Merge pull request #31 from mav7014/opt_counts

Add option to exclude counts from RabbitInAHat output
OHDSI · Apr 8, 2015 · e3aa1d6 · e3aa1d6
2 parents ff14574 + e60e4ee
commit e3aa1d6
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Showing 3 changed files with 41 additions and 10 deletions.
diff --git a/src/org/ohdsi/rabbitInAHat/ETLDocumentGenerator.java b/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();

diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java b/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));
 		}
 	}

diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/ETL.java b/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;
             }