Fix for ticket 503254 - ACT was not validating input file arguments

ChangeLog

@@ -32,14 +32,16 @@ Version 17
 
 	Fixed RT ticket #606061 - Using EBI-Dbfetch on ARTEMIS. Change to DbfetchEntrySource.java due to incorrect regular expression and EBI URL.
 
-	Resized splash screen.
+	Resized splash screen, as it was too small to the accommodate text info.
 
 	Added error handling for dnaplotter template file loading in standalone mode.
 
 	Added Bioconda recipe. RT ticket #341139 .
 
 	Fixed RT ticket #467433 - Genbank DBSOURCE field was not recognised by Artemis. DBLINK was already added.
 
+	Fixed RT ticket #503254 - Act doesn't detect if file does not exist.
+
 	KNOWN ISSUES: 
 		1) Java JDKs 1.8.0_131 and above have a Swing bug related to overlaying of modal dialogs for Mac OS X: https://bugs.openjdk.java.net/browse/JDK-8179335
 		2) There is a current bug in htsjdk whereby calls to the queryMate functionality can throw an exception on reads with secondaries and/or supplementals. 

act

@@ -24,7 +24,7 @@ usage () {
 	echo "        -DuserplotX=FILE[,FILE2]    For sequence 'X' open one or more userplots"
 	echo "        -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)"
 	echo "        -DbamX=FILE[,FILE2,...]     For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files"
-	echo "        -Dchado="h:p/d?u"           Get ACT to open this CHADO database"
+	echo "        -Dchado=\"h:p/d?u\"           Get ACT to open this CHADO database"
 	echo "        -Dread_only                 Open CHADO database read-only"
 	echo "EXAMPLES"
 	echo "        % act"

art

@@ -31,7 +31,7 @@ usage () {
     echo "        -Dshow_cov_plot                Open coverage plot in BamView"
     echo "        -Dshow_forward_lines=?         Hide/show forward frame lines [true,false]"
     echo "        -Dshow_reverse_lines=?         Hide/show reverse frame lines [true,false]"
-    echo "        -Dchado="h:p/d?u"              Get Artemis to open this CHADO database"
+    echo "        -Dchado=\"h:p/d?u\"              Get Artemis to open this CHADO database"
     echo "        -Dread_only                    Open CHADO database read-only"
     echo "EXAMPLES"
     echo "        % art AJ006275.embl" 

uk/ac/sanger/artemis/components/ActMain.java

@@ -39,7 +39,10 @@
 import uk.ac.sanger.artemis.io.SimpleEntryInformation;
 
 import java.awt.event.*;
+import java.io.File;
 import java.io.IOException;
+import java.net.URL;
+
 import javax.swing.JFrame;
 
 /**
@@ -344,35 +347,87 @@ protected void exit()
   {
     System.exit(0);
   }
-
+  
   /**
-   *  Main entry point for ACT
-   **/
-  public static void main(final String [] args) 
+   * Validate the program input arguments and exit
+   * if they are not valid, displaying an error message(s).
+   * @param args String array
+   */
+  protected static void validateStartupArguments(final String[] args)
   {
-    final ActMain main_window = new ActMain();
-    main_window.setVisible(true);
-
-    final InputStreamProgressListener progress_listener =
-      main_window.getInputStreamProgressListener();
-
-    if(args.length >= 3) 
-      ActMain.makeMultiComparator(main_window, progress_listener,
-                                  args);
+	boolean valid = true;
+
+	if(args.length >= 3) 
+    {
+	  // Make sure the files provided are actually valid as far as possible...
+      for (String file : args)
+      {
+    	    if (file.startsWith("ftp") || file.startsWith("http"))
+    	    {
+    	    	  // web resource
+    	    	  try 
+    	    	  {
+    	    	    URL url = new URL(file);
+    	    	  }
+    	    	  catch (Exception e)
+    	    	  {
+    	    		valid = false;
+    			System.err.println("\nError - " + file + " is not a valid URL.");
+    	    	  }
+    	    }
+    	    	else
+    	    	{
+    	    	  // normal file
+		  File argFile = new File(file);
+		  if (!argFile.exists() || !argFile.isFile())
+		  {
+		    	valid = false;
+		    	System.err.println("\nError - " + argFile + " is not a valid file.");
+		  }
+    	    }
+      }
+
+    }
     else 
     {
       if(args.length != 0) 
       {
-        System.err.println("Error - this program needs either no " +
+        System.err.println("\nError - this program needs either no" +
                            " arguments or an odd number\n" +
                            "(3 or more):");
         System.err.println("   act sequence_1 comparison_data sequence_2");
         System.err.println("or");
         System.err.println("   act seq_1 comparison_data_2_v_1 seq_2 comparison_data_3_v_2 seq_3");
         System.err.println("or");
         System.err.println("   act");
-        System.exit(1);
+        valid = false;
       }
+    }  
+
+	if (!valid)
+	{
+	  System.exit(1);
+	}
+
+  }
+
+  /**
+   *  Main entry point for ACT
+   **/
+  public static void main(final String [] args) 
+  {
+	validateStartupArguments(args);
+
+    final ActMain main_window = new ActMain();
+    main_window.setVisible(true);
+
+    final InputStreamProgressListener progress_listener =
+      main_window.getInputStreamProgressListener();
+
+    if(args.length >= 3) 
+    {
+    	  ActMain.makeMultiComparator(main_window, progress_listener,
+                                 args);
     }
   }