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package jalview.ws2.actions.secstructpred; |
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import static org.hamcrest.MatcherAssert.assertThat; |
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import static org.hamcrest.Matchers.contains; |
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import static org.hamcrest.Matchers.equalTo; |
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import java.io.IOException; |
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import java.util.ArrayList; |
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import java.util.List; |
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import static org.mockito.Mockito.mock; |
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import static org.mockito.Mockito.when; |
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import static org.mockito.ArgumentMatchers.any; |
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import static jalview.testutils.ScopeFunctions.apply; |
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import static jalview.testutils.Matchers.matchesSequenceString; |
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import jalview.io.DataSourceType; |
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import jalview.io.FastaFile; |
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import jalview.io.JPredFile; |
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import org.hamcrest.Matcher; |
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import org.hamcrest.Matchers; |
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import org.testng.annotations.BeforeMethod; |
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import org.testng.annotations.DataProvider; |
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import org.testng.annotations.Test; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignViewport; |
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import jalview.ws2.actions.ServiceInputInvalidException; |
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import jalview.ws2.api.Credentials; |
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import jalview.ws2.api.JobStatus; |
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import jalview.ws2.api.WebServiceJobHandle; |
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import jalview.ws2.client.api.SecStructPredWebServiceClientI; |
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import static java.lang.String.format; |
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| 100% |
Uncovered Elements: 0 (48) |
Complexity: 9 |
Complexity Density: 0.24 |
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public class SecStructPredPDBSearchTaskTest |
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{ |
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protected SecStructPredWebServiceClientI mockClient; |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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 @BeforeMethod(alwaysRun = true)... |
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public void setupMockClient() throws IOException |
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{ |
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mockClient = mock(SecStructPredWebServiceClientI.class); |
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when(mockClient.getUrl()).thenReturn("http://example.org"); |
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when(mockClient.getClientName()).thenReturn("mock"); |
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when(mockClient.getLog(any())).thenReturn(""); |
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when(mockClient.getErrorLog(any())).thenReturn(""); |
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} |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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@DataProvider... |
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public Object[][] viewportAndExpectedInputSeq() |
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{ |
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return new Object[][] { |
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{ new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAAA")), |
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"AAAAAAAAAAAAAAAAAAAA", }, |
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{ new AlignViewport(createAlignment("--AAGGAGAG-AGGA----MMMMMMMM")), |
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"AAGGAGAGAGGAMMMMMMMM" }, |
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{ new AlignViewport(createAlignment("AAAANNNCCCCCCCCCCAAAAAA"), |
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apply(new HiddenColumns(), it -> it.hideColumns(4, 6))), |
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"AAAACCCCCCCCCCAAAAAA" }, |
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{ new AlignViewport( |
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createAlignment("NNNNGGGGVVVVVAAAAAAACCMMMMMMMM"), |
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apply(new HiddenColumns(), it -> { |
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it.hideColumns(4, 7); |
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it.hideColumns(20, 21); |
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})), |
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"NNNNVVVVVAAAAAAAMMMMMMMM" } }; |
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} |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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public static AlignmentI createAlignment(String... sequences)... |
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{ |
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var seqArray = new Sequence[sequences.length]; |
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for (int i = 0; i < sequences.length; i++) |
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seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]); |
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return new Alignment(seqArray); |
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} |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
1PASS
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@Test(... |
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groups = { "Functional" }, |
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dataProvider = "viewportAndExpectedInputSeq") |
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public void testPrepareJobs_checkInputSequences(AlignViewport viewport, |
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String expectedSeq) throws Exception |
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{ |
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var task = new SecStructPredPDBSearchTask(mockClient, List.of(), |
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Credentials.empty(), viewport); |
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var jobs = task.prepareJobs(); |
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assertThat(jobs.get(0).getInputSequences(), |
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contains(matchesSequenceString(expectedSeq))); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@DataProvider... |
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public Object[][] viewportWithTooShortSequence() |
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{ |
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return new Object[][] { |
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{ new AlignViewport(createAlignment("")) }, |
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{ new AlignViewport(createAlignment("A")) }, |
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{ new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAA")) }, |
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{ new AlignViewport(createAlignment("AAAAACCCCCAAAAA-----CC")) }, |
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{ new AlignViewport(createAlignment("-------------------------")) }, |
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{ new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAAAAAAAA"), |
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apply(new HiddenColumns(), it -> it.hideColumns(0, 24))) }, |
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{ new AlignViewport(createAlignment("AAAAACCCCCAAAAACCCCCAAAAA"), |
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apply(new HiddenColumns(), it -> it.hideColumns(0, 10))) } }; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
1PASS
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@Test(... |
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groups = { "Functional" }, |
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dataProvider = "viewportWithTooShortSequence", |
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expectedExceptions = ServiceInputInvalidException.class) |
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public void testPrepareJobs_SequenceTooShort_InputInvalidException( |
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AlignViewport viewport) throws ServiceInputInvalidException |
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{ |
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var task = new SecStructPredPDBSearchTask(mockClient, List.of(), |
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Credentials.empty(), viewport); |
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task.prepareJobs(); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@DataProvider... |
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public Object[][] collectResultDataset() throws IOException |
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{ |
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return new Object[][] { |
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{ |
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new AlignViewport(new Alignment(new FastaFile( |
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"examples/testdata/secstrpred/sequence0_input.fa", |
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DataSourceType.FILE).getSeqsAsArray() |
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)), |
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"examples/testdata/secstrpred/sequence0.align", |
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"examples/testdata/secstrpred/sequence0.concise" |
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}, |
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}; |
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} |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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@Test(groups = { "Functional" }, dataProvider = "collectResultDataset")... |
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public void testCollectResult(AlignViewport viewport, String alnFileName, |
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String predFileName) throws Exception |
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{ |
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var alnFile = new FastaFile(alnFileName, DataSourceType.FILE); |
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var predFile = new JPredFile(predFileName, DataSourceType.FILE); |
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when(mockClient.getPredictionFile(any())).thenReturn(predFile); |
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when(mockClient.getAlignmentFile(any())).thenReturn(alnFile); |
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when(mockClient.getStatus(any())).thenReturn(JobStatus.COMPLETED); |
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when(mockClient.submit(any(), any(), any())) |
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.thenReturn(new WebServiceJobHandle("mock", "mock", |
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"http://example.org", "0")); |
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var task = new SecStructPredPDBSearchTask(mockClient, List.of(), |
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Credentials.empty(), viewport); |
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task.init(); |
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task.poll(); |
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task.complete(); |
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var resultAlignment = task.getResult(); |
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var sequences = resultAlignment.getSequences(); |
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{ |
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List<Matcher<? super SequenceI>> matchers = new ArrayList<>(); |
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for (var seq : alnFile.getSeqs()) |
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matchers.add(matchesSequenceString(seq)); |
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assertThat(sequences, Matchers.contains(matchers)); |
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} |
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{ |
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var originalHidden = viewport.getAlignment().getHiddenColumns(); |
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var resultHidden = resultAlignment.getHiddenColumns(); |
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assertThat(resultHidden, equalTo(originalHidden)); |
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} |
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} |
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} |
