formula\n",
+    "        molecule_widgets.properties_widgets[\"smiles\"].value = mol_smiles\n",
+    "        \n",
+    "    elif len(molecules) > 1:\n",
+    "        print(f\"There are more than one molecule in the file: {filename}\")  \n",
+    "    else:\n",
+    "        print(f\"There are no molecules in the file: {filename}\")\n",
+    "    \n",
+    "def create_molecule_openbis(b):\n",
+    "    object_properties = {}\n",
+    "    for prop in CONFIG[\"objects\"][\"Molecule\"][\"properties\"]:\n",
+    "        object_properties[prop] = molecule_widgets.properties_widgets[prop].value\n",
+    "    \n",
+    "    # Check if the molecule is already in openBIS\n",
+    "    smiles_molecules_openbis = [molecule.props['smiles'] for molecule in utils.get_openbis_objects(OPENBIS_SESSION, type =\"MOLECULE\")]\n",
+    "    \n",
+    "    if object_properties[\"smiles\"] in smiles_molecules_openbis:\n",
+    "        display(utils.Javascript(data = \"alert('Molecule is already in openBIS!')\"))\n",
+    "        \n",
+    "        if Path(\"structures/structure.png\").exists():\n",
+    "            os.remove(\"structures/structure.png\")\n",
+    "        \n",
+    "        if Path(\"structures/structure.png\").exists():\n",
+    "            os.remove(\"structures/structure.cdxml\")\n",
+    "    else:\n",
+    "        molecule_object = utils.create_openbis_object(\n",
+    "            OPENBIS_SESSION, type=\"MOLECULE\", \n",
+    "            collection=\"/MATERIALS/MOLECULES/MOLECULE_COLLECTION\", \n",
+    "            props = object_properties\n",
+    "        )\n",
+    "        \n",
+    "        # Send molecule image to openBIS\n",
+    "        if Path(\"structures/structure.png\").exists():\n",
+    "            # Upload cdxml\n",
+    "            utils.create_openbis_dataset(OPENBIS_SESSION, type = \"ELN_PREVIEW\", object = molecule_object, file = \"structures/structure.png\")\n",
+    "            os.remove(\"structures/structure.png\")\n",
+    "        \n",
+    "        if Path(\"structures/structure.png\").exists():\n",
+    "            # Upload cdxml\n",
+    "            utils.create_openbis_dataset(OPENBIS_SESSION, type = \"RAW_DATA\", object = molecule_object, file = \"structures/structure.cdxml\")\n",
+    "            os.remove(\"structures/structure.cdxml\")\n",
+    "        \n",
+    "        # Additional support files\n",
+    "        upload_datasets(molecule_object, molecule_support_files)\n",
+    "        \n",
+    "        display(utils.Javascript(data = \"alert('Upload successful!')\"))\n",
+    "\n",
+    "def upload_datasets(method_object, support_files_widget):\n",
+    "    for filename in support_files_widget.value:\n",
+    "        file_info = support_files_widget.value[filename]\n",
+    "        utils.save_file(file_info['content'], filename)\n",
+    "        utils.create_openbis_dataset(OPENBIS_SESSION, type = 'RAW_DATA', object = method_object, file = filename)\n",
+    "        os.remove(filename)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Create molecule"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Upload CDXML file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "display(molecule_structure)\n",
+    "display(molecule_cdxml_file)\n",
+    "molecule_cdxml_file.observe(load_molecule_structure, names = \"value\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Properties"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "display(molecule_widgets)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Support files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "display(molecule_support_files)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Save results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "display(save_close_buttons_hbox)\n",
+    "display(increase_buttons_size)\n",
+    "create_button.on_click(create_molecule_openbis)\n",
+    "quit_button.on_click(close_notebook)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "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": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}