package jalview.ws2.actions.secstructpred;

import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;

import java.io.IOException;
import java.util.List;

import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import static org.mockito.ArgumentMatchers.any;
import static jalview.testutils.ScopeFunctions.apply;
import static jalview.testutils.Matchers.matchesSequenceString;

import jalview.io.DataSourceType;
import jalview.io.FastaFile;
import jalview.io.JPredFile;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.gui.AlignViewport;
import jalview.ws2.actions.ServiceInputInvalidException;
import jalview.ws2.api.Credentials;
import jalview.ws2.client.api.SecStructPredWebServiceClientI;
import static java.lang.String.format;

public class SecStructPredPDBSearchTaskTest
{
  protected SecStructPredWebServiceClientI mockClient;

  @BeforeMethod(alwaysRun = true)
  public void setupMockClient() throws IOException
  {
    mockClient = mock(SecStructPredWebServiceClientI.class);
    when(mockClient.getUrl()).thenReturn("http://example.org");
    when(mockClient.getClientName()).thenReturn("mock");
    when(mockClient.getLog(any())).thenReturn("");
    when(mockClient.getErrorLog(any())).thenReturn("");
  }

  @DataProvider
  public Object[][] viewportAndExpectedInputSeq()
  {
    return new Object[][] {
        { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAAA")),
            "AAAAAAAAAAAAAAAAAAAA", },
        { new AlignViewport(createAlignment("--AAGGAGAG-AGGA----MMMMMMMM")),
            "AAGGAGAGAGGAMMMMMMMM" },
        { new AlignViewport(createAlignment("AAAANNNCCCCCCCCCCAAAAAA"),
                apply(new HiddenColumns(), it -> it.hideColumns(4, 6))),
            "AAAACCCCCCCCCCAAAAAA" },
        { new AlignViewport(
                createAlignment("NNNNGGGGVVVVVAAAAAAACCMMMMMMMM"),
                apply(new HiddenColumns(), it -> {
                  it.hideColumns(4, 7);
                  it.hideColumns(20, 21);
                })),
            "NNNNVVVVVAAAAAAAMMMMMMMM" } };
  }

  public static AlignmentI createAlignment(String... sequences)
  {
    var seqArray = new Sequence[sequences.length];
    for (int i = 0; i < sequences.length; i++)
      seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]);
    return new Alignment(seqArray);
  }

  @Test(
    groups = { "Functional" },
    dataProvider = "viewportAndExpectedInputSeq")
  public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
          String expectedSeq) throws Exception
  {
    var task = new SecStructPredPDBSearchTask(mockClient, List.of(),
            Credentials.empty(), viewport);
    var jobs = task.prepareJobs();
    assertThat(jobs.get(0).getInputSequences(),
            contains(matchesSequenceString(expectedSeq)));
  }

  @DataProvider
  public Object[][] viewportWithTooShortSequence()
  {
    return new Object[][] { { new AlignViewport(createAlignment("")) },
        { new AlignViewport(createAlignment("A")) },
        { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAA")) },
        { new AlignViewport(createAlignment("AAAAACCCCCAAAAA-----CC")) },
        { new AlignViewport(createAlignment("-------------------------")) },
        { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAAAAAAAA"),
                apply(new HiddenColumns(), it -> it.hideColumns(0, 24))) },
        { new AlignViewport(createAlignment("AAAAACCCCCAAAAACCCCCAAAAA"),
                apply(new HiddenColumns(), it -> it.hideColumns(0, 10))) } };
  }

  @Test(
    groups = { "Functional" },
    dataProvider = "viewportWithTooShortSequence",
    expectedExceptions = ServiceInputInvalidException.class)
  public void testPrepareJobs_SequenceTooShort_InputInvalidException(
          AlignViewport viewport) throws ServiceInputInvalidException
  {
    var task = new SecStructPredPDBSearchTask(mockClient, List.of(),
            Credentials.empty(), viewport);
    task.prepareJobs();
  }

  @DataProvider
  public Object[][] collectResultDataset() throws IOException
  {
    return new Object[][] {
        {
            new AlignViewport(new Alignment(new FastaFile(
                "examples/testdata/secstrpred/sequence0_input.fa",
                DataSourceType.FILE).getSeqsAsArray()
            )),
            "examples/testdata/secstrpred/sequence0.align",
            "examples/testdata/secstrpred/sequence0.concise"
        },
    };
  }

  @Test(
      groups = { "Functional" }
  )
  public void testCollectResult(AlignViewport viewport, String alnFileName, String predFileName) throws Exception
  {
    var alnFile = new FastaFile(alnFileName, DataSourceType.FILE);
    var predFile = new JPredFile(predFileName, DataSourceType.FILE);
  }
}