add metadata schema

notebooks/data_read.ipynb

@@ -134,7 +134,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

notebooks/data_set.ipynb

@@ -153,7 +153,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

notebooks/metadata_schema.ipynb

@@ -0,0 +1,227 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "9058253b-d5f3-4e70-8952-61f7d2992b08",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pyscal_rdf.network.ontology import read_ontology\n",
+    "from rdflib import Graph, Literal, Namespace\n",
+    "import copy"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "4c5d73b6-da02-420c-a223-4eef93c872bc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "onto = read_ontology()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "id": "09f55784-36b9-471d-a766-4a3a017f7696",
+   "metadata": {
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'cmso:hasAltName': cmso:hasAltName,\n",
+       " 'cmso:hasName': cmso:hasName,\n",
+       " 'cmso:hasAngle_alpha': cmso:hasAngle_alpha,\n",
+       " 'cmso:hasAngle_beta': cmso:hasAngle_beta,\n",
+       " 'cmso:hasAngle_gamma': cmso:hasAngle_gamma,\n",
+       " 'cmso:hasChemicalSymbol': cmso:hasChemicalSymbol,\n",
+       " 'cmso:hasSymbol': cmso:hasSymbol,\n",
+       " 'cmso:hasComponent_x': cmso:hasComponent_x,\n",
+       " 'cmso:hasComponent_y': cmso:hasComponent_y,\n",
+       " 'cmso:hasComponent_z': cmso:hasComponent_z,\n",
+       " 'cmso:hasCoordinationNumber': cmso:hasCoordinationNumber,\n",
+       " 'cmso:hasElementRatio': cmso:hasElementRatio,\n",
+       " 'cmso:hasLength_x': cmso:hasLength_x,\n",
+       " 'cmso:hasLength_y': cmso:hasLength_y,\n",
+       " 'cmso:hasLength_z': cmso:hasLength_z,\n",
+       " 'cmso:hasNumberOfAtoms': cmso:hasNumberOfAtoms,\n",
+       " 'cmso:hasReference': cmso:hasReference,\n",
+       " 'cmso:hasRepetition_x': cmso:hasRepetition_x,\n",
+       " 'cmso:hasRepetition_y': cmso:hasRepetition_y,\n",
+       " 'cmso:hasRepetition_z': cmso:hasRepetition_z,\n",
+       " 'cmso:hasSpaceGroupNumber': cmso:hasSpaceGroupNumber,\n",
+       " 'cmso:hasSpaceGroupSymbol': cmso:hasSpaceGroupSymbol,\n",
+       " 'cmso:hasValue': cmso:hasValue,\n",
+       " 'cmso:hasVolume': cmso:hasVolume,\n",
+       " 'pldo:geometricalDegreesOfFreedom': pldo:geometricalDegreesOfFreedom,\n",
+       " 'pldo:hasGBplane': pldo:hasGBplane,\n",
+       " 'pldo:macroscopicDegreesOfFreedom': pldo:macroscopicDegreesOfFreedom,\n",
+       " 'pldo:hasMisorientationAngle': pldo:hasMisorientationAngle,\n",
+       " 'pldo:hasRotationAxis': pldo:hasRotationAxis,\n",
+       " 'pldo:hasSigmaValue': pldo:hasSigmaValue,\n",
+       " 'pldo:microscopicDegreesOfFreedom': pldo:microscopicDegreesOfFreedom,\n",
+       " 'podo:hasNumberOfVacancies': podo:hasNumberOfVacancies,\n",
+       " 'podo:hasVacancyConcentration': podo:hasVacancyConcentration,\n",
+       " 'rdfs:label': rdfs:label}"
+      ]
+     },
+     "execution_count": 23,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "onto.attributes['data_property']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "ce296bb0-8e6a-4ab2-8940-52d6a0121e6f",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['cmso:SimulationCell']"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "onto.attributes['data_property']['cmso:hasVolume'].domain"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "8dc0e696-b128-4ebe-9ebe-3312e8b04124",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def create_dict(datadict, path):\n",
+    "    for p in path:\n",
+    "        datadict[str(p[0])] ={}\n",
+    "        datadict = datadict[str(p[0])]\n",
+    "            #exists\n",
+    "    datadict[str(p[0])] = {str(p[-1]): None}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "7d267c94-b4f2-4fe8-be2e-c44f4300c128",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "collected_dicts = []"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "c87873b0-62d1-40d1-a6f3-9418e0f8c8d2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for key in onto.attributes['data_property']:\n",
+    "    try:\n",
+    "        path = onto.get_path_from_sample(key)\n",
+    "        datadict = {}\n",
+    "        create_dict(datadict, path)\n",
+    "        collected_dicts.append(copy.deepcopy(datadict))\n",
+    "    except:\n",
+    "        pass"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "30d5eae4-d4a4-432d-99cc-7ec8e5944225",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def dict_merge(dct, merge_dct):\n",
+    "    for k, v in merge_dct.items():\n",
+    "        if (k in dct and isinstance(dct[k], dict) and isinstance(merge_dct[k], dict)):  #noqa\n",
+    "            dict_merge(dct[k], merge_dct[k])\n",
+    "        else:\n",
+    "            dct[k] = merge_dct[k]\n",
+    "            \n",
+    "   \n",
+    "collected_dicts = []\n",
+    "\n",
+    "for key in o.attributes['data_node']:\n",
+    "    try:\n",
+    "        path = o.get_path_from_sample(key)\n",
+    "        datadict = {}\n",
+    "        create_dict(datadict, path)\n",
+    "        collected_dicts.append(copy.deepcopy(datadict))\n",
+    "    except:\n",
+    "        pass"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "f407cffc-c1ba-4d51-ae78-0c580a77dea1",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'cmso:ComputationalSample': {'cmso:SimulationCell': {'cmso:Angle': {'cmso:Angle': {'cmso:hasAngle_gamma': None}}}}}"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "collected_dicts[3]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "836f088d-dee5-4ebf-8397-9339d0a1362a",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "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": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

notebooks/schema.yml

@@ -0,0 +1,51 @@
+sample:
+  material:
+    element_ratio:
+      element1: float
+    crystal_structure:
+      altname: string
+      spacegroup_symbol: string
+      spacegroup_number: int
+      unit_cell:
+        bravais_lattice: string
+        lattice_parameter:
+          x: float
+          y: float
+          z: float
+        angle:
+          alpha: float
+          beta: float
+          gamma: float
+    defect:
+      grain_boundary:
+        type: string
+        sigma: int
+        plane: int(3)
+        rotation_axis: int(3)
+        misorientation_angle: float
+      vacancy:
+        type: string
+
+  simulation_cell:
+    volume: float
+    number_of_atoms: int
+    length:
+      x: float
+      y: float
+      z: float
+    vector:
+      x: float(3)
+      y: float(3)
+      z: float(3)
+    angle:
+      alpha: float
+      beta: float
+      gamma: float
+    vacancy_concentration: float
+    number_of_vacancies: int
+
+  calculated_property:
+    - label: string
+      value: float
+      unit: string
+