/*
 * 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.sifts;

import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.PrintStream;

import org.testng.Assert;
import org.testng.FileAssert;
import org.testng.annotations.AfterTest;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;

import MCview.PDBfile;

public class SiftsClientTest
{
  private final ByteArrayOutputStream outContent = new ByteArrayOutputStream();

  private String testPDBId = "1a70";

  private SiftsClient siftsClient = null;

  SequenceI testSeq = new Sequence(
          "P00221",
          "MAAT..TTTMMG..MATTFVPKPQAPPMMAALPSNTGR..SLFGLKT.GSR..GGRMTMA"
                  + "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD"
                  + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", 1, 147);

  int u = SiftsClient.UNASSIGNED;

  int[][] expectedMapping = { { u, u }, { u, u }, { u, u }, { u, u },
      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
      { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { 1, u }, { 2, u },
      { 3, u }, { 4, u }, { 5, u }, { 6, u }, { 7, u }, { 8, u }, { 9, u },
      { 10, u }, { 11, u }, { 12, u }, { 13, u }, { 14, u }, { 15, u },
      { 16, u }, { 17, u }, { 18, u }, { 19, u }, { 20, u }, { 21, u },
      { 22, u }, { 23, u }, { 24, u }, { 25, u }, { 26, u }, { 27, u },
      { 28, u }, { 29, u }, { 30, u }, { 31, u }, { 32, u }, { 33, u },
      { 34, u }, { 35, u }, { 36, u }, { 37, u }, { 38, u }, { 39, u },
      { 40, u }, { 41, u }, { 42, u }, { 43, u }, { 44, u }, { 45, u },
      { 46, u }, { 47, u }, { 48, u }, { 49, u }, { 50, u }, { 51, u },
      { 52, u }, { 53, u }, { 54, u }, { 55, u }, { 56, u }, { 57, u },
      { 58, u }, { 59, u }, { 60, u }, { 61, u }, { 62, u }, { 63, u },
      { 64, u }, { 65, u }, { 66, u }, { 67, u }, { 68, u }, { 69, u },
      { 70, u }, { 71, u }, { 72, u }, { 73, u }, { 74, u }, { 75, u },
      { 76, u }, { 77, u }, { 78, u }, { 79, u }, { 80, u }, { 81, u },
      { 82, u }, { 83, u }, { 84, u }, { 85, u }, { 86, u }, { 87, u },
      { 88, u }, { 89, u }, { 90, u }, { 91, u }, { 92, u }, { 93, u },
      { 94, u }, { 95, u }, { 96, u }, { 97, u } };

  @BeforeTest(alwaysRun = true)
  public void setUpSiftsClient() throws SiftsException
  {
    // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
    // test reproducibility
    File testSiftsFile = new File("test/jalview/io/" + testPDBId
            + ".xml.gz");
    PDBfile pdbFile = new PDBfile(false, false, false);
    siftsClient = new SiftsClient(pdbFile, testSiftsFile);
  }

  @AfterTest(alwaysRun = true)
  public void cleanUpSiftsClient()
  {
    siftsClient = null;
  }

  @BeforeTest(alwaysRun = true)
  public void setUpStreams()
  {
    System.setOut(new PrintStream(outContent));
  }

  @AfterTest(alwaysRun = true)
  public void cleanUpStreams()
  {
    System.setOut(null);
  }

  @Test(groups = { "Functional" })
  public void getSIFTsFileTest() throws SiftsException
  {
    Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
    SiftsClient.getSiftsFile(testPDBId);
    Assert.assertFalse(outContent.toString().contains(
            ">>> SIFTS File already downloaded for " + testPDBId));

    // test for SIFTs file caching
    SiftsClient.getSiftsFile(testPDBId);
    Assert.assertTrue(outContent.toString().contains(
            ">>> SIFTS File already downloaded for " + testPDBId));
  }

  @Test(groups = { "Functional" })
  public void downloadSiftsFileTest() throws SiftsException
  {
    // Assert that file isn't yet downloaded - if already downloaded, assert it
    // is deleted
    Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
    File siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
    FileAssert.assertFile(siftsFile);
    SiftsClient.downloadSiftsFile(testPDBId);
  }

  @Test(groups = { "Functional" })
  public void getAllMappingAccessionTest()
  {
    Assert.assertNotNull(siftsClient);
    Assert.assertNotNull(siftsClient.getAllMappingAccession());
    Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1);
  }

  @Test(groups = { "Functional" })
  public void getGreedyMappingTest()
  {
    Assert.assertNotNull(siftsClient);
    Assert.assertNotNull(testSeq);
    Assert.assertNotNull(expectedMapping);

    // TODO delete when auto-fetching of DBRefEntry is implemented
    DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
    dbRef.setStartRes(1);
    dbRef.setEndRes(147);
    testSeq.addDBRef(dbRef);
    // testSeq.setSourceDBRef(dbRef);

    try
    {
      int[][] actualMapping = siftsClient.getGreedyMapping("A", testSeq,
              null);
      Assert.assertEquals(actualMapping, expectedMapping);
      Assert.assertEquals(testSeq.getStart(), 1);
      Assert.assertEquals(testSeq.getEnd(), 147);
    } catch (Exception e)
    {
      e.printStackTrace();
      Assert.fail("Exception thrown while generating mapping...");
    }
  }

  @Test(groups = { "Functional" })
  private void getAtomIndexTest()
  {
    // siftsClient.getAtomIndex(1, null);
    // Assert.assertTrue(true);
  }

  @Test(
    groups = { "Functional" },
    expectedExceptions = IllegalArgumentException.class)
  private void getAtomIndexNullTest()
  {
    siftsClient.getAtomIndex(1, null);
  }

  @Test(groups = { "Functional" })
  private void padWithGapsTest()
  {

  }

  @Test(groups = { "Functional" })
  private void populateAtomPositionsTest()
  {

  }

  @Test(groups = { "Functional" })
  public void getValidSourceDBRefTest()
  {

  }

  @Test(groups = { "Functional" })
  public void isValidDBRefEntryTest()
  {

  }
}