Add option to exclude counts from RabbitInAHat output

Enable value counts to be excluded from specs file (in both binary or JSON format)
and ETL document appendix via command line argument --no-counts (resolves #29).

src/org/ohdsi/rabbitInAHat/ETLDocumentGenerator.java

@@ -52,16 +52,16 @@ public static void main(String[] args) throws IOException, ClassNotFoundExceptio
 		generate(etl, "C:/Users/mschuemi/Desktop/test.docx");
 	}
 
-	public static void generate(ETL etl, String filename) {
+	public static void generate(ETL etl, String filename, boolean includeCounts) {
 		try {
 			CustomXWPFDocument document = new CustomXWPFDocument();
 
 			addTableLevelSection(document, etl);
 
 			for (Table cdmTable : etl.getCDMDatabase().getTables())
 				addCDMTableSection(document, etl, cdmTable);
-			
-			addSourceTablesAppendix(document, etl);
+
+			if (includeCounts) addSourceTablesAppendix(document, etl);
 
 			document.write(new FileOutputStream(new File(filename)));
 		} catch (FileNotFoundException e) {
@@ -72,6 +72,10 @@ public static void generate(ETL etl, String filename) {
 			e.printStackTrace();
 		}
 	}
+
+	public static void generate(ETL etl, String filename) {
+		generate(etl, filename, true);
+	}
 
 	private static void addSourceTablesAppendix(CustomXWPFDocument document, ETL etl) {
 		XWPFParagraph paragraph = document.createParagraph();

src/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java

@@ -58,12 +58,19 @@ public class RabbitInAHatMain implements ResizeListener, ActionListener {
 	private JScrollPane		scrollPane2;
 	private MappingPanel	tableMappingPanel;
 	private JSplitPane		tableFieldSplitPane;
+	private boolean 		includeCounts;
 
 	public static void main(String[] args) {
-		new RabbitInAHatMain();
+		boolean includeCounts = true;
+		for (String arg: args) {
+			if (arg.equals("--no-counts")) includeCounts = false;
+		}
+		new RabbitInAHatMain(includeCounts);
 	}
 
-	public RabbitInAHatMain() {
+	public RabbitInAHatMain(boolean includeCounts) {
+		this.includeCounts =  includeCounts;
+
 		frame = new JFrame("Rabbit in a hat");
 		frame.addWindowListener(new WindowAdapter() {
 			public void windowClosing(WindowEvent e) {
@@ -247,7 +254,7 @@ private void doSave(String filename) {
 		if (filename != null) {
 			frame.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
 			ETL.FileFormat fileFormat = filename.endsWith("json") ? ETL.FileFormat.Json : ETL.FileFormat.Binary;
-			ObjectExchange.etl.save(filename, fileFormat);
+			ObjectExchange.etl.save(filename, fileFormat, includeCounts);
 			frame.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
 		}
 	}
@@ -281,7 +288,7 @@ private void doOpenScanReport(String filename) {
 	private void doGenerateEtlDoc(String filename) {
 		if (filename != null) {
 			frame.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
-			ETLDocumentGenerator.generate(ObjectExchange.etl, filename);
+			ETLDocumentGenerator.generate(ObjectExchange.etl, filename, includeCounts);
 			frame.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
 		}
 	}

src/org/ohdsi/rabbitInAHat/dataModel/ETL.java

@@ -19,6 +19,7 @@
 
 import com.cedarsoftware.util.io.JsonReader;
 import com.cedarsoftware.util.io.JsonWriter;
+import com.cedarsoftware.util.io.MetaUtils;
 
 import java.io.*;
 import java.nio.file.Files;
@@ -95,13 +96,32 @@ public ItemToItemMap createItemToItemMap(MappableItem source, MappableItem targe
 
     /**
      * Convert into pretty-print JSON
+     * @param includeCounts if false, exclude the valueCounts field from result
      * @return JSON representation of object
      */
+    public String toJson(boolean includeCounts) {
+        Map<String, Object> args = new HashMap<>();
+        if (!includeCounts) {
+            Map<Class, List<String>> fieldSpecifier = new HashMap<>();
+            ArrayList<java.lang.reflect.Field> fieldFields =
+                    new ArrayList<>(MetaUtils.getDeepDeclaredFields(Field.class).values());
+            ArrayList<String> fieldNames = new ArrayList<>();
+            for (java.lang.reflect.Field field : fieldFields) {
+                String fieldName = field.getName();
+                if (Objects.equals(fieldName, "valueCounts")) continue;
+                fieldNames.add(fieldName);
+            }
+            fieldSpecifier.put(Field.class, fieldNames);
+            args.put(JsonWriter.FIELD_SPECIFIERS, fieldSpecifier);
+        }
+        return JsonWriter.formatJson(JsonWriter.objectToJson(this, args));
+    }
+
     public String toJson() {
-        return JsonWriter.formatJson(JsonWriter.objectToJson(this));
+        return toJson(true);
     }
 
-    public void save(String filename, FileFormat format) {
+    public void save(String filename, FileFormat format, boolean includeCounts) {
         try {
             switch (format) {
                 case Binary:
@@ -113,7 +133,7 @@ public void save(String filename, FileFormat format) {
                     }
                     break;
                 case Json:
-                    String json = toJson();
+                    String json = toJson(includeCounts);
                     Files.write(Paths.get(filename), json.getBytes("utf-8"));
                     break;
             }