X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=a5067bee5269d4ea18382b21523a7767199d417d;hb=refs%2Fheads%2Fpatch%2FJAL-3821_ena_rna_moltype;hp=acc3444367f47217a90c69393cb6b02d731c8ee1;hpb=feab9576a4d6f5afe9265abc0b5f942b96d29b2f;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index acc3444..a5067be 100644
--- 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;
@@ -129,6 +136,8 @@ public class CommandLineOperations
 
   private static String modules = null;
 
+  private static String java_exe = null;
+
   public synchronized static String getClassPath()
   {
     if (scanner == null)
@@ -141,6 +150,9 @@ public class CommandLineOperations
       {
         modules.concat(mr.getName());
       }
+      java_exe = System.getProperty("java.home") + File.separator + "bin"
+              + File.separator + "java";
+
     }
     while (classpath == null)
     {
@@ -161,7 +173,8 @@ public class CommandLineOperations
     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
     // not expanded by the shell
     String classpath = getClassPath();
-    String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "")
+    String _cmd = java_exe + " "
+            + (withAwt ? "-Djava.awt.headless=true" : "")
             + " -classpath " + classpath
             + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
                     : "")
@@ -195,17 +208,21 @@ public class CommandLineOperations
     }
     return worker;
   }
-  @BeforeTest(alwaysRun=true)
+
+  @Test(groups = { "Functional" })
   public void reportCurrentWorkingDirectory()
   {
-      try {
-          Path currentRelativePath = Paths.get("");
-          String s = currentRelativePath.toAbsolutePath().toString();
-          System.out.println("Test CWD is "+s);
-      } catch (Exception q) {
-          q.printStackTrace();
-      }
+    try
+    {
+      Path currentRelativePath = Paths.get("");
+      String s = currentRelativePath.toAbsolutePath().toString();
+      System.out.println("Test CWD is " + s);
+    } catch (Exception q)
+    {
+      q.printStackTrace();
+    }
   }
+
   @BeforeTest(alwaysRun = true)
   public void initialize()
   {
@@ -243,7 +260,7 @@ public class CommandLineOperations
     {
       System.out.println(ln);
       successfulCMDs.add(ln);
-      if (++count > 5)
+      if (++count > 25)
       {
         break;
       }
@@ -269,7 +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);
@@ -281,6 +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();
@@ -333,51 +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() }, };
   }
 }