Merge branch 'main' into retrieve-prefix

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 +1,74 @@
+# 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/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/ContextNotFoundException.java

@@ -1,6 +1,6 @@
 package cz.cvut.spipes.exception;
 
-public class ContextNotFoundException  extends RuntimeException {
+public class ContextNotFoundException  extends SPipesException {
 
     public ContextNotFoundException(String contextId) {
         super("Context identified by \"" + contextId + "\" was not found.");

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

@@ -3,7 +3,7 @@
 /**
  * Exception thrown when there is no context defined to search a resource.
  **/
-public class ContextsNotDefinedException extends RuntimeException {
+public class ContextsNotDefinedException extends SPipesException {
 
     public ContextsNotDefinedException(String message, Throwable cause) {
         super(message, cause);

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 SPipesException {
+
+    public ModuleConfigurationInconsistentException(String message) {
+        super(message);
+    }
+}

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

@@ -1,6 +1,6 @@
 package cz.cvut.spipes.exception;
 
-public class ParseException extends RuntimeException {
+public class ParseException extends SPipesException {
 
     public ParseException() {
         super("Could not parse input string");

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

@@ -10,7 +10,7 @@
 /**
  *
  */
-public class ResourceNotFoundException extends RuntimeException {
+public class ResourceNotFoundException extends SPipesException {
 
     public ResourceNotFoundException(String entityId, Set<String> contextUris) {
         super("Resource identified by \"" + entityId + "\" was not found in contexts " + contextUris + ".");

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

@@ -6,7 +6,7 @@
 /**
  * Exception thrown when a resource found is not unique.
  **/
-public class ResourceNotUniqueException extends RuntimeException {
+public class ResourceNotUniqueException extends SPipesException {
 
     public ResourceNotUniqueException(String message) {
         super(message);

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

@@ -0,0 +1,23 @@
+package cz.cvut.spipes.exception;
+
+/**
+ * Runtime exception that should be extended by any specific SPipes exception.
+ */
+public class SPipesException extends RuntimeException {
+
+    public SPipesException(String message) {
+        super(message);
+    }
+
+    public SPipesException(String message, Throwable cause) {
+        super(message, cause);
+    }
+
+    public SPipesException(Throwable cause) {
+        super(cause);
+    }
+
+    public SPipesException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
+        super(message, cause, enableSuppression, writableStackTrace);
+    }
+}

s-pipes-core/src/main/java/cz/cvut/spipes/exception/ValidationConstraintFailed.java → s-pipes-core/src/main/java/cz/cvut/spipes/exception/ValidationConstraintFailedException.java

@@ -1,13 +1,14 @@
 package cz.cvut.spipes.exception;
 
 import cz.cvut.spipes.modules.Module;
-import java.util.Optional;
 import org.jetbrains.annotations.NonNls;
 import org.jetbrains.annotations.NotNull;
 
-public class ValidationConstraintFailed extends RuntimeException {
+import java.util.Optional;
+
+public class ValidationConstraintFailedException extends SPipesException {
 
-    public ValidationConstraintFailed(@NonNls String message, @NotNull Module module) {
+    public ValidationConstraintFailedException(@NonNls String message, @NotNull Module module) {
         super(createModuleInfo(module) + " " +  message);
     }
 

s-pipes-core/src/main/java/cz/cvut/spipes/modules/AbstractModule.java

@@ -7,8 +7,9 @@
 import cz.cvut.spipes.engine.ExecutionContext;
 import cz.cvut.spipes.engine.ExecutionContextFactory;
 import cz.cvut.spipes.engine.VariablesBinding;
-import cz.cvut.spipes.exception.ValidationConstraintFailed;
+import cz.cvut.spipes.exception.ValidationConstraintFailedException;
 import cz.cvut.spipes.util.JenaUtils;
+import cz.cvut.spipes.util.QueryUtils;
 import org.apache.jena.atlas.lib.NotImplemented;
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.query.*;
@@ -293,7 +294,7 @@ private void checkConstraints(Model model, QuerySolution bindings, List<Resource
                         .toString();
                 LOG.error(mergedMsg);
                 if (ExecutionConfig.isExitOnError()) {
-                    throw new ValidationConstraintFailed(mergedMsg, this);
+                    throw new ValidationConstraintFailedException(mergedMsg, this);
                 }
             } else {
                 LOG.debug("Constraint validated for exception \"{}\".", getQueryComment(spinQuery));
@@ -306,9 +307,9 @@ protected String getQueryComment(org.topbraid.spin.model.Query query) {
         if (query.getComment() != null) {
             return query.getComment();
         }
-        String comment = query.toString().split(System.lineSeparator())[0];
-        if (comment.matches("\\s*#.*")) {
-            return comment.split("\\s*#\\s*", 2)[1];
+        String comment = QueryUtils.getQueryComment(query.toString());
+        if (comment != null) {
+            return comment;
         }
 //        Resource obj = query.getPropertyResourceValue(RDFS.comment);
 //        if (obj == null) {

s-pipes-core/src/main/java/cz/cvut/spipes/util/QueryUtils.java

@@ -1,25 +1,18 @@
 package cz.cvut.spipes.util;
 
 
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.regex.Matcher;
-import java.util.stream.Collectors;
-import org.apache.jena.query.ARQ;
-import org.apache.jena.query.ParameterizedSparqlString;
-import org.apache.jena.query.Query;
-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.query.*;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.RDFNode;
 import org.apache.jena.sparql.mgt.Explain;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.util.regex.Matcher;
+import java.util.stream.Collectors;
+
 public class QueryUtils {
 
     private static final Logger LOG = LoggerFactory.getLogger(QueryUtils.class);
@@ -176,4 +169,12 @@ private interface QueryExecutor<T> {
         T execQuery(QueryExecution execution);
     }
 
+    public static String getQueryComment(String query) {
+        String comment = query.split(System.lineSeparator())[0];
+        if (comment.matches("\\s*#.*")) {
+            return comment.split("\\s*#\\s*", 2)[1];
+        }
+        return null;
+    }
+
 }

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 +1,10 @@
+package cz.cvut.spipes.exceptions;
+
+import cz.cvut.spipes.exception.SPipesException;
+
+public class RepositoryAccessException extends SPipesException {
+
+    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 +1,11 @@
+package cz.cvut.spipes.exceptions;
+
+import cz.cvut.spipes.exception.SPipesException;
+
+public class RepositoryAlreadyExistsException extends SPipesException {
+
+    public RepositoryAlreadyExistsException(String repositoryName) {
+        super("Repository " + repositoryName + " already exists.");
+    }
+
+}