generate application profile spec.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 89,
   "id": "identified-north",
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdflib import Graph\n",
    "from rdflib.namespace import OWL, DC, DCTERMS, RDF, RDFS, SKOS, XSD\n",
    "from rdflib import URIRef, BNode, Literal\n",
    "import json\n",
    "import os\n",
    "import pandas as pd\n",
    "import pylode\n",
    "import re"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "id": "german-mainstream",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Graph identifier=N1bb88316860d4a1d88c706ed9db3981e (<class 'rdflib.graph.Graph'>)>"
      ]
     },
     "execution_count": 90,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "g = Graph()\n",
    "##namespace\n",
    "NS = \"https://foodperiodictable.org/ptfi/terms/\"\n",
    "## create ontology\n",
    "ptfi = URIRef(NS)\n",
    "g.add((ptfi, RDF.type, OWL.Ontology)) ## not sure it should be defined as an ontology, so commenting for now\n",
    "g.add((ptfi, DCTERMS.modified, Literal('2022-06-01',datatype=XSD.date))) \n",
    "g.add((ptfi, DCTERMS.title, Literal('PTFI Metadata Terms related to Specimen', lang='en'))) \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "id": "trying-destination",
   "metadata": {},
   "outputs": [],
   "source": [
    "xls = pd.ExcelFile('./Sample_Metadata_PTFI_050222.xlsx')\n",
    "df = pd.read_excel(xls, 'application profile')\n",
    "df.dropna(how='all', axis=1)\n",
    "df.fillna('', inplace=True)\n",
    "\n",
    "\n",
    "for index, row in df.iterrows() :\n",
    "    element_id = row['metadata element IRI/ID']\n",
    "    element_name = row['metadata element name']\n",
    "    element_description = row['definition']\n",
    "    comment = row['comment']\n",
    "    example = row['see']\n",
    "    cardinality = row['occurrence']\n",
    "    obligation = row['obligation']\n",
    "    datatype = row['datatype']\n",
    "    controlled_vocab = row['vocabulary encoding scheme']\n",
    "    module = row['module']\n",
    "    vocab = row['\"in-house\" vocabulary']\n",
    "    \n",
    "    datarange = None\n",
    "    vocabUri = None\n",
    "    \n",
    "    ## if module does not exist, create a class\n",
    "    ##module\n",
    "    moduleUri = URIRef(NS + module.replace(' ', '_'))\n",
    "    if not (None, RDFS.label, Literal(module, lang='en')) in g:\n",
    "        ##create module as owl class\n",
    "        g.add((moduleUri, RDF.type, RDFS.Class))  ## SKOS.Concept\n",
    "        g.add((moduleUri, RDFS.label, Literal(module, lang='en')))\n",
    "        g.add((moduleUri, DCTERMS.issued, Literal('2022-06-01',datatype=XSD.date)))\n",
    "        g.add((moduleUri, RDFS.isDefinedBy, ptfi))\n",
    "        g.add((moduleUri, DCTERMS.description, Literal(module, lang='en')))\n",
    "    ## then for now just create the element, may need to add which element apply for what class\n",
    "    elementURI = URIRef(NS + element_id)\n",
    "    g.add((elementURI, RDFS.label, Literal(element_name, lang='en')))\n",
    "    g.add((elementURI, RDF.type, RDF.Property))\n",
    "    g.add((elementURI, DCTERMS.description, Literal(element_description, lang='en')))\n",
    "    g.add((elementURI, DCTERMS.issued, Literal('2022-06-01',datatype=XSD.date)))\n",
    "    g.add((elementURI, RDFS.isDefinedBy, ptfi))\n",
    "    g.add((elementURI, RDFS.domain, moduleUri))\n",
    "    \n",
    "    if comment:\n",
    "        g.add((elementURI, RDFS.comment, Literal(comment, lang='en')))\n",
    "    if example:\n",
    "        g.add((elementURI, RDFS.seeAlso, Literal(example, lang='en')))\n",
    "    if controlled_vocab:\n",
    "        if controlled_vocab == 'FOODON' and 'food product' in comment:\n",
    "            g.add((elementURI, RDFS.range, URIRef('http://purl.obolibrary.org/obo/FOODON_00002381')))\n",
    "            vocabUri = URIRef('http://purl.obolibrary.org/obo/FOODON_00002381')\n",
    "        elif controlled_vocab == 'FOODON' and 'process' in comment:\n",
    "            g.add((elementURI, RDFS.range, URIRef('http://purl.obolibrary.org/obo/FOODON_00002451')))\n",
    "            vocabUri = URIRef('http://purl.obolibrary.org/obo/FOODON_00002451')\n",
    "        elif controlled_vocab == 'unit ontology':\n",
    "            g.add((elementURI, RDFS.range, URIRef('http://purl.obolibrary.org/obo/UO_0000000')))\n",
    "            vocabUri = URIRef('http://purl.obolibrary.org/obo/UO_0000000')\n",
    "        elif controlled_vocab == 'NCBITaxon':\n",
    "            g.add((elementURI, RDFS.range, URIRef('http://purl.obolibrary.org/obo/NCBITaxon_1')))\n",
    "            vocabUri = URIRef('http://purl.obolibrary.org/obo/NCBITaxon_1')\n",
    "        elif 'vocab' in controlled_vocab:\n",
    "            ## create the in house vocab then add the range to the element\n",
    "            vocabUri = URIRef(NS + controlled_vocab.replace(' ', '_')+'_vocab')\n",
    "            g.add((vocabUri, RDF.type, RDFS.Class))  ## SKOS.Concept\n",
    "            g.add((vocabUri, RDFS.label, Literal(controlled_vocab, lang='en')))\n",
    "            g.add((vocabUri, DCTERMS.issued, Literal('2022-06-01',datatype=XSD.date)))\n",
    "            g.add((vocabUri, RDFS.isDefinedBy, ptfi))\n",
    "            ## add terms to the vocab\n",
    "            for v in vocab.split(\"|\"):\n",
    "                vUri = URIRef(NS + v.replace(' ', '_'))\n",
    "                g.add((vUri, RDF.type, RDFS.Class))  ## SKOS.Concept\n",
    "                g.add((vUri, RDFS.label, Literal(v, lang='en')))\n",
    "                g.add((vUri, DCTERMS.issued, Literal('2022-06-01',datatype=XSD.date)))\n",
    "                g.add((vUri, RDFS.isDefinedBy, ptfi))\n",
    "                g.add((vUri, RDFS.subClassOf, vocabUri))\n",
    "                #g.add((vUri, DCTERMS.description, Literal(module, lang='en')))\n",
    "            ## add range\n",
    "            g.add((elementURI, RDFS.range, vocabUri))\n",
    "        else:\n",
    "            print(element_name)\n",
    "    else:\n",
    "        if datatype == 'date':\n",
    "            g.add((elementURI, RDFS.range, XSD.date))\n",
    "            datarange = XSD.date\n",
    "        elif datatype == 'float':\n",
    "            g.add((elementURI, RDFS.range, XSD.float))\n",
    "            datarange = XSD.float\n",
    "        elif datatype == 'string':\n",
    "            g.add((elementURI, RDFS.range, XSD.string))\n",
    "            datarange = XSD.string\n",
    "        elif datatype == 'binary/image':\n",
    "            g.add((elementURI, RDFS.range, XSD.base64Binary))\n",
    "            datarange = XSD.base64Binary\n",
    "        elif datatype == 'uuid':\n",
    "            g.add((elementURI, RDFS.range, XSD.string))\n",
    "            datarange = XSD.string\n",
    "        elif datatype == 'integer':\n",
    "            g.add((elementURI, RDFS.range, XSD.integer))\n",
    "            datarange = XSD.integer\n",
    "        else:\n",
    "            print(element_name)\n",
    "    if obligation:\n",
    "        if datarange:\n",
    "            if cardinality == 'unique':\n",
    "                br = BNode()\n",
    "                g.add((br, RDF.type, OWL.Restriction))\n",
    "                g.add((br, OWL.onProperty, elementURI))\n",
    "                g.add((br, OWL.qualifiedCardinality, Literal(1)))\n",
    "                g.add((br, OWL.onDataRange, datarange))\n",
    "                g.add((moduleUri, RDFS.subClassOf, br))\n",
    "            else:\n",
    "                br = BNode()\n",
    "                g.add((br, RDF.type, OWL.Restriction))\n",
    "                g.add((br, OWL.onProperty, elementURI))\n",
    "                g.add((br, OWL.minQualifiedCardinality, Literal(1)))\n",
    "                g.add((br, OWL.onDataRange, datarange))\n",
    "                g.add((moduleUri, RDFS.subClassOf, br))\n",
    "        else:\n",
    "            if cardinality == 'unique':\n",
    "                br = BNode()\n",
    "                g.add((br, RDF.type, OWL.Restriction))\n",
    "                g.add((br, OWL.onProperty, elementURI))\n",
    "                g.add((br, OWL.qualifiedCardinality, Literal(1)))\n",
    "                g.add((br, OWL.onClass, vocabUri))\n",
    "                g.add((moduleUri, RDFS.subClassOf, br))\n",
    "            else:\n",
    "                br = BNode()\n",
    "                g.add((br, RDF.type, OWL.Restriction))\n",
    "                g.add((br, OWL.onProperty, elementURI))\n",
    "                g.add((br, OWL.minQualifiedCardinality, Literal(1)))\n",
    "                g.add((br, OWL.onClass, vocabUri))\n",
    "                g.add((moduleUri, RDFS.subClassOf, br))\n",
    "            \n",
    "    else:\n",
    "        if datarange:\n",
    "            if cardinality == 'unique':\n",
    "                br = BNode()\n",
    "                g.add((br, RDF.type, OWL.Restriction))\n",
    "                g.add((br, OWL.onProperty, elementURI))\n",
    "                g.add((br, OWL.maxQualifiedCardinality, Literal(1)))\n",
    "                g.add((br, OWL.onDataRange, datarange))\n",
    "                g.add((moduleUri, RDFS.subClassOf, br))\n",
    "            else:\n",
    "                br = BNode()\n",
    "                g.add((br, RDF.type, OWL.Restriction))\n",
    "                g.add((br, OWL.onProperty, elementURI))\n",
    "                g.add((br, OWL.minQualifiedCardinality, Literal(0)))\n",
    "                g.add((br, OWL.onDataRange, datarange))\n",
    "                g.add((moduleUri, RDFS.subClassOf, br))\n",
    "        else:\n",
    "            if cardinality == 'unique':\n",
    "                br = BNode()\n",
    "                g.add((br, RDF.type, OWL.Restriction))\n",
    "                g.add((br, OWL.onProperty, elementURI))\n",
    "                g.add((br, OWL.maxQualifiedCardinality, Literal(1)))\n",
    "                g.add((br, OWL.onClass, vocabUri))\n",
    "                g.add((moduleUri, RDFS.subClassOf, br))\n",
    "            else:\n",
    "                br = BNode()\n",
    "                g.add((br, RDF.type, OWL.Restriction))\n",
    "                g.add((br, OWL.onProperty, elementURI))\n",
    "                g.add((br, OWL.minQualifiedCardinality, Literal(0)))\n",
    "                g.add((br, OWL.onClass, vocabUri))\n",
    "                g.add((moduleUri, RDFS.subClassOf, br))\n",
    "            \n",
    "            "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "id": "comprehensive-particular",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Print the graph\n",
    "#print(g.serialize(format=\"turtle\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "id": "better-style",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Graph identifier=N1bb88316860d4a1d88c706ed9db3981e (<class 'rdflib.graph.Graph'>)>"
      ]
     },
     "execution_count": 95,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "g.serialize(destination= \"PTFI_application.ttl\", format=\"turtle\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 96,
   "id": "pointed-birth",
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'str' object has no attribute 'decode'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-96-d55279355565>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m### documentation\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m html = pylode.MakeDocco(\n\u001b[0m\u001b[1;32m      3\u001b[0m     \u001b[0minput_data_file\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"PTFI_application_json-ld.json\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m     \u001b[0moutputformat\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"html\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m     \u001b[0mprofile\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"ontdoc\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python3.9/site-packages/pylode/common.py\u001b[0m in \u001b[0;36mdocument\u001b[0;34m(self, destination)\u001b[0m\n\u001b[1;32m    217\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    218\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 219\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgenerate_document\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/usr/local/lib/python3.9/site-packages/pylode/profiles/ontdoc.py\u001b[0m in \u001b[0;36mgenerate_document\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m   1429\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mCLASSES\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0muri\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"has_members\"\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhtml\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1430\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1431\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_make_document\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/usr/local/lib/python3.9/site-packages/pylode/profiles/ontdoc.py\u001b[0m in \u001b[0;36m_make_document\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m   1233\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1234\u001b[0m         return self._load_template(\"document.\" + self.outputformat).render(\n\u001b[0;32m-> 1235\u001b[0;31m             \u001b[0mschemaorg\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_make_schemaorg_metadata\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m  \u001b[0;31m# only does something for the HTML templates\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1236\u001b[0m             \u001b[0mtitle\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mMETADATA\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"title\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1237\u001b[0m             \u001b[0mmetadata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_make_metadata\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python3.9/site-packages/pylode/profiles/base.py\u001b[0m in \u001b[0;36m_make_schemaorg_metadata\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    457\u001b[0m             \u001b[0mg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0muri\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mSDO\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcodeRepository\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrepository\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    458\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 459\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mserialize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"json-ld\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"utf-8\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    460\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    461\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_make_agent_link\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0memail\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maffiliation\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'str' object has no attribute 'decode'"
     ]
    }
   ],
   "source": [
    "### documentation\n",
    "html = pylode.MakeDocco(\n",
    "    input_data_file=\"PTFI_application_json-ld.json\",\n",
    "    outputformat=\"html\",\n",
    "    profile=\"ontdoc\"\n",
    ").document()\n",
    "f = open('documentation.html', 'w' )\n",
    "f.write( html )\n",
    "f.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "boolean-dylan",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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