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

import jalview.api.DBRefEntryI;
import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingClient.StructureMappingException;
import jalview.xml.binding.sifts.Entry.Entity;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;

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

import MCview.Atom;
import MCview.PDBfile;

public class SiftsClientTest
{

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

  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
          .getProperty("user.home")
          + File.separatorChar
          + ".sifts_downloads" + File.separatorChar;

  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;

  HashMap<Integer, int[]> expectedMapping = new HashMap<Integer, int[]>();

  @BeforeTest(alwaysRun = true)
  public void populateExpectedMapping() throws SiftsException
  {
    expectedMapping.put(51, new int[] { 1, 2 });
    expectedMapping.put(52, new int[] { 2, 7 });
    expectedMapping.put(53, new int[] { 3, 12 });
    expectedMapping.put(54, new int[] { 4, 24 });
    expectedMapping.put(55, new int[] { 5, 33 });
    expectedMapping.put(56, new int[] { 6, 40 });
    expectedMapping.put(57, new int[] { 7, 47 });
    expectedMapping.put(58, new int[] { 8, 55 });
    expectedMapping.put(59, new int[] { 9, 62 });
    expectedMapping.put(60, new int[] { 10, 69 });
    expectedMapping.put(61, new int[] { 11, 76 });
    expectedMapping.put(62, new int[] { 12, 83 });
    expectedMapping.put(63, new int[] { 13, 87 });
    expectedMapping.put(64, new int[] { 14, 95 });
    expectedMapping.put(65, new int[] { 15, 102 });
    expectedMapping.put(66, new int[] { 16, 111 });
    expectedMapping.put(67, new int[] { 17, 122 });
    expectedMapping.put(68, new int[] { 18, 131 });
    expectedMapping.put(69, new int[] { 19, 137 });
    expectedMapping.put(70, new int[] { 20, 144 });
    expectedMapping.put(71, new int[] { 21, 152 });
    expectedMapping.put(72, new int[] { 22, 160 });
    expectedMapping.put(73, new int[] { 23, 167 });
    expectedMapping.put(74, new int[] { 24, 179 });
    expectedMapping.put(75, new int[] { 25, 187 });
    expectedMapping.put(76, new int[] { 26, 195 });
    expectedMapping.put(77, new int[] { 27, 203 });
    expectedMapping.put(78, new int[] { 28, 208 });
    expectedMapping.put(79, new int[] { 29, 213 });
    expectedMapping.put(80, new int[] { 30, 222 });
    expectedMapping.put(81, new int[] { 31, 231 });
    expectedMapping.put(82, new int[] { 32, 240 });
    expectedMapping.put(83, new int[] { 33, 244 });
    expectedMapping.put(84, new int[] { 34, 252 });
    expectedMapping.put(85, new int[] { 35, 260 });
    expectedMapping.put(86, new int[] { 36, 268 });
    expectedMapping.put(87, new int[] { 37, 275 });
    expectedMapping.put(88, new int[] { 38, 287 });
    expectedMapping.put(89, new int[] { 39, 293 });
    expectedMapping.put(90, new int[] { 40, 299 });
    expectedMapping.put(91, new int[] { 41, 310 });
    expectedMapping.put(92, new int[] { 42, 315 });
    expectedMapping.put(93, new int[] { 43, 319 });
    expectedMapping.put(94, new int[] { 44, 325 });
    expectedMapping.put(95, new int[] { 45, 331 });
    expectedMapping.put(96, new int[] { 46, 337 });
    expectedMapping.put(97, new int[] { 47, 343 });
    expectedMapping.put(98, new int[] { 48, 349 });
    expectedMapping.put(99, new int[] { 49, 354 });
    expectedMapping.put(100, new int[] { 50, 358 });
    expectedMapping.put(101, new int[] { 51, 367 });
    expectedMapping.put(102, new int[] { 52, 375 });
    expectedMapping.put(103, new int[] { 53, 384 });
    expectedMapping.put(104, new int[] { 54, 391 });
    expectedMapping.put(105, new int[] { 55, 395 });
    expectedMapping.put(106, new int[] { 56, 401 });
    expectedMapping.put(107, new int[] { 57, 409 });
    expectedMapping.put(108, new int[] { 58, 417 });
    expectedMapping.put(109, new int[] { 59, 426 });
    expectedMapping.put(110, new int[] { 60, 434 });
    expectedMapping.put(111, new int[] { 61, 442 });
    expectedMapping.put(112, new int[] { 62, 451 });
    expectedMapping.put(113, new int[] { 63, 457 });
    expectedMapping.put(114, new int[] { 64, 468 });
    expectedMapping.put(115, new int[] { 65, 476 });
    expectedMapping.put(116, new int[] { 66, 484 });
    expectedMapping.put(117, new int[] { 67, 492 });
    expectedMapping.put(118, new int[] { 68, 500 });
    expectedMapping.put(119, new int[] { 69, 509 });
    expectedMapping.put(120, new int[] { 70, 517 });
    expectedMapping.put(121, new int[] { 71, 525 });
    expectedMapping.put(122, new int[] { 72, 534 });
    expectedMapping.put(123, new int[] { 73, 538 });
    expectedMapping.put(124, new int[] { 74, 552 });
    expectedMapping.put(125, new int[] { 75, 559 });
    expectedMapping.put(126, new int[] { 76, 567 });
    expectedMapping.put(127, new int[] { 77, 574 });
    expectedMapping.put(128, new int[] { 78, 580 });
    expectedMapping.put(129, new int[] { 79, 585 });
    expectedMapping.put(130, new int[] { 80, 590 });
    expectedMapping.put(131, new int[] { 81, 602 });
    expectedMapping.put(132, new int[] { 82, 609 });
    expectedMapping.put(133, new int[] { 83, 616 });
    expectedMapping.put(134, new int[] { 84, 622 });
    expectedMapping.put(135, new int[] { 85, 630 });
    expectedMapping.put(136, new int[] { 86, 637 });
    expectedMapping.put(137, new int[] { 87, 644 });
    expectedMapping.put(138, new int[] { 88, 652 });
    expectedMapping.put(139, new int[] { 89, 661 });
    expectedMapping.put(140, new int[] { 90, 668 });
    expectedMapping.put(141, new int[] { 91, 678 });
    expectedMapping.put(142, new int[] { 92, 687 });
    expectedMapping.put(143, new int[] { 93, 696 });
    expectedMapping.put(144, new int[] { 94, 705 });
    expectedMapping.put(145, new int[] { 95, 714 });
    expectedMapping.put(146, new int[] { 96, 722 });
    expectedMapping.put(147, new int[] { 97, 729 });
  }

  @BeforeTest(alwaysRun = true)
  public void setUpSiftsClient() throws SiftsException, IOException
  {
    // read test props before manipulating config
    Cache.loadProperties("test/jalview/io/testProps.jvprops");
    // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
    // test reproducibility
    new SiftsSettings();
    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
            "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
    SiftsSettings.setMapWithSifts(true);
    SiftsSettings.setCacheThresholdInDays("2");
    SiftsSettings.setFailSafePIDThreshold("70");
    PDBfile pdbFile;
    pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
            + testPDBId + ".pdb", DataSourceType.FILE);
    siftsClient = new SiftsClient(pdbFile);
  }

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

  @Test(groups = { "Network" })
  public void getSIFTsFileTest() throws SiftsException, IOException
  {
    File siftsFile;
    siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
    FileAssert.assertFile(siftsFile);
    long t1 = siftsFile.lastModified();

    // re-read file should be returned from cache
    siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
    FileAssert.assertFile(siftsFile);
    long t2 = siftsFile.lastModified();
    assertEquals(t1, t2);

    /*
     * force fetch by having 0 expiry of cache
     * also wait one second, because file timestamp does not
     * give millisecond resolution :-(
     */
    synchronized (this)
    {
      try
      {
        wait(1000);
      } catch (InterruptedException e)
      {
      }
    }
    SiftsSettings.setCacheThresholdInDays("0");
    siftsFile = SiftsClient.getSiftsFile(testPDBId);
    FileAssert.assertFile(siftsFile);
    long t3 = siftsFile.lastModified();
    assertTrue(t3 > t2, "file timestamp unchanged at " + t3);

    SiftsSettings.setCacheThresholdInDays("2");
  }

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

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

  @Test(groups = { "Network" })
  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");
    testSeq.addDBRef(dbRef);
    // testSeq.setSourceDBRef(dbRef);

    try
    {
      HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
              "A", testSeq, null);
      Assert.assertEquals(testSeq.getStart(), 1);
      Assert.assertEquals(testSeq.getEnd(), 147);
<<<<<<< HEAD
      // Can't do Assert.assertEquals(actualMapping, expectedMapping);
      // because this fails in our version of TestNG
      Assert.assertEquals(actualMapping.size(), expectedMapping.size());
      Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
              .iterator();
      while (it.hasNext())
      {
        Map.Entry<Integer, int[]> pair = it.next();
        Assert.assertTrue(actualMapping.containsKey(pair.getKey()));
        Assert.assertEquals(actualMapping.get(pair.getKey()),
                pair.getValue());
      }

=======
      // Assert.assertEquals(actualMapping, expectedMapping);
      Assert.assertEquals(actualMapping.size(), expectedMapping.size());
      // Test key set
      Assert.assertEquals(actualMapping.keySet(), expectedMapping.keySet());
      // Test entry set
      for (int key : expectedMapping.keySet())
      {
        Assert.assertTrue(Arrays.equals(expectedMapping.get(key),
                actualMapping.get(key)));
      }
>>>>>>> f80180a53bf16dc72ecdd4ace0f70c83cb0d274a
    } catch (Exception e)
    {
      e.printStackTrace();
      Assert.fail("Exception thrown while generating mapping...");
    }
  }

  @Test(groups = { "Network" })
  private void getAtomIndexTest()
  {
    ArrayList<Atom> atoms = new ArrayList<Atom>();
    Atom atom = new Atom(u, u, u);
    atom.resNumber = 43;
    atom.atomIndex = 7;
    atoms.add(atom);
    int actualAtomIndex = siftsClient.getAtomIndex(1, atoms);
    Assert.assertEquals(actualAtomIndex, -1);
    actualAtomIndex = siftsClient.getAtomIndex(43, atoms);
    Assert.assertEquals(actualAtomIndex, 7);
  }

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

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

  }

  @Test(
groups = { "Network" },
    expectedExceptions = StructureMappingException.class)
  private void populateAtomPositionsNullTest1()
          throws IllegalArgumentException, StructureMappingException
  {
    siftsClient.populateAtomPositions(null, null);
  }

  @Test(
groups = { "Network" },
    expectedExceptions = StructureMappingException.class)
  private void populateAtomPositionsNullTest2()
          throws IllegalArgumentException, StructureMappingException
  {
    siftsClient.populateAtomPositions("A", null);
  }

  @Test(groups = { "Network" })
  public void getValidSourceDBRefTest() throws SiftsException
  {
    DBRefEntryI actualValidSrcDBRef = siftsClient
            .getValidSourceDBRef(testSeq);
    DBRefEntryI expectedDBRef = new DBRefEntry();
    expectedDBRef.setSource(DBRefSource.UNIPROT);
    expectedDBRef.setAccessionId("P00221");
    expectedDBRef.setVersion("");
    Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
  }

  @Test(
groups = { "Network" },
    expectedExceptions = SiftsException.class)
  public void getValidSourceDBRefExceptionTest() throws SiftsException
  {
    SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
    siftsClient.getValidSourceDBRef(invalidTestSeq);
  }

  @Test(
groups = { "Network" },
    expectedExceptions = SiftsException.class)
  public void getValidSourceDBRefExceptionXTest() throws SiftsException
  {
    SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
    DBRefEntry invalidDBRef = new DBRefEntry();
    invalidDBRef.setAccessionId("BLAR");
    invalidTestSeq.addDBRef(invalidDBRef);
    siftsClient.getValidSourceDBRef(invalidTestSeq);
  }

  @Test(groups = { "Network" })
  public void isValidDBRefEntryTest()
  {
    DBRefEntryI validDBRef = new DBRefEntry();
    validDBRef.setSource(DBRefSource.UNIPROT);
    validDBRef.setAccessionId("P00221");
    validDBRef.setVersion("");
    Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
  }

  @Test(groups = { "Network" })
  public void getSiftsStructureMappingTest()
          throws StructureMappingException, Exception
  {
    Assert.assertTrue(SiftsSettings.isMapWithSifts());
    StructureMapping strucMapping = siftsClient.getStructureMapping(
            testSeq, testPDBId, "A");
    String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
            + "Method: SIFTS\n\n"
            + "P00221 :  51 - 147 Maps to \n"
            + "1A70|A :  1 - 97\n\n"
            + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
            + "       |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
            + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"

            + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n"
            + "       |||||||||||||||||||||||||| |||||\n"
            + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" +

            "Length of alignment = 97\n" + "Percentage ID = 98.97\n";

    Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
            expectedMappingOutput);

<<<<<<< HEAD
    // Can't do Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
    // because this fails in our version of TestNG
    Assert.assertEquals(strucMapping.getMapping().size(),
            expectedMapping.size());
    Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
            .iterator();
    while (it.hasNext())
    {
      Map.Entry<Integer, int[]> pair = it.next();
      Assert.assertTrue(strucMapping.getMapping()
              .containsKey(pair.getKey()));
      Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
              pair.getValue());
=======
    // Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
    Assert.assertEquals(strucMapping.getMapping().size(),
            expectedMapping.size());
    // Test key set
    Assert.assertEquals(strucMapping.getMapping().keySet(),
            expectedMapping.keySet());
    // Test entry set
    for (int key : expectedMapping.keySet())
    {
      Assert.assertTrue(Arrays.equals(expectedMapping.get(key),
              strucMapping.getMapping().get(key)));
>>>>>>> f80180a53bf16dc72ecdd4ace0f70c83cb0d274a
    }
  }

  @Test(groups = { "Network" })
  public void getEntityCountTest()
  {
    int actualEntityCount = siftsClient.getEntityCount();
    System.out.println("actual entity count : " + actualEntityCount);
    Assert.assertEquals(actualEntityCount, 1);
  }

  @Test(groups = { "Network" })
  public void getDbAccessionIdTest()
  {
    String actualDbAccId = siftsClient.getDbAccessionId();
    System.out.println("Actual Db Accession Id: " + actualDbAccId);
    Assert.assertEquals(actualDbAccId, "1a70");
  }

  @Test(groups = { "Network" })
  public void getDbCoordSysTest()
  {
    String actualDbCoordSys = siftsClient.getDbCoordSys();
    System.out.println("Actual DbCoordSys: " + actualDbCoordSys);
    Assert.assertEquals(actualDbCoordSys, "PDBe");
  }

  @Test(groups = { "Network" })
  public void getDbSourceTest()
  {
    String actualDbSource = siftsClient.getDbSource();
    System.out.println("Actual DbSource: " + actualDbSource);
    Assert.assertEquals(actualDbSource, "PDBe");
  }

  @Test(groups = { "Network" })
  public void getDbVersionTest()
  {
    String actualDbVersion = siftsClient.getDbVersion();
    System.out.println("Actual DbVersion: " + actualDbVersion);
    Assert.assertEquals(actualDbVersion, "2.0");
  }

  @Test(groups = { "Network" })
  public void getEntityByMostOptimalMatchedIdTest1() throws IOException,
          SiftsException
  {
    SiftsClient siftsClientX = null;
    PDBfile pdbFile;
    pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
            + ".pdb", DataSourceType.FILE);
    siftsClientX = new SiftsClient(pdbFile);
    Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
    Assert.assertEquals(entityA.getEntityId(), "A");
    Entity entityB = siftsClientX.getEntityByMostOptimalMatchedId("B");
    Assert.assertEquals(entityB.getEntityId(), "C");
    Entity entityC = siftsClientX.getEntityByMostOptimalMatchedId("C");
    Assert.assertEquals(entityC.getEntityId(), "B");
    Entity entityD = siftsClientX.getEntityByMostOptimalMatchedId("D");
    Assert.assertEquals(entityD.getEntityId(), "D");

  }

  @Test(groups = { "Network" })
  public void getEntityByMostOptimalMatchedIdTest2() throws IOException,
          SiftsException
  {
    // This test is for a SIFTS file in which entity A should map to chain P for
    // the given PDB Id. All the other chains shouldn't be mapped as there are
    // no SIFTS entity records for them.
    SiftsClient siftsClientX = null;
    PDBfile pdbFile;
    pdbFile = new PDBfile(false, false, false, "test/jalview/io/3ucu.cif",
            DataSourceType.FILE);
    siftsClientX = new SiftsClient(pdbFile);
    Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P");
    Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A");
    Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");
    Assert.assertEquals(entityA.getEntityId(), "A");
    Assert.assertNotEquals(entityR, "A");
    Assert.assertNotEquals(entityP, "A");
    Assert.assertNotEquals(entityR, "R");
    Assert.assertNotEquals(entityP, "P");
    Assert.assertNull(entityR);
    Assert.assertNull(entityP);

  }
}