Merge branch '29-add-aegis-flag' into 'master'

Resolve "Add AEGIS flag"

Closes #29

See merge request !23

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

@@ -87,6 +87,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
 import swing2swt.layout.BorderLayout;
+import org.eclipse.swt.events.KeyAdapter;
+import org.eclipse.swt.events.KeyEvent;
 
 public class PushDialog extends Dialog {
 	private static final Logger _log = Logger.getLogger(PushDialog.class);
@@ -212,6 +214,14 @@ public class PushDialog extends Dialog {
 		createContents();
 
 		logAppender = new SwtLogAppender(this.txtJson);
+		txtJson.addKeyListener(new KeyAdapter() {
+			@Override
+			public void keyPressed(KeyEvent e) {
+				if (e.character == 'k' && (e.stateMask == SWT.COMMAND || e.stateMask == SWT.CTRL)) {
+					logAppender.clearBuffer();
+				}
+			}
+		});
 		
 		Composite composite = new Composite(shell, SWT.NO_FOCUS);
 		composite.setLayoutData(BorderLayout.SOUTH);
@@ -297,6 +307,9 @@ public class PushDialog extends Dialog {
 
 				for (int i = futures.size() - 1; i >= 0; i--) {
 					Future<?> future = futures.get(i);
+					if (future == null) {
+						continue;
+					}
 					if (future.isDone() || future.isCancelled()) {
 						futures.remove(future);
 					} else {
@@ -512,9 +525,12 @@ public class PushDialog extends Dialog {
 				long lastTime = 0;
 				do {
 					for (int i = futures.size() - 1; i >= 0; i--) {
-						Future<?> f = futures.get(i);
-						if (f.isDone()) {
-							futures.remove(f);
+						Future<?> future = futures.get(i);
+						if (future == null) {
+							continue;
+						}
+						if (future.isDone()) {
+							futures.remove(future);
 						}
 					}
 
@@ -676,7 +692,7 @@ public class PushDialog extends Dialog {
 
 								// If filtering, check INSTCODE is listed
 								if (instCodesFilter.size() > 0 && !(isBlackList ^ instCodesFilter.contains(accessionInstCode))) {
-									_log.info("Ignoring accessions with inst code : " + accessionInstCode);
+									_log.debug("Ignoring accessions with inst code : " + accessionInstCode);
 									continue;
 								}
 

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

@@ -47,6 +47,17 @@ public class SwtLogAppender extends WriterAppender {
 		patternLayout.setConversionPattern(DEFAULT_LAYOUT_PATTERN);
 		setLayout(patternLayout);
 	}
+	
+	public void clearBuffer() {
+		synchronized (logBuffer) {
+			display.asyncExec(() -> {
+				if (text != null) {
+					text.setText("");
+				}
+			});
+			logBuffer.delete(0, logBuffer.length());
+		}
+	}
 
 	public void setConversionPattern(String conversionPattern) {
 		PatternLayout patternLayout = (PatternLayout) getLayout();
@@ -75,14 +86,16 @@ public class SwtLogAppender extends WriterAppender {
 			}
 		}
 		final String mes = layout.format(loggingEvent) + (throwableStr == null ? "" : sb.toString());
-		logBuffer.append(mes);
-		if (logBuffer.length() > maxBufferSize && text.getSelectionCount() == 0) {
-			// System.err.println("CLEARING POOL len=" + logBuffer.length() +
-			// " removing=" + (logBuffer.length() - maxBufferSize));
-			logBuffer.replace(0, logBuffer.length() - maxBufferSize, "");
-			int pos = logBuffer.indexOf("\n");
-			if (pos >= 0) {
-				logBuffer.replace(0, pos + 1, "");
+		synchronized (logBuffer) {
+			logBuffer.append(mes);
+			if (logBuffer.length() > maxBufferSize) {
+				// System.err.println("CLEARING POOL len=" + logBuffer.length() +
+				// " removing=" + (logBuffer.length() - maxBufferSize));
+				logBuffer.replace(0, logBuffer.length() - maxBufferSize, "");
+				int pos = logBuffer.indexOf("\n");
+				if (pos >= 0) {
+					logBuffer.replace(0, pos + 1, "");
+				}
 			}
 		}
 

anno-gui/src/main/java/org/genesys2/anno/predefined/GenesysJSON.java

@@ -225,6 +225,9 @@ public class GenesysJSON {
 		columnDef = new JsonField(Api1Constants.Accession.MLSSTAT, RdfMCPD.MLSSTAT).setType(boolean.class);
 		columns.add(columnDef);
 
+		columnDef = new JsonField(Api1Constants.Accession.AEGIS, RdfMCPD.AEGIS).setType(boolean.class);
+		columns.add(columnDef);
+
 		columnDef = new JsonField(Api1Constants.Accession.INTRUST, RdfMCPD.FAOINTRUST).setType(boolean.class);
 		columns.add(columnDef);
 

anno-gui/src/main/java/org/genesys2/anno/predefined/MCPD.java

@@ -164,6 +164,9 @@ public class MCPD {
 		columnDef = new ColumnDef("MLSSTAT", "MLS status of the accession", ColumnDataType.BOOLEAN, false, RdfMCPD.MLSSTAT).setIncludeNull(false);
 		columns.add(columnDef);
 
+		columnDef = new ColumnDef("AEGIS", "Aegis status of the accession", ColumnDataType.BOOLEAN, false, RdfMCPD.AEGIS).setIncludeNull(false);
+		columns.add(columnDef);
+
 		columnDef = new ColumnDef("REMARKS", "Remarks", ColumnDataType.TEXT, false, RdfMCPD.REMARKS).setAllowMultiple(true);
 		columns.add(columnDef);
 

anno-gui/src/main/java/org/genesys2/anno/predefined/RdfMCPD.java

@@ -23,6 +23,7 @@ public class RdfMCPD {
 	public static final String ACCENUMB = "http://purl.org/germplasm/germplasmTerm#germplasmID";
 
 	public static final String ACCENUMB_NEW = "https://www.genesys-pgr.org/rdf/mcpd#newAcceNumb";
+	public static final String AEGIS = "https://www.genesys-pgr.org/rdf/mcpd#aegis";
 
 	public static final String GENUS = "http://rs.tdwg.org/dwc/terms/genus";
 	public static final String GENUS_NEW = "https://www.genesys-pgr.org/rdf/mcpd#newGenus";