Add relative file resolver base path to mapping launcher.

src/main/scala/com/herminiogarcia/shexml/MappingLauncher.scala

@@ -6,13 +6,15 @@ import com.herminiogarcia.shexml.helper.{OrphanBNodeRemover, ParallelExecutionCo
 import com.herminiogarcia.shexml.parser.ASTCreatorVisitor
 import com.herminiogarcia.shexml.shex._
 import com.herminiogarcia.shexml.visitor.{PushedOrPoppedValueSearchVisitor, RDFGeneratorVisitor, RMLGeneratorVisitor, VarTableBuilderVisitor}
+import com.typesafe.scalalogging.Logger
 import org.antlr.v4.runtime.{CharStreams, CommonTokenStream}
 import org.apache.jena.query.{Dataset, DatasetFactory}
 import org.apache.jena.riot.{RDFDataMgr, RDFFormat, RDFLanguages}
-import com.typesafe.scalalogging.Logger
+
 import java.io.ByteArrayOutputStream
-import scala.collection.JavaConverters._
+import java.nio.file.Path
 import java.util.concurrent.ConcurrentLinkedQueue
+import scala.collection.JavaConverters._
 import scala.collection.mutable
 
 /**
@@ -21,7 +23,21 @@ import scala.collection.mutable
 class MappingLauncher(val username: String = "", val password: String = "", drivers: String = "",
                       val inferenceDatatype: Boolean = false,
                       val normaliseURIs: Boolean = false,
-                      val parallelCollectionConfigurator: ParallelExecutionConfigurator = new ParallelExecutionConfigurator(Map(), None)) {
+                      val parallelCollectionConfigurator: ParallelExecutionConfigurator = new ParallelExecutionConfigurator(Map(), None),
+                      val basePath: Path = Path.of("")) {
+
+  /**
+   * Java compatibility constructor.
+   */
+  def this(
+    username: String,
+    password: String,
+    drivers: String,
+    inferenceDatatype: Boolean,
+    normaliseURIs: Boolean,
+    parallelCollectionConfigurator: ParallelExecutionConfigurator) = {
+      this(username, password, drivers, inferenceDatatype, normaliseURIs, parallelCollectionConfigurator, Path.of(""))
+    }
 
   private val logger = Logger[MappingLauncher]
 
@@ -158,7 +174,8 @@ class MappingLauncher(val username: String = "", val password: String = "", driv
       pushedOrPoppedFieldsPresent = pushedOrPoppedFields,
       inferenceDatatype = inferenceDatatype,
       normaliseURIs = normaliseURIs,
-      parallelCollectionConfigurator = parallelCollectionConfigurator).doVisit(ast, null)
+      parallelCollectionConfigurator = parallelCollectionConfigurator,
+      basePath = basePath).doVisit(ast, null)
     //val in = new ByteArrayInputStream(output.toString().getBytes)
     //val model = ModelFactory.createDefaultModel()
     //model.read(in, null, "TURTLE")
@@ -167,7 +184,7 @@ class MappingLauncher(val username: String = "", val password: String = "", driv
 
   private def generateResultingRML(ast: AST, varTable: mutable.HashMap[Variable, VarResult], prettify: Boolean): Dataset = {
     val output = DatasetFactory.create()
-    new RMLGeneratorVisitor(output, varTable.toMap, prettify, username, password).doVisit(ast, null)
+    new RMLGeneratorVisitor(output, varTable.toMap, prettify, username, password, basePath = basePath).doVisit(ast, null)
     output
   }
 
@@ -179,7 +196,9 @@ class MappingLauncher(val username: String = "", val password: String = "", driv
       pushedOrPoppedFieldsPresent = searchForPushedOrPoppedFields(ast),
       inferenceDatatype = inferenceDatatype,
       normaliseURIs = normaliseURIs,
-      parallelCollectionConfigurator = parallelCollectionConfigurator).doVisit(ast, null)
+      parallelCollectionConfigurator = parallelCollectionConfigurator,
+      basePath = basePath
+    ).doVisit(ast, null)
   }
 
   private def generateShapeMaps(ast: AST, varTable: mutable.HashMap[Variable, VarResult]): List[ShapeMapInference] = {
@@ -191,7 +210,9 @@ class MappingLauncher(val username: String = "", val password: String = "", driv
       pushedOrPoppedFieldsPresent = searchForPushedOrPoppedFields(ast),
       inferenceDatatype = inferenceDatatype,
       normaliseURIs = normaliseURIs,
-      parallelCollectionConfigurator = parallelCollectionConfigurator).doVisit(ast, null)
+      parallelCollectionConfigurator = parallelCollectionConfigurator,
+      basePath = basePath
+    ).doVisit(ast, null)
     shapeMapTable.asScala.toList
   }
 
@@ -206,13 +227,13 @@ class MappingLauncher(val username: String = "", val password: String = "", driv
   private def searchForPushedOrPoppedFields(ast: AST): Boolean = new PushedOrPoppedValueSearchVisitor().doVisit(ast, null)
 
   private def resolveImports(mappingRules: String): String = {
-    val sourceHelper = new SourceHelper()
+    val sourceHelper = SourceHelper()
     val regex = "[Ii][Mm][Pp][Oo][Rr][Tt]\\s*<(.+)>".r
     regex.replaceAllIn(mappingRules, matchedPart => {
       val importSource = matchedPart.group(1)
       val loadedSource =
         if(importSource.contains("://")) sourceHelper.getURLContent(importSource)
-        else sourceHelper.getContentFromRelativePath(importSource)
+        else sourceHelper.getContentFromRelativePath(importSource, basePath)
       java.util.regex.Matcher.quoteReplacement(loadedSource.fileContent)
     })
   }

src/main/scala/com/herminiogarcia/shexml/helper/SourceHelper.scala

@@ -2,40 +2,44 @@ package com.herminiogarcia.shexml.helper
 
 import com.herminiogarcia.shexml.helper.SourceHelper.{saveFileResult, searchFileResult}
 
+import java.nio.charset.StandardCharsets
+import java.nio.file.Path
 import scala.collection.mutable
 
 /**
   * Created by herminio on 21/2/18.
   */
-class SourceHelper {
+case class SourceHelper() {
 
   def getURLContent(url: String): LoadedSource = searchFileResult(url) match {
     case Some(result) => result
     case None =>
       val parsedURL = new java.net.URL(url)
-      val file = scala.io.Source.fromURL(parsedURL, "UTF-8")
+      val file = scala.io.Source.fromURL(parsedURL, StandardCharsets.UTF_8.toString)
       try {
         val content = LoadedSource(file.mkString, url)
         saveFileResult(url, content)
         content
       } finally { file.close() }
   }
 
-  def getContentFromRelativePath(path: String): LoadedSource = searchFileResult(path) match {
-    case Some(result) => result
-    case None =>
-      val file = scala.io.Source.fromFile(path, "UTF-8")
-      try {
-        val content = LoadedSource(file.mkString, path)
-        saveFileResult(path, content)
-        content
-      } finally { file.close() }
+  def getContentFromRelativePath(path: String, base: Path = Path.of("")): LoadedSource = {
+    val fullPath = base.resolve(path).normalize().toString
+    searchFileResult(fullPath) match {
+      case Some(result) => result
+      case None =>
+        val file = scala.io.Source.fromFile(fullPath, StandardCharsets.UTF_8.toString)
+        try {
+          val content = LoadedSource(file.mkString, fullPath)
+          saveFileResult(fullPath, content)
+          content
+        } finally { file.close() }
+    }
   }
 
   def getStdinContents(): LoadedSource = {
     LoadedSource(scala.io.Source.stdin.mkString, "-")
   }
-
 }
 
 object SourceHelper {

src/main/scala/com/herminiogarcia/shexml/visitor/QuerySearcher.scala

@@ -28,7 +28,7 @@ class QuerySearcher(val varTable: Map[Variable, VarResult]) {
   private def getURLContents(u: URL): QueryClause = {
     val parts = u.value.split('.')
     val extension = parts(parts.length - 1)
-    val file = new SourceHelper().getURLContent(u.value)
+    val file = SourceHelper().getURLContent(u.value)
     if(extension == "xpath") {
       XmlPath(file.fileContent)
     } else if(extension == "jsonpath") {

src/main/scala/com/herminiogarcia/shexml/visitor/RDFGeneratorVisitor.scala

@@ -18,6 +18,7 @@ import org.apache.jena.util.SplitIRI
 
 import scala.collection.concurrent
 import java.io.{File, StringReader}
+import java.nio.file.Path
 import java.sql.DriverManager
 import java.util.concurrent.ConcurrentLinkedQueue
 import javax.xml.transform.stream.StreamSource
@@ -35,7 +36,8 @@ class RDFGeneratorVisitor(dataset: Dataset, varTable: Map[Variable, VarResult],
                           pushedOrPoppedFieldsPresent: Boolean = true,
                           inferenceDatatype: Boolean = false,
                           normaliseURIs: Boolean = false,
-                          parallelCollectionConfigurator: ParallelExecutionConfigurator = new ParallelExecutionConfigurator(Map(), None))
+                          parallelCollectionConfigurator: ParallelExecutionConfigurator = new ParallelExecutionConfigurator(Map(), None),
+                          basePath: Path)
   extends DefaultVisitor[Any, Any] with JdbcDriverRegistry {
 
   protected val prefixTable = concurrent.TrieMap[String, String](("rdf:", "http://www.w3.org/1999/02/22-rdf-syntax-ns#"))
@@ -49,6 +51,7 @@ class RDFGeneratorVisitor(dataset: Dataset, varTable: Map[Variable, VarResult],
   protected val xpathQueryResultsCache = new XpathQueryResultsCache(pushedOrPoppedFieldsPresent)
   protected val xmlDocumentCache = new XMLDocumentCache()
   protected val functionHubExecuterCache = new FunctionHubExecutorCache()
+  protected val sourceHelper: SourceHelper = SourceHelper()
   protected val defaultModel = dataset.getDefaultModel
   protected val jsonPathConfiguration = Configuration.defaultConfiguration()
     .addOptions(com.jayway.jsonpath.Option.ALWAYS_RETURN_LIST)
@@ -614,7 +617,7 @@ class RDFGeneratorVisitor(dataset: Dataset, varTable: Map[Variable, VarResult],
       else if(url.contains('*'))
         throw new Exception("* wildcard not allowed over remote files")
       else
-        List(new SourceHelper().getURLContent(url))
+        List(sourceHelper.getURLContent(url))
 
     case RelativePath(path) =>
       if(isRDFSource(path)) {
@@ -625,11 +628,11 @@ class RDFGeneratorVisitor(dataset: Dataset, varTable: Map[Variable, VarResult],
         List(LoadedSource("", fileProtocol + fileAbsolutePath))
       }
       else if(path.contains('*')) getAllFilesContents(path)
-      else List(new SourceHelper().getContentFromRelativePath(path))
+      else List(sourceHelper.getContentFromRelativePath(path, basePath))
 
     case JdbcURL(url) => List(LoadedSource("", url))
 
-    case Stdin() => List(new SourceHelper().getStdinContents())
+    case Stdin() => List(sourceHelper.getStdinContents())
 
 
     case default => visit(default, optionalArgument)
@@ -1007,10 +1010,11 @@ class RDFGeneratorVisitor(dataset: Dataset, varTable: Map[Variable, VarResult],
     val fileBeginning = slices(0).splitAt(slices(0).lastIndexOf("/"))._2.replace("/", "")
     val fileEnding = slices(1).splitAt(slices(1).lastIndexOf("."))._1
     val fileExtension = slices(1).splitAt(slices(1).lastIndexOf("."))._2
-    val files = new File(path).listFiles().filter(_.isFile)
+    val normPath = basePath.resolve(path).normalize()
+    val files = normPath.toFile.listFiles().filter(_.isFile)
       .filter(_.getName.endsWith(fileEnding + fileExtension)).filter(_.getName.startsWith(fileBeginning))
     val fileProtocol = if(path.startsWith("/")) "file://" else "file:///"
-    files.map(file => new SourceHelper().getURLContent(fileProtocol + file.getAbsolutePath.replaceAll("\\\\", "/"))).toList
+    files.map(file => sourceHelper.getURLContent(fileProtocol + file.getAbsolutePath.replaceAll("\\\\", "/"))).toList
   }
 
   private def visitAction(actionOrLiteral: ActionOrLiteral, predicateObjectsList: List[Any], optionalArgument: Any): List[Result] = actionOrLiteral match {

src/main/scala/com/herminiogarcia/shexml/visitor/RMLGeneratorVisitor.scala

@@ -5,8 +5,10 @@ import com.typesafe.scalalogging.Logger
 import org.apache.jena.query.Dataset
 import org.apache.jena.rdf.model.{Resource, Statement}
 
-class RMLGeneratorVisitor(dataset: Dataset, varTable: Map[Variable, VarResult], prettify: Boolean ,username: String, password: String)
-  extends RDFGeneratorVisitor(dataset, varTable, username, password) with JdbcDriverRegistry {
+import java.nio.file.Path
+
+class RMLGeneratorVisitor(dataset: Dataset, varTable: Map[Variable, VarResult], prettify: Boolean ,username: String, password: String, basePath: Path)
+  extends RDFGeneratorVisitor(dataset, varTable, username, password, basePath = basePath) with JdbcDriverRegistry {
 
   private val mapPrefix = "http://mapping.example.com/"
   private val rmlPrefix = "http://semweb.mmlab.be/ns/rml#"

src/test/scala/com/herminiogarcia/shexml/FilmsStdin.scala

@@ -48,7 +48,7 @@ class FilmsStdin extends AnyFunSuite
 
   override def beforeAll(configMap: ConfigMap): Unit = {
     super.beforeAll(configMap)
-    val stream = new ByteArrayInputStream(new SourceHelper().getContentFromRelativePath("./src/test/resources/filmsAlt.json").fileContent.getBytes())
+    val stream = new ByteArrayInputStream(SourceHelper().getContentFromRelativePath("./src/test/resources/filmsAlt.json").fileContent.getBytes())
     System.setIn(stream)
     stream.close()
     output = mappingLauncher.launchMapping(example).getDefaultModel

src/test/scala/com/herminiogarcia/shexml/MultipleElementIteratorExpressionWithCSVFromStdinTest.scala

@@ -57,7 +57,7 @@ class MultipleElementIteratorExpressionWithCSVFromStdinTest extends AnyFunSuite
 
   override def beforeAll(configMap: ConfigMap): Unit = {
     super.beforeAll(configMap)
-    val stream = new ByteArrayInputStream(new SourceHelper().getURLContent("https://rawgit.com/herminiogg/ShExML/enhancement-%239/src/test/resources/films.csv").fileContent.getBytes())
+    val stream = new ByteArrayInputStream(SourceHelper().getURLContent("https://rawgit.com/herminiogg/ShExML/enhancement-%239/src/test/resources/films.csv").fileContent.getBytes())
     System.setIn(stream)
     stream.close()
     output = mappingLauncher.launchMapping(example).getDefaultModel

src/test/scala/com/herminiogarcia/shexml/ParallelConfigFixtures.scala

@@ -3,6 +3,8 @@ package com.herminiogarcia.shexml
 import com.herminiogarcia.shexml.helper.ParallelExecutionConfigurator
 import org.scalatest.{BeforeAndAfterAllConfigMap, ConfigMap, TestSuite}
 
+import java.nio.file.Path
+
 
 trait ParallelConfigInferenceDatatypesNormaliseURIsFixture extends BeforeAndAfterAllConfigMap with MappingLauncherInitializer { this: TestSuite =>
   var mappingLauncher: MappingLauncher = _
@@ -49,6 +51,17 @@ trait ParallelConfigSparql extends BeforeAndAfterAllConfigMap with MappingLaunch
   }
 }
 
+trait ParallelConfigBasePath extends BeforeAndAfterAllConfigMap with MappingLauncherInitializer { this: TestSuite =>
+  var mappingLauncher: MappingLauncher = _
+
+  def relativeBasePath: Path
+
+  override def beforeAll(configMap: ConfigMap): Unit = {
+    mappingLauncher = configMapToParallelConfiguration(configMap).parallelConfigurationBasePath(relativeBasePath)
+    super.beforeAll(configMap)
+  }
+}
+
 trait ParallelConfigValidation extends BeforeAndAfterAllConfigMap with MappingLauncherInitializer { this: TestSuite =>
   var parallelConfiguration: ParallelExecutionConfigurator = _
 

src/test/scala/com/herminiogarcia/shexml/ParallelConfigurations.scala

@@ -2,6 +2,8 @@ package com.herminiogarcia.shexml
 
 import com.herminiogarcia.shexml.helper.ParallelExecutionConfigurator
 
+import java.nio.file.Path
+
 class ParallelConfigurations(val parallelConfiguration: ParallelExecutionConfigurator) {
 
   val parallelConfigurationInferenceDatatypesNormaliseURIs = new MappingLauncher(
@@ -34,6 +36,11 @@ class ParallelConfigurations(val parallelConfiguration: ParallelExecutionConfigu
     "root",
     parallelCollectionConfigurator = parallelConfiguration
   )
+
+  def parallelConfigurationBasePath(basePath: Path) = new MappingLauncher(
+    parallelCollectionConfigurator = parallelConfiguration,
+    basePath = basePath
+  )
 }
 
 object ParallelConfigurations {