Fixes to address problems reported by COPO, linked to issues #67 #63,…

… as well as a few others.

* Add missing STUDY_SET element to study.xml output
* Modifications to SraExportPipelineComponent for new and updated assay types supported by SRA 1.5

Note, some of these changes may affect ISAcreator and ISAconfigurator builds. Until tested with those, keep these changes in this hotfix/copo-sra-export branch.

import_layer/src/main/java/org/isatools/isatab/commandline/ConverterShellCommand.java

@@ -93,9 +93,13 @@ public static void main(String[] args) {
 				ISATABReducedMapper mapper = new ISATABReducedMapper(new BIIObjectStore(), loader.load());
 				ISAConfiguratorValidator validator = new ISAConfiguratorValidator(mapper.map());
 				log.info("Running validator");
-				if (validator.validate() != GUIInvokerResult.SUCCESS) {
-					log.warn("Validation failed");
+				GUIInvokerResult validationResult = validator.validate();
+				if (validationResult == GUIInvokerResult.ERROR) {
+					throw new Exception("Validation failed");
 				} else {
+					if (validationResult == GUIInvokerResult.WARNING) {
+						log.warn("Validation succceded with warnings");
+					}
 					log.info("Using SraExporter");
 					SraExporter exporter = new SraExporter(store, sourceDirPath, exportPath);
 					exporter.export();