/*
 * 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.io;

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;

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[][] expectedMapping = { { 0, 0 }, { 0, 1 }, { 0, 2 }, { 0, 3 },
      { 0, 4 }, { 0, 5 }, { 0, 6 }, { 0, 7 }, { 0, 8 }, { 0, 9 },
      { 0, 10 }, { 0, 11 }, { 0, 12 }, { 0, 13 }, { 0, 14 }, { 0, 15 },
      { 0, 16 }, { 0, 17 }, { 0, 18 }, { 0, 19 }, { 0, 20 }, { 0, 21 },
      { 0, 22 }, { 0, 23 }, { 0, 24 }, { 0, 25 }, { 0, 26 }, { 0, 27 },
      { 0, 28 }, { 0, 29 }, { 0, 30 }, { 0, 31 }, { 0, 32 }, { 0, 33 },
      { 0, 34 }, { 0, 35 }, { 0, 36 }, { 0, 37 }, { 0, 38 }, { 0, 39 },
      { 0, 40 }, { 0, 41 }, { 0, 42 }, { 0, 43 }, { 0, 44 }, { 0, 45 },
      { 0, 46 }, { 0, 47 }, { 0, 48 }, { 0, 49 }, { 0, 50 }, { 1, 51 },
      { 2, 52 }, { 3, 53 }, { 4, 54 }, { 5, 55 }, { 6, 56 }, { 7, 57 },
      { 8, 58 }, { 9, 59 }, { 10, 60 }, { 11, 61 }, { 12, 62 }, { 13, 63 },
      { 14, 64 }, { 15, 65 }, { 16, 66 }, { 17, 67 }, { 18, 68 },
      { 19, 69 }, { 20, 70 }, { 21, 71 }, { 22, 72 }, { 23, 73 },
      { 24, 74 }, { 25, 75 }, { 26, 76 }, { 27, 77 }, { 28, 78 },
      { 29, 79 }, { 30, 80 }, { 31, 81 }, { 32, 82 }, { 33, 83 },
      { 34, 84 }, { 35, 85 }, { 36, 86 }, { 37, 87 }, { 38, 88 },
      { 39, 89 }, { 40, 90 }, { 41, 91 }, { 42, 92 }, { 43, 93 },
      { 44, 94 }, { 45, 95 }, { 46, 96 }, { 47, 97 }, { 48, 98 },
      { 49, 99 }, { 50, 100 }, { 51, 101 }, { 52, 102 }, { 53, 103 },
      { 54, 104 }, { 55, 105 }, { 56, 106 }, { 57, 107 }, { 58, 108 },
      { 59, 109 }, { 60, 110 }, { 61, 111 }, { 62, 112 }, { 63, 113 },
      { 64, 114 }, { 65, 115 }, { 66, 116 }, { 67, 117 }, { 68, 118 },
      { 69, 119 }, { 70, 120 }, { 71, 121 }, { 72, 122 }, { 73, 123 },
      { 74, 124 }, { 75, 125 }, { 76, 126 }, { 77, 127 }, { 78, 128 },
      { 79, 129 }, { 80, 130 }, { 81, 131 }, { 82, 132 }, { 83, 133 },
      { 84, 134 }, { 85, 135 }, { 86, 136 }, { 87, 137 }, { 88, 138 },
      { 89, 139 }, { 90, 140 }, { 91, 141 }, { 92, 142 }, { 93, 143 },
      { 94, 144 }, { 95, 145 }, { 96, 146 } };

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

  }

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

  }
}