Catch error in RowConverter when row contains less items than defined

columns (stopped the parser thread)
Increased Batch size for load and push, reduced queue size

anno-gui/src/main/java/org/genesys2/anno/converter/RowConverter.java

@@ -42,6 +42,12 @@ public class RowConverter {
 
 		List<Column> columns = dataSourceSheet.getColumns();
 		for (int i = 0; i < columns.size(); i++) {
+
+			if (i >= row.length) {
+				_log.warn("Row has less than " + (i + 1) + " columns: " + ArrayUtils.toString(row));
+				continue;
+			}
+
 			Column column = columns.get(i);
 			ColumnDef columnDef = findColumnDef(column, columnDefs.getColumnDefs());
 			if (columnDef == null) {
@@ -181,7 +187,7 @@ public class RowConverter {
 		ObjectNode rowNode = mapper.createObjectNode();
 
 		for (GenesysJSON.JsonField jsonField : genesysJson.getJsonFields()) {
-			if (! row.containsKey(jsonField.getRdfTerm())) 
+			if (!row.containsKey(jsonField.getRdfTerm()))
 				continue;
 			Object rdfValues = row.get(jsonField.getRdfTerm());
 			add(rowNode, jsonField, rdfValues);

anno-gui/src/main/java/org/genesys2/anno/gui/PushDialog.java

@@ -45,7 +45,7 @@ import com.fasterxml.jackson.databind.node.ObjectNode;
 
 public class PushDialog extends Dialog {
 	private static final Logger _log = Logger.getLogger(PushDialog.class);
-	protected static final int BATCH_SIZE = 25;
+	protected static final int BATCH_SIZE = 50;
 
 	@Autowired
 	private Settings settings;
@@ -53,7 +53,7 @@ public class PushDialog extends Dialog {
 	@Autowired
 	protected DataSourceLoader dataSourceLoader;
 
-	BlockingQueue<Runnable> linkedBlockingDeque = new LinkedBlockingDeque<Runnable>(100);
+	BlockingQueue<Runnable> linkedBlockingDeque = new LinkedBlockingDeque<Runnable>(4);
 	private ThreadPoolExecutor executorService = new ThreadPoolExecutor(1, 2, 30, TimeUnit.SECONDS, linkedBlockingDeque, new ThreadPoolExecutor.CallerRunsPolicy());
 
 	protected Object result;
@@ -267,7 +267,7 @@ public class PushDialog extends Dialog {
 					try {
 
 						do {
-							List<Object[]> rows = rowReader.readRows(10);
+							List<Object[]> rows = rowReader.readRows(100);
 
 							if (rows.size() == 0) {
 								_log.info("Exhausted data source.");
@@ -323,7 +323,10 @@ public class PushDialog extends Dialog {
 						_log.error(e.getMessage(), e);
 					} catch (InterruptedException e) {
 						_log.info("Execution was interrupted");
+					} catch (Throwable e) {
+						_log.error(e.getMessage(), e);
 					} finally {
+						_log.info("Reader finished.");
 						try {
 							rowReader.close();
 						} catch (IOException e) {
@@ -375,6 +378,12 @@ public class PushDialog extends Dialog {
 			public void run() {
 				try {
 					_log.info("Pushing data for instCode=" + instCode + " size=" + accns.size());
+					if (_log.isDebugEnabled()) {
+						for (ObjectNode o : accns) {
+							_log.debug(o);
+						}
+					}
+
 					genesysClient.updateAccessions(instCode, accns);
 				} catch (OAuthAuthenticationException e) {
 					_log.error(e.getMessage(), e);

anno-gui/src/main/java/org/genesys2/anno/gui/SettingsDialog.java

@@ -236,7 +236,7 @@ public class SettingsDialog extends Dialog {
 			_log.warn(e.getMessage());
 			String authorizationUrl = genesysClient.getAuthorizationUrl(null);
 			VerifierDialog vd = new VerifierDialog(getParent(), SWT.NONE);
-			String verifierCode = vd.open(authorizationUrl);
+			String verifierCode = vd.open(authorizationUrl).trim();
 			_log.info("Got verifier code: " + verifierCode);
 			if (StringUtils.isNotBlank(verifierCode)) {
 				genesysClient.authenticate(verifierCode);

anno-gui/src/main/java/org/genesys2/anno/gui/SwtLogAppender.java

@@ -15,7 +15,7 @@ import org.eclipse.swt.widgets.Text;
 
 public class SwtLogAppender extends WriterAppender {
 
-	private static final String DEFAULT_LAYOUT_PATTERN = "%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n";
+	private static final String DEFAULT_LAYOUT_PATTERN = "%d{yyyy-MM-dd HH:mm:ss} %t %-5p %c{1}:%L - %m%n";
 	private Text text;
 	private Display display;
 	private int maxBufferSize = 100000;