Reusable server code split up and moved to the com.atomgraph.server…

… artifact (which `com.atomgraph.processor` now depends on) ResourceBase constructor catches `QueryParseException` and wraps it into `OntologyException` Removed unused classes
AtomGraph · Jul 9, 2023 · 9bc7fd9 · 9bc7fd9
1 parent e6e1b15
commit 9bc7fd9
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Showing 46 changed files with 72 additions and 1,677 deletions.
diff --git a/pom.xml b/pom.xml
@@ -7,7 +7,7 @@
     <packaging>${packaging.type}</packaging>
 
     <name>AtomGraph Processor</name>
-    <description>Ontology-driven Linked Data processor and server for SPARQL backends</description>
+    <description>Ontology-driven Linked Data processor</description>
     <url>https://github.com/AtomGraph/Processor</url>
     <inceptionYear>2015</inceptionYear>
 
@@ -78,18 +78,8 @@
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
-            <artifactId>twirl</artifactId>
-            <version>1.0.32</version>
-        </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>core</artifactId>
-            <version>4.0.3</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.jena</groupId>
-            <artifactId>jena-shacl</artifactId>
-            <version>4.7.0</version>
+            <artifactId>server</artifactId>
+            <version>${project.version}</version>
         </dependency>
     </dependencies>
 

diff --git a/src/main/java/com/atomgraph/processor/exception/OntologyException.java b/src/main/java/com/atomgraph/processor/exception/OntologyException.java
diff --git a/...graph/server/factory/OntologyFactory.java → ...ph/processor/factory/OntologyFactory.java b/...graph/server/factory/OntologyFactory.java → ...ph/processor/factory/OntologyFactory.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.atomgraph.server.factory;
+package com.atomgraph.processor.factory;
 
 import java.util.Optional;
 import jakarta.ws.rs.ext.Provider;

diff --git a/...h/server/factory/TemplateCallFactory.java → ...rocessor/factory/TemplateCallFactory.java b/...h/server/factory/TemplateCallFactory.java → ...rocessor/factory/TemplateCallFactory.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.atomgraph.server.factory;
+package com.atomgraph.processor.factory;
 
 import com.atomgraph.processor.model.Template;
 import com.atomgraph.processor.model.TemplateCall;

diff --git a/src/main/java/com/atomgraph/processor/model/impl/TemplateImpl.java b/src/main/java/com/atomgraph/processor/model/impl/TemplateImpl.java
@@ -33,7 +33,7 @@
 import org.apache.jena.rdf.model.Statement;
 import org.apache.jena.rdf.model.StmtIterator;
 import org.apache.jena.vocabulary.RDF;
-import com.atomgraph.processor.exception.OntologyException;
+import com.atomgraph.server.exception.OntologyException;
 import com.atomgraph.processor.model.Template;
 import com.atomgraph.processor.vocabulary.LDT;
 import org.apache.jena.rdf.model.RDFList;

diff --git a/...ava/com/atomgraph/server/Application.java → ...omgraph/processor/server/Application.java b/...ava/com/atomgraph/server/Application.java → ...omgraph/processor/server/Application.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.atomgraph.server;
+package com.atomgraph.processor.server;
 
 import com.atomgraph.core.MediaTypes;
 import com.atomgraph.core.exception.ConfigurationException;
@@ -26,7 +26,7 @@
 import org.apache.jena.enhanced.BuiltinPersonalities;
 import org.apache.jena.util.LocationMapper;
 import com.atomgraph.core.factory.DataManagerFactory;
-import com.atomgraph.server.model.impl.ResourceBase;
+import com.atomgraph.processor.server.model.impl.ResourceBase;
 import com.atomgraph.core.provider.QueryParamProvider;
 import com.atomgraph.core.io.ResultSetProvider;
 import com.atomgraph.core.io.UpdateRequestProvider;
@@ -35,7 +35,7 @@
 import com.atomgraph.server.mapper.ConfigurationExceptionMapper;
 import com.atomgraph.server.mapper.ModelExceptionMapper;
 import com.atomgraph.server.mapper.NotFoundExceptionMapper;
-import com.atomgraph.server.mapper.ParameterExceptionMapper;
+import com.atomgraph.processor.server.mapper.ParameterExceptionMapper;
 import com.atomgraph.server.mapper.jena.DatatypeFormatExceptionMapper;
 import com.atomgraph.server.mapper.jena.QueryParseExceptionMapper;
 import com.atomgraph.server.mapper.jena.RiotExceptionMapper;
@@ -44,8 +44,8 @@
 import com.atomgraph.processor.model.impl.TemplateImpl;
 import com.atomgraph.processor.vocabulary.AP;
 import com.atomgraph.server.mapper.OntologyExceptionMapper;
-import com.atomgraph.server.util.OntologyLoader;
-import com.atomgraph.server.io.SkolemizingModelProvider;
+import com.atomgraph.processor.util.OntologyLoader;
+import com.atomgraph.processor.server.io.SkolemizingModelProvider;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import com.atomgraph.processor.model.Parameter;
@@ -62,12 +62,12 @@
 import com.atomgraph.core.util.jena.DataManagerImpl;
 import com.atomgraph.processor.model.TemplateCall;
 import com.atomgraph.processor.model.impl.ApplicationImpl;
-import com.atomgraph.server.factory.OntologyFactory;
+import com.atomgraph.processor.factory.OntologyFactory;
 import com.atomgraph.server.mapper.BadGatewayExceptionMapper;
 import com.atomgraph.server.mapper.NotAcceptableExceptionMapper;
 import com.atomgraph.server.mapper.NotSupportedExceptionMapper;
-import com.atomgraph.server.factory.TemplateCallFactory;
-import com.atomgraph.server.filter.response.ResponseHeaderFilter;
+import com.atomgraph.processor.factory.TemplateCallFactory;
+import com.atomgraph.processor.server.filter.response.ResponseHeaderFilter;
 import com.atomgraph.server.mapper.SHACLConstraintViolationExceptionMapper;
 import com.atomgraph.spinrdf.vocabulary.SP;
 import java.util.HashMap;

diff --git a/...filter/response/ResponseHeaderFilter.java → ...filter/response/ResponseHeaderFilter.java b/...filter/response/ResponseHeaderFilter.java → ...filter/response/ResponseHeaderFilter.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.atomgraph.server.filter.response;
+package com.atomgraph.processor.server.filter.response;
 
 import com.atomgraph.core.util.Link;
 import com.atomgraph.processor.model.TemplateCall;

diff --git a/...server/io/SkolemizingDatasetProvider.java → ...server/io/SkolemizingDatasetProvider.java b/...server/io/SkolemizingDatasetProvider.java → ...server/io/SkolemizingDatasetProvider.java
@@ -13,10 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.atomgraph.server.io;
+package com.atomgraph.processor.server.io;
 
 import com.atomgraph.processor.util.Skolemizer;
 import com.atomgraph.server.exception.SkolemizationException;
+import com.atomgraph.server.io.ValidatingDatasetProvider;
 import java.util.Iterator;
 import jakarta.ws.rs.core.Context;
 import jakarta.ws.rs.core.Request;

diff --git a/...h/server/io/SkolemizingModelProvider.java → ...r/server/io/SkolemizingModelProvider.java b/...h/server/io/SkolemizingModelProvider.java → ...r/server/io/SkolemizingModelProvider.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.atomgraph.server.io;
+package com.atomgraph.processor.server.io;
 
 import org.apache.jena.ontology.Ontology;
 import org.apache.jena.rdf.model.Model;
@@ -23,6 +23,7 @@
 import jakarta.ws.rs.core.UriBuilder;
 import com.atomgraph.server.exception.SkolemizationException;
 import com.atomgraph.processor.util.Skolemizer;
+import com.atomgraph.server.io.ValidatingModelProvider;
 import jakarta.ws.rs.HttpMethod;
 import org.apache.jena.rdf.model.ResIterator;
 import org.apache.jena.rdf.model.Resource;

diff --git a/...rver/mapper/ParameterExceptionMapper.java → ...rver/mapper/ParameterExceptionMapper.java b/...rver/mapper/ParameterExceptionMapper.java → ...rver/mapper/ParameterExceptionMapper.java
@@ -14,13 +14,14 @@
  * limitations under the License.
  */
 
-package com.atomgraph.server.mapper;
+package com.atomgraph.processor.server.mapper;
 
 import com.atomgraph.core.MediaTypes;
 import org.apache.jena.rdf.model.ResourceFactory;
 import jakarta.ws.rs.core.Response;
 import jakarta.ws.rs.ext.ExceptionMapper;
 import com.atomgraph.processor.exception.ParameterException;
+import com.atomgraph.server.mapper.ExceptionMapperBase;
 import jakarta.inject.Inject;
 
 /**

diff --git a/...omgraph/server/model/QueriedResource.java → ...ocessor/server/model/QueriedResource.java b/...omgraph/server/model/QueriedResource.java → ...ocessor/server/model/QueriedResource.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.atomgraph.server.model;
+package com.atomgraph.processor.server.model;
 
 import org.apache.jena.update.UpdateRequest;
 
@@ -27,9 +27,9 @@ public interface QueriedResource extends com.atomgraph.core.model.QueriedResourc
 {
 
     /**
-     * Returns the SPARQL query that is used to retrieve RDF description of this resource.
+     * Returns the SPARQL update that is used to update the RDF description of this resource.
      * 
-     * @return query builder
+     * @return update request
      */
     public UpdateRequest getUpdate();
 

diff --git a/.../com/atomgraph/server/model/Resource.java → ...raph/processor/server/model/Resource.java b/.../com/atomgraph/server/model/Resource.java → ...raph/processor/server/model/Resource.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.atomgraph.server.model;
+package com.atomgraph.processor.server.model;
 
 import com.atomgraph.processor.model.Application;
 import com.atomgraph.processor.model.TemplateCall;

diff --git a/...graph/server/model/impl/ResourceBase.java → ...essor/server/model/impl/ResourceBase.java b/...graph/server/model/impl/ResourceBase.java → ...essor/server/model/impl/ResourceBase.java
@@ -14,7 +14,7 @@
  *  limitations under the License.
  *
  */
-package com.atomgraph.server.model.impl;
+package com.atomgraph.processor.server.model.impl;
 
 import com.atomgraph.core.MediaTypes;
 import org.apache.jena.ontology.*;
@@ -28,9 +28,9 @@
 import jakarta.ws.rs.core.*;
 import com.atomgraph.core.model.Service;
 import com.atomgraph.core.model.impl.QueriedResourceBase;
-import com.atomgraph.processor.exception.OntologyException;
+import com.atomgraph.server.exception.OntologyException;
 import com.atomgraph.processor.model.TemplateCall;
-import com.atomgraph.server.util.InsertDataBuilder;
+import com.atomgraph.processor.util.InsertDataBuilder;
 import com.atomgraph.spinrdf.vocabulary.SPIN;
 import java.io.IOException;
 import java.util.Collections;
@@ -54,7 +54,7 @@
  * @see <a href="http://www.w3.org/TR/sparql11-query/#solutionModifiers">15 Solution Sequences and Modifiers</a>
  */
 @Path("/")
-public class ResourceBase extends QueriedResourceBase implements com.atomgraph.server.model.Resource, com.atomgraph.server.model.QueriedResource
+public class ResourceBase extends QueriedResourceBase implements com.atomgraph.processor.server.model.Resource, com.atomgraph.processor.server.model.QueriedResource
 {
     private static final Logger log = LoggerFactory.getLogger(ResourceBase.class);
 
@@ -125,16 +125,24 @@ protected ResourceBase(final UriInfo uriInfo, final Request request, final Media
             queryResource = templateCall.get().getTemplate().getQuery();
             if (queryResource != null)
             {
-                if (queryResource.canAs(com.atomgraph.spinrdf.model.TemplateCall.class))
-                    query = new ParameterizedSparqlString(queryResource.as(com.atomgraph.spinrdf.model.TemplateCall.class).getTemplate().getBody().getText(),
-                        querySolutionMap, uriInfo.getBaseUri().toString()).asQuery();
-                else
+                try
                 {
-                    if (queryResource.canAs(com.atomgraph.spinrdf.model.Query.class))
-                        query = new ParameterizedSparqlString(queryResource.as(com.atomgraph.spinrdf.model.Query.class).getText(),
+                    if (queryResource.canAs(com.atomgraph.spinrdf.model.TemplateCall.class))
+                        query = new ParameterizedSparqlString(queryResource.as(com.atomgraph.spinrdf.model.TemplateCall.class).getTemplate().getBody().getText(),
                             querySolutionMap, uriInfo.getBaseUri().toString()).asQuery();
                     else
-                        query = null;
+                    {
+                        if (queryResource.canAs(com.atomgraph.spinrdf.model.Query.class))
+                            query = new ParameterizedSparqlString(queryResource.as(com.atomgraph.spinrdf.model.Query.class).getText(),
+                                querySolutionMap, uriInfo.getBaseUri().toString()).asQuery();
+                        else
+                            query = null;
+                    }
+                }
+                catch (QueryParseException ex)
+                {
+                    if (log.isDebugEnabled()) log.debug("Query resource contains an invalid SPARQL string: {}", queryResource);
+                    throw new OntologyException(ex);
                 }
             }
             else
@@ -143,16 +151,24 @@ protected ResourceBase(final UriInfo uriInfo, final Request request, final Media
             updateResource = templateCall.get().getTemplate().getUpdate();
             if (updateResource != null)
             {
-                if (updateResource.canAs(com.atomgraph.spinrdf.model.TemplateCall.class))
-                    update = new ParameterizedSparqlString(updateResource.as(com.atomgraph.spinrdf.model.TemplateCall.class).getTemplate().getBody().getText(),
-                        querySolutionMap, uriInfo.getBaseUri().toString()).asUpdate();
-                else
+                try
                 {
-                    if (updateResource.canAs(com.atomgraph.spinrdf.model.update.Update.class))
-                        update = new ParameterizedSparqlString(updateResource.as(com.atomgraph.spinrdf.model.update.Update.class).getText(),
+                    if (updateResource.canAs(com.atomgraph.spinrdf.model.TemplateCall.class))
+                        update = new ParameterizedSparqlString(updateResource.as(com.atomgraph.spinrdf.model.TemplateCall.class).getTemplate().getBody().getText(),
                             querySolutionMap, uriInfo.getBaseUri().toString()).asUpdate();
                     else
-                        update = null;
+                    {
+                        if (updateResource.canAs(com.atomgraph.spinrdf.model.update.Update.class))
+                            update = new ParameterizedSparqlString(updateResource.as(com.atomgraph.spinrdf.model.update.Update.class).getText(),
+                                querySolutionMap, uriInfo.getBaseUri().toString()).asUpdate();
+                        else
+                            update = null;
+                    }
+                }
+                catch (QueryParseException ex)
+                {
+                    if (log.isDebugEnabled()) log.debug("Update resource contains an invalid SPARQL string: {}", updateResource);
+                    throw new OntologyException(ex);
                 }
             }
             else

diff --git a/...atomgraph/server/resource/graph/Item.java → ...processor/server/resource/graph/Item.java b/...atomgraph/server/resource/graph/Item.java → ...processor/server/resource/graph/Item.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.atomgraph.server.resource.graph;
+package com.atomgraph.processor.server.resource.graph;
 
 import com.atomgraph.core.MediaTypes;
 import org.apache.jena.ontology.Ontology;
@@ -25,7 +25,7 @@
 import jakarta.ws.rs.core.Response;
 import jakarta.ws.rs.core.UriInfo;
 import com.atomgraph.core.model.Service;
-import com.atomgraph.server.model.impl.ResourceBase;
+import com.atomgraph.processor.server.model.impl.ResourceBase;
 import com.atomgraph.processor.model.TemplateCall;
 import java.util.Optional;
 import jakarta.inject.Inject;
@@ -42,7 +42,7 @@
  * @see com.atomgraph.core.model.GraphStore
  * @see <a href="http://www.w3.org/TR/sparql11-http-rdf-update/#direct-graph-identification">4.1 Direct Graph Identification</a>
  */
-public class Item extends ResourceBase // TO-DO: extends GraphStore
+public class Item extends ResourceBase
 {
 
     private static final Logger log = LoggerFactory.getLogger(Item.class);

diff --git a/...mgraph/server/util/InsertDataBuilder.java → ...aph/processor/util/InsertDataBuilder.java b/...mgraph/server/util/InsertDataBuilder.java → ...aph/processor/util/InsertDataBuilder.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.atomgraph.server.util;
+package com.atomgraph.processor.util;
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;