package jalview.gui;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;

import jalview.analysis.AlignmentGenerator;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;

import java.io.File;
import java.io.IOException;
import java.io.PrintStream;

import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;

public class FreeUpMemoryTest
{
  private static final int ONE_MB = 1000 * 1000;

  /**
   * Configure (read-only) Jalview property settings for test
   */
  @BeforeClass(alwaysRun = true)
  public void setUp()
  {
    Jalview.main(new String[] { "-nonews", "-props",
        "test/jalview/testProps.jvprops" });
    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("SHOW_QUALITY",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
            Boolean.TRUE.toString());
  }

  /**
   * A simple test that memory is released when all windows are closed.
   * <ul>
   * <li>generates a reasonably large alignment and loads it</li>
   * <li>performs various operations on the alignment</li>
   * <li>closes all windows</li>
   * <li>requests garbage collection</li>
   * <li>asserts that the remaining memory footprint (heap usage) is 'not large'
   * </li>
   * </ul>
   * If the test fails, this suggests that a reference to some large object
   * (perhaps the alignment data, or some annotation / Tree / PCA data) has
   * failed to be garbage collected. If this is the case, the heap will need to
   * be inspected manually (suggest using jvisualvm) in order to track down
   * where large objects are still referenced. The code (for example
   * AlignmentViewport.dispose()) should then be updated to ensure references to
   * large objects are set to null when they are no longer required.
   * 
   * @throws IOException
   */
  @Test(groups = "Memory")
  public void testFreeMemoryOnClose() throws IOException
  {
    File f = generateAlignment();
    f.deleteOnExit();

    doStuffInJalview(f);

    Desktop.instance.closeAll_actionPerformed(null);

    checkUsedMemory(35L);
  }

  /**
   * Requests garbage collection and then checks whether remaining memory in use
   * is less than the expected value (in Megabytes)
   * 
   * @param expectedMax
   */
  protected void checkUsedMemory(long expectedMax)
  {
    /*
     * request garbage collection and wait briefly for it to run;
     * NB there is no guarantee when, or whether, it will do so
     */
    System.gc();
    waitFor(100);

    /*
     * a second gc() call should not be necessary - but it is!
     * the test passes with it, and fails without it
     */
    System.gc();
    waitFor(100);

    /*
     * check used memory is 'reasonably low'
     */
    long availableMemory = Runtime.getRuntime().totalMemory() / ONE_MB;
    long freeMemory = Runtime.getRuntime().freeMemory() / ONE_MB;
    long usedMemory = availableMemory - freeMemory;

    /*
     * sanity check - fails if any frame was added after
     * closeAll_actionPerformed
     */
    assertEquals(Desktop.instance.getAllFrames().length, 0);

    /*
     * if this assertion fails
     * - set a breakpoint here
     * - run jvisualvm to inspect a heap dump of Jalview
     * - identify large objects in the heap and their referers
     * - fix code as necessary to null the references on close
     */
    System.out.println("Used memory after gc = " + usedMemory + "MB");
    assertTrue(usedMemory < expectedMax, String.format(
            "Used memory %d should be less than %d (Recommend running test manually to verify)",
            usedMemory,
            expectedMax));
  }

  /**
   * Loads an alignment from file and exercises various operations in Jalview
   * 
   * @param f
   */
  protected void doStuffInJalview(File f)
  {
    /*
     * load alignment, wait for consensus and other threads to complete
     */
    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(f.getPath(),
            DataSourceType.FILE);
    while (af.getViewport().isCalcInProgress())
    {
      waitFor(200);
    }

    /*
     * set a selection group - potential memory leak if it retains
     * a reference to the alignment
     */
    SequenceGroup sg = new SequenceGroup();
    sg.setStartRes(0);
    sg.setEndRes(100);
    AlignmentI al = af.viewport.getAlignment();
    for (int i = 0; i < al.getHeight(); i++)
    {
      sg.addSequence(al.getSequenceAt(i), false);
    }
    af.viewport.setSelectionGroup(sg);

    /*
     * compute Tree and PCA (on all sequences, 100 columns)
     */
    af.openTreePcaDialog();
    CalculationChooser dialog = af.alignPanel.getCalculationDialog();
    dialog.openPcaPanel("BLOSUM62", dialog.getSimilarityParameters(true));
    dialog.openTreePanel("BLOSUM62", dialog.getSimilarityParameters(false));

    /*
     * wait until Tree and PCA have been computed
     */
    while (af.viewport.getCurrentTree() == null
            && dialog.getPcaPanel().isWorking())
    {
      waitFor(10);
    }

    /*
     * give Swing time to add the PCA panel (?!?)
     */
    waitFor(100);
  }

  /**
   * Wait for waitMs miliseconds
   * 
   * @param waitMs
   */
  protected void waitFor(int waitMs)
  {
    try
    {
      Thread.sleep(waitMs);
    } catch (InterruptedException e)
    {
    }
  }

  /**
   * Generates an alignment and saves it in a temporary file, to be loaded by
   * Jalview. We use a peptide alignment (so Conservation and Quality are
   * calculated), which is wide enough to ensure Consensus, Conservation and
   * Occupancy have a significant memory footprint (if not removed from the
   * heap).
   * 
   * @return
   * @throws IOException
   */
  private File generateAlignment() throws IOException
  {
    File f = File.createTempFile("MemoryTest", "fa");
    PrintStream ps = new PrintStream(f);
    AlignmentGenerator ag = new AlignmentGenerator(false, ps);
    int width = 100000;
    int height = 100;
    ag.generate(width, height, 0, 10, 15);
    return f;
  }
}