*/
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;
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;
import org.testng.annotations.Test;
import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ModuleRef;
import io.github.classgraph.ScanResult;
public class CommandLineOperations
private static String classpath = null;
+ private static String modules = null;
+
+ private static String java_exe = null;
+
public synchronized static String getClassPath()
{
if (scanner == null)
scanner = new ClassGraph();
ScanResult scan = scanner.scan();
classpath = scan.getClasspath();
+ modules = "";
+ for (ModuleRef mr : scan.getModules())
+ {
+ modules.concat(mr.getName());
+ }
+ java_exe = System.getProperty("java.home") + File.separator + "bin"
+ + File.separator + "java";
+
}
while (classpath == null)
{
// 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" : "")
- + " -classpath " + classpath + " jalview.bin.Jalview ";
+ String _cmd = java_exe + " "
+ + (withAwt ? "-Djava.awt.headless=true" : "")
+ + " -classpath " + classpath
+ + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
+ : "")
+ + " jalview.bin.Jalview ";
Process ls2_proc = null;
Worker worker = null;
try
return worker;
}
+ @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();
+ }
+ }
+
@BeforeTest(alwaysRun = true)
public void initialize()
{
{
System.out.println(ln);
successfulCMDs.add(ln);
- if (++count > 5)
+ if (++count > 25)
{
break;
}
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);
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();
@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,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ " -eps", workingDir + "test_uniref50_out.eps", true,
+ MINFILESIZE_BIG, TEST_TIMEOUT, null },
{ "nodisplay -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.eps", false,
+ MINFILESIZE_BIG, TEST_TIMEOUT, null },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT, null },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.eps", false,
+ MINFILESIZE_BIG, TEST_TIMEOUT, null },
{ "headless -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT, null },
{ "headless -open examples/uniref50.fa", " -svg",
- "test/jalview/bin/test_uniref50_out.svg", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.svg", false,
+ MINFILESIZE_BIG, TEST_TIMEOUT, null },
{ "headless -open examples/uniref50.fa", " -png",
- "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT, null },
{ "headless -open examples/uniref50.fa", " -html",
- "test/jalview/bin/test_uniref50_out.html", true,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.html", true,
+ MINFILESIZE_BIG, TEST_TIMEOUT, null },
{ "headless -open examples/uniref50.fa", " -fasta",
- "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT, FileFormat.Fasta.toString() },
{ "headless -open examples/uniref50.fa", " -clustal",
- "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT, FileFormat.Clustal.toString() },
{ "headless -open examples/uniref50.fa", " -msf",
- "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT, FileFormat.MSF.toString() },
{ "headless -open examples/uniref50.fa", " -pileup",
- "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT, FileFormat.Pileup.toString() },
{ "headless -open examples/uniref50.fa", " -pir",
- "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT, FileFormat.PIR.toString() },
{ "headless -open examples/uniref50.fa", " -pfam",
- "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT, FileFormat.Pfam.toString() },
{ "headless -open examples/uniref50.fa", " -blc",
- "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT, FileFormat.BLC.toString() },
{ "headless -open examples/uniref50.fa", " -jalview",
- "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT }, };
+ workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT, FileFormat.Jalview.toString() }, };
}
}
git://source.jalview.org / jalview.git / blobdiff