Merge branch 'cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat' into Jalview...

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fea99fb..b8aa928 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -73,7 +73,6 @@ import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
-//import netscape.javascript.JSObject;
 
 /**
  * Main class for Jalview Application <br>
@@ -1038,28 +1037,43 @@ public class Jalview implements ApplicationSingletonI
                 "Creating image map: " + imageFile.getAbsolutePath());
         continue;
       default:
-        format = FileFormats.getInstance().forName(outputFormat);
-        if (format == null)
-        {
-          System.out.println("Invalid file format: " + outputFormat);
-          break;
-        }
-        fname = new File(aparser.nextValue()).getAbsolutePath();
-        af.saveAlignment(fname, format);
-        if (!af.isSaveAlignmentSuccessful())
-        {
-          System.out.println("Error writing file " + fname + " in " + format
-                  + " format!!");
-          break;
-        }
-        continue;
+         // fall through - try to parse as an alignment data export format
+          FileFormatI outFormat=null;
+          try {
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP) {
+          }
+          if (outFormat==null) {
+            System.out.println("Couldn't parse "+outputFormat+" as a valid Jalview format string.");
+           continue;
+         }
+          if (!outFormat.isWritable())
+          {
+            System.out.println(
+                    "This version of Jalview does not support alignment export as "
+                            + outputFormat);
+           continue;
+          }
+          // record file as it was passed to Jalview so it is recognisable to the CLI caller
+          String file;
+         fname = new File(file=aparser.nextValue()).getAbsolutePath();
+         // JBPNote - yuck - really wish we did have a bean returned from this which gave success/fail like before !
+         af.saveAlignment(fname, outFormat);
+         if (!af.isSaveAlignmentSuccessful())
+          {
+              System.out.println("Written alignment in " + outputFormat
+                      + " format to " + file);
+             continue;
+          } else {
+                System.out.println("Error writing file " + file + " in "
+                        + outputFormat + " format!!");
+          }
       }
-      System.out.println("Unknown arg: " + outputFormat);      
-      break;
     }
+    // ??? Should report - 'ignoring' extra args here...
     while (aparser.getSize() > 0)
     {
-      System.out.println("Unknown arg: " + aparser.nextValue());
+      System.out.println("Ignoring extra argument: " + aparser.nextValue());
     }
   }
 

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 59fc79d..a5067be 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -20,10 +20,17 @@
  */
 package jalview.bin;
 
+import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertTrue;
 
 import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.IdentifyFile;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -279,7 +286,7 @@ public class CommandLineOperations
     dataProvider = "headlessModeOutputOperationsData")
   public void testHeadlessModeOutputOperations(String harg, String type,
           String fileName, boolean withAWT, int expectedMinFileSize,
-          int timeout)
+          int timeout, String fileFormatType)
   {
     String cmd = harg + type + " " + fileName;
     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
@@ -291,6 +298,25 @@ public class CommandLineOperations
     assertTrue(file.exists(), msg);
     FileAssert.assertFile(file, msg);
     FileAssert.assertMinLength(file, expectedMinFileSize);
+    if (fileFormatType!=null && fileFormatType.length()>0)
+    {
+      FileFormatI format = FileFormats.getInstance()
+              .forName(fileFormatType);
+      if (format!=null)
+      {
+        try
+        {
+          FileFormatI exportedType = new IdentifyFile()
+                  .identify(file.getAbsolutePath(), DataSourceType.FILE);
+          assertEquals(exportedType, format,
+                  "Exported file type was wrong");
+        } catch (FileFormatException e)
+        {
+          Assert.fail("Couldn't identify file " + file
+                  + " as an alignment format", e);
+        }
+      }
+    }
     if (worker != null && worker.exit == null)
     {
       worker.interrupt();
@@ -343,51 +369,51 @@ public class CommandLineOperations
     String workingDir = "test/jalview/bin/";
     return new Object[][] { { "nodisplay -open examples/uniref50.fa",
         " -eps", workingDir + "test_uniref50_out.eps", true,
-        MINFILESIZE_BIG, TEST_TIMEOUT },
+        MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "nodisplay -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "nogui -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, null },
         { "nogui -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -svg",
             workingDir + "test_uniref50_out.svg", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -png",
             workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -html",
             workingDir + "test_uniref50_out.html", true,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -fasta",
             workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.Fasta.toString() },
         { "headless -open examples/uniref50.fa", " -clustal",
             workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.Clustal.toString() },
         { "headless -open examples/uniref50.fa", " -msf",
             workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.MSF.toString() },
         { "headless -open examples/uniref50.fa", " -pileup",
             workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.Pileup.toString() },
         { "headless -open examples/uniref50.fa", " -pir",
             workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.PIR.toString() },
         { "headless -open examples/uniref50.fa", " -pfam",
             workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.Pfam.toString() },
         { "headless -open examples/uniref50.fa", " -blc",
             workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.BLC.toString() },
         { "headless -open examples/uniref50.fa", " -jalview",
             workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT }, };
+            TEST_TIMEOUT, FileFormat.Jalview.toString() }, };
   }
 }