Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews

[jalview.git] / test / jalview / bin / argparser / ArgParserTest.java

diff --git a/test/jalview/bin/argparser/ArgParserTest.java b/test/jalview/bin/argparser/ArgParserTest.java
index 9beba17..3ba096e 100644 (file)
--- a/test/jalview/bin/argparser/ArgParserTest.java
+++ b/test/jalview/bin/argparser/ArgParserTest.java
@@ -279,9 +279,15 @@ public class ArgParserTest
   }
 
   @Test(groups = "Functional", dataProvider = "allLinkedIdsData")
-  public void allLinkedIdsTest(String commandLineArgs, Arg a,
+  public void allLinkedIdsTest(String pwd, String commandLineArgs, Arg a,
           String[] values, String[] nonvalues)
   {
+    String userDir = System.getProperty("user.dir");
+    if (pwd != null)
+    {
+      File pwdFile = new File(pwd);
+      System.setProperty("user.dir", pwdFile.getAbsolutePath());
+    }
     String[] args = commandLineArgs.split("\\s+");
     ArgParser argparser = new ArgParser(args);
 
@@ -306,12 +312,13 @@ public class ArgParserTest
         ArgValues avs = avm.getArgValues(a);
         ArgValue av = avs.getArgValue();
         String v = av.getValue();
-        value = new File(value).getAbsolutePath();
+        value = new File(value).getPath();
         Assert.assertEquals(v, value, "Arg value for " + a.argString()
                 + " not applied correctly to linkedId '" + linkedId + "'");
       }
     }
 
+    System.setProperty("user.dir", userDir);
   }
 
   @DataProvider(name = "allLinkedIdsData")
@@ -321,22 +328,33 @@ public class ArgParserTest
         //
         /*
         */
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+        { null,
+            "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
             Arg.CLOSE, new String[]
             { null, null, null },
             null },
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+        { null,
+            "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
             Arg.OUTPUT, new String[]
             { "test/jalview/bin/argparser/testfiles/test1.stk",
                 "test/jalview/bin/argparser/testfiles/test2.stk",
                 "test/jalview/bin/argparser/testfiles/test3.stk", },
             null },
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+        { null,
+            "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
             Arg.IMAGE, new String[]
             { "test/jalview/bin/argparser/testfiles/test1.png",
                 "test/jalview/bin/argparser/testfiles/test2.png",
                 "test/jalview/bin/argparser/testfiles/test3.png", },
             null },
+        /*
+         * Find a way to change pwd reliably -- need to match "*.fa" against some files!
+         { "test/jalview/bin/argparser/testfiles",
+         
+            "--open=*.fa --image={dirname}/{basename}.png --close",
+            Arg.IMAGE, new String[]
+            { "./test1.png", "./test2.png", "./test3.png", }, null },
+            */
         //
     };
   }
@@ -414,4 +432,4 @@ public class ArgParserTest
     };
   }
 
-}
+}
\ No newline at end of file