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

[jalview.git] / test / jalview / bin / CommandLineOperationsNG.java

diff --git a/test/jalview/bin/CommandLineOperationsNG.java b/test/jalview/bin/CommandLineOperationsNG.java
index 30a1b9f..56d4300 100644 (file)
--- a/test/jalview/bin/CommandLineOperationsNG.java
+++ b/test/jalview/bin/CommandLineOperationsNG.java
@@ -27,6 +27,7 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
@@ -161,6 +162,12 @@ public class CommandLineOperationsNG
   private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
           int timeout)
   {
+    return getJalviewDesktopRunner(withAwt, cmd, timeout, true);
+  }
+
+  private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+          int timeout, boolean testoutput)
+  {
     /*
     boolean win = System.getProperty("os.name").indexOf("Win") >= 0;
     String pwd = "";
@@ -193,7 +200,7 @@ public class CommandLineOperationsNG
     Worker worker = null;
     try
     {
-      cmd = " --testoutput " + cmd;
+      cmd = cmd + (testoutput ? " --testoutput " : "");
       System.out.println("Running '" + _cmd + cmd + "'");
       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
     } catch (Throwable e1)
@@ -368,6 +375,42 @@ public class CommandLineOperationsNG
     file.delete();
   }
 
+  @Test(
+    groups =
+    { "Functional", "testTask1" },
+    dataProvider = "headlessModeOutputToStdout")
+  public void testHeadlessModeOutputToStdout(String args,
+          String comparisonFile, int timeout)
+  {
+    String cmd = args;
+    File file = new File(comparisonFile);
+    Worker worker = getJalviewDesktopRunner(true, cmd, timeout, false);
+    int b = -1;
+    StringBuilder sb = new StringBuilder();
+    try
+    {
+      while ((b = worker.getOutputReader().read()) != -1)
+      {
+        sb.append(Character.toChars(b));
+      }
+    } catch (IOException e)
+    {
+      Assert.fail("IOException whilst trying to read from jalview process");
+    }
+
+    String comparisonContent = null;
+    try
+    {
+      comparisonContent = new String(Files.readAllBytes(file.toPath()));
+    } catch (IOException e)
+    {
+      Assert.fail("IOException whilst trying to read comparison file");
+    }
+
+    Assert.assertEquals(sb.toString(), comparisonContent,
+            "STDOUT from jalview command did not match the comparison file");
+  }
+
   @DataProvider(name = "allInputOperationsData")
   public Object[][] getHeadlessModeInputParams()
   {
@@ -459,4 +502,36 @@ public class CommandLineOperationsNG
         //
     };
   }
+
+  @DataProvider(name = "headlessModeOutputToStdout")
+  public static Object[][] getHeadlessModeOutputToStdout()
+  {
+    // JBPNote: I'm not clear why need to specify full path for output file
+    // when running tests on build server, but we will keep this patch for now
+    // since it works.
+    // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
+    String workingDir = "test/jalview/bin";
+    return new Object[][] {
+        //
+        { "--open=examples/uniref50.fa --output=-",
+            workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
+        { "--open examples/uniref50.fa --output -",
+            workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
+        { "--open examples/uniref50.fa --output=[format=blc]-",
+            workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+        { "--open examples/uniref50.fa --output - --format blc",
+            workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+        { "./examples/uniref50.fa --output=-",
+            workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
+        { "./examples/uniref50.fa --output - --format blc",
+            workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+        // remember you can't use shell wildcards for filenames in a test
+        { "./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -",
+            workingDir + "/test1-3.fa", TEST_TIMEOUT },
+        // but you can use java wildcards when using an equals sign
+        { "--open=./test/jalview/bin/argparser/testfiles/test*.fa --all --output -",
+            workingDir + "/test1-3.fa", TEST_TIMEOUT },
+        //
+    };
+  }
 }