package jalview.ws2.actions.secstructpred;

import static org.hamcrest.MatcherAssert.assertThat;

import static jalview.testutils.Matchers.matchesSequenceString;
import static jalview.testutils.ScopeFunctions.apply;
import static jalview.testutils.ScopeFunctions.run;
import org.hamcrest.Matcher;
import org.hamcrest.Matchers;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyList;
import static org.hamcrest.Matchers.contains;

import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.doAnswer;
import static org.mockito.Mockito.doThrow;
import static org.mockito.Mockito.inOrder;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;

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

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.ws2.api.Credentials;
import jalview.ws2.client.api.SecStructPredWebServiceClientI;

import static java.lang.String.format;

public class SecStructPredTaskTest
{
  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[][] alignmentWithExpectedInput()
  {
    return new Object[][] {
        {
            new AlignViewport(createAlignment("AAAAAAAAAAAA", "AAAAAAAAAAAA",
                "AAAAAAAAAAAA")),
            List.of("AAAAAAAAAAAA", "AAAAAAAAAAAA", "AAAAAAAAAAAA") },
        {
            new AlignViewport(createAlignment("AAAA--NNNNAAAA",
                "AA--AANNNNAAAA", "AA--AARRRRAAAA")),
            List.of("AAAA--NNNNAAAA", "AA--AANNNNAAAA", "AA--AARRRRAAAA") },
        {
            new AlignViewport(createAlignment("AAAANNNNAAAA--",
                "AAAARRRRAAAA--", "AAAARRRRAAAA--")),
            List.of("AAAANNNNAAAA--", "AAAARRRRAAAA--", "AAAARRRRAAAA--") },
        {
            new AlignViewport(createAlignment("AAAA--NNNNAAAA",
                "AAAA--NNNNAAAA", "AAAA--NNNNAAAA")),
            List.of("AAAA--NNNNAAAA", "AAAA--NNNNAAAA", "AAAA--NNNNAAAA") },
        {
            new AlignViewport(createAlignment("AAAACCCCNNNN", "------------",
                "AAAADDDDNNNN")),
            List.of("AAAACCCCNNNN", "AAAADDDDNNNN") },
        {
            new AlignViewport(createAlignment("AAAACC--NNNN", "AAAACCDDNNNN"),
                apply(new HiddenColumns(), it -> it.hideColumns(6, 7))),
            List.of("AAAACCNNNN", "AAAACCNNNN") },
        {
            new AlignViewport(
                createAlignment("CCAAAACC--MMMM", "--AAAAGGGGMMMM"),
                apply(new HiddenColumns(), it -> {
                  it.hideColumns(0, 1);
                  it.hideColumns(8, 9);
                })),
            List.of("AAAACCMMMM", "AAAAGGMMMM") },
        {
            new AlignViewport(
                createAlignment("CCAAAACC--MMMM", "CCAAAACC--MMMM"),
                apply(new HiddenColumns(), it -> it.hideColumns(2, 5))),
            List.of("CCCC--MMMM", "CCCC--MMMM") } };
  }

  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 = "alignmentWithExpectedInput")
  public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
      List<String> expectedInput) throws Exception
  {
    var task = new SecStructPredMsaTask(mockClient, List.of(), Credentials.empty(),
        viewport);
    var jobs = task.prepareJobs();
    List<Matcher<? super SequenceI>> seqMatchers = new ArrayList<>(
        expectedInput.size());
    for (var seqStr : expectedInput)
      seqMatchers.add(matchesSequenceString(seqStr));
    assertThat(jobs.get(0).getInputSequences(),
        Matchers.<SequenceI> contains(seqMatchers));
  }
}