Merge branch 'sbgfixes' into develop

README.md

@@ -18,7 +18,7 @@ Once the download has been completed, unpack the downloaded archive.
 The following command will automatically download and unpack the archive in the newly created `rabix` directory:
 
 ```sh
-wget https://github.com/rabix/bunny/releases/download/v1.0.4-1/rabix-1.0.4.tar.gz -O rabix-1.0.4.tar.gz && tar -xvf rabix-1.0.4.tar.gz
+wget https://github.com/rabix/bunny/releases/download/v1.0.4-4/rabix-1.0.4.tar.gz -O rabix-1.0.4.tar.gz && tar -xvf rabix-1.0.4.tar.gz
 ```
 
 

rabix-bindings-cwl/src/main/java/org/rabix/bindings/cwl/processor/callback/CWLStageInputProcessorCallback.java

@@ -105,7 +105,7 @@ private String stagePath(String path, StageInput stageInput) throws BindingExcep
       return destinationFile.toString();
     case LINK:
         try {
-          Files.createLink(destinationFile, file);
+          Files.createSymbolicLink(destinationFile, file);
         } catch (IOException e) {
           throw new BindingException(e);
         }

rabix-bindings-sb/src/main/java/org/rabix/bindings/sb/SBProcessor.java

@@ -380,6 +380,10 @@ public static List<Map<String, Object>> getSecondaryFiles(SBJob job, HashAlgorit
         Path pathToSec = Paths.get(secondaryFilePath);
         if (Files.exists(pathToSec) || !onlyExisting) {
           Map<String, Object> file = SBFileValueHelper.pathToRawFile(pathToSec, hashAlgorithm, Paths.get(SBFileValueHelper.getPath(fileValue)));
+          boolean loadContents = SBBindingHelper.loadContents(binding);
+          if (loadContents) {
+            SBFileValueHelper.setContents(file);
+          }
           secondaryFileMaps.add(file);
         }
       } catch (IOException | URISyntaxException e) {

rabix-bindings-sb/src/main/java/org/rabix/bindings/sb/processor/callback/SBStageInputProcessorCallback.java

@@ -109,7 +109,7 @@ private String stagePath(String path, StageInput stageInput) throws BindingExcep
       return destinationFile.getAbsolutePath();
     case LINK:
         try {
-          Files.createLink(destinationFile.toPath(), file.toPath());
+          Files.createSymbolicLink(destinationFile.toPath(), file.toPath());
         } catch (IOException e) {
           throw new BindingException(e);
         }

rabix-bindings-sb/src/main/java/org/rabix/bindings/sb/service/impl/SBGlobServiceImpl.java

@@ -81,7 +81,7 @@ public FileVisitResult visitFileFailed(Path file, IOException exc) throws IOExce
           @Override
           public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) throws IOException {
             if(dir.getFileName() != null) {
-              if (matcher.matches(dir.getFileName()) && isDir) {
+              if (matcher.matches(dir.getFileName()) && isDir && !dir.equals(globDir.toPath())) {
                 files.add(dir.toFile());
               }
             }

rabix-engine/src/main/java/org/rabix/engine/processor/handler/impl/JobStatusEventHandler.java

@@ -87,8 +87,6 @@ public JobStatusEventHandler(final DAGNodeService dagNodeService, final AppServi
 
   @Override
   public void handle(JobStatusEvent event, EventHandlingMode mode) throws EventHandlerException {
-    logger.info(event.toString());
-
     JobRecord jobRecord = jobRecordService.find(event.getJobId(), event.getContextId());
     if (jobRecord == null) {
       logger.info("Possible stale message. Job {} for root {} doesn't exist.", event.getJobId(), event.getContextId());