JAL-3130 JAL-1889 report absolute paths for CommandLineTests

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

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index ace1868..acc3444 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -29,6 +29,8 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 
 import org.testng.Assert;
@@ -39,6 +41,7 @@ import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ModuleRef;
 import io.github.classgraph.ScanResult;
 
 public class CommandLineOperations
@@ -124,6 +127,8 @@ public class CommandLineOperations
 
   private static String classpath = null;
 
+  private static String modules = null;
+
   public synchronized static String getClassPath()
   {
     if (scanner == null)
@@ -131,6 +136,11 @@ public class CommandLineOperations
       scanner = new ClassGraph();
       ScanResult scan = scanner.scan();
       classpath = scan.getClasspath();
+      modules = "";
+      for (ModuleRef mr : scan.getModules())
+      {
+        modules.concat(mr.getName());
+      }
     }
     while (classpath == null)
     {
@@ -152,7 +162,10 @@ public class CommandLineOperations
     // not expanded by the shell
     String classpath = getClassPath();
     String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "")
-            + " -classpath " + classpath + " jalview.bin.Jalview ";
+            + " -classpath " + classpath
+            + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
+                    : "")
+            + " jalview.bin.Jalview ";
     Process ls2_proc = null;
     Worker worker = null;
     try
@@ -182,7 +195,17 @@ public class CommandLineOperations
     }
     return worker;
   }
-
+  @BeforeTest(alwaysRun=true)
+  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();
+      }
+  }
   @BeforeTest(alwaysRun = true)
   public void initialize()
   {
@@ -303,53 +326,58 @@ public class CommandLineOperations
   @DataProvider(name = "headlessModeOutputOperationsData")
   public static Object[][] getHeadlessModeOutputParams()
   {
+    // 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[][] { { "nodisplay -open examples/uniref50.fa",
-        " -eps", "test/jalview/bin/test_uniref50_out.eps", true,
+        " -eps", workingDir + "test_uniref50_out.eps", true,
         MINFILESIZE_BIG, TEST_TIMEOUT },
         { "nodisplay -open examples/uniref50.fa", " -eps",
-            "test/jalview/bin/test_uniref50_out.eps", false,
+            workingDir + "test_uniref50_out.eps", false,
             MINFILESIZE_BIG, TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
-            "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
-            "test/jalview/bin/test_uniref50_out.eps", false,
+            workingDir + "test_uniref50_out.eps", false,
             MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -eps",
-            "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -svg",
-            "test/jalview/bin/test_uniref50_out.svg", false,
+            workingDir + "test_uniref50_out.svg", false,
             MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -png",
-            "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
+            workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -html",
-            "test/jalview/bin/test_uniref50_out.html", true,
+            workingDir + "test_uniref50_out.html", true,
             MINFILESIZE_BIG, TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -fasta",
-            "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -clustal",
-            "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -msf",
-            "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pileup",
-            "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pir",
-            "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -pfam",
-            "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -blc",
-            "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -jalview",
-            "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
+            workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT }, };
   }
 }