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

   1 package jalview.ws2.actions.secstructpred;
   2
   3 import static org.hamcrest.MatcherAssert.assertThat;
   4 import static org.hamcrest.Matchers.contains;
   5 import static org.hamcrest.Matchers.equalTo;
   6
   7 import java.io.IOException;
   8 import java.util.ArrayList;
   9 import java.util.List;
  10
  11 import static org.mockito.Mockito.mock;
  12 import static org.mockito.Mockito.when;
  13 import static org.mockito.ArgumentMatchers.any;
  14 import static jalview.testutils.ScopeFunctions.apply;
  15 import static jalview.testutils.Matchers.matchesSequenceString;
  16
  17 import jalview.io.DataSourceType;
  18 import jalview.io.FastaFile;
  19 import jalview.io.JPredFile;
  20
  21 import org.hamcrest.Matcher;
  22 import org.hamcrest.Matchers;
  23 import org.testng.annotations.BeforeMethod;
  24 import org.testng.annotations.DataProvider;
  25 import org.testng.annotations.Test;
  26
  27 import jalview.datamodel.Alignment;
  28 import jalview.datamodel.AlignmentI;
  29 import jalview.datamodel.HiddenColumns;
  30 import jalview.datamodel.Sequence;
  31 import jalview.datamodel.SequenceI;
  32 import jalview.gui.AlignViewport;
  33 import jalview.ws2.actions.ServiceInputInvalidException;
  34 import jalview.ws2.api.Credentials;
  35 import jalview.ws2.api.JobStatus;
  36 import jalview.ws2.api.WebServiceJobHandle;
  37 import jalview.ws2.client.api.SecStructPredWebServiceClientI;
  38 import static java.lang.String.format;
  39
  40 public class SecStructPredPDBSearchTaskTest
  41 {
  42   protected SecStructPredWebServiceClientI mockClient;
  43
  44   @BeforeMethod(alwaysRun = true)
  45   public void setupMockClient() throws IOException
  46   {
  47     mockClient = mock(SecStructPredWebServiceClientI.class);
  48     when(mockClient.getUrl()).thenReturn("http://example.org");
  49     when(mockClient.getClientName()).thenReturn("mock");
  50     when(mockClient.getLog(any())).thenReturn("");
  51     when(mockClient.getErrorLog(any())).thenReturn("");
  52   }
  53
  54   @DataProvider
  55   public Object[][] viewportAndExpectedInputSeq()
  56   {
  57     return new Object[][] {
  58         { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAAA")),
  59             "AAAAAAAAAAAAAAAAAAAA", },
  60         { new AlignViewport(createAlignment("--AAGGAGAG-AGGA----MMMMMMMM")),
  61             "AAGGAGAGAGGAMMMMMMMM" },
  62         { new AlignViewport(createAlignment("AAAANNNCCCCCCCCCCAAAAAA"),
  63                 apply(new HiddenColumns(), it -> it.hideColumns(4, 6))),
  64             "AAAACCCCCCCCCCAAAAAA" },
  65         { new AlignViewport(
  66                 createAlignment("NNNNGGGGVVVVVAAAAAAACCMMMMMMMM"),
  67                 apply(new HiddenColumns(), it -> {
  68                   it.hideColumns(4, 7);
  69                   it.hideColumns(20, 21);
  70                 })),
  71             "NNNNVVVVVAAAAAAAMMMMMMMM" } };
  72   }
  73
  74   public static AlignmentI createAlignment(String... sequences)
  75   {
  76     var seqArray = new Sequence[sequences.length];
  77     for (int i = 0; i < sequences.length; i++)
  78       seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]);
  79     return new Alignment(seqArray);
  80   }
  81
  82   @Test(
  83     groups = { "Functional" },
  84     dataProvider = "viewportAndExpectedInputSeq")
  85   public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
  86           String expectedSeq) throws Exception
  87   {
  88     var task = new SecStructPredPDBSearchTask(mockClient, List.of(),
  89             Credentials.empty(), viewport);
  90     var jobs = task.prepareJobs();
  91     assertThat(jobs.get(0).getInputSequences(),
  92             contains(matchesSequenceString(expectedSeq)));
  93   }
  94
  95   @DataProvider
  96   public Object[][] viewportWithTooShortSequence()
  97   {
  98     return new Object[][] {
  99         { new AlignViewport(createAlignment("")) },
 100         { new AlignViewport(createAlignment("A")) },
 101         { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAA")) },
 102         { new AlignViewport(createAlignment("AAAAACCCCCAAAAA-----CC")) },
 103         { new AlignViewport(createAlignment("-------------------------")) },
 104         { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAAAAAAAA"),
 105                 apply(new HiddenColumns(), it -> it.hideColumns(0, 24))) },
 106         { new AlignViewport(createAlignment("AAAAACCCCCAAAAACCCCCAAAAA"),
 107                 apply(new HiddenColumns(), it -> it.hideColumns(0, 10))) } };
 108   }
 109
 110   @Test(
 111     groups = { "Functional" },
 112     dataProvider = "viewportWithTooShortSequence",
 113     expectedExceptions = ServiceInputInvalidException.class)
 114   public void testPrepareJobs_SequenceTooShort_InputInvalidException(
 115           AlignViewport viewport) throws ServiceInputInvalidException
 116   {
 117     var task = new SecStructPredPDBSearchTask(mockClient, List.of(),
 118             Credentials.empty(), viewport);
 119     task.prepareJobs();
 120   }
 121
 122   @DataProvider
 123   public Object[][] collectResultDataset() throws IOException
 124   {
 125     return new Object[][] {
 126         {
 127             new AlignViewport(new Alignment(new FastaFile(
 128                 "examples/testdata/secstrpred/sequence0_input.fa",
 129                 DataSourceType.FILE).getSeqsAsArray()
 130             )),
 131             "examples/testdata/secstrpred/sequence0.align",
 132             "examples/testdata/secstrpred/sequence0.concise"
 133         },
 134     };
 135   }
 136
 137   @Test(groups = { "Functional" }, dataProvider = "collectResultDataset")
 138   public void testCollectResult(AlignViewport viewport, String alnFileName,
 139           String predFileName) throws Exception
 140   {
 141     var alnFile = new FastaFile(alnFileName, DataSourceType.FILE);
 142     var predFile = new JPredFile(predFileName, DataSourceType.FILE);
 143     when(mockClient.getPredictionFile(any())).thenReturn(predFile);
 144     when(mockClient.getAlignmentFile(any())).thenReturn(alnFile);
 145     when(mockClient.getStatus(any())).thenReturn(JobStatus.COMPLETED);
 146     when(mockClient.submit(any(), any(), any()))
 147             .thenReturn(new WebServiceJobHandle("mock", "mock",
 148                     "http://example.org", "0"));
 149
 150     var task = new SecStructPredPDBSearchTask(mockClient, List.of(),
 151             Credentials.empty(), viewport);
 152     task.init();
 153     task.poll();
 154     task.complete();
 155     var resultAlignment = task.getResult();
 156     var sequences = resultAlignment.getSequences();
 157
 158     {
 159       List<Matcher<? super SequenceI>> matchers = new ArrayList<>();
 160       for (var seq : alnFile.getSeqs())
 161         matchers.add(matchesSequenceString(seq));
 162       assertThat(sequences, Matchers.contains(matchers));
 163     }
 164
 165     {
 166       var originalHidden = viewport.getAlignment().getHiddenColumns();
 167       var resultHidden = resultAlignment.getHiddenColumns();
 168       assertThat(resultHidden, equalTo(originalHidden));
 169     }
 170   }
 171 }