Merge pull request #273 from kbss-cvut/258-refactor-parameter-annotat…

…ion-to-use-iri

[#258] Refactor @parameter to include iri instead of (urlPrefix, name)

s-pipes-cli/src/main/java/cz/cvut/spipes/cli/ExecuteModuleCLI.java

@@ -133,7 +133,7 @@ public static void main(String[] args) throws IOException {
         // ----- execute pipeline
         ExecutionEngine engine = ExecutionEngineFactory.createEngine();
         Module module = scriptManager.loadFunction(asArgs.executionTarget);
-//          module =  PipelineFactory.loadModulePipeline(inputDataModel.listObjectsOfProperty(SM.returnModule).next().asResource());
+//          module =  PipelineFactory.loadModulePipeline(inputDataModel.listObjectsOfProperty(SM.JENA.returnModule).next().asResource());
 
         if ( module == null ) {
             throw new RuntimeException("Cannot load module/function with id=" + asArgs.executionTarget);

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

@@ -1,7 +1,8 @@
 package cz.cvut.spipes.constants;
 
 import org.apache.jena.rdf.model.Property;
-import org.apache.jena.rdf.model.ResourceFactory;
+
+import static org.apache.jena.rdf.model.ResourceFactory.createProperty;
 
 public class KBSS_MODULE {
 
@@ -10,17 +11,25 @@ public class KBSS_MODULE {
      */
     public static final String uri = "http://onto.fel.cvut.cz/ontologies/lib/module/";
 
-    protected static final Property property(String local )
-    { return ResourceFactory.createProperty( uri, local ); }
-
-    public static final Property has_input_graph_constraint = property("has-input-graph-constraint");
-    public static final Property has_output_graph_constraint = property("has-output-graph-constraint");
-    public static final Property has_target_module_flag = property("has-target-module-flag");
-    public static final Property has_debug_mode_flag = property("has-debug-mode-flag");
-    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 String has_input_graph_constraint = uri + "has-input-graph-constraint";
+    public static final String has_output_graph_constraint = uri + "has-output-graph-constraint";
+    public static final String has_target_module_flag = uri + "has-target-module-flag";
+    public static final String has_debug_mode_flag = uri + "has-debug-mode-flag";
+    public static final String is_parse_text = uri + "is-parse-text";
+    public static final String has_max_iteration_count = uri + "has-max-iteration-count";
+    public static final String has_resource_uri = uri + "has-resource-uri";
 
     // states that reified statement belongs to specific named graph identified by uri
-    public static final Property is_part_of_graph = property("is-part-of-graph");
+    public static final String is_part_of_graph = uri + "is-part-of-graph";
+
+    public static class JENA {
+        public static final Property has_input_graph_constraint = createProperty(KBSS_MODULE.has_input_graph_constraint);
+        public static final Property has_output_graph_constraint = createProperty(KBSS_MODULE.has_output_graph_constraint);
+        public static final Property has_target_module_flag = createProperty(KBSS_MODULE.has_target_module_flag);
+        public static final Property has_debug_mode_flag = createProperty(KBSS_MODULE.has_debug_mode_flag);
+        public static final Property is_parse_text = createProperty(KBSS_MODULE.is_parse_text);
+        public static final Property has_max_iteration_count = createProperty(KBSS_MODULE.has_max_iteration_count);
+        public static final Property has_resource_uri = createProperty(KBSS_MODULE.has_resource_uri);
+        public static final Property is_part_of_graph = createProperty(KBSS_MODULE.is_part_of_graph);
+    }
 }

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

@@ -1,8 +1,9 @@
 package cz.cvut.spipes.constants;
 
 import org.apache.jena.rdf.model.Property;
-import org.apache.jena.rdf.model.Resource;
-import org.apache.jena.rdf.model.ResourceFactory;
+
+import static org.apache.jena.rdf.model.ResourceFactory.createProperty;
+import static org.apache.jena.rdf.model.ResourceFactory.createResource;
 
 public class SM {
 
@@ -11,18 +12,22 @@ public class SM {
      */
     public static final String uri = "http://topbraid.org/sparqlmotion#";
 
-    protected static final Resource resource(String local )
-    { return ResourceFactory.createResource( uri + local ); }
+    public static final String next = uri + "next";
+    public static final String outputVariable = uri + "outputVariable";
+    public static final String returnModule = uri + "returnModule";
 
-    protected static final Property property(String local )
-    { return ResourceFactory.createProperty( uri, local ); }
+    public static final String Function = uri + "Function";
+    public static final String Module = uri + "Module";
+    public static final String Modules = uri + "Modules";
 
 
-    public static final Property next = property("next");
-    public static final Property outputVariable = property("outputVariable");
-    public static final Property returnModule = property("returnModule");
+    public static class JENA {
+        public static final Property next = createProperty(SM.next);
+        public static final Property outputVariable = createProperty(SM.outputVariable);
+        public static final Property returnModule = createProperty(SM.returnModule);
 
-    public static final Resource Function = resource("Function");
-    public static final Resource Module = resource("Module");
-    public static final Resource Modules = resource("Modules");
+        public static final org.apache.jena.rdf.model.Resource Function = createResource(SM.Function);
+        public static final org.apache.jena.rdf.model.Resource Module = createResource(SM.Module);
+        public static final org.apache.jena.rdf.model.Resource Modules = createResource(SM.Modules);
+    }
 }

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

@@ -2,7 +2,9 @@
 
 import org.apache.jena.rdf.model.Property;
 import org.apache.jena.rdf.model.Resource;
-import org.apache.jena.rdf.model.ResourceFactory;
+
+import static org.apache.jena.rdf.model.ResourceFactory.createProperty;
+import static org.apache.jena.rdf.model.ResourceFactory.createResource;
 
 public class SML {
 
@@ -11,32 +13,49 @@ public class SML {
      */
     public static final String uri = "http://topbraid.org/sparqlmotionlib#";
 
-    protected static final org.apache.jena.rdf.model.Resource resource(String local )
-    { return ResourceFactory.createResource( uri + local ); }
-
-    protected static final Property property(String local )
-    { return ResourceFactory.createProperty( uri, local ); }
-
-    public static final Property replace = property( "replace");
-    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");
-    public static final Property baseURI = property("baseURI");
-    public static final Property serialization = property("serialization");
-    public static final Property ignoreImports = property("ignoreImports");
-
-    public static final Resource ApplyConstruct = resource("ApplyConstruct");
-    public static final Resource ExportToRDFFile = resource("ExportToRDFFile");
-    public static final Resource ImportRDFFromWorkspace = resource("ImportRDFFromWorkspace");
-    public static final Resource ImportFileFromURL = resource("ImportFileFromURL");
-    public static final Resource BindWithConstant = resource("BindWithConstant");
-    public static final Resource BindBySelect = resource("BindBySelect");
-    public static final Resource Merge = resource("Merge");
-    public static final Resource ReturnRDF = resource("ReturnRDF");
-
-    public static final Resource JSONLD = resource("JSONLD");
+    public static final String replace = uri + "replace";
+    public static final String constructQuery = uri + "constructQuery";
+    public static final String value = uri + "value";
+    public static final String selectQuery = uri + "selectQuery";
+    public static final String updateQuery = uri + "updateQuery";
+    public static final String sourceFilePath = uri + "sourceFilePath";
+    public static final String url = uri + "url";
+    public static final String targetFilePath = uri + "targetFilePath";
+    public static final String baseURI = uri + "baseURI";
+    public static final String serialization = uri + "serialization";
+    public static final String ignoreImports = uri + "ignoreImports";
+
+    public static final String ApplyConstruct = uri + "ApplyConstruct";
+    public static final String ExportToRDFFile = uri + "ExportToRDFFile";
+    public static final String ImportRDFFromWorkspace = uri + "ImportRDFFromWorkspace";
+    public static final String ImportFileFromURL = uri + "ImportFileFromURL";
+    public static final String BindWithConstant = uri + "BindWithConstant";
+    public static final String BindBySelect = uri + "BindBySelect";
+    public static final String Merge = uri + "Merge";
+    public static final String ReturnRDF = uri + "ReturnRDF";
+    public static final String JSONLD = uri + "JSONLD";
+
+    public static class JENA {
+        public static final Property replace = createProperty(SML.replace);
+        public static final Property constructQuery = createProperty(SML.constructQuery);
+        public static final Property value = createProperty(SML.value);
+        public static final Property selectQuery = createProperty(SML.selectQuery);
+        public static final Property updateQuery = createProperty(SML.updateQuery);
+        public static final Property sourceFilePath = createProperty(SML.sourceFilePath);
+        public static final Property url = createProperty(SML.url);
+        public static final Property targetFilePath = createProperty(SML.targetFilePath);
+        public static final Property baseURI = createProperty(SML.baseURI);
+        public static final Property serialization = createProperty(SML.serialization);
+        public static final Property ignoreImports = createProperty(SML.ignoreImports);
+
+        public static final Resource ApplyConstruct = createResource(SML.ApplyConstruct);
+        public static final Resource ExportToRDFFile = createResource(SML.ExportToRDFFile);
+        public static final Resource ImportRDFFromWorkspace = createResource(SML.ImportRDFFromWorkspace);
+        public static final Resource ImportFileFromURL = createResource(SML.ImportFileFromURL);
+        public static final Resource BindWithConstant = createResource(SML.BindWithConstant);
+        public static final Resource BindBySelect = createResource(SML.BindBySelect);
+        public static final Resource Merge = createResource(SML.Merge);
+        public static final Resource ReturnRDF = createResource(SML.ReturnRDF);
+        public static final Resource JSONLD = createResource(SML.JSONLD);
+    }
 }

s-pipes-core/src/main/java/cz/cvut/spipes/engine/PipelineFactory.java

@@ -4,15 +4,6 @@
 import cz.cvut.spipes.function.ARQFunction;
 import cz.cvut.spipes.modules.Module;
 import cz.cvut.spipes.util.JenaPipelineUtils;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.lang.reflect.Modifier;
-import java.nio.file.Path;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.stream.Collectors;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
@@ -28,6 +19,16 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.lang.reflect.Modifier;
+import java.nio.file.Path;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
 public class PipelineFactory {
 
     private static final Logger log = LoggerFactory.getLogger(PipelineFactory.class);
@@ -166,7 +167,7 @@ private static Map<Resource, Module> loadAllModules(@NotNull Model configModel)
                     Resource res = e.getKey();
 
                     // set up input modules
-                    res.listProperties(SM.next).toList().stream()
+                    res.listProperties(SM.JENA.next).toList().stream()
                             .map(st -> {
                                 Module m = res2ModuleMap.get(st.getObject().asResource());
                                 if (m == null) {

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

@@ -213,13 +213,13 @@ protected String saveFullModelToTemporaryFile(OntModel model) {
     }
 
     private void loadModuleConstraints() {
-        inputConstraintQueries = getResourcesByProperty(KBSS_MODULE.has_input_graph_constraint);
-        outputConstraintQueries = getResourcesByProperty(KBSS_MODULE.has_output_graph_constraint);
+        inputConstraintQueries = getResourcesByProperty(KBSS_MODULE.JENA.has_input_graph_constraint);
+        outputConstraintQueries = getResourcesByProperty(KBSS_MODULE.JENA.has_output_graph_constraint);
     }
 
     private void loadModuleFlags() {
-        isTargetModule = getPropertyValue(KBSS_MODULE.has_debug_mode_flag, false);
-        isInDebugMode = getPropertyValue(KBSS_MODULE.has_debug_mode_flag, false);
+        isTargetModule = getPropertyValue(KBSS_MODULE.JENA.has_debug_mode_flag, false);
+        isInDebugMode = getPropertyValue(KBSS_MODULE.JENA.has_debug_mode_flag, false);
     }
 
 

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

@@ -1,15 +1,15 @@
 package cz.cvut.spipes.modules;
 
-import java.lang.reflect.Field;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
 import cz.cvut.spipes.modules.handlers.*;
 import org.apache.jena.rdf.model.ResourceFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.lang.reflect.Field;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 /**
  * The `AnnotatedAbstractModule` class extends the `AbstractModule` class and provides
  * an implementation for loading the module's configuration using {@link Parameter} annotation.
@@ -35,10 +35,10 @@ public void loadConfiguration() {
             final Parameter p = f.getAnnotation(Parameter.class);
             if ( p == null ) {
                 continue;
-            } else if (vars.containsKey(p.name())) {
-                throw new RuntimeException(String.format("Two parameters are named the same %s, except prefix", p.name()));
+            } else if (vars.containsKey(p.iri())) {
+                throw new RuntimeException(String.format("Two parameters have same iri %s", p.iri()));
             } else {
-                vars.put(p.name(), f);
+                vars.put(p.iri(), f);
             }
 
             log.trace("Processing parameter {} ", f.getName());
@@ -51,7 +51,7 @@ public void loadConfiguration() {
             }
             HandlerRegistry handlerRegistry = HandlerRegistry.getInstance();
             Handler<?> handler = handlerRegistry.getHandler(f.getType(), resource, executionContext, setter);
-            handler.setValueByProperty(ResourceFactory.createProperty(p.urlPrefix()+p.name()));
+            handler.setValueByProperty(ResourceFactory.createProperty(p.iri()));
         }
     }
 }

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

@@ -31,22 +31,18 @@ public class ApplyConstructModule extends AnnotatedAbstractModule {
 
     private static final Logger log = LoggerFactory.getLogger(ApplyConstructModule.class);
 
-    //sml:constructQuery
-    @Parameter(urlPrefix = SML.uri, name = "constructQuery")
+    @Parameter(iri = SML.constructQuery)
     private List<Resource> constructQueries;
 
-    //sml:replace
-    @Parameter(urlPrefix = SML.uri, name = "replace")
+    @Parameter(iri = SML.replace)
     private boolean isReplace = false;
 
-    //kbss:parseText
     /**
      * Whether the query should be taken from sp:text property instead of from SPIN serialization
      */
-    @Parameter(urlPrefix = KBSS_MODULE.uri, name = "is-parse-text")
+    @Parameter(iri = KBSS_MODULE.is_parse_text)
     private boolean parseText = false;
 
-    //kbss:iterationCount
     /**
      * Maximal number of iterations of the whole rule set. 0 means 0 iterations. The actual number of iterations can be smaller,
      * if no new inferences are generated any more.
@@ -59,7 +55,7 @@ public class ApplyConstructModule extends AnnotatedAbstractModule {
      * <p>
      * Within each iteration, all queries are evaluated on the same model.
      */
-    @Parameter(urlPrefix = KBSS_MODULE.uri, name = "has-max-iteration-count")
+    @Parameter(iri = KBSS_MODULE.has_max_iteration_count)
     private int iterationCount = 1;
 
     public ApplyConstructModule() {
@@ -166,7 +162,7 @@ public ExecutionContext executeSelf() {
 
     @Override
     public String getTypeURI() {
-        return SML.ApplyConstruct.getURI();
+        return SML.ApplyConstruct;
     }
 
 }

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

@@ -5,26 +5,20 @@
 import cz.cvut.spipes.engine.ExecutionContextFactory;
 import cz.cvut.spipes.engine.VariablesBinding;
 import cz.cvut.spipes.util.QueryUtils;
-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.ModelFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.topbraid.spin.arq.ARQFactory;
 import org.topbraid.spin.model.Select;
 
 public class BindBySelectModule extends AnnotatedAbstractModule {
 
     private static final Logger log = LoggerFactory.getLogger(BindBySelectModule.class);
 
-    @Parameter(urlPrefix = SML.uri, name = "selectQuery")
+    @Parameter(iri = SML.selectQuery)
     private Select selectQuery;
 
-    //sml:replace
-    @Parameter(urlPrefix = SML.uri, name = "replace")
+    @Parameter(iri = SML.replace)
     private boolean isReplace = false;
 
     @Override
@@ -60,7 +54,7 @@ public ExecutionContext executeSelf() {
 
     @Override
     public String getTypeURI() {
-        return SML.BindBySelect.getURI();
+        return SML.BindBySelect;
     }
 
     public Select getSelectQuery() {

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

@@ -14,7 +14,7 @@
 public class BindRDFContentHashModule extends AnnotatedAbstractModule {
 
     private static final Logger log = LoggerFactory.getLogger(BindRDFContentHashModule.class);
-    @Parameter(urlPrefix =  SM.uri, name="outputVariable")
+    @Parameter(iri =  SM.outputVariable)
     String outputVariable;
 
     @Override