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