Partial refactoring of the s-pipes-core

s-pipes-core/src/main/java/cz/cvut/spipes/config/AuditConfig.java

@@ -1,16 +1,16 @@
 package cz.cvut.spipes.config;
 
-import cz.cvut.spipes.util.CoreConfigProperies;
+import cz.cvut.spipes.util.CoreConfigProperties;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
 public class AuditConfig {
 
     public static Path getResourcesPath() {
-        return Paths.get(CoreConfigProperies.get("audit.resourcesPath"));
+        return Paths.get(CoreConfigProperties.get("audit.resourcesPath"));
     }
 
     public static boolean isEnabled() {
-        return Boolean.parseBoolean(CoreConfigProperies.get("audit.enable"));
+        return Boolean.parseBoolean(CoreConfigProperties.get("audit.enable"));
     }
 }

s-pipes-core/src/main/java/cz/cvut/spipes/config/CompatibilityConfig.java

@@ -1,10 +1,10 @@
 package cz.cvut.spipes.config;
 
-import cz.cvut.spipes.util.CoreConfigProperies;
+import cz.cvut.spipes.util.CoreConfigProperties;
 
 public class CompatibilityConfig {
 
     public static boolean isLoadSparqlMotionFiles() {
-        return Boolean.parseBoolean(CoreConfigProperies.get("compatibility.loadSparqlMotionFiles", "false"));
+        return Boolean.parseBoolean(CoreConfigProperties.get("compatibility.loadSparqlMotionFiles", "false"));
     }
 }

s-pipes-core/src/main/java/cz/cvut/spipes/config/ContextsConfig.java

@@ -1,6 +1,6 @@
 package cz.cvut.spipes.config;
 
-import cz.cvut.spipes.util.CoreConfigProperies;
+import cz.cvut.spipes.util.CoreConfigProperties;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Arrays;
@@ -12,8 +12,8 @@ public class ContextsConfig {
 
     public static List<Path> getScriptPaths() {
         return Arrays
-                .stream(CoreConfigProperies.get("contexts.scriptPaths").split(";"))
-                .map(path -> Paths.get(path))
+                .stream(CoreConfigProperties.get("contexts.scriptPaths").split(";"))
+                .map(Paths::get)
                 .collect(Collectors.toList());
     }
 }

s-pipes-core/src/main/java/cz/cvut/spipes/config/ExecutionConfig.java

@@ -1,43 +1,43 @@
 package cz.cvut.spipes.config;
 
-import cz.cvut.spipes.util.CoreConfigProperies;
+import cz.cvut.spipes.util.CoreConfigProperties;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
 public class ExecutionConfig {
 
     public static Path getTempDirectoryPath() {
-        return Paths.get(CoreConfigProperies.get("execution.tempDirectoryPath", System.getProperty("java.io.tmpdir")));
+        return Paths.get(CoreConfigProperties.get("execution.tempDirectoryPath", System.getProperty("java.io.tmpdir")));
     }
 
     public static boolean isExitOnError() {
-        return Boolean.parseBoolean(CoreConfigProperies.get(
+        return Boolean.parseBoolean(CoreConfigProperties.get(
                 "execution.exitOnError",
                 "false"));
     }
 
     public static boolean isCheckValidationConstrains() {
-        return Boolean.parseBoolean(CoreConfigProperies.get(
+        return Boolean.parseBoolean(CoreConfigProperties.get(
                 "execution.validation.checkConstraints",
                 "true"));
     }
 
     public static int getEvidenceNumber() {
-        return Integer.parseInt(CoreConfigProperies.get("execution.validation.maxNumberOfConstraintFailureEvidences", "3"));
+        return Integer.parseInt(CoreConfigProperties.get("execution.validation.maxNumberOfConstraintFailureEvidences", "3"));
     }
 
     public static String getConfigUrl() {
-        return CoreConfigProperies.get("execution.configUrl", "config.ttl");
+        return CoreConfigProperties.get("execution.configUrl", "config.ttl");
     }
 
     public static Environment getEnvironment() {
-        return  Environment.valueOf(CoreConfigProperies.get(
+        return  Environment.valueOf(CoreConfigProperties.get(
             "execution.environment",
             Environment.production.toString())
         );
     }
 
     public static String getDevelopmentServiceUrl() {
-        return CoreConfigProperies.get("execution.developmentServiceUrl", "http://localhost:8080/s-pipes/");
+        return CoreConfigProperties.get("execution.developmentServiceUrl", "http://localhost:8080/s-pipes/");
     }
 }

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

@@ -10,6 +10,6 @@ public class KBSS_TIMEF {
      */
     public static final String uri = "http://onto.fel.cvut.cz/ontologies/lib/function/time/";
 
-    protected static final Property property(String local )
+    protected static Property property(String local)
     { return ResourceFactory.createProperty( uri, local ); }
 }

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

@@ -10,6 +10,6 @@ public class SPIF {
      */
     public static final String uri = "http://spinrdf.org/spif#";
 
-    protected static final Property property(String local )
+    protected static Property property(String local)
     { return ResourceFactory.createProperty( uri, local ); }
 }

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

@@ -11,10 +11,10 @@ public class SPIPES {
      */
     public static final String uri = "http://onto.fel.cvut.cz/ontologies/s-pipes/";
 
-    protected static final org.apache.jena.rdf.model.Resource resource(String local )
+    protected static org.apache.jena.rdf.model.Resource resource(String local)
     { return ResourceFactory.createResource( uri + local ); }
 
-    protected static final Property property(String local )
+    protected static Property property(String local)
     { return ResourceFactory.createProperty( uri, local ); }
 
     public static final Resource ProgressListener = resource("progress-listener");

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

@@ -12,10 +12,10 @@ public class SPL {
      */
     private static final String uri = "http://spinrdf.org/spl#";
 
-    protected static final Resource resource(String local )
+    protected static Resource resource(String local)
     { return ResourceFactory.createResource( uri + local ); }
 
-    protected static final Property property(String local )
+    protected static Property property(String local)
     { return ResourceFactory.createProperty( uri, local ); }
 
     public static final Resource tarql = resource("Argument");

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

@@ -74,5 +74,5 @@ public interface ExecutionContext {
 
     // TODO named graphs ? -- in merge rather having multiple graphs (for debugging)
     // TODO variable binding supporting stream etc .. ?
-    // TODO prefixe map ??
+    // TODO prefix map ??
 }

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

@@ -8,9 +8,7 @@
 
 public class ExecutionContextFactory {
 
-    /**
-     * @return
-     */
+
     public static ExecutionContext createEmptyContext() {
         ExecutionContextImpl context = new ExecutionContextImpl();
         context.setDefaultModel(ModelFactory.createDefaultModel());

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

@@ -53,7 +53,7 @@ private ExecutionContext _executePipeline(long pipelineExecutionId, Module modul
             return module.getOutputContext();
         }
 
-        // module has no predeccesor
+        // module has no predecessor
         if (module.getInputModules().isEmpty()) {
             fire((l) -> {l.moduleExecutionStarted(pipelineExecutionId, moduleExecutionId, module, context, predecessorId); return null;});
 
@@ -62,7 +62,7 @@ private ExecutionContext _executePipeline(long pipelineExecutionId, Module modul
             } else {
                 module.setInputContext(context);
 
-                log.info(" ##### " + module.getLabel());
+                log.info(" ##### {}", module.getLabel());
                 if (log.isTraceEnabled()) {
                     log.trace("Using input context {}", context.toTruncatedSimpleString()); //TODO redundant code -> merge
                 }
@@ -80,7 +80,7 @@ private ExecutionContext _executePipeline(long pipelineExecutionId, Module modul
                 .collect(Collectors.toMap(Module::getResource, mod -> this._executePipeline(pipelineExecutionId, mod, context, moduleExecutionId)));
 
 
-        log.info(" ##### " + module.getLabel());
+        log.info(" ##### {}", module.getLabel());
         ExecutionContext mergedContext = mergeContexts(resource2ContextMap);
         if (log.isTraceEnabled()) {
             log.trace("Using input merged context {}", mergedContext.toTruncatedSimpleString());
@@ -114,21 +114,18 @@ private ExecutionContext mergeContexts(Map<Resource, ExecutionContext> resource2
         VariablesBinding variablesBinding = new VariablesBinding();
 
 
-        resource2ContextMap.entrySet().stream().forEach(e -> {
-
-            Resource modRes = e.getKey();
-            ExecutionContext context = e.getValue();
+        resource2ContextMap.forEach((modRes, context) -> {
 
             // merge models
             newModel.add(context.getDefaultModel());
 
             // merge variable bindings
-            VariablesBinding b = e.getValue().getVariablesBinding();
+            VariablesBinding b = context.getVariablesBinding();
 
             VariablesBinding conflictingBinding = variablesBinding.extendConsistently(b);
 
-            if (! conflictingBinding.isEmpty()) {
-                log.warn("Module {} has conflicting variables binding {} with sibling modules ocurring in pipeline. ", modRes, context);
+            if (!conflictingBinding.isEmpty()) {
+                log.warn("Module {} has conflicting variables binding {} with sibling modules occurring in pipeline. ", modRes, context);
             }
         });
 

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

@@ -21,20 +21,18 @@
 
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
+import java.lang.reflect.InvocationTargetException;
 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.*;
 import java.util.stream.Collectors;
 
 public class PipelineFactory {
 
     private static final Logger log = LoggerFactory.getLogger(PipelineFactory.class);
 
-    // TODO inheritence not involved, not static context
-    static Map<Resource, Class<? extends Module>> moduleTypes = new HashMap<>();
+    // TODO inheritance not involved, not static context
+    static final Map<Resource, Class<? extends Module>> moduleTypes = new HashMap<>();
 
     //TODO move to ModuleRegistry
     static {
@@ -75,7 +73,7 @@ public static void registerModuleTypesOnClassPath() {
 
         List<Class<? extends Module>> moduleClasses = reflections.getSubTypesOf(Module.class).stream().filter(
                 c -> !Modifier.isAbstract(c.getModifiers())
-        ).collect(Collectors.toList());
+        ).toList();
 
         moduleClasses.forEach(
                 mClass -> {
@@ -96,7 +94,7 @@ public static void registerFunctionsOnClassPath() {
 
         List<Class<? extends ARQFunction>> functionClasses = reflections.getSubTypesOf(ARQFunction.class).stream().filter(
             c -> !Modifier.isAbstract(c.getModifiers())
-        ).collect(Collectors.toList());
+        ).toList();
 
         functionClasses.forEach(
             fClass -> {
@@ -124,13 +122,13 @@ public static Module loadModule(@NotNull Resource moduleRes) {
     // TODO not very effective
     public static Module loadPipeline(@NotNull Resource resource) {
         return loadPipelines(resource.getModel()).stream().filter(m -> {
-            //TODO does not work on annonymous node
+            //TODO does not work on anonymous node
             return resource.getURI().equals(m.getResource().getURI());
         }).findAny().orElse(null);
     }
 
     /**
-     * @param configModel
+     * @param configModel configuration model containing pipeline definition
      * @return List of output modules.
      */
     public static List<Module> loadPipelines(@NotNull Model configModel) {
@@ -139,7 +137,7 @@ public static List<Module> loadPipelines(@NotNull Model configModel) {
 
         Set<Module> inputModulesSet = res2ModuleMap.values().stream().flatMap(m -> m.getInputModules().stream()).collect(Collectors.toSet());
 
-        List<Module> outputModulesList = res2ModuleMap.values().stream().collect(Collectors.toList());
+        List<Module> outputModulesList = new ArrayList<>(res2ModuleMap.values());
         outputModulesList.removeAll(inputModulesSet);
 
         return outputModulesList;
@@ -151,37 +149,31 @@ private static Map<Resource, Module> loadAllModules(@NotNull Model configModel)
         Map<Resource, Module> res2ModuleMap = new HashMap<>();
 
         JenaPipelineUtils.getAllModulesWithTypes(configModel)
-                .entrySet()
-                .forEach(e -> {
-                    Module m = loadModule(e.getKey(), e.getValue());
+                .forEach((key, value) -> {
+                    Module m = loadModule(key, value);
                     if (m != null) {
-                        res2ModuleMap.put(e.getKey(), m);
+                        res2ModuleMap.put(key, m);
                     }
                 });
         //      .collect(Collectors.toMap(Map.Entry::getKey, e -> loadModule(e.getKey(), e.getValue())));
 
 
         // set appropriate links //TODO problem 2 files reusing module inconsistently ? do i need to solve it ?
-        res2ModuleMap.entrySet()
-                .forEach(e -> {
-                    Resource res = e.getKey();
-
-                    // set up input modules
-                    res.listProperties(SM.JENA.next).toList().stream()
-                            .map(st -> {
-                                Module m = res2ModuleMap.get(st.getObject().asResource());
-                                if (m == null) {
-                                    log.error("Ignoring statement {}. The object of the triple must have rdf:type {}.", st, SM.Module);
-                                }
-                                return m;
-                            }).filter(m -> (m != null)).forEach(
-                            m -> {
-
-                                m.getInputModules().add(e.getValue());
-                            }
+        res2ModuleMap.forEach((res, value) -> {
+
+            // set up input modules
+            res.listProperties(SM.JENA.next).toList().stream()
+                    .map(st -> {
+                        Module m = res2ModuleMap.get(st.getObject().asResource());
+                        if (m == null) {
+                            log.error("Ignoring statement {}. The object of the triple must have rdf:type {}.", st, SM.Module);
+                        }
+                        return m;
+                    }).filter(Objects::nonNull).forEach(
+                            m -> m.getInputModules().add(value)
                     );
 
-                });
+        });
 
         return res2ModuleMap;
     }
@@ -195,12 +187,12 @@ private static Module loadModule(@NotNull Resource moduleRes, @NotNull Resource
             return null;
         }
 
-        Module module = null;
+        Module module;
 
         try {
-            module = moduleClass.newInstance();
+            module = moduleClass.getDeclaredConstructor().newInstance();
             module.setConfigurationResource(moduleRes);
-        } catch (InstantiationException | IllegalAccessException e) {
+        } catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
             throw new IllegalArgumentException("Could not instantiate module of type " + moduleTypeRes, e);
         }
 
@@ -209,16 +201,16 @@ private static Module loadModule(@NotNull Resource moduleRes, @NotNull Resource
 
     public static Module instantiateModule(Class<? extends Module> moduleClass) {
         try {
-            return moduleClass.newInstance();
-        } catch (InstantiationException | IllegalAccessException e) {
+            return moduleClass.getDeclaredConstructor().newInstance();
+        } catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
             throw new IllegalArgumentException("Could not instantiate module of type " +  moduleClass);
         }
     }
 
     public static ARQFunction instantiateFunction(Class<? extends ARQFunction> functionClass) {
         try {
-            return functionClass.newInstance();
-        } catch (InstantiationException | IllegalAccessException e) {
+            return functionClass.getDeclaredConstructor().newInstance();
+        } catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
             throw new IllegalArgumentException("Could not instantiate function of type " +  functionClass);
         }
     }
@@ -232,7 +224,7 @@ public static Module loadModule(@NotNull Path configFilePath, @NotNull String mo
             configModel.read(new FileInputStream(configFilePath.toFile()), null, FileUtils.langTurtle);
             return PipelineFactory.loadModule(configModel.createResource(moduleResourceUri));
         } catch (FileNotFoundException e) {
-            e.printStackTrace();
+            log.error("Loading of module failed.", e);
             throw new RuntimeException("Loading of module failed.");
         }
     }