/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.ws.jabaws;

import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;

import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.slivkaws.SlivkaWSDiscoverer;

import java.util.ArrayList;
import java.util.List;

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

/*
 * All methods in this class are set to the Network group because setUpBeforeClass will fail
 * if there is no network.
 */
@Test(singleThreaded = true)
public class AAConAnnotAndSettingsIO
{

  @BeforeClass(alwaysRun = true)
  public void setUpJvOptionPane()
  {
    JvOptionPane.setInteractiveMode(false);
    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  }

  public static String testseqs = "examples/uniref50.fa";

  public static Jws2Discoverer disc;

  public static List<ServiceWithParameters[]> aacon;

  jalview.ws.jws2.SeqAnnotationServiceCalcWorker aaconClient;

  public static jalview.gui.AlignFrame af = null;

  @BeforeClass(alwaysRun = true)
  public static void setUpBeforeClass() throws Exception
  {
    Cache.loadProperties("test/jalview/io/testProps.jvprops");
    Cache.initLogger();
    disc = JalviewJabawsTestUtils.getJabawsDiscoverer();

    while (disc.isRunning())
    {
      // don't get services until discoverer has finished
      Thread.sleep(100);
    }


    aacon = new ArrayList<>();
    for (ServiceWithParameters svc : disc.getServices())
    {
      if (svc.getNameURI().toLowerCase().contains("aacon"))
      {
        aacon.add(new ServiceWithParameters[] { svc });
      }
    }

    for (ServiceWithParameters svc : SlivkaWSDiscoverer.getServices())
    {
      if (svc.getNameURI().toLowerCase().contains("aacon"))
      {
        aacon.add(new ServiceWithParameters[] { svc });
      }
    }
    assertTrue("Couldn't discover any AACon services to use to test.",
            aacon.size() > 0);
  }

  @AfterClass(alwaysRun = true)
  public static void tearDownAfterClass() throws Exception
  {
    if (af != null)
    {
      af.setVisible(false);
      af.dispose();
      af = null;
    }
  }

  @DataProvider(name = "aacons")
  public Object[][] getAaconArray()
  {

    Object[][] rtn = new Object[aacon.size()][1];
    int i = 0;
    for (ServiceWithParameters[] aa : aacon)
    {
      rtn[i++] = aa;
    }
    return rtn;
  }
  /**
   * Run AACon on an alignment with defaults and verify Just Shenkin annotation
   * appears
   */
  @Test(groups = { "External", "Network" }, dataProvider = "aacons")
  public void testAAConAnnotAndRecovery(ServiceWithParameters service)
  {
    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
    AlignFrame _af = fl.LoadFileWaitTillLoaded(testseqs,
            jalview.io.DataSourceType.FILE);
    assertNotNull("Couldn't load test data ('" + testseqs + "')", _af);
    af = _af;
    try
    {
    testAAConClient(_af, service);
    } finally
    {
      af = null;
      _af.setVisible(false);
      _af.dispose();
      _af = null;

    }
  }

  /**
   * triggers the given aacon worker on the alignment, waits for 5s and gives up
   * or verifies SHENKIN annotation is produced.
   * 
   * @param af
   *          - test data in an alignment frame
   * @param aacon
   *          - the service to test
   */
  static void testAAConClient(AlignFrame af, ServiceWithParameters aacon)
  {
    SeqAnnotationServiceCalcWorker aaconClient = new SeqAnnotationServiceCalcWorker(
            aacon, af, null,
            null);
    long current = System.currentTimeMillis(), limit = 15;
    af.getViewport().getCalcManager().startWorker(aaconClient);
    do
    {
      try
      {
        Thread.sleep(50);
      } catch (InterruptedException x)
      {
      }
      ;
      assertTrue(
              "Waited " + limit + "s for " + aacon.getHostURL()
                      + " - giving up.",
              (System.currentTimeMillis() - current) < limit * 1000);
    } while (af.getViewport().getCalcManager().isWorking());
    AlignmentI orig_alig = af.getViewport().getAlignment();
    boolean foundShenkin = false;
    Iterable<AlignmentAnnotation> _aa=orig_alig
            .findAnnotation(aacon.getAlignAnalysisUI().getCalcId());
    assertTrue("No annotation from service",
            _aa != null && _aa.iterator().hasNext());

    for (AlignmentAnnotation aa : _aa)
    {
      assertTrue("AACon annotation not marked as autocalculated!",
              aa.autoCalculated);
      if ("shenkin".equals(aa.label.toLowerCase()))
      {
        foundShenkin = true;
        break;
      }
    }
    assertTrue("Failed to locate 'SHENKIN' annotation row.", foundShenkin);
  }
}