Misc minor updates in examples and code description

README_code_architecture.txt

@@ -1,29 +1,33 @@
+Below we describe the architecture of classes regarding the treatment of RDBs. This can easily be adapted to the MongoDB case.
+
 base.MorphProperties
     Is a java.util.Properties.
     Holds members for each property definable in the configuration file 
-    (defaults to examples/morph.properties, set in MorphRDBRunner main)
+    (defaults to example_mysql/morph.properties, set in project morph-xr2rml-dist, MorphRunner main)
+
+The base.engine.MorphBaseRunnerFactory class is an abstract class that builds an morph.base.engine.MorphBaseRunner.
+Database-specific methods are implemented in concrete factory classes like r2rml.rdb.engine.MorphRDBRunnerFactory. 
 
 r2rml.rdb.engine.MorphRDBRunnerFactory < base.engine.MorphBaseRunnerFactory
-    Build an r2rml.rdb.engine.MorphRDBRunner object to initialize:
+    Provides methods to initialize:
+    - a mapping document (R2RMLMappingDocument): read the xR2RML mapping file into a JENA model, then create an R2RMLMappingDocument
+      that consists of a set of classMappings, namely triples maps (R2RMLTriplesMap).
     - a DB connection
     - a data source reader (MorphBaseDataSourceReader) of which concrete class name (MorphRDBDataSourceReader) 
-      is passed as contruct parameter. The data source reader provides methods to set the connection and run 
-      queries against the DB.
-    - a mapping document (R2RMLMappingDocument): read the R2RML mapping into a JENA model, then create an R2RMLMappingDocument
-      that consists of a set of classMappings, namely triples maps (R2RMLTriplesMap).
+      is passed as contruct parameter. The data source reader provides methods to open, configure, and close the connection, 
+      run queries against the DB, and possibly manage strategies to store results to avoid executing the same query several times in the case of joint queries.
     - an unfolder (MorphRDBUnfolder < MorphBaseUnfolder) to create SQL queries using a table name or query
-    - a data materializer (MorphBaseMaterializer) basically consists of a proper JENA model (either in mem or db)
-      initialized with a name space etc. The model is used to create statements from subject, predicate, objects read
-      from the database.
     - a data translator (MorphRDBDataTranslator < MorphBaseDataTranslator) that actually makes the translation: it runs
       SQL queries created by the unfolder, then generates RDF triples from the results.
+    - a data materializer (MorphBaseMaterializer) basically consists of a properly initialized (name space, etc.) 
+      JENA model, either in mem or db. The model is used to store statements created from subjects, predicates and objects read
+      from the database.
     - a query translator, query result writer and query result processor
 
-r2rml.rdb.engine.MorphRDBRunner < base.engine.MorphBaseRunner
-    Main: 
+fr.unice.i3s.morph.xr2rml.engine.MorphRunner provide the main class to run the process:
     - Load the properties
-    - Create a singleton MorphRDBRunner using the MorphRDBRunnerFactory that creates
-      a R2RMLMappingDocument, MorphRDBUnfoldern MorphRDBDataMaterializer and MorphRDBDataTranslator (see above).
+    - Create a singleton MorphBaseRunner using the MorphRDBRunnerFactory that creates
+      a R2RMLMappingDocument, MorphRDBUnfolder, MorphRDBDataMaterializer and MorphRDBDataTranslator (see above).
     - Run the process using either materialization (MorphBaseRunner.materializeMappingDocuments) or query rewriting
     - Load the RDF graph produced in a JENA model and save a serialization into a file using the requested RDF syntax.
 

morph-xr2rml-dist/example_mongo/mapping.ttl

@@ -2,15 +2,13 @@
 @prefix rr:  <http://www.w3.org/ns/r2rml#> .
 @prefix ex:  <http://example.com/> .
 @prefix rml: <http://semweb.mmlab.be/ns/rml#> .
-@prefix ql:	 <http://semweb.mmlab.be/ns/ql#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 <#Students>
     a rr:TriplesMap;
     xrr:logicalSource [
     	# Jongo needs strings in singles quotes (difference with MongoDB shell)
         xrr:query """db.students.find( { 'FullName' : {$exists: 1} } )""";
-        xrr:referenceFormulation ql:JSONPath;
     ];
     rr:subjectMap [ 
     	rr:template "http://example.org/student/{$._id.*}";
@@ -51,7 +49,6 @@
     a rr:TriplesMap;
     xrr:logicalSource [
         xrr:query "db.movies.find( { movies: { $exists: true} } )";
-        xrr:referenceFormulation ql:JSONPath;
         rml:iterator "$.movies.*";
     ];
     rr:subjectMap [ 
@@ -63,7 +60,6 @@
     a rr:TriplesMap;
     xrr:logicalSource [
         xrr:query "db.movies.find( { directors: { $exists: true} } )";
-        xrr:referenceFormulation ql:JSONPath;
         rml:iterator "$.directors.*";
     ];
     rr:subjectMap [ rr:template "http://example.org/director/{$.name}"; ];

morph-xr2rml-dist/src/main/resources/log4j.properties

@@ -1,6 +1,6 @@
 # Logging properties
 #log4j.rootCategory=file,console
-log4j.rootLogger=TRACE,file,console
+log4j.rootLogger=INFO,file,console
 
 layout.fileLayout=%d{yyyy-MM-dd HH:mm:ss} %-5p %C{1}.%M:%L %x - %m%n
 layout.consoleLayout=%d{yyyy-MM-dd HH:mm:ss} %-5p [%t] (%F:%L) - %m%n

morph-xr2rml-dist/src/main/scala/fr/unice/i3s/morph/xr2rml/engine/MorphRunner.scala

@@ -47,11 +47,12 @@ object MorphRunner {
             logger.info("properties Directory = " + configDir)
             logger.info("properties File      = " + configFile)
 
-            // Create the runner, parse the mapping document, create the unfolder, data materializer, data translator etc.
             val properties = MorphProperties(configDir, configFile)
 
-            val runnerFactInstance = Class.forName(properties.runnerFactoryClassName).newInstance()
-            val runnerFact = runnerFactInstance.asInstanceOf[MorphBaseRunnerFactory]
+            // Create the runner factory based on the class name given in configuration file
+            val runnerFact = Class.forName(properties.runnerFactoryClassName).newInstance().asInstanceOf[MorphBaseRunnerFactory]
+
+            // Create the runner, parse the mapping document, create the unfolder, data materializer, data translator etc.
             val runner = runnerFact.createRunner(properties);
 
             // Start the translation process

morph-xr2rml-jsondoc/src/main/scala/fr/unice/i3s/morph/xr2rml/jsondoc/engine/MorphJsondocDataTranslator.scala

@@ -45,7 +45,7 @@ class MorphJsondocDataTranslator(
         extends MorphBaseDataTranslator(md, materializer, unfolder, dataSourceReader, connection, properties)
         with MorphR2RMLElementVisitor {
 
-    /** Store already executed queries do avoid running them several times */
+    /** Store already executed queries to avoid running them several times */
     private var executedQueries: scala.collection.mutable.Map[String, List[String]] = new scala.collection.mutable.HashMap
 
     override val logger = Logger.getLogger(this.getClass().getName());
@@ -353,34 +353,6 @@ class MorphJsondocDataTranslator(
         result
     }
 
-    private def getResultSetValue(termMap: R2RMLTermMap, rs: ResultSet, pColumnName: String): Object = {
-        try {
-            val zConstant = MorphSQLConstant(pColumnName, ZConstant.COLUMNNAME);
-            val tableName = zConstant.table;
-            val columnName = {
-                if (tableName != null) {
-                    tableName + "." + zConstant.column
-                } else
-                    zConstant.column
-            }
-
-            val result = if (termMap.datatype == null) {
-                rs.getString(columnName);
-            } else if (termMap.datatype.equals(XSDDatatype.XSDdateTime.getURI())) {
-                rs.getDate(columnName).toString();
-            } else {
-                rs.getObject(columnName);
-            }
-            result
-        } catch {
-            case e: Exception => {
-                e.printStackTrace();
-                logger.error("An error occured when reading the SQL result set : " + e.getMessage());
-                null
-            }
-        }
-    }
-
     /**
      * Create a JENA literal resource with optional data type and language tag.
      * This method is overriden in the case of JSON to enable the mapping between JSON data types