test/jalview/ws2/actions/secstructpred/SecStructPredTaskTest.java

   1 package jalview.ws2.actions.secstructpred;
   2
   3 import static org.hamcrest.MatcherAssert.assertThat;
   4
   5 import static jalview.testutils.Matchers.matchesSequenceString;
   6 import static jalview.testutils.ScopeFunctions.apply;
   7 import static jalview.testutils.ScopeFunctions.run;
   8 import org.hamcrest.Matcher;
   9 import org.hamcrest.Matchers;
  10 import org.testng.annotations.BeforeMethod;
  11 import org.testng.annotations.DataProvider;
  12 import org.testng.annotations.Test;
  13
  14 import static org.mockito.ArgumentMatchers.any;
  15 import static org.mockito.ArgumentMatchers.anyList;
  16 import static org.hamcrest.Matchers.contains;
  17
  18 import static org.mockito.ArgumentMatchers.eq;
  19 import static org.mockito.Mockito.doAnswer;
  20 import static org.mockito.Mockito.doThrow;
  21 import static org.mockito.Mockito.inOrder;
  22 import static org.mockito.Mockito.mock;
  23 import static org.mockito.Mockito.verify;
  24 import static org.mockito.Mockito.when;
  25
  26 import java.io.IOException;
  27 import java.util.ArrayList;
  28 import java.util.List;
  29
  30 import jalview.datamodel.Alignment;
  31 import jalview.datamodel.AlignmentI;
  32 import jalview.datamodel.HiddenColumns;
  33 import jalview.datamodel.Sequence;
  34 import jalview.datamodel.SequenceI;
  35 import jalview.gui.AlignViewport;
  36 import jalview.ws2.api.Credentials;
  37 import jalview.ws2.client.api.SecStructPredWebServiceClientI;
  38
  39 import static java.lang.String.format;
  40
  41 public class SecStructPredTaskTest
  42 {
  43   protected SecStructPredWebServiceClientI mockClient;
  44
  45   @BeforeMethod(alwaysRun = true)
  46   public void setupMockClient() throws IOException
  47   {
  48     mockClient = mock(SecStructPredWebServiceClientI.class);
  49     when(mockClient.getUrl()).thenReturn("http://example.org");
  50     when(mockClient.getClientName()).thenReturn("mock");
  51     when(mockClient.getLog(any())).thenReturn("");
  52     when(mockClient.getErrorLog(any())).thenReturn("");
  53   }
  54
  55   @DataProvider
  56   public Object[][] alignmentWithExpectedInput()
  57   {
  58     return new Object[][] {
  59         {
  60             new AlignViewport(createAlignment("AAAAAAAAAAAA", "AAAAAAAAAAAA",
  61                 "AAAAAAAAAAAA")),
  62             List.of("AAAAAAAAAAAA", "AAAAAAAAAAAA", "AAAAAAAAAAAA") },
  63         {
  64             new AlignViewport(createAlignment("AAAA--NNNNAAAA",
  65                 "AA--AANNNNAAAA", "AA--AARRRRAAAA")),
  66             List.of("AAAA--NNNNAAAA", "AA--AANNNNAAAA", "AA--AARRRRAAAA") },
  67         {
  68             new AlignViewport(createAlignment("AAAANNNNAAAA--",
  69                 "AAAARRRRAAAA--", "AAAARRRRAAAA--")),
  70             List.of("AAAANNNNAAAA--", "AAAARRRRAAAA--", "AAAARRRRAAAA--") },
  71         {
  72             new AlignViewport(createAlignment("AAAA--NNNNAAAA",
  73                 "AAAA--NNNNAAAA", "AAAA--NNNNAAAA")),
  74             List.of("AAAA--NNNNAAAA", "AAAA--NNNNAAAA", "AAAA--NNNNAAAA") },
  75         {
  76             new AlignViewport(createAlignment("AAAACCCCNNNN", "------------",
  77                 "AAAADDDDNNNN")),
  78             List.of("AAAACCCCNNNN", "AAAADDDDNNNN") },
  79         {
  80             new AlignViewport(createAlignment("AAAACC--NNNN", "AAAACCDDNNNN"),
  81                 apply(new HiddenColumns(), it -> it.hideColumns(6, 7))),
  82             List.of("AAAACCNNNN", "AAAACCNNNN") },
  83         {
  84             new AlignViewport(
  85                 createAlignment("CCAAAACC--MMMM", "--AAAAGGGGMMMM"),
  86                 apply(new HiddenColumns(), it -> {
  87                   it.hideColumns(0, 1);
  88                   it.hideColumns(8, 9);
  89                 })),
  90             List.of("AAAACCMMMM", "AAAAGGMMMM") },
  91         {
  92             new AlignViewport(
  93                 createAlignment("CCAAAACC--MMMM", "CCAAAACC--MMMM"),
  94                 apply(new HiddenColumns(), it -> it.hideColumns(2, 5))),
  95             List.of("CCCC--MMMM", "CCCC--MMMM") } };
  96   }
  97
  98   public static AlignmentI createAlignment(String... sequences)
  99   {
 100     var seqArray = new Sequence[sequences.length];
 101     for (int i = 0; i < sequences.length; i++)
 102       seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]);
 103     return new Alignment(seqArray);
 104   }
 105
 106   @Test(groups = { "functional" }, dataProvider = "alignmentWithExpectedInput")
 107   public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
 108       List<String> expectedInput) throws Exception
 109   {
 110     var task = new SecStructPredMsaTask(mockClient, List.of(), Credentials.empty(),
 111         viewport);
 112     var jobs = task.prepareJobs();
 113     List<Matcher<? super SequenceI>> seqMatchers = new ArrayList<>(
 114         expectedInput.size());
 115     for (var seqStr : expectedInput)
 116       seqMatchers.add(matchesSequenceString(seqStr));
 117     assertThat(jobs.get(0).getInputSequences(),
 118         Matchers.<SequenceI> contains(seqMatchers));
 119   }
 120 }