[#274] Add loadManualConfiguration and refactor all modules

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

@@ -71,6 +71,7 @@ public abstract class AbstractModule implements Module {
     public ExecutionContext execute() {
         loadModuleFlags();
         loadConfiguration();
+        loadManualConfiguration();
         loadModuleConstraints();
         String inputModelFilePath = null;
         if (AuditConfig.isEnabled() || isInDebugMode) {

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

@@ -54,4 +54,7 @@ public void loadConfiguration() {
             handler.setValueByProperty(ResourceFactory.createProperty(p.iri()));
         }
     }
+
+    @Override
+    public void loadManualConfiguration(){}
 }

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

@@ -41,6 +41,8 @@ public interface Module {
      */
     void loadConfiguration();
 
+    void loadManualConfiguration();
+
     Resource getResource();
 
     void setInputModules(List<Module> inputModules);

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

@@ -43,9 +43,8 @@ public class ImportE5XModule extends AnnotatedAbstractModule {
 
     // 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
     // TODO - we should be able to annotate directly "StreamResource e5xResource" instead
-    @Parameter(iri = KBSS_MODULE.has_resource_uri, comment = "Uri of a resource referencing content of an e5x file.")
-    private String e5xResourceUriStr;
 
+    @Parameter(iri = KBSS_MODULE.has_resource_uri, comment = "Uri of a resource referencing content of an e5x file.")
     StreamResource e5xResource;
 
     private boolean computeEccairsToAviationSafetyOntologyMapping = true;
@@ -151,21 +150,4 @@ public String getTypeURI() {
         return KBSS_MODULE.uri + "import-e5x";
     }
 
-    @Override
-    public void loadConfiguration() {
-        e5xResourceUriStr = getEffectiveValue(KBSS_MODULE.JENA.has_resource_uri).asLiteral().toString();
-        e5xResource = getResourceByUri(e5xResourceUriStr);
-    }
-
-    @NotNull
-    private StreamResource getResourceByUri(@NotNull String e5xResourceUriStr) {
-
-        StreamResource res = StreamResourceRegistry.getInstance().getResourceByUrl(e5xResourceUriStr);
-
-        if (res == null) {
-            throw new ResourceNotFoundException("Stream resource " + e5xResourceUriStr + " not found. ");
-        }
-        return res;
-    }
-
 }

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

@@ -30,7 +30,7 @@
 
 @Slf4j
 @SPipesModule(label = "temporal v0.1", comment = "Annotate temporal expressions in literals in input model.")
-public class SUTimeModule extends AbstractModule {
+public class SUTimeModule extends AnnotatedAbstractModule {
 
     public static final String TYPE_URI = KBSS_MODULE.uri + "temporal-v0.1";
 
@@ -40,7 +40,6 @@ public class SUTimeModule extends AbstractModule {
     @Parameter(iri = DescriptorModel.has_document_date, comment = "Document date format.") // TODO - revise comment
     private String documentDate; // TODO support other formats ?
 
-
     public SUTimeModule() {
     }
 
@@ -49,17 +48,6 @@ public String getTypeURI() {
         return TYPE_URI;
     }
 
-    @Override
-    public void loadConfiguration() {
-
-        if (this.resource.getProperty(DescriptorModel.JENA.has_document_date) != null) { // TODO set current date if not specified
-            documentDate = getEffectiveValue(DescriptorModel.JENA.has_document_date).asLiteral().toString();
-        }
-
-        if (this.resource.getProperty(DescriptorModel.JENA.has_rule_file) != null) { //TODO support more rule files
-            ruleFilePaths.add(Paths.get(getEffectiveValue(DescriptorModel.JENA.has_rule_file).asLiteral().toString()));
-        }
-    }
 
     @Override
 
@@ -70,12 +58,8 @@ ExecutionContext executeSelf() {
     }
 
     private Model analyzeModel(Model m) {
-
-
-
         AnnotationPipeline pipeline = loadPipeline();
 
-
         DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd");
         List<ReifiedStatement> temporalAnnotationStmts = new LinkedList<>();
         m.listStatements()
@@ -199,7 +183,4 @@ private AnnotationPipeline loadPipeline() {
         return pipeline;
     }
 
-
-
-
 }

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

@@ -15,6 +15,8 @@
 import edu.stanford.nlp.time.TimeAnnotator;
 import edu.stanford.nlp.time.TimeExpression;
 import edu.stanford.nlp.util.CoreMap;
+import lombok.Getter;
+import lombok.Setter;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryFactory;
@@ -29,11 +31,15 @@
 import java.nio.file.Paths;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
+import java.time.LocalDate;
+import java.time.format.DateTimeFormatter;
 import java.util.*;
 
 @Slf4j
+@Getter
+@Setter
 @SPipesModule(label = "temporal-v1", comment = "Module annotates input triples using NLP analysis of time using library SUTime.")
-public class SUTimeModuleNew extends AbstractModule {
+public class SUTimeModuleNew extends AnnotatedAbstractModule {
 
     private static final String TYPE_URI = KBSS_MODULE.uri + "temporal-v1";
     private static final String TYPE_PREFIX = TYPE_URI + "/";
@@ -49,18 +55,18 @@ public class SUTimeModuleNew extends AbstractModule {
     private List<Resource> constructQueries;
 
     @Parameter(iri = SML.replace, comment = "Replace context flag. Default value is false." )
-    private boolean isReplace;
+    private boolean isReplace = false;
 
     @Parameter(iri = KBSS_MODULE.is_parse_text,
         comment = "Whether the query should be taken from sp:text property instead of from SPIN serialization," +
             " default is true.")
-    private boolean parseText;
+    private boolean parseText = true;
 
     @Parameter(iri = DescriptorModel.has_rule_file, comment = "Rule file, multivalued.")// TODO - review comment
     private List<Path> ruleFilePaths = new LinkedList<>();
 
     @Parameter(iri = DescriptorModel.has_document_date, comment = "Document date format.")// TODO - review comment
-    private String documentDate; // TODO support other formats ?
+    private String documentDate = LocalDate.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd")); // TODO support other formats ?
     private AnnotationPipeline pipeline;
 
     public SUTimeModuleNew() {
@@ -72,30 +78,6 @@ public String getTypeURI() {
         return TYPE_URI;
     }
 
-    public int getPageSize() {
-        return pageSize;
-    }
-
-    public void setPageSize(int pageSize) {
-        this.pageSize = pageSize;
-    }
-
-    @Override
-    public void loadConfiguration() {
-        if (this.resource.getProperty(DescriptorModel.JENA.has_document_date) != null) { // TODO set current date if not specified
-            documentDate = getEffectiveValue(DescriptorModel.JENA.has_document_date).asLiteral().toString();
-        }
-
-        if (this.resource.getProperty(DescriptorModel.JENA.has_rule_file) != null) { //TODO support more rule files
-            ruleFilePaths.add(Paths.get(getEffectiveValue(DescriptorModel.JENA.has_rule_file).asLiteral().toString()));
-        }
-        parseText = this.getPropertyValue(KBSS_MODULE.JENA.is_parse_text, true);
-        pageSize = this.getPropertyValue(P_PAGE_SIZE, DEFAULT_PAGE_SIZE);
-        constructQueries = getResourcesByProperty(SML.JENA.constructQuery);
-
-        isReplace = this.getPropertyValue(SML.JENA.replace, false);
-    }
-
     @Override
     public ExecutionContext executeSelf() {
 

s-pipes-modules/module-rdf4j/src/main/java/cz/cvut/spipes/modules/Rdf4jCreateRepositoryModule.java

@@ -17,7 +17,7 @@
 
 @Slf4j
 @SPipesModule(label = "rdf4j create repository", comment = "Module creates native store rdf4j repository on the given server with the given name.")
-public class Rdf4jCreateRepositoryModule extends AbstractModule {
+public class Rdf4jCreateRepositoryModule extends AnnotatedAbstractModule {
     private static final String TYPE_URI = KBSS_MODULE.uri + "rdf4j-create-repository";
     private static final String PROPERTY_PREFIX_URI = KBSS_MODULE.uri + "rdf4j";
 
@@ -34,8 +34,9 @@ public class Rdf4jCreateRepositoryModule extends AbstractModule {
 
     @Parameter(iri = PROPERTY_PREFIX_URI + "/" + "p-rdf4j-ignore-if-exists",
             comment = "Don't try to create new repository if it already exists (Default value is false)")
-    private boolean rdf4jIgnoreIfExists;
+    private boolean rdf4jIgnoreIfExists = false;
 
+    @Parameter(iri = PROPERTY_PREFIX_URI + "/" + "p-rdf4j-server-url", comment = "URL of the Rdf4j server")
     private RepositoryManager repositoryManager;
 
     public String getRdf4jServerURL() {
@@ -101,15 +102,7 @@ public String getTypeURI() {
     }
 
     @Override
-    public void loadConfiguration() {
-        rdf4jServerURL = getEffectiveValue(P_RDF4J_SERVER_URL).asLiteral().getString();
-        rdf4jRepositoryName = getEffectiveValue(P_RDF4J_REPOSITORY_NAME).asLiteral().getString();
-        try {
-            rdf4jIgnoreIfExists = (Objects.equals(getEffectiveValue(P_RDF4J_IGNORE_IF_EXISTS).asLiteral().getString(), "true"));
-        }
-        catch (NullPointerException e){
-            rdf4jIgnoreIfExists = false;
-        }
+    public void loadManualConfiguration() {
         repositoryManager = new RemoteRepositoryManager(rdf4jServerURL);
     }
 }

s-pipes-modules/module-rdf4j/src/main/java/cz/cvut/spipes/modules/Rdf4jDeployModule.java

@@ -40,7 +40,7 @@
         "Module deploys content of input execution context into default context of repository (if p-rdf4j-context-iri " +
         "is not specified) or concrete context (if p-rdf4j-context-iri is specified)."
 )
-public class Rdf4jDeployModule extends AbstractModule {
+public class Rdf4jDeployModule extends AnnotatedAbstractModule {
 
     private final static String TYPE_URI = KBSS_MODULE.uri + "deploy";
     private final static String PROPERTY_PREFIX_URI = KBSS_MODULE.uri + "rdf4j";
@@ -66,8 +66,8 @@ private static Property getParameter(final String name) {
     @Parameter(iri = PROPERTY_PREFIX_URI + "/" + "p-rdf4j-infer-context-iris",
         comment = "IRI of contexts is inferred from annotated input triples. Only reified triples that contain triple " +
             "?reifiedStatement kbss-module:is-part-of-graph ?graph are processed." +
-            " Actual triples related to reified statement are not processed/needed.")
-    private boolean inferContextIRIs;
+            " Actual triples related to reified statement are not processed/needed. Default is false.")
+    private boolean inferContextIRIs = false;
 
     static final Property P_RDF4J_REPOSITORY_USERNAME = getParameter("p-rdf4j-secured-username-variable");
     @Parameter(iri = PROPERTY_PREFIX_URI + "/" + "p-rdf4j-secured-username-variable", comment = "User name if the repository requires authentication.")
@@ -89,7 +89,7 @@ public void setRepositoryManager(RepositoryManager repositoryManager) {
     @Parameter(iri = PROPERTY_PREFIX_URI + "/" + "p-is-replace", comment =
             "Whether data should be replaced (true) / appended (false) into the specified context or repository.\n" +
             "Default is false.")
-    private boolean isReplaceContext;
+    private boolean isReplaceContext = false;
 
     public String getRdf4jServerURL() {
         return rdf4jServerURL;
@@ -238,19 +238,7 @@ public String getTypeURI() {
     }
 
     @Override
-    public void loadConfiguration() {
-        rdf4jServerURL = getEffectiveValue(P_RDF4J_SERVER_URL).asLiteral().getString();
-        rdf4jRepositoryName = getEffectiveValue(P_RDF4J_REPOSITORY_NAME).asLiteral().getString();
-        if (this.getPropertyValue(P_RDF4J_CONTEXT_IRI) != null) {
-            rdf4jContextIRI = getEffectiveValue(P_RDF4J_CONTEXT_IRI).asLiteral().getString();
-        }
-        isReplaceContext = this.getPropertyValue(P_IS_REPLACE_CONTEXT_IRI, false);
-        rdf4jSecuredUsernameVariable = Optional.ofNullable(
-            getEffectiveValue(P_RDF4J_REPOSITORY_USERNAME)).map(n -> n.asLiteral().getString()
-        ).orElse(null);
-        rdf4jSecuredPasswordVariable = Optional.ofNullable(
-            getEffectiveValue(P_RDF4J_REPOSITORY_PASSWORD)).map(n -> n.asLiteral().getString()
-        ).orElse(null);
+    public void loadManualConfiguration() {
         if (repositoryManager != null && rdf4jServerURL != null) {
             throw new ModuleConfigurationInconsistentException(
                     "Repository manager is already initialized. Trying to override its configuration from RDF.");
@@ -263,7 +251,6 @@ public void loadConfiguration() {
             remoteRepositoryManager.setUsernameAndPassword(username, password);
         }
         repository = repositoryManager.getRepository(rdf4jRepositoryName);
-        inferContextIRIs = getPropertyValue(P_RDF4J_INFER_CONTEXT_IRIS,false);
         log.debug("Inferring contexts from annotated input triples.");
     }
     private static @Nullable String getConfigurationVariable(String variableName) {

s-pipes-modules/module-rdf4j/src/main/java/cz/cvut/spipes/modules/Rdf4jUpdateModule.java

@@ -30,7 +30,7 @@
 @SPipesModule(label = "rdf4j update", comment = "Updates sparql endpoint configured in rdf4jServerURL" +
     " using specified list updateQueries. The list of queries can be executed multiple times specified by " +
     " `has-max-iteration-count` property.")
-public class Rdf4jUpdateModule extends AbstractModule {
+public class Rdf4jUpdateModule extends AnnotatedAbstractModule {
     private static final String TYPE_URI = KBSS_MODULE.uri + "rdf4j-update";
     private static final String PROPERTY_PREFIX_URI = KBSS_MODULE.uri + "rdf4j";
 
@@ -56,13 +56,13 @@ public class Rdf4jUpdateModule extends AbstractModule {
     @Parameter(iri = PROPERTY_PREFIX_URI + "/" + "p-stop-iteration-on-stable-triple-count",
             comment = "Stops iteration (i.e. execution of list of queries) if triple count " +
                 "in the last iteration did not change. Default is false.")
-    private boolean onlyIfTripleCountChanges;
+    private boolean onlyIfTripleCountChanges = false;
 
     @Parameter(iri = PROPERTY_PREFIX_URI + "/" + "has-max-iteration-count",
             comment = "Limits the number of iterations (i.e. executions of list of queries)" +
                 " to the specified value. Default value is 1, which means that all" +
                 " update queries are executed only once.")
-    private int iterationCount;
+    private int iterationCount = 1;
 
     private Repository updateRepository;
 
@@ -189,11 +189,7 @@ public String getTypeURI() {
     }
 
     @Override
-    public void loadConfiguration() {
-        rdf4jServerURL = getEffectiveValue(P_RDF4J_SERVER_URL).asLiteral().getString();
-        rdf4jRepositoryName = getEffectiveValue(P_RDF4J_REPOSITORY_NAME).asLiteral().getString();
-        iterationCount = getPropertyValue(KBSS_MODULE.JENA.has_max_iteration_count,1);
-        onlyIfTripleCountChanges = getPropertyValue(P_RDF4J_STOP_ITERATION_ON_STABLE_TRIPLE_COUNT,false);
+    public void loadManualConfiguration() {
         log.debug("Iteration count={}\nOnlyIf...Changes={}"
                 ,iterationCount
                 ,onlyIfTripleCountChanges);

s-pipes-modules/module-sparql-endpoint/src/main/java/cz/cvut/spipes/modules/ApplyConstructV2Module.java

@@ -20,7 +20,7 @@ public String getTypeURI() {
 
 
     @Override
-    public void loadConfiguration() {
+    public void loadManualConfiguration() {
         super.loadConfiguration();
         iterationCount = this.getPropertyValue(KBSS_MODULE.JENA.has_max_iteration_count, 1);
     }

s-pipes-modules/module-sparql-endpoint/src/main/java/cz/cvut/spipes/modules/ApplyConstructWithChunkedValuesAndScrollableCursorModule.java

@@ -106,13 +106,10 @@ protected String substituteQueryMarkers(int currentIteration, String queryStr) {
 
 
     @Override
-    public void loadConfiguration() {
+    public void loadManualConfiguration() {
         super.loadConfiguration();
+        super.loadManualConfiguration();
         //iterationCount = this.getPropertyValue(KBSS_MODULE.JENA.s_max_iteration_count, 1);
-        parseText = this.getPropertyValue(KBSS_MODULE.JENA.is_parse_text, true);
-        chunkSize = this.getPropertyValue(P_CHUNK_SIZE, DEFAULT_CHUNK_SIZE);
-        selectQuery = getPropertyValue(SML.JENA.selectQuery).asResource().as(Select.class);
-        pageSize = this.getPropertyValue(P_PAGE_SIZE, DEFAULT_PAGE_SIZE);
     }
 
     @NotNull

s-pipes-modules/module-sparql-endpoint/src/main/java/cz/cvut/spipes/modules/ApplyConstructWithChunkedValuesModule.java

@@ -113,12 +113,9 @@ protected String substituteQueryMarkers(int currentIteration, String queryStr) {
 
 
     @Override
-    public void loadConfiguration() {
+    public void loadManualConfiguration() {
         super.loadConfiguration();
         //iterationCount = this.getPropertyValue(KBSS_MODULE.JENA.s_max_iteration_count, 1);
-        parseText = this.getPropertyValue(KBSS_MODULE.JENA.is_parse_text, true);
-        chunkSize = this.getPropertyValue(P_CHUNK_SIZE, DEFAULT_CHUNK_SIZE);
-        selectQuery = getPropertyValue(SML.JENA.selectQuery).asResource().as(Select.class);
     }
 
     @NotNull

s-pipes-modules/module-sparql-endpoint/src/main/java/cz/cvut/spipes/modules/ApplyConstructWithScrollableCursorModule.java

@@ -76,10 +76,8 @@ protected String substituteQueryMarkers(int currentIteration, String queryStr) {
 
 
     @Override
-    public void loadConfiguration() {
+    public void loadManualConfiguration() {
         super.loadConfiguration();
         //iterationCount = this.getPropertyValue(KBSS_MODULE.JENA.s_max_iteration_count, 1);
-        parseText = this.getPropertyValue(KBSS_MODULE.JENA.is_parse_text, true);
-        pageSize = this.getPropertyValue(P_PAGE_SIZE , DEFAULT_PAGE_SIZE);
     }
 }

s-pipes-modules/module-sparql-endpoint/src/main/java/cz/cvut/spipes/modules/ImproveSPOWithMarginalsModule.java

@@ -380,12 +380,8 @@ public String getTypeURI() {
     }
 
     @Override
-    public void loadConfiguration() {
+    public void loadManualConfiguration() {
         super.loadConfiguration();
-        marginalConstraint = getEffectiveStringValue(TYPE_PREFIX + "marginal-constraint");
-        marginalsDefsFileUrl = getEffectiveStringValue(TYPE_PREFIX + "marginals-defs-file-url");
-        marginalsFileUrl = getEffectiveStringValue(TYPE_PREFIX + "marginals-file-url");
-        dataServiceUrl = getEffectiveStringValue(TYPE_PREFIX + "data-service-url");
     }
 
     private @NotNull