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Setting up Virtuoso on Ubuntu 18.04

I recently needed to setup a local instance of Virtuoso on my Ubuntu 18.04 laptop. In particular I needed to be able to specify the directory that Virtuoso is installed. This meant that using a Linux package manager was not an option. I therefore opted to install Virtuoso from source.

  1. Here are the steps I followed to do this:
    We are using Virtuoso 7.2.2. in our production environment, hence I downloaded virtuoso-opensource-7.2.2.tar.gz from Virtuoso downloads.
  2. Then I followed the instructions to build Virtuoso from Building from Upstream Source.
    1. Check build environment by running the following commands:
      sudo apt-get install dpkg-dev build-essential 
      sudo apt-get install autoconf automake libtool flex bison gperf gawk m4 make odbcinst libxml2-dev libssl-dev libreadline-dev
      
    2. Extract the file:
      tar xvpfz virtuoso-opensource-7.2.2.tar.gz
    3. Now to configure Virtuoso to install to a directory of your choice, in the directory you extracted the .tar.gz, run the following:
      ./configure --prefix=directory_of_choice
      
    4. To build Virtuoso, run:
      make nice
      

      This step failed for me with an error message that looks something like the following

      make[3]: Entering directory '~/virtuoso-opensource/libsrc/Wi'
      /bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../libsrc/Dk    -fno-strict-aliasing -O2  -Wall  -DNDEBUG -DPOINTER_64   -I/home/klimek/virtuoso-opensource/libsrc/Xml.new  -DOPENSSL_NO_KRB5 -Dlinux -D_GNU_SOURCE -DFILE64 -D_LARGEFILE64_SOURCE   -I../../libsrc -I../../libsrc/Dk -I../../libsrc/zlib -I. -I../../libsrc/langfunc -I../../libsrc/plugin -I../../libsrc/Tidy -I../../libsrc/Xml.new -I../../libsrc/odbcsdk/include -DVAD -DDBP -DBIF_XPER -DOPSYS=\"Linux\" -DHOST=\"x86_64-unknown-linux-gnu\" -g -O2 -MT libwi_la-bif_crypto.lo -MD -MP -MF .deps/libwi_la-bif_crypto.Tpo -c -o libwi_la-bif_crypto.lo `test -f 'bif_crypto.c' || echo './'`bif_crypto.c
      libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../libsrc/Dk -fno-strict-aliasing -O2 -Wall -DNDEBUG -DPOINTER_64 -I/home/klimek/virtuoso-opensource/libsrc/Xml.new -DOPENSSL_NO_KRB5 -Dlinux -D_GNU_SOURCE -DFILE64 -D_LARGEFILE64_SOURCE -I../../libsrc -I../../libsrc/Dk -I../../libsrc/zlib -I. -I../../libsrc/langfunc -I../../libsrc/plugin -I../../libsrc/Tidy -I../../libsrc/Xml.new -I../../libsrc/odbcsdk/include -DVAD -DDBP -DBIF_XPER -DOPSYS=\"Linux\" -DHOST=\"x86_64-unknown-linux-gnu\" -g -O2 -MT libwi_la-bif_crypto.lo -MD -MP -MF .deps/libwi_la-bif_crypto.Tpo -c bif_crypto.c  -fPIC -DPIC -o .libs/libwi_la-bif_crypto.o
      bif_crypto.c: In function ‘box_hmac’:
      bif_crypto.c:184:12: error: storage size of ‘ctx’ isn’t known
         HMAC_CTX ctx;
                  ^~~
      bif_crypto.c:190:3: warning: ‘HMAC_Init’ is deprecated [-Wdeprecated-declarations]
         HMAC_Init (&ctx, key, box_length (key) - DV_STRINGP (key) ? 1 : 0, md);
       ...

      which I fixed by installing libssl1.0-dev with

      sudo apt-get install libssl1.0-dev
      

      You can read more on this error here.
      After this re-run make nice.

    5. Lastly, I ran
      make install
      

      because I installed Virtuoso in my home directory. If you are not installing it in you home directory, you will need to run

      sudo make install
      
  3. To test your installation, go to localhost:8890.

 

Getting started with Ontotext GraphDB and Jena

In my previous post I explained how you can create an GraphDB repository and how you can update and query your repository using RDF4J. In this post I provide an example of how you can update and query a GraphDB repository using Jena. However, even though the code works, there are some pitfalls.

A Quick Example

First you need to add Jena as a Maven dependency:

<dependency>
 <groupId>org.apache.jena</groupId>
 <artifactId>apache-jena-libs</artifactId>
 <version>3.7.0</version>
 <type>pom</type>
</dependency>  

The Java code is straightforward:

package org.graphdb.jena.tutorial;

import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.ResultSet;
import org.apache.jena.update.UpdateExecutionFactory;
import org.apache.jena.update.UpdateFactory;
import org.apache.jena.update.UpdateProcessor;
import org.apache.jena.update.UpdateRequest;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.slf4j.Marker;
import org.slf4j.MarkerFactory;

public class SimpleInsertQueryExample {
  private static Logger logger = LoggerFactory.getLogger(SimpleInsertQueryExample.class);
  // Why This Failure marker
  private static final Marker WTF_MARKER = MarkerFactory.getMarker("WTF");
  
  // GraphDB 
  private static final String PERSONDATA_REPO_QUERY = 
      "http://localhost:7200/repositories/PersonData";
  private static final String PERSONDATA_REPO_UPDATE = 
      "http://localhost:7200/repositories/PersonData/statements";


  private static String strInsert;
  private static String strQuery;
  
  static {
    strInsert = 
        "INSERT DATA {"
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://dbpedia.org/ontology/birthDate>"
         + " \"1906-12-09\"^^<http://www.w3.org/2001/XMLSchema#date> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://dbpedia.org/ontology/birthPlace> "
         + "<http://dbpedia.org/resource/New_York_City> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://dbpedia.org/ontology/deathDate>"
         + " \"1992-01-01\"^^<http://www.w3.org/2001/XMLSchema#date> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://dbpedia.org/ontology/deathPlace> "
         + "<http://dbpedia.org/resource/Arlington_County,_Virginia> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://purl.org/dc/terms/description>"
         + " \"American computer scientist and United States Navy officer.\" ."
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
         + "<http://dbpedia.org/ontology/Person> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://xmlns.com/foaf/0.1/gender> \"female\" ."
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://xmlns.com/foaf/0.1/givenName> \"Grace\" ."
         + "<http://dbpedia.org/resource/Grace_Hopper> "
         + "<http://xmlns.com/foaf/0.1/name> \"Grace Hopper\" ."
         + "<http://dbpedia.org/resource/Grace_Hopper>"
         + " <http://xmlns.com/foaf/0.1/surname> \"Hopper\" ."        
         + "}";
    
    strQuery = 
        "SELECT ?name WHERE {?s <http://xmlns.com/foaf/0.1/name> ?name .}";
  }   
  
  private static void insert() {
    UpdateRequest updateRequest = UpdateFactory.create(strInsert);
    UpdateProcessor updateProcessor = UpdateExecutionFactory
        .createRemote(updateRequest, 
        PERSONDATA_REPO_UPDATE);
    updateProcessor.execute();
  }
  
  private static void query() {
    QueryExecution queryExecution = QueryExecutionFactory
        .sparqlService(PERSONDATA_REPO_QUERY, strQuery);
    for (ResultSet results = queryExecution.execSelect(); results.hasNext();) {
      QuerySolution qs = results.next();
      String strName = qs.get("?name").toString();
      logger.trace("name = " + strName);
    }    
    queryExecution.close();
  }

  
  public static void main(String[] args) {
    try {
      insert(); 
      query();      
    } catch (Throwable t) {
      logger.error(WTF_MARKER, t.getMessage(), t);
    }   
  }  
}

Some Pitfalls

The example I provided will insert RDF data into GraphDB and query it successfully. However, the data is inserted into the repository in the absence of a transaction. The transaction API of Jena is based on a Dataset. Historically Ontotext provided a Jena adapter with which a Jena Dataset could be created. However, based on my question on Stack Overflow in this regard, the Jena adapter is no longer supported by Ontotext. Hence, currently it is not clear to me how to enable transactions when using Jena to access GraphDB. So, if you know how to address this, please be so kind as to leave a comment with your insight!

Conclusion

In this post I provided a quick example of how you can access GraphDB using Jena. However, this example does not support transactions, and therefore you may want to look at rather using RDF4J with GraphDB. You can find this code at github.

Getting started with Ontotext GraphDB and RDF4J

In this post I will explain how to quickly get started with the free version of Ontotext GraphDB and RDF4J. Ontotext GraphDB is an RDF datastore and RDF4J is a Java framework for accessing RDF datastores (not just GraphDB). I will explain

  1. how to install and start GraphDB, as well as how to use the workbench to add a repository, and
  2. how to do SPARQL queries against GraphDB using RDF4J.

Install and start GraphDB and create a Repository

To gain access to the free version of GraphDB you have to email Ontotext. They will respond with an email with links to a desktop and stand-alone server version of GraphDB. You want to download the stand-alone server version. This is a graphdb-free-VERSION-dist.zip file, that you can extract somewhere on your filesystem, which I will refer to here as $GRAPHDB_ROOT. To start GraphDB, go to $GRAPHDB_ROOT/bin and run ./graphdb.

To access the workbench you can go to http://localhost:7200. To create a new repository, in the left-hand side menu navigate to Setup>Repositories. Click the Create new repository button. For our simple example we will use PersonData as an Repository ID. The rest of the settings we leave as-is. At the bottom of the page you can press the Create button.

Accessing a GraphDB Repository using RDF4J

To access our PersonData repository we will use RDF4J. Since GraphDB is based on the RDF4J libraries, we only need to include the GraphDB dependencies since these already include RDF4J. Thus, in our pom.xml file we only need to add the following:

 <dependency>
   <groupId>com.ontotext.graphdb</groupId>
   <artifactId>graphdb-free-runtime</artifactId>
   <version>8.5.0</version>
 </dependency>

In our example Java code we first insert some RDF data and then do a query based on the added data. For inserting data we start a transaction and commit it, or, if it fails we do a rollback. For querying the data we iterate through the TupleQueryResult, retrieving values for the binding variables we are interested in (i.e. name in this case). In line with the TupleQueryResult documentation, we close the TupleQueryResult once we are done.

package org.graphdb.rdf4j.tutorial;
package org.graphdb.rdf4j.tutorial;

import org.eclipse.rdf4j.model.impl.SimpleLiteral;
import org.eclipse.rdf4j.query.BindingSet;
import org.eclipse.rdf4j.query.QueryEvaluationException;
import org.eclipse.rdf4j.query.QueryLanguage;
import org.eclipse.rdf4j.query.TupleQuery;
import org.eclipse.rdf4j.query.TupleQueryResult;
import org.eclipse.rdf4j.query.Update;
import org.eclipse.rdf4j.repository.Repository;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.eclipse.rdf4j.repository.http.HTTPRepository;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.slf4j.Marker;
import org.slf4j.MarkerFactory;

public class SimpleInsertQueryExample {
  private static Logger logger = 
    LoggerFactory.getLogger(SimpleInsertQueryExample.class);
  // Why This Failure marker
  private static final Marker WTF_MARKER = 
    MarkerFactory.getMarker("WTF");
  
  // GraphDB 
  private static final String GRAPHDB_SERVER = 
    "http://localhost:7200/";
  private static final String REPOSITORY_ID = "PersonData";

  private static String strInsert;
  private static String strQuery;
  
  static {
    strInsert = 
        "INSERT DATA {"
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://dbpedia.org/ontology/birthDate> \"1906-12-09\"^^<http://www.w3.org/2001/XMLSchema#date> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://dbpedia.org/ontology/birthPlace> <http://dbpedia.org/resource/New_York_City> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://dbpedia.org/ontology/deathDate> \"1992-01-01\"^^<http://www.w3.org/2001/XMLSchema#date> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://dbpedia.org/ontology/deathPlace> <http://dbpedia.org/resource/Arlington_County,_Virginia> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://purl.org/dc/terms/description> \"American computer scientist and United States Navy officer.\" ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://dbpedia.org/ontology/Person> ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://xmlns.com/foaf/0.1/gender> \"female\" ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://xmlns.com/foaf/0.1/givenName> \"Grace\" ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://xmlns.com/foaf/0.1/name> \"Grace Hopper\" ."
         + "<http://dbpedia.org/resource/Grace_Hopper> <http://xmlns.com/foaf/0.1/surname> \"Hopper\" ."        
         + "}";
    
    strQuery = 
        "SELECT ?name FROM DEFAULT WHERE {" +
        "?s <http://xmlns.com/foaf/0.1/name> ?name .}";
  }  
  
  private static RepositoryConnection getRepositoryConnection() {
    Repository repository = new HTTPRepository(
      GRAPHDB_SERVER, REPOSITORY_ID);
    repository.initialize();
    RepositoryConnection repositoryConnection = 
      repository.getConnection();
    return repositoryConnection;
  }
  
  private static void insert(
    RepositoryConnection repositoryConnection) {
    
    repositoryConnection.begin();    
    Update updateOperation = repositoryConnection
      .prepareUpdate(QueryLanguage.SPARQL, strInsert);
    updateOperation.execute();
    
    try {
      repositoryConnection.commit();
    } catch (Exception e) {
      if (repositoryConnection.isActive())
        repositoryConnection.rollback();
    }
  }

  private static void query(
    RepositoryConnection repositoryConnection) {
    
    TupleQuery tupleQuery = repositoryConnection
      .prepareTupleQuery(QueryLanguage.SPARQL, strQuery);
    TupleQueryResult result = null;
    try {
      result = tupleQuery.evaluate();
      while (result.hasNext()) {
        BindingSet bindingSet = result.next();

        SimpleLiteral name = 
          (SimpleLiteral)bindingSet.getValue("name");
        logger.trace("name = " + name.stringValue());
      }
    }
    catch (QueryEvaluationException qee) {
      logger.error(WTF_MARKER, 
        qee.getStackTrace().toString(), qee);
    } finally {
      result.close();
    }    
  }  
  
  public static void main(String[] args) {
    RepositoryConnection repositoryConnection = null;
    try {   
      repositoryConnection = getRepositoryConnection();
      
      insert(repositoryConnection);
      query(repositoryConnection);      
      
    } catch (Throwable t) {
      logger.error(WTF_MARKER, t.getMessage(), t);
    } finally {
      repositoryConnection.close();
    }
  }  
}

Conclusion

In this brief post I gave a quick example of how you can setup a simple GraphDB repository and query it using SPARQL. You can find sample code on github.