Depndency on com.atomgraph.server instead of com.atomgraph.processor (#177)

namedgraph · web-flow · commit d3b8ef54e58d · 2023-07-10T09:50:05.000+02:00
* `com.atomgraph.linkeddatahub` depends on the new `com.atomgraph.server` instead of `com.atomgraph.processor`
Caching ontologies by default
Registered Server's `NotAcceptableExceptionMapper`

* Copied vocabulary files from Processor -- they were missing since LDH now only depends on Server, which does not include them

* Bumped Server to 4.1.0-SNAPSHOT

* Bump to Server 4.1.2
diff --git a/pom.xml b/pom.xml
@@ -128,8 +128,8 @@
         <!-- TO-DO: replace with AtomGraph Core -->
         <dependency>
             <groupId>${project.groupId}</groupId>
-            <artifactId>processor</artifactId>
-            <version>4.0.1</version>
+            <artifactId>server</artifactId>
+            <version>4.1.2</version>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
diff --git a/src/main/java/com/atomgraph/linkeddatahub/Application.java b/src/main/java/com/atomgraph/linkeddatahub/Application.java
@@ -124,10 +124,9 @@
 import com.atomgraph.linkeddatahub.writer.XSLTWriterBase;
 import com.atomgraph.linkeddatahub.writer.factory.ModeFactory;
 import com.atomgraph.linkeddatahub.writer.function.DecodeURI;
-import com.atomgraph.processor.vocabulary.AP;
-import com.atomgraph.processor.vocabulary.LDT;
+import com.atomgraph.server.mapper.NotAcceptableExceptionMapper;
+import com.atomgraph.server.vocabulary.LDT;
 import com.atomgraph.server.mapper.OntologyExceptionMapper;
-import com.atomgraph.server.mapper.ParameterExceptionMapper;
 import com.atomgraph.server.mapper.jena.DatatypeFormatExceptionMapper;
 import com.atomgraph.server.mapper.jena.QueryParseExceptionMapper;
 import com.atomgraph.server.mapper.jena.RiotExceptionMapper;
@@ -304,7 +303,6 @@ public Application(@Context ServletConfig servletConfig) throws URISyntaxExcepti
             servletConfig.getServletContext().getInitParameter(A.maxGetRequestSize.getURI()) != null ? Integer.valueOf(servletConfig.getServletContext().getInitParameter(A.maxGetRequestSize.getURI())) : null,
             servletConfig.getServletContext().getInitParameter(A.cacheModelLoads.getURI()) != null ? Boolean.parseBoolean(servletConfig.getServletContext().getInitParameter(A.cacheModelLoads.getURI())) : true,
             servletConfig.getServletContext().getInitParameter(A.preemptiveAuth.getURI()) != null ? Boolean.parseBoolean(servletConfig.getServletContext().getInitParameter(A.preemptiveAuth.getURI())) : false,
-            servletConfig.getServletContext().getInitParameter(AP.cacheSitemap.getURI()) != null ? Boolean.parseBoolean(servletConfig.getServletContext().getInitParameter(AP.cacheSitemap.getURI())) : true,
             new PrefixMapper(servletConfig.getServletContext().getInitParameter(AC.prefixMapping.getURI()) != null ? servletConfig.getServletContext().getInitParameter(AC.prefixMapping.getURI()) : null),
             com.atomgraph.client.Application.getSource(servletConfig.getServletContext(), servletConfig.getServletContext().getInitParameter(AC.stylesheet.getURI()) != null ? servletConfig.getServletContext().getInitParameter(AC.stylesheet.getURI()) : null),
             servletConfig.getServletContext().getInitParameter(AC.cacheStylesheet.getURI()) != null ? Boolean.parseBoolean(servletConfig.getServletContext().getInitParameter(AC.cacheStylesheet.getURI())) : false,
@@ -363,7 +361,6 @@ public Application(@Context ServletConfig servletConfig) throws URISyntaxExcepti
      * @param maxGetRequestSize maximum <code>GET</code> request size
      * @param cacheModelLoads true if model loads should be cached
      * @param preemptiveAuth true if HTTP Basic auth credentials should be sent preemptively
-     * @param cacheSitemap true if app's ontology should be cached
      * @param locationMapper Jena's <code>LocationMapper</code> instance
      * @param stylesheet stylesheet URI
      * @param cacheStylesheet true if stylesheet should be cached
@@ -404,7 +401,7 @@ public Application(@Context ServletConfig servletConfig) throws URISyntaxExcepti
      * @param googleClientSecret client secret for Google's OAuth
      */
     public Application(final ServletConfig servletConfig, final MediaTypes mediaTypes,
-            final Integer maxGetRequestSize, final boolean cacheModelLoads, final boolean preemptiveAuth, final boolean cacheSitemap,
+            final Integer maxGetRequestSize, final boolean cacheModelLoads, final boolean preemptiveAuth,
             final LocationMapper locationMapper, final Source stylesheet, final boolean cacheStylesheet, final boolean resolvingUncached,
             final String clientKeyStoreURIString, final String clientKeyStorePassword,
             final String secretaryCertAlias,
@@ -671,7 +668,7 @@ public Application(final ServletConfig servletConfig, final MediaTypes mediaType
             ontModelSpec = OntModelSpec.OWL_MEM_RDFS_INF;
             ontModelSpec.setImportModelGetter(dataManager);
             OntDocumentManager.getInstance().setFileManager((FileManager)dataManager);
-            OntDocumentManager.getInstance().setCacheModels(cacheSitemap); // need to re-set after changing FileManager
+            OntDocumentManager.getInstance().setCacheModels(true); // need to re-set after changing FileManager
             ontModelSpec.setDocumentManager(OntDocumentManager.getInstance());
 
             if (mailUser != null && mailPassword !=  null) // enable SMTP authentication
@@ -969,10 +966,10 @@ protected void registerExceptionMappers()
         register(SPINConstraintViolationExceptionMapper.class);
         register(SHACLConstraintViolationExceptionMapper.class);
         register(DatatypeFormatExceptionMapper.class);
-        register(ParameterExceptionMapper.class);
         register(QueryExecExceptionMapper.class);
         register(RiotExceptionMapper.class);
         register(RiotParseExceptionMapper.class); // move to Processor?
+        register(NotAcceptableExceptionMapper.class);
         register(ClientErrorExceptionMapper.class);
         register(HttpHostConnectExceptionMapper.class);
         register(BadGatewayExceptionMapper.class);
diff --git a/src/main/java/com/atomgraph/linkeddatahub/apps/model/Application.java b/src/main/java/com/atomgraph/linkeddatahub/apps/model/Application.java
@@ -26,14 +26,21 @@
  * 
  * @author Martynas Jusevičius {@literal <martynas@atomgraph.com>}
  */
-public interface Application extends Resource, com.atomgraph.processor.model.Application
+public interface Application extends Resource, com.atomgraph.core.model.Application
 {
     
     /**
      * The relative path of the content-addressed file container.
      */
     public static final String UPLOADS_PATH = "uploads";
 
+    /**
+     * Returns the application's namespace ontology.
+     * 
+     * @return ontology resource
+     */
+    Resource getOntology();
+
     /**
      * Returns the agent who created this application.
      * 
diff --git a/src/main/java/com/atomgraph/linkeddatahub/apps/model/impl/ApplicationImpl.java b/src/main/java/com/atomgraph/linkeddatahub/apps/model/impl/ApplicationImpl.java
@@ -21,7 +21,7 @@
 import com.atomgraph.linkeddatahub.model.Service;
 import com.atomgraph.linkeddatahub.vocabulary.FOAF;
 import com.atomgraph.linkeddatahub.vocabulary.LAPP;
-import com.atomgraph.processor.vocabulary.LDT;
+import com.atomgraph.server.vocabulary.LDT;
 import org.apache.jena.enhanced.EnhGraph;
 import org.apache.jena.graph.Node;
 import org.apache.jena.rdf.model.Resource;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/apps/model/impl/DatasetImpl.java b/src/main/java/com/atomgraph/linkeddatahub/apps/model/impl/DatasetImpl.java
@@ -19,7 +19,7 @@
 import com.atomgraph.linkeddatahub.apps.model.Dataset;
 import com.atomgraph.linkeddatahub.model.Service;
 import com.atomgraph.linkeddatahub.vocabulary.LAPP;
-import com.atomgraph.processor.vocabulary.LDT;
+import com.atomgraph.server.vocabulary.LDT;
 import java.net.URI;
 import jakarta.ws.rs.core.UriBuilder;
 import org.apache.jena.enhanced.EnhGraph;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/model/impl/UserAccountImpl.java b/src/main/java/com/atomgraph/linkeddatahub/model/impl/UserAccountImpl.java
@@ -18,7 +18,7 @@
 
 import org.apache.jena.graph.Node;
 import com.atomgraph.linkeddatahub.model.UserAccount;
-import com.atomgraph.processor.vocabulary.SIOC;
+import com.atomgraph.linkeddatahub.vocabulary.SIOC;
 import org.apache.jena.enhanced.EnhGraph;
 import org.apache.jena.enhanced.EnhNode;
 import org.apache.jena.enhanced.Implementation;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/resource/Generate.java b/src/main/java/com/atomgraph/linkeddatahub/resource/Generate.java
@@ -27,8 +27,8 @@
 import com.atomgraph.linkeddatahub.server.util.Skolemizer;
 import com.atomgraph.linkeddatahub.vocabulary.LDH;
 import com.atomgraph.linkeddatahub.vocabulary.VoID;
-import com.atomgraph.processor.vocabulary.DH;
-import com.atomgraph.processor.vocabulary.SIOC;
+import com.atomgraph.linkeddatahub.vocabulary.DH;
+import com.atomgraph.linkeddatahub.vocabulary.SIOC;
 import com.atomgraph.spinrdf.vocabulary.SP;
 import com.atomgraph.spinrdf.vocabulary.SPIN;
 import java.net.URI;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/resource/admin/SignUp.java b/src/main/java/com/atomgraph/linkeddatahub/resource/admin/SignUp.java
@@ -35,8 +35,8 @@
 import com.atomgraph.linkeddatahub.vocabulary.Cert;
 import com.atomgraph.linkeddatahub.vocabulary.FOAF;
 import com.atomgraph.linkeddatahub.vocabulary.LACL;
-import com.atomgraph.processor.vocabulary.DH;
-import com.atomgraph.processor.vocabulary.SIOC;
+import com.atomgraph.linkeddatahub.vocabulary.DH;
+import com.atomgraph.linkeddatahub.vocabulary.SIOC;
 import com.atomgraph.server.exception.SPINConstraintViolationException;
 import com.atomgraph.server.exception.SkolemizationException;
 import com.atomgraph.spinrdf.constraints.ConstraintViolation;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/resource/admin/oauth2/Login.java b/src/main/java/com/atomgraph/linkeddatahub/resource/admin/oauth2/Login.java
@@ -36,8 +36,8 @@
 import com.atomgraph.linkeddatahub.vocabulary.FOAF;
 import com.atomgraph.linkeddatahub.vocabulary.Google;
 import com.atomgraph.linkeddatahub.vocabulary.LACL;
-import com.atomgraph.processor.vocabulary.DH;
-import com.atomgraph.processor.vocabulary.SIOC;
+import com.atomgraph.linkeddatahub.vocabulary.DH;
+import com.atomgraph.linkeddatahub.vocabulary.SIOC;
 import com.auth0.jwt.JWT;
 import com.auth0.jwt.interfaces.DecodedJWT;
 import java.io.IOException;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/AuthorizationFilter.java b/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/AuthorizationFilter.java
@@ -26,7 +26,7 @@
 import com.atomgraph.linkeddatahub.server.security.AuthorizationContext;
 import com.atomgraph.linkeddatahub.vocabulary.ACL;
 import com.atomgraph.linkeddatahub.vocabulary.LACL;
-import com.atomgraph.processor.vocabulary.LDT;
+import com.atomgraph.server.vocabulary.LDT;
 import com.atomgraph.spinrdf.vocabulary.SPIN;
 import java.io.IOException;
 import java.util.Collections;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/OntologyFilter.java b/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/OntologyFilter.java
@@ -19,7 +19,7 @@
 import com.atomgraph.linkeddatahub.apps.model.Application;
 import com.atomgraph.linkeddatahub.apps.model.EndUserApplication;
 import com.atomgraph.linkeddatahub.vocabulary.LAPP;
-import com.atomgraph.processor.exception.OntologyException;
+import com.atomgraph.server.exception.OntologyException;
 import com.atomgraph.linkeddatahub.server.util.OntologyModelGetter;
 import java.io.IOException;
 import java.net.URI;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/auth/IDTokenFilter.java b/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/auth/IDTokenFilter.java
@@ -26,7 +26,7 @@
 import com.atomgraph.linkeddatahub.vocabulary.FOAF;
 import com.atomgraph.linkeddatahub.vocabulary.Google;
 import com.atomgraph.linkeddatahub.vocabulary.LACL;
-import com.atomgraph.processor.vocabulary.SIOC;
+import com.atomgraph.linkeddatahub.vocabulary.SIOC;
 import com.auth0.jwt.JWT;
 import com.auth0.jwt.exceptions.TokenExpiredException;
 import com.auth0.jwt.interfaces.DecodedJWT;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/io/ValidatingModelProvider.java b/src/main/java/com/atomgraph/linkeddatahub/server/io/ValidatingModelProvider.java
@@ -36,7 +36,7 @@
 import jakarta.ws.rs.core.Context;
 import jakarta.ws.rs.core.UriInfo;
 import org.apache.jena.riot.Lang;
-import com.atomgraph.processor.vocabulary.SIOC;
+import com.atomgraph.linkeddatahub.vocabulary.SIOC;
 import com.atomgraph.server.exception.SPINConstraintViolationException;
 import com.atomgraph.spinrdf.constraints.ConstraintViolation;
 import com.atomgraph.spinrdf.constraints.ObjectPropertyPath;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/mapper/ModelExceptionMapper.java b/src/main/java/com/atomgraph/linkeddatahub/server/mapper/ModelExceptionMapper.java
@@ -17,10 +17,6 @@
 package com.atomgraph.linkeddatahub.server.mapper;
 
 import com.atomgraph.core.MediaTypes;
-import jakarta.ws.rs.core.Context;
-import jakarta.ws.rs.core.Response;
-import com.atomgraph.server.exception.ModelException;
-import com.atomgraph.server.model.QueriedResource;
 import jakarta.inject.Inject;
 import jakarta.ws.rs.container.ResourceContext;
 
@@ -32,7 +28,7 @@
 public class ModelExceptionMapper extends com.atomgraph.server.mapper.ModelExceptionMapper
 {
 
-    @Context ResourceContext resourceContext;
+//    @Context ResourceContext resourceContext;
     
     /**
      * Constructs mapper from media types.
@@ -45,32 +41,32 @@ public ModelExceptionMapper(MediaTypes mediaTypes)
         super(mediaTypes);
     }
 
-    @Override
-    public Response toResponse(ModelException ex)
-    {
-        if (getQueriedResource() != null) ex.getModel().add(getQueriedResource().describe());
-        
-        return super.toResponse(ex);
-    }
+//    @Override
+//    public Response toResponse(ModelException ex)
+//    {
+//        if (getQueriedResource() != null) ex.getModel().add(getQueriedResource().describe());
+//        
+//        return super.toResponse(ex);
+//    }
     
     /**
      * Returns the current RDF resource.
      * 
      * @return RDF resource
      */
-    public QueriedResource getQueriedResource()
-    {
-        return getResourceContext().getResource(QueriedResource.class);
-    }
+//    public QueriedResource getQueriedResource()
+//    {
+//        return getResourceContext().getResource(QueriedResource.class);
+//    }
     
     /**
      * Returns JAX-RS resource context.
      * 
      * @return resource context
      */
-    public ResourceContext getResourceContext()
-    {
-        return resourceContext;
-    }
+//    public ResourceContext getResourceContext()
+//    {
+//        return resourceContext;
+//    }
     
 }
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/mapper/jena/QueryExecExceptionMapper.java b/src/main/java/com/atomgraph/linkeddatahub/server/mapper/jena/QueryExecExceptionMapper.java
@@ -48,10 +48,10 @@ public QueryExecExceptionMapper(MediaTypes mediaTypes)
     @Override
     public Response toResponse(QueryExecException ex)
     {
-        return getResponseBuilder(toResource(ex, Response.Status.INTERNAL_SERVER_ERROR,
-                    ResourceFactory.createResource("http://www.w3.org/2011/http-statusCodes#InternalServerError")).
+        return getResponseBuilder(toResource(ex, Response.Status.BAD_REQUEST,
+                    ResourceFactory.createResource("http://www.w3.org/2011/http-statusCodes#BadRequest")).
                 getModel()).
-            status(Response.Status.INTERNAL_SERVER_ERROR).
+            status(Response.Status.BAD_REQUEST).
             build();
     }
 
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/model/impl/GraphStoreImpl.java b/src/main/java/com/atomgraph/linkeddatahub/server/model/impl/GraphStoreImpl.java
@@ -27,8 +27,8 @@
 import com.atomgraph.linkeddatahub.server.util.Skolemizer;
 import com.atomgraph.linkeddatahub.vocabulary.Default;
 import com.atomgraph.linkeddatahub.vocabulary.NFO;
-import com.atomgraph.processor.vocabulary.DH;
-import com.atomgraph.processor.vocabulary.SIOC;
+import com.atomgraph.linkeddatahub.vocabulary.DH;
+import com.atomgraph.linkeddatahub.vocabulary.SIOC;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/util/OntologyModelGetter.java b/src/main/java/com/atomgraph/linkeddatahub/server/util/OntologyModelGetter.java
@@ -19,7 +19,7 @@
 import com.atomgraph.client.vocabulary.LDT;
 import com.atomgraph.core.MediaTypes;
 import com.atomgraph.linkeddatahub.apps.model.EndUserApplication;
-import com.atomgraph.processor.exception.OntologyException;
+import com.atomgraph.server.exception.OntologyException;
 import jakarta.ws.rs.client.Client;
 import org.apache.jena.ontology.OntModelSpec;
 import org.apache.jena.query.ParameterizedSparqlString;
diff --git a/src/main/java/com/atomgraph/linkeddatahub/vocabulary/DH.java b/src/main/java/com/atomgraph/linkeddatahub/vocabulary/DH.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright 2016 Martynas Jusevičius <martynas@atomgraph.com>.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package com.atomgraph.linkeddatahub.vocabulary;
+
+import org.apache.jena.ontology.DatatypeProperty;
+import org.apache.jena.ontology.ObjectProperty;
+import org.apache.jena.ontology.OntClass;
+import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntModelSpec;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Resource;
+
+/**
+ *
+ * @author Martynas Jusevičius {@literal <martynas@atomgraph.com>}
+ */
+public class DH
+{
+
+    /** <p>The RDF model that holds the vocabulary terms</p> */
+    private static OntModel m_model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, null);
+    
+    /** <p>The namespace of the vocabulary as a string</p> */
+    public static final String NS = "https://www.w3.org/ns/ldt/document-hierarchy#";
+    
+    /** <p>The namespace of the vocabulary as a string</p>
+     *  @see #NS */
+    public static String getURI()
+    {
+        return NS;
+    }
+    
+    /** <p>The namespace of the vocabulary as a resource</p> */
+    public static final Resource NAMESPACE = m_model.createResource( NS );
+
+    public static final OntClass Document = m_model.createClass( NS + "Document" );
+    
+    public static final OntClass Container = m_model.createClass( NS + "Container" );
+    
+    public static final OntClass Item = m_model.createClass( NS + "Item" );
+    
+    public static final DatatypeProperty slug = m_model.createDatatypeProperty( NS + "slug" );
+
+    public static final ObjectProperty select = m_model.createObjectProperty( NS + "select");
+    
+}
diff --git a/src/main/java/com/atomgraph/linkeddatahub/vocabulary/SIOC.java b/src/main/java/com/atomgraph/linkeddatahub/vocabulary/SIOC.java
diff --git a/src/main/resources/com/atomgraph/linkeddatahub/c.ttl b/src/main/resources/com/atomgraph/linkeddatahub/c.ttl
diff --git a/src/main/resources/com/atomgraph/linkeddatahub/dh.ttl b/src/main/resources/com/atomgraph/linkeddatahub/dh.ttl
diff --git a/src/main/resources/com/atomgraph/linkeddatahub/http-statusCodes.rdf b/src/main/resources/com/atomgraph/linkeddatahub/http-statusCodes.rdf
diff --git a/src/main/resources/com/atomgraph/linkeddatahub/http.owl b/src/main/resources/com/atomgraph/linkeddatahub/http.owl
diff --git a/src/main/resources/com/atomgraph/linkeddatahub/ldt.ttl b/src/main/resources/com/atomgraph/linkeddatahub/ldt.ttl
diff --git a/src/main/resources/com/atomgraph/linkeddatahub/sparql-service.owl b/src/main/resources/com/atomgraph/linkeddatahub/sparql-service.owl
diff --git a/src/main/resources/location-mapping.ttl b/src/main/resources/location-mapping.ttl
diff --git a/src/main/resources/prefix-mapping.ttl b/src/main/resources/prefix-mapping.ttl
