Excel feature framework operational.

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>org.ndextools</groupId>
     <artifactId>morphcx</artifactId>
-    <version>2.4.0-Beta-1d</version>
+    <version>2.4.0-Beta-1e</version>
     <packaging>jar</packaging>
 
     <url>http://www.ndextools.org</url>

src/main/java/org/ndextools/morphcx/shared/Configuration.java

@@ -12,14 +12,15 @@
  * finalizes the runtime configuration used by the application.
  */
 public final class Configuration {
-    public final boolean EXCEL_FEATURE_DISABLED = false;  // TODO: 2/7/19 temporary, remove when Excel feature goes alpha
+    public final boolean EXCEL_FEATURE_DISABLED = true;  // TODO: temporary, remove when Excel feature goes alpha
     private String[] args;
     private boolean isHelp;
     private Operation operation;
     private boolean inputIsFile;
     private boolean outputIsFile;
     private Newline newline;
     private boolean isServer;
+    private boolean isDebugMode;
     private String inputFilename;
     private String outputFilename;
     private char delimiter;
@@ -130,6 +131,13 @@ private CommandLine defineParams() throws ParseException {
                         .build()
         );
 
+        getCSVParameterOptions().addOption(
+                Option.builder(ConfigurationConstants.OPT_DEBUG)
+                        .longOpt(ConfigurationConstants.LONG_OPT_DEBUG)
+                        .desc("A flag used for debugging and development purposes. < -X | --DEBUG >")
+                        .build()
+        );
+
         // Apache Commons CLI - Step #2 of 3: Parse all command-line parameters
         CommandLine parsed;
         CommandLineParser parser = new DefaultParser();
@@ -224,6 +232,10 @@ private final void resolve(CommandLine parsed) {
         if (parsed.hasOption(ConfigurationConstants.OPT_SERVER)) {
             setIsServer(true);
         }
+
+        if (parsed.hasOption(ConfigurationConstants.OPT_DEBUG)) {
+            setIsDebugMode(true);
+        }
     }
 
     private final void preValidationAdjustments() {
@@ -312,6 +324,10 @@ public void printHelpText() {
 
     void setIsServer(boolean value) { this.isServer = value; }
 
+    public boolean isDebugMode() { return this.isDebugMode; }
+
+    void setIsDebugMode(boolean value) { this.isDebugMode = value; }
+
     public String getInputFilename() { return this.inputFilename; }
 
     void setInputFilename(String filename) { this.inputFilename = filename; }
@@ -346,6 +362,9 @@ public static class ConfigurationConstants {
 
         private static final String OPT_SERVER = "S";
 
+        private static final String OPT_DEBUG =  "X";
+        private static final String LONG_OPT_DEBUG =  "DEBUG";
+
         private static final String CONVERT_CSV = "CSV";
         private static final String CONVERT_TSV = "TSV";
         private static final String CONVERT_EXCEL = "EXCEL";

src/main/java/org/ndextools/morphcx/tables/ExcelApp.java

@@ -0,0 +1,50 @@
+package org.ndextools.morphcx.tables;
+
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.ndexbio.model.cx.NiceCXNetwork;
+import org.ndextools.morphcx.shared.Configuration;
+import org.ndextools.morphcx.writers.TableToPOI;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.List;
+
+public class ExcelApp implements Table3D {
+    private final Configuration cfg;
+    private final NiceCXNetwork niceCX;
+    private final TableToPOI writer;
+    private final OutputStream outStream;
+    private final XSSFWorkbook wb;
+
+    public ExcelApp(Configuration cfg,
+                    NiceCXNetwork niceCX,
+                    TableToPOI writer,
+                    XSSFWorkbook wb,
+                    OutputStream outStream) {
+        this.cfg = cfg;
+        this.niceCX = niceCX;
+        this.writer = writer;
+        this.outStream = outStream;
+        this.wb = wb;
+    }
+
+    @Override
+    public void morphThisCX() throws IOException {
+
+        Sheet sheet1 = wb.createSheet("Mike 1");
+        Row row = sheet1.createRow(0);
+        row.createCell(0).setCellValue("Cell-0");
+        row.createCell(1).setCellValue("Cell-1");
+        row.createCell(2).setCellValue("Cell-2");
+        row.createCell(3).setCellValue("Cell-3");
+        writer.outputAll();
+
+    }
+
+    @Override
+    public List<String> buildColumnHeadings() {
+        return null;  // TODO: 2/7/19 CANT BE NULL!
+    }
+}

src/main/java/org/ndextools/morphcx/tables/TablesRoot.java

@@ -1,19 +1,16 @@
 package org.ndextools.morphcx.tables;
 
-import java.io.File;
-import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.io.PrintStream;
 
-import org.apache.commons.csv.CSVPrinter;
-import org.apache.poi.ss.usermodel.Workbook;
-import org.apache.poi.ss.usermodel.WorkbookFactory;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
 import org.ndexbio.model.cx.NiceCXNetwork;
 import org.ndextools.morphcx.shared.CXReader;
 import org.ndextools.morphcx.shared.Configuration;
 import org.ndextools.morphcx.shared.Utilities;
-import org.ndextools.morphcx.writers.TableToCSV;
+import org.ndextools.morphcx.writers.TableToPOI;
 import org.ndextools.morphcx.writers.TableWritable;
 import org.ndextools.morphcx.writers.WriterFactory;
 
@@ -23,85 +20,87 @@
 public class TablesRoot {
 
     /**
-     * Converts the JSON-format NDEx CX Network into a NiceCXNetwork object, then uses a factory
-     * class to instantiate the class of writer needed by the operation.  Finally, control is passed
-     * to the class which morphs the NiceCXNetwork object to the desired output format.
+     * Converts the JSON-format NDEx CX Network into a NiceCXNetwork object, Then control
+     * is passed to the class which morphs the NiceCXNetwork object to the desired output format.
      *
      * @param cfg reference to a Configuration class object
      * @throws Exception base class exception when there is an IO or other processing error
      */
     public void execute(final Configuration cfg) throws Exception {
+
         String msg = String.format("%s: expecting MorphCX.appConfig() !=null, actual=%s ",
                 TablesRoot.class.getSimpleName(), cfg);
         Utilities.nullReferenceCheck(cfg, msg);
 
-        NiceCXNetwork niceCX = LoadInputCxNetwork(cfg);
-
-        switch (cfg.getOperation())
-        {
-            case EXCEL:
-                // TODO: BEGIN *************************************************************
-                // TODO: Remove feature disabled conditional when features goes alpha
-                if (cfg.EXCEL_FEATURE_DISABLED) {
-                    System.err.println("The Excel feature is still being developed!");
-                    return;
-                } else {
-
-                    try ( Workbook writer = setupPOIOutputWriter(cfg) ) {
-                        Table3D morph = new CXToExcel(cfg, niceCX, writer);
-                        morph.morphThisCX();
-                    } catch (Exception e) {
-                        throw new Exception(e);
-                    }
-                    break;
-                }
-                // TODO: END **************************************************************
+        // Transform input stream to a NiceCXNetwork object.
+        CXReader cxReader = new CXReader(cfg);
+        NiceCXNetwork niceCX = cxReader.produceNiceCX();
 
+        // Prepare for and run a morphing operation on the NiceCXNetwork object.
+        switch (cfg.getOperation()) {
             case TSV:
             case CSV:
             case NOT_SPECIFIED:
 
                 try ( TableWritable writer = setupCSVOutputWriter(cfg) ) {
-                    Table2D morph = new Webapp( cfg, niceCX, writer);
+                    Table2D morph = new WebApp( cfg, niceCX, writer);
                     morph.morphThisCX();
                 } catch (Exception e) {
                     throw new Exception(e);
                 }
                 break;
 
-        }
-    }
+            case EXCEL:
 
-    private static NiceCXNetwork LoadInputCxNetwork(Configuration cfg) throws IOException {
-        CXReader cxReader = new CXReader(cfg);
-        return cxReader.produceNiceCX();
+                // TODO: BEGIN ****************************************************************
+                // TODO: Remove/comment this code when excel feature is released for testing
+                if ( (cfg.EXCEL_FEATURE_DISABLED) && (!cfg.isDebugMode()) ) {
+                    System.out.println("The Excel feature is being developed!");
+                    return;
+                }
+                // TODO: END ******************************************************************
+
+                if (cfg.outputIsFile()) {
+                    setupForPOIAsFile(cfg, niceCX);
+                } else {
+                    setupForPOIAsStdout(cfg, niceCX);
+                    return;
+                }
+                break;
+
+            default:
+                String errMsg = String.format("%s: \'%s\' is not a valid operation",
+                        TablesRoot.class.getSimpleName(), cfg.getOperation());
+                throw new Exception(errMsg);
+        }
     }
 
     private static TableWritable setupCSVOutputWriter(Configuration cfg) throws Exception {
         WriterFactory wf = new WriterFactory(cfg);
-        return wf.getWriter();
+        return wf.getCSVWriter();
     }
 
+    void setupForPOIAsFile(Configuration cfg, NiceCXNetwork niceCX) throws Exception {
 
-    private Workbook setupPOIOutputWriter(Configuration cfg) throws Exception {
-        Workbook workbook;
-
-        try
-        {
+        try (OutputStream outputStream = new FileOutputStream(cfg.getOutputFilename());
+             XSSFWorkbook workbook = new XSSFWorkbook() ) {
+            TableToPOI writer = new TableToPOI(outputStream, workbook);
+            Table3D morph = new ExcelApp(cfg, niceCX, writer, workbook, outputStream);
+            morph.morphThisCX();
+        } catch (Exception e) {
+            throw new Exception(e);
+        }
+    }
 
-        // Determine whether the output is to a file or stdout.
-            if (cfg.outputIsFile()) {
-                Workbook wb = WorkbookFactory.create(new File(cfg.getOutputFilename()));
-                return wb;
-            } else {
-                Workbook wb = WorkbookFactory.create(new FileInputStream(cfg.getOutputFilename()));
-                return wb;
-            }
+    void setupForPOIAsStdout(Configuration cfg, NiceCXNetwork niceCX) throws Exception {
 
-        }
-            catch (Exception e) {
-            String msg = this.getClass().getSimpleName() + ": " + e.getMessage();
-            throw new Exception(msg);
+        try (OutputStream outputStream = new PrintStream(System.out);
+             XSSFWorkbook workbook = new XSSFWorkbook() ) {
+            TableToPOI writer = new TableToPOI(outputStream, workbook);
+            Table3D morph = new ExcelApp(cfg, niceCX, writer, workbook, outputStream);
+            morph.morphThisCX();
+        } catch (Exception e) {
+            throw new Exception(e);
         }
     }
 

src/main/java/org/ndextools/morphcx/tables/Webapp.java → src/main/java/org/ndextools/morphcx/tables/WebApp.java

@@ -12,9 +12,9 @@
 import java.util.*;
 
 /**
- *  The subclass of Table that customizes output according to the NDEx Webapp table schema.
+ *  The subclass of Table that customizes output according to the NDEx WebApp table schema.
  */
-public class Webapp extends Table implements Table2D {
+public class WebApp extends Table implements Table2D {
 
     // column header labels used in this table, presented in column sequence order
     protected final static String LABEL_SOURCE_NODE = "Source Node";
@@ -38,7 +38,7 @@ public class Webapp extends Table implements Table2D {
      * @param niceCX reference to NiceCXNetwork class object
      * @param cxWriter reference to output writer class object
      */
-    public Webapp(Configuration cfg, NiceCXNetwork niceCX, TableWritable cxWriter) {
+    public WebApp(Configuration cfg, NiceCXNetwork niceCX, TableWritable cxWriter) {
         super(cfg, niceCX, cxWriter);
     }
 

src/main/java/org/ndextools/morphcx/writers/POIWritable.java

@@ -0,0 +1,7 @@
+package org.ndextools.morphcx.writers;
+
+public interface POIWritable extends AutoCloseable {
+
+    void outputAll() throws Exception;
+
+}

src/main/java/org/ndextools/morphcx/writers/TableToCSV.java

@@ -45,11 +45,19 @@ public void outputRow(final List<String> columns) throws IOException {
      */
     @Override
     public void close() throws IOException {
-        if (printer != null) {
-            printer.flush();
-        }
-        if (printer != null) {
-            printer.close();
+
+        try
+        {
+            if (printer != null) {
+                printer.flush();
+            }
+
+            if (printer != null) {
+                printer.close();
+            }
+
+        } catch (IOException e) {
+            throw new IOException(e);
         }
     }