Merge branch 'JAL-1601-direct-jpred4-rest-service' into development/Release_2_12_Branch

[jalview.git] / test / jalview / ws2 / actions / secstructpred / SecStructPredPDBSearchTaskTest.java

diff --git a/test/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTaskTest.java b/test/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTaskTest.java
new file mode 100644 (file)
index 0000000..ca88cf3
--- /dev/null
+++ b/test/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTaskTest.java
@@ -0,0 +1,171 @@
+package jalview.ws2.actions.secstructpred;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.equalTo;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+import static org.mockito.ArgumentMatchers.any;
+import static jalview.testutils.ScopeFunctions.apply;
+import static jalview.testutils.Matchers.matchesSequenceString;
+
+import jalview.io.DataSourceType;
+import jalview.io.FastaFile;
+import jalview.io.JPredFile;
+
+import org.hamcrest.Matcher;
+import org.hamcrest.Matchers;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.ws2.actions.ServiceInputInvalidException;
+import jalview.ws2.api.Credentials;
+import jalview.ws2.api.JobStatus;
+import jalview.ws2.api.WebServiceJobHandle;
+import jalview.ws2.client.api.SecStructPredWebServiceClientI;
+import static java.lang.String.format;
+
+public class SecStructPredPDBSearchTaskTest
+{
+  protected SecStructPredWebServiceClientI mockClient;
+
+  @BeforeMethod(alwaysRun = true)
+  public void setupMockClient() throws IOException
+  {
+    mockClient = mock(SecStructPredWebServiceClientI.class);
+    when(mockClient.getUrl()).thenReturn("http://example.org");
+    when(mockClient.getClientName()).thenReturn("mock");
+    when(mockClient.getLog(any())).thenReturn("");
+    when(mockClient.getErrorLog(any())).thenReturn("");
+  }
+
+  @DataProvider
+  public Object[][] viewportAndExpectedInputSeq()
+  {
+    return new Object[][] {
+        { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAAA")),
+            "AAAAAAAAAAAAAAAAAAAA", },
+        { new AlignViewport(createAlignment("--AAGGAGAG-AGGA----MMMMMMMM")),
+            "AAGGAGAGAGGAMMMMMMMM" },
+        { new AlignViewport(createAlignment("AAAANNNCCCCCCCCCCAAAAAA"),
+                apply(new HiddenColumns(), it -> it.hideColumns(4, 6))),
+            "AAAACCCCCCCCCCAAAAAA" },
+        { new AlignViewport(
+                createAlignment("NNNNGGGGVVVVVAAAAAAACCMMMMMMMM"),
+                apply(new HiddenColumns(), it -> {
+                  it.hideColumns(4, 7);
+                  it.hideColumns(20, 21);
+                })),
+            "NNNNVVVVVAAAAAAAMMMMMMMM" } };
+  }
+
+  public static AlignmentI createAlignment(String... sequences)
+  {
+    var seqArray = new Sequence[sequences.length];
+    for (int i = 0; i < sequences.length; i++)
+      seqArray[i] = new Sequence(format("Seq%d", i), sequences[i]);
+    return new Alignment(seqArray);
+  }
+
+  @Test(
+    groups = { "Functional" },
+    dataProvider = "viewportAndExpectedInputSeq")
+  public void testPrepareJobs_checkInputSequences(AlignViewport viewport,
+          String expectedSeq) throws Exception
+  {
+    var task = new SecStructPredPDBSearchTask(mockClient, List.of(),
+            Credentials.empty(), viewport);
+    var jobs = task.prepareJobs();
+    assertThat(jobs.get(0).getInputSequences(),
+            contains(matchesSequenceString(expectedSeq)));
+  }
+
+  @DataProvider
+  public Object[][] viewportWithTooShortSequence()
+  {
+    return new Object[][] {
+        { new AlignViewport(createAlignment("")) },
+        { new AlignViewport(createAlignment("A")) },
+        { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAA")) },
+        { new AlignViewport(createAlignment("AAAAACCCCCAAAAA-----CC")) },
+        { new AlignViewport(createAlignment("-------------------------")) },
+        { new AlignViewport(createAlignment("AAAAAAAAAAAAAAAAAAAAAAAAA"),
+                apply(new HiddenColumns(), it -> it.hideColumns(0, 24))) },
+        { new AlignViewport(createAlignment("AAAAACCCCCAAAAACCCCCAAAAA"),
+                apply(new HiddenColumns(), it -> it.hideColumns(0, 10))) } };
+  }
+
+  @Test(
+    groups = { "Functional" },
+    dataProvider = "viewportWithTooShortSequence",
+    expectedExceptions = ServiceInputInvalidException.class)
+  public void testPrepareJobs_SequenceTooShort_InputInvalidException(
+          AlignViewport viewport) throws ServiceInputInvalidException
+  {
+    var task = new SecStructPredPDBSearchTask(mockClient, List.of(),
+            Credentials.empty(), viewport);
+    task.prepareJobs();
+  }
+
+  @DataProvider
+  public Object[][] collectResultDataset() throws IOException
+  {
+    return new Object[][] {
+        {
+            new AlignViewport(new Alignment(new FastaFile(
+                "examples/testdata/secstrpred/sequence0_input.fa",
+                DataSourceType.FILE).getSeqsAsArray()
+            )),
+            "examples/testdata/secstrpred/sequence0.align",
+            "examples/testdata/secstrpred/sequence0.concise"
+        },
+    };
+  }
+
+  @Test(groups = { "Functional" }, dataProvider = "collectResultDataset")
+  public void testCollectResult(AlignViewport viewport, String alnFileName,
+          String predFileName) throws Exception
+  {
+    var alnFile = new FastaFile(alnFileName, DataSourceType.FILE);
+    var predFile = new JPredFile(predFileName, DataSourceType.FILE);
+    when(mockClient.getPredictionFile(any())).thenReturn(predFile);
+    when(mockClient.getAlignmentFile(any())).thenReturn(alnFile);
+    when(mockClient.getStatus(any())).thenReturn(JobStatus.COMPLETED);
+    when(mockClient.submit(any(), any(), any()))
+            .thenReturn(new WebServiceJobHandle("mock", "mock",
+                    "http://example.org", "0"));
+
+    var task = new SecStructPredPDBSearchTask(mockClient, List.of(),
+            Credentials.empty(), viewport);
+    task.init();
+    task.poll();
+    task.complete();
+    var resultAlignment = task.getResult();
+    var sequences = resultAlignment.getSequences();
+
+    {
+      List<Matcher<? super SequenceI>> matchers = new ArrayList<>();
+      for (var seq : alnFile.getSeqs())
+        matchers.add(matchesSequenceString(seq));
+      assertThat(sequences, Matchers.contains(matchers));
+    }
+
+    {
+      var originalHidden = viewport.getAlignment().getHiddenColumns();
+      var resultHidden = resultAlignment.getHiddenColumns();
+      assertThat(resultHidden, equalTo(originalHidden));
+    }
+  }
+}