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

   1 package jalview.ws2.actions.secstructpred;
   2
   3 import jalview.datamodel.Alignment;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.HiddenColumns;
   7 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.gui.AlignViewport;
  10 import jalview.io.DataSourceType;
  11 import jalview.io.FastaFile;
  12 import jalview.io.JPredFile;
  13 import jalview.ws2.api.Credentials;
  14 import jalview.ws2.api.JobStatus;
  15 import jalview.ws2.api.WebServiceJobHandle;
  16 import jalview.ws2.client.api.SecStructPredWebServiceClientI;
  17 import org.hamcrest.Matcher;
  18 import org.hamcrest.Matchers;
  19 import org.testng.annotations.BeforeMethod;
  20 import org.testng.annotations.DataProvider;
  21 import org.testng.annotations.Test;
  22
  23 import java.io.IOException;
  24 import java.util.ArrayList;
  25 import java.util.List;
  26
  27 import static jalview.testutils.Matchers.matchesAnnotations;
  28 import static jalview.testutils.Matchers.matchesSequenceString;
  29 import static jalview.testutils.ScopeFunctions.apply;
  30 import static java.lang.String.format;
  31 import static org.hamcrest.MatcherAssert.assertThat;
  32 import static org.hamcrest.Matchers.allOf;
  33 import static org.hamcrest.Matchers.containsInAnyOrder;
  34 import static org.hamcrest.Matchers.equalTo;
  35 import static org.hamcrest.Matchers.hasProperty;
  36 import static org.mockito.ArgumentMatchers.any;
  37 import static org.mockito.Mockito.mock;
  38 import static org.mockito.Mockito.when;
  39
  40 public class SecStructPredMsaTaskTest
  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.submit(any(), any(), any()))
  51             .thenReturn(new WebServiceJobHandle("mock", "mock",
  52                     "http://example.org", "0"));
  53     when(mockClient.getLog(any())).thenReturn("");
  54     when(mockClient.getErrorLog(any())).thenReturn("");
  55     when(mockClient.getStatus(any())).thenReturn(JobStatus.COMPLETED);
  56   }
  57
  58   @DataProvider
  59   public Object[][] alignmentWithExpectedInput()
  60   {
  61     return new Object[][] { {
  62         new AlignViewport(createAlignment("AAAAAAAAAAAA", "AAAAAAAAAAAA",
  63                 "AAAAAAAAAAAA")),
  64         List.of("AAAAAAAAAAAA", "AAAAAAAAAAAA", "AAAAAAAAAAAA") },
  65         { new AlignViewport(createAlignment("AAAA--NNNNAAAA",
  66                 "AA--AANNNNAAAA", "AA--AARRRRAAAA")),
  67             List.of("AAAA--NNNNAAAA", "AA--AANNNNAAAA", "AA--AARRRRAAAA") },
  68         { new AlignViewport(createAlignment("AAAANNNNAAAA--",
  69                 "AAAARRRRAAAA--", "AAAARRRRAAAA--")),
  70             List.of("AAAANNNNAAAA--", "AAAARRRRAAAA--", "AAAARRRRAAAA--") },
  71         { new AlignViewport(createAlignment("AAAA--NNNNAAAA",
  72                 "AAAA--NNNNAAAA", "AAAA--NNNNAAAA")),
  73             List.of("AAAA--NNNNAAAA", "AAAA--NNNNAAAA", "AAAA--NNNNAAAA") },
  74         { new AlignViewport(createAlignment("AAAACCCCNNNN", "------------",
  75                 "AAAADDDDNNNN")),
  76             List.of("AAAACCCCNNNN", "AAAADDDDNNNN") },
  77         { new AlignViewport(createAlignment("AAAACC--NNNN", "AAAACCDDNNNN"),
  78                 apply(new HiddenColumns(), it -> it.hideColumns(6, 7))),
  79             List.of("AAAACCNNNN", "AAAACCNNNN") },
  80         { new AlignViewport(
  81                 createAlignment("CCAAAACC--MMMM", "--AAAAGGGGMMMM"),
  82                 apply(new HiddenColumns(), it -> {
  83                   it.hideColumns(0, 1);
  84                   it.hideColumns(8, 9);
  85                 })),
  86             List.of("AAAACCMMMM", "AAAAGGMMMM") },
  87         { new AlignViewport(
  88                 createAlignment("CCAAAACC--MMMM", "CCAAAACC--MMMM"),
  89                 apply(new HiddenColumns(), it -> it.hideColumns(2, 5))),
  90             List.of("CCCC--MMMM", "CCCC--MMMM") } };
  91   }
  92
  93   public static AlignmentI createAlignment(String... sequences)
  94   {
  95     var seqArray = new Sequence[sequences.length];
  96     for (int i = 0; i < sequences.length; i++)
  97       seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]);
  98     return new Alignment(seqArray);
  99   }
 100
 101   @Test(
 102     groups =
 103     { "Functional" },
 104     dataProvider = "alignmentWithExpectedInput")
 105   public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
 106           List<String> expectedInput) throws Exception
 107   {
 108     var task = new SecStructPredMsaTask(mockClient, List.of(),
 109             Credentials.empty(), viewport);
 110     var jobs = task.prepareJobs();
 111     List<Matcher<? super SequenceI>> seqMatchers = new ArrayList<>(
 112             expectedInput.size());
 113     for (var seqStr : expectedInput)
 114       seqMatchers.add(matchesSequenceString(seqStr));
 115     assertThat(jobs.get(0).getInputSequences(),
 116             Matchers.<SequenceI> contains(seqMatchers));
 117   }
 118
 119   @DataProvider
 120   public Object[][] viewportWithServiceOutput() throws IOException
 121   {
 122
 123     return new Object[][] {
 124       {
 125           new AlignViewport(new Alignment(new FastaFile(
 126                   "examples/testdata/secstrpred/alignment0_aln.fa",
 127                   DataSourceType.FILE).getSeqsAsArray())),
 128           "examples/testdata/secstrpred/alignment0.fa",
 129           "examples/testdata/secstrpred/alignment0.concise"
 130       },
 131       {
 132         new AlignViewport(new Alignment(new FastaFile(
 133                 "examples/testdata/secstrpred/alignment0a_aln.fa",
 134                 DataSourceType.FILE).getSeqsAsArray()),
 135                 apply(new HiddenColumns(), it -> it.hideColumns(3, 7))),
 136         "examples/testdata/secstrpred/alignment0.fa",
 137         "examples/testdata/secstrpred/alignment0.concise"
 138       }
 139     };
 140   }
 141
 142   @Test(groups = "Functional", dataProvider = "viewportWithServiceOutput")
 143   public void testCollectResults(AlignViewport viewport, String alnFileName, String predFileName) throws Exception
 144   {
 145     var alnFile = new FastaFile(alnFileName, DataSourceType.FILE);
 146     var predFile = new JPredFile(predFileName, DataSourceType.FILE);
 147     when(mockClient.getPredictionFile(any())).thenReturn(predFile);
 148     when(mockClient.getAlignmentFile(any())).thenReturn(alnFile);
 149
 150     var task = new SecStructPredMsaTask(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     // Test output alignment matches original
 159     {
 160       List<Matcher<? super SequenceI>> matchers = new ArrayList<>();
 161       for (var seq : viewport.getAlignment().getSequences())
 162         matchers.add(matchesSequenceString(seq));
 163       assertThat(sequences, Matchers.contains(matchers));
 164     }
 165     // Test output sequence names match original
 166     {
 167       List<Matcher<? super SequenceI>> matchers = new ArrayList<>();
 168       for (var seq : viewport.getAlignment().getSequences())
 169         matchers.add(hasProperty("name", equalTo(seq.getName())));
 170       assertThat(sequences, Matchers.contains(matchers));
 171     }
 172     // Test hidden columns
 173     {
 174       var originalHidden = viewport.getAlignment().getHiddenColumns();
 175       var resultHidden = resultAlignment.getHiddenColumns();
 176       assertThat(resultHidden, equalTo(originalHidden));
 177     }
 178     // Test annotations present on the alignment
 179     {
 180       var hiddenColumns = viewport.getAlignment().getHiddenColumns();
 181       List<Matcher<? super AlignmentAnnotation>> matchers = new ArrayList<>();
 182       for (var annot : predFile.getAnnotations())
 183         matchers.add(allOf(
 184                 hasProperty("label", equalTo(annot.label)),
 185                 hasProperty("annotations", matchesAnnotations(annot.annotations))
 186         ));
 187       List<AlignmentAnnotation> annotations = new ArrayList<>();
 188       for (var annot : resultAlignment.getAlignmentAnnotation())
 189         annotations.add(new AlignmentAnnotation(annot, hiddenColumns));
 190       assertThat(annotations, containsInAnyOrder(matchers));
 191     }
 192
 193   }
 194 }