Fix issues #205, #206 and #216

s-pipes-modules-utils/s-pipes-module-creator-maven-plugin/src/main/java/RdfAnnotationProcessorMojo.java

@@ -139,8 +139,9 @@ private void generateRdfForAllModules() throws MalformedURLException, ClassNotFo
             for (Class<?> moduleClass : moduleClasses) {
                 getLog().info("Creating RDF for module '" + moduleClass.getCanonicalName() + "'");
                 var moduleAnnotation = readModuleAnnotationFromClass(moduleClass);
+                var extendedModuleAnnotation = readExtendedModuleAnnotationFromClass(moduleClass);
                 var constraints = readConstraintsFromClass(moduleClass);
-                writeConstraintsToModel(model, constraints, moduleAnnotation);
+                writeConstraintsToModel(model, constraints, moduleAnnotation, extendedModuleAnnotation);
             }
 
             getLog().info("--------------------------------------");
@@ -154,14 +155,27 @@ private void generateRdfForAllModules() throws MalformedURLException, ClassNotFo
         getLog().info("======================================");
     }
 
+    private SPipesModule readExtendedModuleAnnotationFromClass(Class<?> moduleClass) {
+
+        SPipesModule ret = null;
+        Class cls = moduleClass.getSuperclass();
+        while(ret == null && cls != null) {
+            ret = readModuleAnnotationFromClass(cls);
+            cls = cls.getSuperclass();
+        }
+
+        return ret;
+    }
+
     private void generateRdfForModule() throws MojoExecutionException {
         try {
             Set<Class<?>> moduleClasses = readAllModuleClasses(this.project);
             var model = readModelFromDefaultFile();
             for (Class<?> moduleClass : moduleClasses) {
                 var moduleAnnotation = readModuleAnnotationFromClass(moduleClass);
+                var extendedModuleAnnotation = readExtendedModuleAnnotationFromClass(moduleClass);
                 var constraints = readConstraintsFromClass(moduleClass);
-                writeConstraintsToModel(model, constraints, moduleAnnotation);
+                writeConstraintsToModel(model, constraints, moduleAnnotation, extendedModuleAnnotation);
             }
 
             var ontologyPath = modulePackageName.replaceAll("[.]", "/") + "/" + ontologyFilename;
@@ -269,25 +283,27 @@ private Model readModelFromDefaultFile() {
 
     private void writeConstraintsToModel(Model baseRdfModel,
                                          List<cz.cvut.spipes.modules.Parameter> constraintAnnotations,
-                                         SPipesModule moduleAnnotation) {
+                                         SPipesModule moduleAnnotation,
+                                         SPipesModule extendedModuleAnnotation) {
         final var root = ResourceFactory.createResource(KBSS_MODULE.uri + moduleAnnotation.label().replaceAll(" ", "-").toLowerCase()); //todo can be added to the annotation
+        // set extended uri
+        Optional.ofNullable(extendedModuleAnnotation)
+                .map(a -> ResourceFactory.createResource(
+                        KBSS_MODULE.uri + a.label().replaceAll(" ", "-").toLowerCase()) //todo can be added to the annotation
+                ).ifPresent(r -> baseRdfModel.add(root, RDFS.subClassOf, r));
+
         baseRdfModel.add(root, RDF.type, SM.Module);
         baseRdfModel.add(root, RDFS.comment, moduleAnnotation.comment());
         baseRdfModel.add(root, RDFS.label, moduleAnnotation.label());
-        final var statements = baseRdfModel.listStatements(null, RDF.type, SM.Module);
-        while (statements.hasNext()) {
-            final var statement = statements.next();
-            final var subject = statement.getSubject();
-            for (var annotation : constraintAnnotations) {
-                final var modelConstraint = ResourceFactory.createResource();
-                baseRdfModel.add(modelConstraint, RDF.type, SPL.Argument);
-                baseRdfModel.add(modelConstraint, SPL.predicate, annotation.urlPrefix() + annotation.name());
-                baseRdfModel.add(modelConstraint, RDFS.comment, "Automatically generated field: " + annotation.name());
-                baseRdfModel.add(subject, SPIN.constraint, modelConstraint);
-
-                getLog().debug("Added model constraint based on annotation: " +
-                        "(name = " + annotation.name() + ", urlPrefix = " + annotation.urlPrefix() + ")");
-            }
+        for (var annotation : constraintAnnotations) {
+            final var modelConstraint = ResourceFactory.createResource();
+            baseRdfModel.add(modelConstraint, RDF.type, SPL.Argument);
+            baseRdfModel.add(modelConstraint, SPL.predicate, ResourceFactory.createResource(annotation.urlPrefix() + annotation.name()));
+            baseRdfModel.add(modelConstraint, RDFS.comment, "Automatically generated field: " + annotation.name());
+            baseRdfModel.add(root, SPIN.constraint, modelConstraint);
+
+            getLog().debug("Added model constraint based on annotation: " +
+                    "(name = " + annotation.name() + ", urlPrefix = " + annotation.urlPrefix() + ")");
         }
     }
 

s-pipes-modules/module-ckan2rdf/src/main/java/cz/cvut/spipes/modules/Ckan2RdfModule.java

@@ -5,6 +5,7 @@
 import cz.cvut.kbss.jopa.model.descriptors.EntityDescriptor;
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.engine.ExecutionContext;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import eu.trentorise.opendata.jackan.CkanClient;
 import eu.trentorise.opendata.jackan.exceptions.CkanException;
 import eu.trentorise.opendata.jackan.model.CkanCatalog;
@@ -26,6 +27,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@SPipesModule(label = "ckan2rdf-v1", comment = "Convert ckan to rdf.")
 public class Ckan2RdfModule extends AnnotatedAbstractModule {
 
     public static final String TYPE_URI = KBSS_MODULE.uri + "ckan2rdf-v1";

s-pipes-modules/module-ckan2rdf/src/main/java/cz/cvut/spipes/modules/SparqlEndpointDatasetExplorerModule.java

@@ -5,6 +5,8 @@
 import cz.cvut.spipes.engine.ExecutionContextFactory;
 import java.time.Instant;
 import java.util.Calendar;
+
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import org.apache.commons.io.IOUtils;
 import org.apache.jena.query.ParameterizedSparqlString;
 import org.apache.jena.query.Query;
@@ -18,6 +20,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@SPipesModule(label = "sparqlEndpointDatasetExplorer-v1", comment = "TODO")
 public class SparqlEndpointDatasetExplorerModule extends AnnotatedAbstractModule {
 
     public static final String TYPE_URI = KBSS_MODULE.uri + "sparqlEndpointDatasetExplorer-v1";

s-pipes-modules/module-dataset-discovery/src/main/java/cz/cvut/spipes/modules/DatasetDiscoveryModule.java

@@ -10,6 +10,8 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.TimeZone;
+
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import org.apache.jena.query.QueryExecution;
 import org.apache.jena.query.QueryExecutionFactory;
 import org.apache.jena.query.QueryFactory;
@@ -24,6 +26,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@SPipesModule(label = "dataset discovery v1", comment =
+        "Discovers dataset based on keyword userInput in repository linked.opendata.cz-federated-descriptor-faceted-search " +
+        "hosted at http://onto.fel.cvut.cz/rdf4j-server.")
 public class DatasetDiscoveryModule extends AbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(DatasetDiscoveryModule.class);
@@ -34,6 +39,7 @@ public class DatasetDiscoveryModule extends AbstractModule {
      * URL of the Sesame server.
      */
     private static final Property P_USER_INPUT = getParameter("prp-user-input");
+    @Parameter(urlPrefix = TYPE_URI + "/", name = "prp-user-inpu")
     private String userInput;
 
     private static Property getParameter(final String name) {

s-pipes-modules/module-dataset-discovery/src/main/java/cz/cvut/spipes/modules/GetDatasetDescriptorsModule.java

@@ -4,6 +4,9 @@
 import cz.cvut.spipes.engine.ExecutionContext;
 import java.io.IOException;
 import java.util.Collections;
+import java.util.Optional;
+
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryExecution;
 import org.apache.jena.query.QueryExecutionFactory;
@@ -19,21 +22,27 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@SPipesModule(label = "get dataset descriptors v1", comment = "Retrieve dataset descriptor for dataset with dataset-iri in endpoint-url.")
 public class GetDatasetDescriptorsModule extends AbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(GetDatasetDescriptorsModule.class);
 
     private static final String TYPE_URI = KBSS_MODULE.uri + "get-dataset-descriptors-v1";
+    private static final String PARAM_URI = TYPE_URI + "/";
 
     /**
      * URL of the Sesame server.
      */
     private static final Property P_DATASET_IRI = getParameter("p-dataset-iri");
+    private static final Property P_ENDPOINT_URL = getParameter("endpoint-url");
+
+    @Parameter(urlPrefix = PARAM_URI, name = "dataset-iri")
     private String prpDatasetIri;
 
     /**
      * URL of the SPARQL endpoint.
      */
+    @Parameter(urlPrefix = PARAM_URI, name = "endpoint-url")
     private String endpointUrl = "http://onto.fel.cvut.cz/rdf4j-server/repositories/descriptors-metadata";
 
     private static Property getParameter(final String name) {
@@ -95,5 +104,6 @@ public String getTypeURI() {
     @Override
     public void loadConfiguration() {
         prpDatasetIri = this.getStringPropertyValue(P_DATASET_IRI);
+        endpointUrl = Optional.ofNullable(this.getStringPropertyValue(P_ENDPOINT_URL)).orElse(endpointUrl);
     }
 }

s-pipes-modules/module-eccairs/src/main/java/cz/cvut/spipes/modules/ImportE5XModule.java

@@ -15,6 +15,7 @@
 import cz.cvut.spipes.engine.ExecutionContext;
 import cz.cvut.spipes.engine.ExecutionContextFactory;
 import cz.cvut.spipes.exception.ResourceNotFoundException;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import cz.cvut.spipes.modules.eccairs.EccairsAccessFactory;
 import cz.cvut.spipes.modules.eccairs.JopaPersistenceUtils;
 import cz.cvut.spipes.modules.eccairs.SesameDataDao;
@@ -34,10 +35,15 @@
 import java.net.URI;
 import java.util.Arrays;
 
+@SPipesModule(label = "import-e5x", comment = "Convert e5x xml files to rdf.")
 public class ImportE5XModule extends AbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(ImportE5XModule.class);
 
+    // TODO - this parameter id defined with IRI <http://onto.fel.cvut.cz/ontologies/lib/module-param/has-resource-uri> in  s-pipes-modules\module.sms.ttl
+    @Parameter(name = "has-resource-uri")
+    private String e5xResourceUriStr;
+
     StreamResource e5xResource;
 
     private boolean computeEccairsToAviationSafetyOntologyMapping = true;
@@ -145,7 +151,7 @@ public String getTypeURI() {
 
     @Override
     public void loadConfiguration() {
-        String e5xResourceUriStr = getEffectiveValue(KBSS_MODULE.has_resource_uri).asLiteral().toString();
+        e5xResourceUriStr = getEffectiveValue(KBSS_MODULE.has_resource_uri).asLiteral().toString();
         e5xResource = getResourceByUri(e5xResourceUriStr);
     }
 

s-pipes-modules/module-form/src/main/java/cz/cvut/spipes/modules/ConstructFormMetadataModule.java

@@ -4,6 +4,7 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.jena.rdf.model.*;
 import org.apache.jena.vocabulary.RDF;
@@ -21,6 +22,7 @@
 /**
  * Compute form:has-origin-path and form:has-origin-path-id properties.
  */
+@SPipesModule(label = "construct form metadata", comment = "Compute form:has-origin-path and form:has-origin-path-id properties.")
 public class ConstructFormMetadataModule extends AnnotatedAbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(ConstructFormMetadataModule.class);

s-pipes-modules/module-form/src/main/java/cz/cvut/spipes/modules/ConstructTextualViewModule.java

@@ -12,6 +12,7 @@
 import cz.cvut.spipes.engine.ExecutionContext;
 import cz.cvut.spipes.form.JenaFormUtils;
 import cz.cvut.spipes.form.JopaPersistenceUtils;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
@@ -25,6 +26,10 @@
  * For input Q&A models constructs textual view of specified questions. Each textual view represent the question
  * and its sub-questions recursively.
  */
+@SPipesModule(label = "construct textual view", comment =
+        "For input Q&A models constructs textual view of specified questions. Each textual" +
+        " view represent the question and its sub-questions recursively."
+)
 public class ConstructTextualViewModule extends AnnotatedAbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(ConstructTextualViewModule.class);

s-pipes-modules/module-form/src/main/java/cz/cvut/spipes/modules/FetchPossibleValuesModule.java

@@ -6,6 +6,7 @@
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
 import cz.cvut.spipes.form.JenaFormUtils;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
@@ -19,6 +20,10 @@
  * Inputs are forms using Q&A model. Possible values of questions are added to questions that does not have
  * any value attached and contains possible value query.
  */
+@SPipesModule(label = "fetch possible values", comment =
+        "Fetches possible values for answers of questions. Inputs are forms using Q&A model. Possible values of " +
+        "questions are added to questions that does not have any value attached and contains possible value query."
+)
 public class FetchPossibleValuesModule extends AnnotatedAbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(FetchPossibleValuesModule.class);

s-pipes-modules/module-form/src/main/java/cz/cvut/spipes/modules/MergeFormMetadataModule.java

@@ -6,6 +6,7 @@
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
 import cz.cvut.spipes.form.JenaFormUtils;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
@@ -20,6 +21,11 @@
  * question origin combined with executionId. New question instances are created using questionInstanceTemplate
  * which defaults to "doc:question-{_questionOriginHash}-{_executionId}".
  */
+@SPipesModule(label = "merge form metadata", comment =
+        "Merges form metadata. Inputs are sample form and Q&A model. Questions from both models are remapped to new" +
+        "IRIs based on question origin combined with executionId. New question instances are created using" +
+        "questionInstanceTemplate which defaults to \"doc:question-{_questionOriginHash}-{_executionId}\"."
+)
 public class MergeFormMetadataModule extends AnnotatedAbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(MergeFormMetadataModule.class);

s-pipes-modules/module-identity/src/main/java/cz/cvut/spipes/modules/IdentityModule.java

@@ -2,9 +2,11 @@
 
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.engine.ExecutionContext;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@SPipesModule(label = "identity", comment = "Implements a no-op.")
 public class IdentityModule extends AnnotatedAbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(IdentityModule.class);

s-pipes-modules/module-nlp/src/main/java/cz/cvut/spipes/modules/SUTimeModule.java

@@ -3,6 +3,7 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.engine.ExecutionContext;
 import cz.cvut.spipes.engine.ExecutionContextFactory;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import cz.cvut.spipes.sutime.AnnforModel;
 import cz.cvut.spipes.sutime.DescriptorModel;
 import edu.stanford.nlp.ling.CoreAnnotations;
@@ -27,13 +28,17 @@
 import java.nio.file.Paths;
 
 
+@SPipesModule(label = "temporal v0.1", comment = "Annotate temporal expressions in literals in input model.")
 public class SUTimeModule extends AbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(SUTimeModule.class);
 
     public static final String TYPE_URI = KBSS_MODULE.getURI() + "temporal-v0.1";
 
+    @Parameter(urlPrefix = DescriptorModel.prefix, name = "has-document-date")
     private List<Path> ruleFilePaths = new LinkedList<>();
+
+    @Parameter(urlPrefix = DescriptorModel.prefix, name = "has-rule-file")
     private String documentDate; // TODO support other formats ?
 
 

s-pipes-modules/module-nlp/src/main/java/cz/cvut/spipes/modules/SUTimeModuleNew.java

@@ -3,6 +3,7 @@
 import cz.cvut.spipes.constants.KBSS_MODULE;
 import cz.cvut.spipes.constants.SML;
 import cz.cvut.spipes.engine.ExecutionContext;
+import cz.cvut.spipes.modules.annotations.SPipesModule;
 import cz.cvut.spipes.sutime.AnnforModel;
 import cz.cvut.spipes.sutime.DescriptorModel;
 import cz.cvut.spipes.util.JenaUtils;
@@ -33,6 +34,7 @@
 import java.util.*;
 
 
+@SPipesModule(label = "temporal-v1", comment = "Annotate temporal expressions in literals in input model.")
 public class SUTimeModuleNew extends AbstractModule {
 
     private static final Logger LOG = LoggerFactory.getLogger(SUTimeModuleNew.class);
@@ -43,16 +45,24 @@ public class SUTimeModuleNew extends AbstractModule {
     private static final String LIMIT_OFFSET_CLAUSE_MARKER_NAME = "LIMIT_OFFSET";
     private static final Property P_PAGE_SIZE = ResourceFactory.createProperty(TYPE_PREFIX + "page-size");
     private Integer pageSize = DEFAULT_PAGE_SIZE;
+
+    @Parameter(urlPrefix = SML.uri, name = "constructQuery")
     private List<Resource> constructQueries;
+
     //sml:replace
+    @Parameter(urlPrefix = SML.uri, name = "replace")
     private boolean isReplace;
 
     //kbss:parseText
     /**
      * Whether the query should be taken from sp:text property instead of from SPIN serialization
      */
+    @Parameter(name = "is-parse-text")
     private boolean parseText;
+
+    @Parameter(urlPrefix = DescriptorModel.prefix, name = "has-document-date")
     private List<Path> ruleFilePaths = new LinkedList<>();
+    @Parameter(urlPrefix = DescriptorModel.prefix, name = "has-rule-file")
     private String documentDate; // TODO support other formats ?
     private AnnotationPipeline pipeline;
 

s-pipes-modules/module-nlp/src/main/java/cz/cvut/spipes/sutime/DescriptorModel.java

@@ -9,7 +9,7 @@ public class DescriptorModel {
     /**
      * The namespace of the vocabulary as a string
      */
-    private static final String prefix = "http://onto.fel.cvut.cz/ontologies/dataset-descriptor/temporal-v1/";
+    public static final String prefix = "http://onto.fel.cvut.cz/ontologies/dataset-descriptor/temporal-v1/";
 
     protected static final Resource resource(String local )
     { return ResourceFactory.createResource( prefix +  local ); }