Set "Include null" to true by default

- Except CROPNAME and booleans

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

@@ -203,6 +203,7 @@ public class DataSourceSheet extends AbstractModelObject implements IDataSourceS
 						column.setRdfTerm(columnDef.getRdfTerm());
 						column.setMultiple(columnDef.hasAllowMultiple());
 						column.setDescription(columnDef.getTitle());
+						column.setIncludeNull(columnDef.hasIncludeNull());
 					}
 				}
 			}

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

@@ -154,6 +154,7 @@ public class DwcaBuilder extends AbstractModelObject {
 					column.put("pattern", sourceColumn.getPattern());
 					column.put("separator", sourceColumn.getSeparator());
 					column.put("groupPattern", sourceColumn.getGroupPattern());
+					column.put("includeNull", sourceColumn.isIncludeNull());
 					columns.put(column);
 				}
 			}
@@ -273,6 +274,8 @@ public class DwcaBuilder extends AbstractModelObject {
 							sourceColumn.setDataType(ColumnDataType.valueOf(column.getString("dataType")));
 						if (column.has("multiple"))
 							sourceColumn.setMultiple(column.getBoolean("multiple"));
+						if (column.has("includeNull"))
+							sourceColumn.setIncludeNull(column.getBoolean("includeNull"));
 
 						if (loadedColumns.contains(sourceColumn)) {
 							columnList.add(sourceColumn);

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

@@ -28,11 +28,6 @@ import java.util.concurrent.ThreadPoolExecutor;
 import java.util.concurrent.TimeUnit;
 import java.util.function.Consumer;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.log4j.Level;
 import org.apache.log4j.LogManager;
@@ -66,6 +61,11 @@ import org.genesys2.client.oauth.PleaseRetryException;
 import org.genesys2.client.oauth.api.accession.Api1Constants;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
 import swing2swt.layout.BorderLayout;
 
 public class PushDialog extends Dialog {
@@ -89,7 +89,7 @@ public class PushDialog extends Dialog {
 	protected DataSourceLoader dataSourceLoader;
 
 	BlockingQueue<Runnable> linkedBlockingDeque = new LinkedBlockingDeque<Runnable>(4);
-	private ThreadPoolExecutor executorService = new ThreadPoolExecutor(1, 2, 30, TimeUnit.SECONDS, linkedBlockingDeque, new ThreadPoolExecutor.CallerRunsPolicy());
+	private ThreadPoolExecutor executorService = new ThreadPoolExecutor(1, 4, 30, TimeUnit.SECONDS, linkedBlockingDeque, new ThreadPoolExecutor.CallerRunsPolicy());
 
 	protected Object result;
 	protected Shell shell;
@@ -482,8 +482,6 @@ public class PushDialog extends Dialog {
 					if (_log.isDebugEnabled())
 						_log.debug(serverResponse);
 
-					_log.info("Push done.");
-
 					try {
 						JsonNode ri = objectMapper.readTree(serverResponse);
 						ri.forEach(new Consumer<JsonNode>() {
@@ -497,6 +495,8 @@ public class PushDialog extends Dialog {
 							}
 						});
 
+						_log.info("Push done.");
+
 					} catch (IOException e) {
 						// TODO Auto-generated catch block
 						e.printStackTrace();

anno-gui/src/main/java/org/genesys2/anno/model/Column.java

@@ -28,17 +28,18 @@ public class Column extends AbstractModelObject {
 	private String separator = ";";
 	private String pattern;
 	private String groupPattern;
-	private boolean includeNull = false;
+	private boolean includeNull = true;
 
 	public Column() {
 	}
 
-	public Column(String preferredName, ColumnDataType dataType, boolean multiple, boolean unique, String rdfTerm) {
+	public Column(String preferredName, ColumnDataType dataType, boolean multiple, boolean unique, String rdfTerm, boolean includeNull) {
 		this.preferredName = preferredName;
 		this.dataType = dataType;
 		this.multiple = multiple;
 		this.unique = unique;
 		this.rdfTerm = rdfTerm;
+		this.includeNull = includeNull;
 	}
 
 	public String getPreferredName() {

anno-gui/src/main/java/org/genesys2/anno/model/ColumnDef.java

@@ -28,6 +28,7 @@ public class ColumnDef extends AbstractModelObject {
 	private Set<ColumnValidator> validators = new HashSet<ColumnValidator>();
 	private String title;
 	private boolean allowMultiple = false;
+	private boolean includeNull = true;
 
 	public ColumnDef() {
 	}
@@ -96,4 +97,13 @@ public class ColumnDef extends AbstractModelObject {
 		this.allowMultiple = allowMultiple;
 		return this;
 	}
+
+	public boolean hasIncludeNull() {
+		return this.includeNull;
+	}
+	
+	public ColumnDef setIncludeNull(boolean includeNull) {
+		this.includeNull = includeNull;
+		return this;
+	}
 }

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

@@ -74,7 +74,7 @@ public class MCPD {
 		columnDef = new ColumnDef("SUBTAUTHOR", "Subtaxon authority", ColumnDataType.TEXT, false, RdfMCPD.SUBTAUTHOR);
 		columns.add(columnDef);
 
-		columnDef = new ColumnDef("CROPNAME", "Common crop name", ColumnDataType.TEXT, false, RdfMCPD.CROPNAME);
+		columnDef = new ColumnDef("CROPNAME", "Common crop name", ColumnDataType.TEXT, false, RdfMCPD.CROPNAME).setIncludeNull(false);
 		columns.add(columnDef);
 
 		columnDef = new ColumnDef("ACCENAME", "Accession name", ColumnDataType.TEXT, false, RdfMCPD.ACCENAME).setAllowMultiple(true);
@@ -158,20 +158,20 @@ public class MCPD {
 		columnDef = new ColumnDef("STORAGE", "Type of germplasm storage", ColumnDataType.TEXT, false, RdfMCPD.STORAGE).setAllowMultiple(true);
 		columns.add(columnDef);
 
-		columnDef = new ColumnDef("MLSSTAT", "MLS status of the accession", ColumnDataType.BOOLEAN, false, RdfMCPD.MLSSTAT);
+		columnDef = new ColumnDef("MLSSTAT", "MLS status of the accession", ColumnDataType.BOOLEAN, false, RdfMCPD.MLSSTAT).setIncludeNull(false);
 		columns.add(columnDef);
 
 		columnDef = new ColumnDef("REMARKS", "Remarks", ColumnDataType.TEXT, false, RdfMCPD.REMARKS).setAllowMultiple(true);
 		columns.add(columnDef);
 
 		// Genesys specific
-		columnDef = new ColumnDef("INTRUST", "FAO in Trust", ColumnDataType.BOOLEAN, false, RdfMCPD.FAOINTRUST);
+		columnDef = new ColumnDef("INTRUST", "FAO in Trust", ColumnDataType.BOOLEAN, false, RdfMCPD.FAOINTRUST).setIncludeNull(false);
 		columns.add(columnDef);
 
-		columnDef = new ColumnDef("AVAILABLE", "Accession is available for distribution", ColumnDataType.BOOLEAN, false, RdfMCPD.AVAILABLE);
+		columnDef = new ColumnDef("AVAILABLE", "Accession is available for distribution", ColumnDataType.BOOLEAN, false, RdfMCPD.AVAILABLE).setIncludeNull(false);
 		columns.add(columnDef);
 
-		columnDef = new ColumnDef("HISTORIC", "Historic entry", ColumnDataType.BOOLEAN, false, RdfMCPD.HISTORIC);
+		columnDef = new ColumnDef("HISTORIC", "Historic entry", ColumnDataType.BOOLEAN, false, RdfMCPD.HISTORIC).setIncludeNull(false);
 		columns.add(columnDef);
 
 		columnDef = new ColumnDef("ACCEURL", "Accession URL", ColumnDataType.TEXT, false, RdfMCPD.ACCEURL);