Merge pull request #172 from kbss-cvut/rdf4j-update-module

Rdf4j update module

README.md

@@ -29,6 +29,7 @@ SPipes loads pipelines by recursive traversal of configured directories, searchi
 SPipes script construction, execution, and execution history tracking is explained 
 in [Hello world example](doc/examples/hello-world/hello-world.md).
 Script debugging is explained in [skosify example](doc/examples/skosify/skosify.md).
+Working with RDF4J repository is explained in [rdf4j example](doc/examples/rdf4j-update/rdf4j-update.md).
 Constraint validation is described in [constraint validation example](doc/examples/constraint-validation/constraint-validation.md).
 
 

doc/examples/rdf4j-update/rdf4j-update.md

@@ -0,0 +1,71 @@
+# RDF4J update example
+
+RDF4J update example explains how to update RDF4J repository.
+
+## Introduction
+
+This example explains script [rdf4j-update.sms.ttl](./rdf4j-update.sms.ttl]) that contain one pipeline. It creates RDF4J repository and performs update query. For more details about script construction and execution you can see [hello-world-example](../hello-world/hello-world.md).
+
+## Script structure
+
+Script performs following steps:
+1) Creates RDF4J repository using `kbss:rdf4j-create-repository` module. Repository is specified by parameters `rdf4j:p-rdf4j-server-url` and `rdf4j:p-rdf4j-repository-name`. Parameter `rdf4j:p-rdf4j-ignore-if-exists` defines behavior of the module in case when defined repository already exists:
+in case if it is set to be "true", module will not do anything if repository with given ID already exists on the server.  
+
+
+    :create-repository
+        a kbss:rdf4j-create-repository ;
+        rdf4j:p-rdf4j-server-url "http://localhost:8080/rdf4j-server/" ;
+        rdf4j:p-rdf4j-repository-name "test-update" ;
+        rdf4j:p-rdf4j-ignore-if-exists "true" ;
+        sm:next :update ;
+    .
+
+2) Perform an update on repository using `kbss:rdf4j-update` module. Repository is defined in the same way as in `:create-repository`. Update query is set by string in `sp:text` section.
+
+
+    :update-repository
+        a kbss:rdf4j-update ;
+        sm:next :update-repository_Return ;
+        sml:updateQuery [
+            a sp:Update ;
+            sp:text """
+    PREFIX ex-people: <http://example.org/people/>
+    DELETE {
+        ex-people:john ex-people:age ?oldAge .
+    }
+    INSERT {
+        ex-people:john ex-people:age ?newAge .
+    } WHERE {
+        OPTIONAL {
+        ex-people:john ex-people:age ?oldAge .
+        }
+        BIND(COALESCE(?oldAge+1, 1) as ?newAge)
+    }
+            """ ;
+        ];
+        rdf4j:p-rdf4j-server-url "http://localhost:8080/rdf4j-server/" ;
+        rdf4j:p-rdf4j-repository-name "test-update" ;
+    .
+
+## Script execution
+
+Let's assume that SPipes web application is running at `http://localhost:8080/s-pipes`. We can call the *pipeline* with:
+
+    http://localhost:8080/s-pipes/service?_pId=update-repository
+
+Note, that rdf4j server should be running on the URL that is specified in script (`http://localhost:8080/rdf4j-server/` for example).
+You can see following logs while execution:
+
+    [http-nio-8080-exec-7] INFO  c.c.s.e.ExecutionEngineImpl -  ##### create-repository
+    ...
+    [http-nio-8080-exec-1] INFO  c.c.s.m.Rdf4jUpdateModule - Server url: http://localhost:8080/rdf4j-server/, Repsitory name: test-update, Ignore if repository exist: true
+    [http-nio-8080-exec-6] INFO  c.c.s.m.Rdf4jUpdateModule - Repository "test-update" already exists
+    ...
+    [http-nio-8080-exec-7] INFO  c.c.s.e.ExecutionEngineImpl -  ##### Make insert update
+    ...
+    [http-nio-8080-exec-7] DEBUG c.c.s.m.Rdf4jUpdateModule - Connected to test-update
+    [http-nio-8080-exec-7] DEBUG  c.c.s.m.Rdf4jUpdateModule - Update successful
+
+This log will occur when Ignore flag is set to true and repository already exists:
+`[http-nio-8080-exec-6] INFO  c.c.s.m.Rdf4jUpdateModule - Repository "test-update" already exists`

doc/examples/rdf4j-update/rdf4j-update.sms.ttl

@@ -0,0 +1,69 @@
+# baseURI: http://onto.fel.cvut.cz/ontologies/s-pipes/rdf-update-example
+# imports: http://onto.fel.cvut.cz/ontologies/s-pipes-lib
+
+@prefix : <http://onto.fel.cvut.cz/ontologies/s-pipes/rdf-update-example/> .
+@prefix doc: <http://onto.fel.cvut.cz/ontologies/documentation/> .
+@prefix kbss: <http://onto.fel.cvut.cz/ontologies/lib/module/> .
+@prefix km-sesame: <http://onto.fel.cvut.cz/ontologies/lib/module/sesame/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix sm: <http://topbraid.org/sparqlmotion#> .
+@prefix sml: <http://topbraid.org/sparqlmotionlib#> .
+@prefix sp: <http://spinrdf.org/sp#> .
+@prefix spif: <http://spinrdf.org/spif#> .
+@prefix spin: <http://spinrdf.org/spin#> .
+@prefix spl: <http://spinrdf.org/spl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdf4j: <http://onto.fel.cvut.cz/ontologies/lib/module/rdf4j/> .
+
+<http://onto.fel.cvut.cz/ontologies/s-pipes/rdf-update-example>
+  a owl:Ontology ;
+  owl:imports <http://onto.fel.cvut.cz/ontologies/s-pipes-lib> ;
+.
+
+:create-repository
+  a kbss:rdf4j-create-repository ;
+  rdf4j:p-rdf4j-server-url "http://localhost:8080/rdf4j-server/" ;
+  rdf4j:p-rdf4j-repository-name "test-update" ;
+  rdf4j:p-rdf4j-ignore-if-exists "true" ;
+  sm:next :update-repository ;
+.
+
+:update-repository
+  a kbss:rdf4j-update ;
+  sm:next :update-repository_Return ;
+  sml:updateQuery [
+      a sp:Update ;
+      sp:text """
+PREFIX ex-people: <http://example.org/people/>
+DELETE {
+	ex-people:john ex-people:age ?oldAge .
+}
+INSERT {
+	ex-people:john ex-people:age ?newAge .
+} WHERE {
+   OPTIONAL {
+      ex-people:john ex-people:age ?oldAge .
+   }
+   BIND(COALESCE(?oldAge+1, 1) as ?newAge)
+}
+      """ ;
+    ];
+  kbss:has-max-iteration-count 5 ;
+  kbss:only-if-triple-count-changes false;
+  rdf4j:p-rdf4j-server-url "http://localhost:8080/rdf4j-server/" ;
+  rdf4j:p-rdf4j-repository-name "test-update" ;
+.
+
+:update-repository_Return
+  a sml:ReturnRDF ;
+  sml:serialization sml:JSONLD ;
+  rdfs:label "Update repository" ;
+.
+
+:update-repository
+   a sm:Function ;
+   sm:returnModule :update-repository_Return ;
+   rdfs:subClassOf sm:Functions ;
+.

s-pipes-core/src/main/java/cz/cvut/spipes/constants/KBSS_MODULE.java

@@ -20,6 +20,7 @@ protected static final Property property(String local )
     public static final Property is_parse_text = property("is-parse-text");
     public static final Property has_max_iteration_count = property("has-max-iteration-count");
     public static final Property has_resource_uri = property("has-resource-uri");
+    public static final Property stop_iteration_on_stable_triple_count = property("stop-iteration-on-stable-triple-count");
 
     /**
      returns the URI for this schema

s-pipes-core/src/main/java/cz/cvut/spipes/constants/SML.java

@@ -21,6 +21,7 @@ protected static final Property property(String local )
     public static final Property constructQuery = property("constructQuery");
     public static final Property value = property("value");
     public static final Property selectQuery = property("selectQuery");
+    public static final Property updateQuery = property("updateQuery");
     public static final Property sourceFilePath = property("sourceFilePath");
     public static final Property url = property("url");
     public static final Property targetFilePath = property("targetFilePath");

s-pipes-core/src/main/java/cz/cvut/spipes/exception/ModuleConfigurationInconsistentException.java

@@ -0,0 +1,11 @@
+package cz.cvut.spipes.exception;
+
+/**
+ * Indicate that SPipes Module was incorrectly configured.
+ */
+public class ModuleConfigurationInconsistentException extends RuntimeException {
+
+    public ModuleConfigurationInconsistentException(String message) {
+        super(message);
+    }
+}

s-pipes-core/src/test/java/cz/cvut/spipes/modules/RetrievePrefixesModuleTest.java

@@ -7,7 +7,6 @@
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.ontology.OntModelSpec;
 import org.apache.jena.rdf.model.ModelFactory;
-import org.apache.jena.shared.PrefixMapping;
 import org.apache.jena.util.FileManager;
 import org.apache.jena.util.FileUtils;
 import org.apache.jena.vocabulary.OWL;
@@ -52,7 +51,7 @@ void setUp() {
     }
 
     @Test
-    void testExecuteSelf() {
+    void executeSelfReturnPrefixes() {
         given(ontoDocManager.getRegisteredOntologyUris()).willReturn(uri2ontModel.keySet());
         uri2ontModel.forEach((key, value) -> {
             doReturn(value).when(ontoDocManager).getOntology(key);

s-pipes-modules/module-rdf4j/pom.xml

@@ -44,6 +44,16 @@
             <artifactId>junit-jupiter-api</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-junit-jupiter</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-core</artifactId>
+            <scope>test</scope>
+        </dependency>
 
         <!-- TODO needed -->
         <!--<dependency>-->

s-pipes-modules/module-rdf4j/src/main/java/cz/cvut/spipes/exceptions/RepositoryAccessException.java

@@ -0,0 +1,8 @@
+package cz.cvut.spipes.exceptions;
+
+public class RepositoryAccessException extends RuntimeException {
+
+    public RepositoryAccessException(String repositoryName, Throwable cause) {
+        super("Cannot connect to repository " + repositoryName + ".", cause);
+    }
+}

s-pipes-modules/module-rdf4j/src/main/java/cz/cvut/spipes/exceptions/RepositoryAlreadyExistsException.java

@@ -0,0 +1,9 @@
+package cz.cvut.spipes.exceptions;
+
+public class RepositoryAlreadyExistsException extends RuntimeException {
+
+    public RepositoryAlreadyExistsException(String repositoryName) {
+        super("Repository " + repositoryName + " already exists.");
+    }
+
+}

s-pipes-modules/module-rdf4j/src/main/java/cz/cvut/spipes/modules/Rdf4jCreateRepositoryModule.java

@@ -0,0 +1,120 @@
+package cz.cvut.spipes.modules;
+
+import cz.cvut.spipes.constants.KBSS_MODULE;
+import cz.cvut.spipes.engine.ExecutionContext;
+import cz.cvut.spipes.exceptions.RepositoryAlreadyExistsException;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.ResourceFactory;
+import org.eclipse.rdf4j.repository.config.RepositoryConfig;
+import org.eclipse.rdf4j.repository.manager.RemoteRepositoryManager;
+import org.eclipse.rdf4j.repository.manager.RepositoryManager;
+import org.eclipse.rdf4j.repository.sail.config.SailRepositoryConfig;
+import org.eclipse.rdf4j.sail.nativerdf.config.NativeStoreConfig;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Objects;
+
+/**
+ * Module creates native store rdf4j repository on the given server with the given name
+ */
+public class Rdf4jCreateRepositoryModule extends AbstractModule {
+    private static final Logger LOG = LoggerFactory.getLogger(Rdf4jUpdateModule.class.getName());
+    private static final String TYPE_URI = KBSS_MODULE.getURI() + "rdf4j-create-repository";
+    private static final String PROPERTY_PREFIX_URI = KBSS_MODULE.getURI() + "rdf4j";
+
+    /**
+     * URL of the Rdf4j server
+     */
+    static final Property P_RDF4J_SERVER_URL = getParameter("p-rdf4j-server-url");
+    private String rdf4jServerURL;
+
+    /**
+     * Rdf4j repository ID
+     */
+    static final Property P_RDF4J_REPOSITORY_NAME = getParameter("p-rdf4j-repository-name");
+    private String rdf4jRepositoryName;
+
+    /**
+     * Don't try to create new repository if it already exists (Default value is false)
+     */
+    static final Property P_RDF4J_IGNORE_IF_EXISTS = getParameter("p-rdf4j-ignore-if-exists");
+    private boolean rdf4jIgnoreIfExists;
+
+    private RepositoryManager repositoryManager;
+
+    public String getRdf4jServerURL() {
+        return rdf4jServerURL;
+    }
+
+    public void setRdf4jServerURL(String rdf4jServerURL) {
+        this.rdf4jServerURL = rdf4jServerURL;
+    }
+
+    public String getRdf4jRepositoryName() {
+        return rdf4jRepositoryName;
+    }
+
+    public void setRdf4jRepositoryName(String rdf4jRepositoryName) {
+        this.rdf4jRepositoryName = rdf4jRepositoryName;
+    }
+
+    public boolean isRdf4jIgnoreIfExists() {
+        return rdf4jIgnoreIfExists;
+    }
+
+    public void setRdf4jIgnoreIfExists(boolean rdf4jIgnoreIfExists) {
+        this.rdf4jIgnoreIfExists = rdf4jIgnoreIfExists;
+    }
+
+    private static Property getParameter(final String name) {
+        return ResourceFactory.createProperty(PROPERTY_PREFIX_URI + "/" + name);
+    }
+
+    void setRepositoryManager(RepositoryManager repositoryManager) {
+        this.repositoryManager = repositoryManager;
+    }
+
+    @Override
+    ExecutionContext executeSelf() {
+        NativeStoreConfig nativeStoreConfig = new NativeStoreConfig();
+        SailRepositoryConfig sailRepositoryConfig = new SailRepositoryConfig(nativeStoreConfig);
+
+        repositoryManager.init();
+        LOG.info("Server url:{}, Repsitory name:{}, Ignore if repository exist:{}.",
+                rdf4jServerURL,
+                rdf4jRepositoryName,
+                rdf4jIgnoreIfExists);
+
+        if((!rdf4jIgnoreIfExists) && repositoryManager.hasRepositoryConfig(rdf4jRepositoryName)){
+
+            LOG.info("Repository \"{}\" already exists",
+                    rdf4jRepositoryName);
+            throw new RepositoryAlreadyExistsException(rdf4jRepositoryName);
+        }
+
+        RepositoryConfig repositoryConfig = new RepositoryConfig(rdf4jRepositoryName,sailRepositoryConfig);
+        repositoryManager.addRepositoryConfig(repositoryConfig);
+        repositoryManager.getRepository(rdf4jRepositoryName).init();
+
+        return executionContext;
+    }
+
+    @Override
+    public String getTypeURI() {
+        return TYPE_URI;
+    }
+
+    @Override
+    public void loadConfiguration() {
+        rdf4jServerURL = getEffectiveValue(P_RDF4J_SERVER_URL).asLiteral().getString();
+        rdf4jRepositoryName = getEffectiveValue(P_RDF4J_REPOSITORY_NAME).asLiteral().getString();
+        try {
+            rdf4jIgnoreIfExists = (Objects.equals(getEffectiveValue(P_RDF4J_IGNORE_IF_EXISTS).asLiteral().getString(), "true"));
+        }
+        catch (NullPointerException e){
+            rdf4jIgnoreIfExists = false;
+        }
+        repositoryManager = new RemoteRepositoryManager(rdf4jServerURL);
+    }
+}