linkedbuildingdata · GeorgFerdinandSchneider · May 21, 2019 · May 21, 2019 · May 21, 2019 · May 23, 2019
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,9 @@
+# Intellij
+
+*.iml
+.idea
+
+.ipynb_checkpoints/
+
+# virtualenv
+env/
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,64 @@
+FROM openjdk:11.0.3-jdk
+MAINTAINER Rui de Klerk <rui.klerk@campus.ul.pt>
+
+# Dockerfile copied and adapted from Spencer Park: https://github.com/SpencerPark/ijava-binder/blob/master/Dockerfile
+
+RUN apt-get update
+RUN apt-get install -y python3-pip
+
+# add requirements.txt, written this way to gracefully ignore a missing file
+COPY . .
+RUN ([ -f requirements.txt ] \
+    && pip3 install --no-cache-dir -r requirements.txt) \
+        || pip3 install --no-cache-dir jupyter jupyterlab
+
+USER root
+
+# Download the kernel release
+RUN curl -L https://github.com/SpencerPark/IJava/releases/download/v1.3.0/ijava-1.3.0.zip > ijava-kernel.zip
+
+# Unpack and install the kernel
+RUN unzip ijava-kernel.zip -d ijava-kernel \
+  && cd ijava-kernel \
+  && python3 install.py --sys-prefix
+
+# -- WIP --
+# Download Apache Jena
+#RUN curl -L http://mirrors.up.pt/pub/apache/jena/binaries/apache-jena-3.11.0.zip > apache-jena-3.11.0.zip
+
+# Unpack and install Jena
+#RUN unzip apache-jena-3.11.0.zip -d apache-jena 
+
+# Download Apache Jena Fuseki
+#RUN curl -L http://mirrors.up.pt/pub/apache/jena/binaries/apache-jena-fuseki-3.11.0.zip > apache-jena-fuseki-3.11.0.zip
+
+# Unpack and install Apache Jena Fuseki
+#RUN unzip apache-jena-fuseki-3.11.0.zip -d fuseki
+# -- WIP --
+
+# Set up the user environment
+
+#ENV IJAVA_CLASSPATH apache-jena/lib/* ; fuseki/lib/*
+
+ENV NB_USER jovyan
+ENV NB_UID 1000
+ENV HOME /home/$NB_USER
+
+# -- WIP --
+#RUN java -classpath apache-jena/lib/* ;\
+#  fuseki/lib/*
+# -- WIP --
+
+RUN adduser --disabled-password \
+    --gecos "Default user" \
+    --uid $NB_UID \
+    $NB_USER
+
+COPY . $HOME
+RUN chown -R $NB_UID $HOME
+
+USER $NB_USER
+
+# Launch the notebook server
+WORKDIR $HOME
+CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
diff --git a/Java Notebooks/3rdPartyDependency.ipynb b/Java Notebooks/3rdPartyDependency.ipynb
diff --git a/Java Notebooks/BOT_reasoning.ipynb b/Java Notebooks/BOT_reasoning.ipynb
@@ -0,0 +1,310 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Jena Reasoning on a simple BOT instance\n",
+    "\n",
+    "In order to run Jena using the IJava kernel on Jupyter notebooks, first we need to use some [IJava Magics](https://github.com/SpencerPark/IJava/blob/7f5aa9ab858859a010fd228364b080606399ae60/docs/magics.md#line-magic-2) to load it:\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%loadFromPOM\n",
+    "<dependency>\n",
+    "    <groupId>org.apache.jena</groupId>\n",
+    "    <artifactId>apache-jena-libs</artifactId>\n",
+    "    <type>pom</type>\n",
+    "    <version>3.11.0</version>\n",
+    "</dependency>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%loadFromPOM\n",
+    "<dependencies>\n",
+    "  <dependency>\n",
+    "    <groupId> org.apache.cassandra</groupId>\n",
+    "    <artifactId>cassandra-all</artifactId>\n",
+    "    <version>0.8.1</version>\n",
+    "\n",
+    "    <exclusions>\n",
+    "      <exclusion> \n",
+    "        <groupId>org.slf4j</groupId>\n",
+    "        <artifactId>slf4j-log4j12</artifactId>\n",
+    "      </exclusion>\n",
+    "      <exclusion> \n",
+    "        <groupId>log4j</groupId>\n",
+    "        <artifactId>log4j</artifactId>\n",
+    "      </exclusion>\n",
+    "    </exclusions> \n",
+    "\n",
+    "  </dependency>\n",
+    "</dependencies>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Setting up Jena \n",
+    "\n",
+    "first, lets import all the Classes we will need for reasoning"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import org.apache.jena.reasoner.*;\n",
+    "import org.apache.jena.rdf.model.InfModel;\n",
+    "import org.apache.jena.rdf.model.Statement;\n",
+    "import org.apache.jena.util.*;\n",
+    "import org.apache.jena.rdf.model.*;\n",
+    "import org.apache.jena.ontology.*;\n",
+    "import org.apache.jena.vocabulary.OWL ;\n",
+    "import org.apache.jena.vocabulary.RDF ;\n",
+    "import org.apache.jena.vocabulary.RDFS;"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Load an ABox from the the documentation example\n",
+    "Now,load a simple model that has been created similar to the example in the BOT documentation on https://w3c-lbd-cg.github.io/bot/?tab=0#two-storey-building \n",
+    "\n",
+    "This is provided in the `../data` directory\n",
+    "\n",
+    "it consist of just a number of statements:\n",
+    "\n",
+    "```\n",
+    ":SiteA a bot:Site ;\n",
+    "    bot:hasBuilding :BuildingA .\n",
+    "    \n",
+    ":BuildingA bot:hasStorey :Storey00 , :Storey01 .\n",
+    "\n",
+    ":Storey00 bot:hasSpace :SpaceA , :SpaceB .\n",
+    "\n",
+    ":Storey01 bot:hasSpace :SpaceC , :SpaceD .\n",
+    "```\n",
+    "\n",
+    "Let's print out what is known abou the :BuildingA\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/***************** facts BEFORE inference ****************/\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#hasStorey> <https://ldac.org/house#Storey01>)\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#hasStorey> <https://ldac.org/house#Storey00>)\n"
+     ]
+    }
+   ],
+   "source": [
+    "// load a simple instance file from the example az\n",
+    "// https://w3c-lbd-cg.github.io/bot/?tab=0#two-storey-building\n",
+    "/****** the A-BOX *************/\n",
+    "Model simple_house = FileManager.get().loadModel(\"../data/simple_bot.ttl\");\n",
+    "System.out.println (\"/***************** facts BEFORE inference ****************/\");\n",
+    "Resource Site = simple_house.getResource(\"https://ldac.org/house#BuildingA\");\n",
+    "for (StmtIterator i = ((Model)simple_house).listStatements(new SimpleSelector( Site, null, (RDFNode)null )); i.hasNext();){\n",
+    "    Statement stmt = i.nextStatement();\n",
+    "    System.out.println (PrintUtil.print(stmt));\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Load the BOT TBox \n",
+    "Up to know, these are just the \"stupid\" facts asserted in the above snipptes. No knowledge about what the Resources actually are is present at present. \n",
+    "\n",
+    "In a second step the TBOX is loaded directly from its source.\n",
+    "\n",
+    "A Reasoner is created in that combines TBox and Abox and starts to make inferences"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "/***************** facts AFTER inference ****************/\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#hasStorey> <https://ldac.org/house#Storey01>)\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#hasStorey> <https://ldac.org/house#Storey00>)\n",
+      "(<https://ldac.org/house#BuildingA> rdf:type owl:Thing)\n",
+      "(<https://ldac.org/house#BuildingA> rdf:type <https://w3id.org/bot#Building>)\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#containsZone> <https://ldac.org/house#Storey01>)\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#containsZone> <https://ldac.org/house#Storey00>)\n",
+      "(<https://ldac.org/house#BuildingA> rdf:type <https://w3id.org/bot#Zone>)\n",
+      "(<https://ldac.org/house#BuildingA> rdf:type rdfs:Resource)\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#containsZone> <https://ldac.org/house#SpaceD>)\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#containsZone> <https://ldac.org/house#SpaceC>)\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#containsZone> <https://ldac.org/house#SpaceB>)\n",
+      "(<https://ldac.org/house#BuildingA> <https://w3id.org/bot#containsZone> <https://ldac.org/house#SpaceA>)\n",
+      "(<https://ldac.org/house#BuildingA> owl:sameAs <https://ldac.org/house#BuildingA>)\n",
+      "(<https://ldac.org/house#BuildingA> owl:differentFrom <https://ldac.org/house#SpaceD>)\n",
+      "(<https://ldac.org/house#BuildingA> owl:differentFrom <https://ldac.org/house#SpaceC>)\n",
+      "(<https://ldac.org/house#BuildingA> owl:differentFrom <https://ldac.org/house#SpaceB>)\n",
+      "(<https://ldac.org/house#BuildingA> owl:differentFrom <https://ldac.org/house#SpaceA>)\n",
+      "(<https://ldac.org/house#BuildingA> owl:differentFrom <https://ldac.org/house#Storey01>)\n",
+      "(<https://ldac.org/house#BuildingA> owl:differentFrom <https://ldac.org/house#Storey00>)\n",
+      "(<https://ldac.org/house#BuildingA> owl:differentFrom <https://ldac.org/house#SiteA>)\n"
+     ]
+    }
+   ],
+   "source": [
+    "// import the BOT Ontology from the source via HTTP\n",
+    "/****** the T-BOX *************/\n",
+    "Model bot = FileManager.get().loadModel(\"https://w3id.org/bot#\");\n",
+    "\n",
+    "// create on OWL reasoner and feed it the bot ontology model\n",
+    "Reasoner reasoner = ReasonerRegistry.getOWLReasoner();\n",
+    "reasoner = reasoner.bindSchema(bot);\n",
+    "\n",
+    "//create inferences from \n",
+    "InfModel infmodel = ModelFactory.createInfModel(reasoner, simple_house);\n",
+    "System.out.println (\"\\n\\n/***************** facts AFTER inference ****************/\");\n",
+    "// print out all statements asserted and inferred \n",
+    "Resource Site = infmodel.getResource(\"https://ldac.org/house#BuildingA\");\n",
+    "for (StmtIterator i = ((Model)infmodel).listStatements(new SimpleSelector( Site, null, (RDFNode)null )); i.hasNext();){\n",
+    "    Statement stmt = i.nextStatement();\n",
+    "    System.out.println (PrintUtil.print(stmt));\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Extend the BOT ontology with a \"connectivity\" property\n",
+    "\n",
+    "A simple extension is loaded that consists of the following three statements:\n",
+    "```\n",
+    "@prefix bot:  <https://w3id.org/bot#> .\n",
+    "@prefix conn:  <https://ldac.org/connection#> .\n",
+    "@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .\n",
+    "@prefix owl:  <http://www.w3.org/2002/07/owl#> .\n",
+    "\n",
+    "conn:isConnectedTo a owl:SymmetricProperty;\n",
+    "             a owl:TransitiveProperty;\n",
+    "             rdfs:range bot:Zone.\n",
+    "```\n",
+    "\n",
+    "The `owl:SymmetricProperty` means that \n",
+    "- if A is connected to B \n",
+    "- then it follows that B is connected to A\n",
+    "\n",
+    "The `owl:TransitiveProperty` means that\n",
+    "- if A is connected to B\n",
+    "- and B is connected to C\n",
+    "- then A is connected to C\n",
+    "\n",
+    "combining both also means \n",
+    "- C is connected to A\n",
+    "\n",
+    "In our ABox, we  a few statements to that end have been added:\n",
+    "```\n",
+    ":SpaceA conn:isConnectedTo :SpaceB .\n",
+    ":SpaceB conn:isConnectedTo :SpaceC .\n",
+    ":Storey00 conn:isConnectedTo :SpaceA .\n",
+    "```\n",
+    "\n",
+    "Lets take a look at `:Storey00`\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(<https://ldac.org/house#Storey00> <https://ldac.org/connection#isConnectedTo> <https://ldac.org/house#SpaceA>)\n",
+      "(<https://ldac.org/house#Storey00> <https://w3id.org/bot#hasSpace> <https://ldac.org/house#SpaceB>)\n",
+      "(<https://ldac.org/house#Storey00> <https://w3id.org/bot#hasSpace> <https://ldac.org/house#SpaceA>)\n",
+      "(<https://ldac.org/house#Storey00> rdf:type <https://w3id.org/bot#Storey>)\n",
+      "(<https://ldac.org/house#Storey00> rdf:type owl:Thing)\n",
+      "(<https://ldac.org/house#Storey00> <https://w3id.org/bot#containsZone> <https://ldac.org/house#SpaceB>)\n",
+      "(<https://ldac.org/house#Storey00> <https://w3id.org/bot#containsZone> <https://ldac.org/house#SpaceA>)\n",
+      "(<https://ldac.org/house#Storey00> rdf:type <https://w3id.org/bot#Zone>)\n",
+      "(<https://ldac.org/house#Storey00> <https://ldac.org/connection#isConnectedTo> <https://ldac.org/house#SpaceB>)\n",
+      "(<https://ldac.org/house#Storey00> <https://ldac.org/connection#isConnectedTo> <https://ldac.org/house#SpaceC>)\n",
+      "(<https://ldac.org/house#Storey00> <https://ldac.org/connection#isConnectedTo> <https://ldac.org/house#Storey00>)\n",
+      "(<https://ldac.org/house#Storey00> rdf:type rdfs:Resource)\n",
+      "(<https://ldac.org/house#Storey00> owl:sameAs <https://ldac.org/house#Storey00>)\n",
+      "(<https://ldac.org/house#Storey00> owl:differentFrom <https://ldac.org/house#SiteA>)\n",
+      "(<https://ldac.org/house#Storey00> owl:differentFrom <https://ldac.org/house#BuildingA>)\n",
+      "(<https://ldac.org/house#Storey00> owl:differentFrom <https://ldac.org/house#SpaceD>)\n",
+      "(<https://ldac.org/house#Storey00> owl:differentFrom <https://ldac.org/house#SpaceC>)\n",
+      "(<https://ldac.org/house#Storey00> owl:differentFrom <https://ldac.org/house#SpaceB>)\n",
+      "(<https://ldac.org/house#Storey00> owl:differentFrom <https://ldac.org/house#SpaceA>)\n"
+     ]
+    }
+   ],
+   "source": [
+    "Model conn = FileManager.get().loadModel(\"../data/conn.ttl\");\n",
+    "bot.add(conn);\n",
+    "\n",
+    "Reasoner reasoner = ReasonerRegistry.getOWLReasoner();\n",
+    "reasoner = reasoner.bindSchema(bot);\n",
+    "\n",
+    "//create inferences from \n",
+    "InfModel infmodel = ModelFactory.createInfModel(reasoner, simple_house);\n",
+    "\n",
+    "//simple_house.write(System.out,\"RDF/XML\");\n",
+    "Resource Site = infmodel.getResource(\"https://ldac.org/house#Storey00\");\n",
+    "for (StmtIterator i = ((Model)infmodel).listStatements(new SimpleSelector( Site, null, (RDFNode)null )); i.hasNext();){\n",
+    "    Statement stmt = i.nextStatement();\n",
+    "    System.out.println (PrintUtil.print(stmt));\n",
+    "}"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Java",
+   "language": "java",
+   "name": "java"
+  },
+  "language_info": {
+   "codemirror_mode": "java",
+   "file_extension": ".jshell",
+   "mimetype": "text/x-java-source",
+   "name": "Java",
+   "pygments_lexer": "java",
+   "version": "12.0.1+12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}