Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL...

[jalview.git] / test / jalview / ws / dbsources / RemoteFormatTest.java

diff --git a/test/jalview/ws/dbsources/RemoteFormatTest.java b/test/jalview/ws/dbsources/RemoteFormatTest.java
new file mode 100644 (file)
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+++ b/test/jalview/ws/dbsources/RemoteFormatTest.java
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+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.ext.ensembl.EnsemblGenomes;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.uniprot.UniProtFTSRestClient;
+import jalview.ws.SequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+/**
+ * A class to verify that remotely fetched data has an expected format and can
+ * be successfully processed by Jalview. This is intended as a first line of
+ * defence and early warning of service affecting changes to data fetched
+ * externally.
+ * <p>
+ * This is class is not intended to cover remote services e.g. alignment. Nor
+ * should it duplicate tests already provided by other classes (such as
+ * PDBFTSRestClientTest). Or maybe we will relocate those tests here...
+ */
+public class RemoteFormatTest
+{
+  SequenceFetcher sf;
+
+  @BeforeTest(alwaysRun = true)
+  public void setUp() throws Exception
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    // ensure 'add annotation from structure' is selected
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+
+    sf = new SequenceFetcher(false);
+  }
+
+  @DataProvider(name = "AccessionData")
+  protected Object[][] getAccessions()
+  {
+    return new Object[][] { { DBRefSource.UNIPROT, "P30419" },
+        { DBRefSource.PDB, "1QIP" }, { DBRefSource.EMBL, "X53828" },
+        { DBRefSource.EMBLCDS, "CAA37824" },
+        { DBRefSource.ENSEMBL, "ENSG00000157764" },
+        { new EnsemblGenomes().getDbSource(), "DDB_G0283883" },
+        { new PfamFull().getDbSource(), "PF03760" },
+        { new PfamSeed().getDbSource(), "PF03760" },
+        { new RfamSeed().getDbSource(), "RF00014" } };
+  }
+
+  @Test(groups = "Network", dataProvider = "AccessionData")
+  public void testFetchAccession(String dbSource, String accessionId)
+          throws Exception
+  {
+    System.out.println("Fetching " + accessionId + " from " + dbSource);
+    List<DbSourceProxy> sps = sf.getSourceProxy(dbSource);
+    assertFalse(sps.isEmpty());
+    AlignmentI al = sps.get(0).getSequenceRecords(accessionId);
+    assertNotNull(al);
+    assertTrue(al.getHeight() > 0);
+    SequenceI sq = al.getSequenceAt(0);
+    // suppress this check as only Uniprot and PDB acquire PDB refs
+    // assertTrue(sq.getAllPDBEntries().size() > 0, "No PDBEntry on sequence.");
+    assertTrue(sq.getDBRefs().length > 0, "No DBRef on sequence.");
+    // suppress this test as only certain databases provide 'primary' dbrefs
+    // assertFalse(sq.getPrimaryDBRefs().isEmpty());
+    int length = AlignSeq.extractGaps("-. ", sq.getSequenceAsString())
+            .length();
+    assertEquals(sq.getEnd() - sq.getStart() + 1, length,
+            "Sequence start/end doesn't match number of residues in sequence");
+  }
+
+  @Test(groups = { "Network" })
+  public void testUniprotFreeTextSearch() throws Exception
+  {
+    List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+    FTSRestClientI client = UniProtFTSRestClient.getInstance();
+    wantedFields.add(client.getDataColumnByNameOrCode("id"));
+    wantedFields.add(client.getDataColumnByNameOrCode("entry name"));
+    wantedFields.add(client.getDataColumnByNameOrCode("organism"));
+    wantedFields.add(client.getDataColumnByNameOrCode("reviewed")); // Status
+    wantedFields.add(client.getDataColumnByNameOrCode("length"));
+  
+    FTSRestRequest request = new FTSRestRequest();
+    request.setAllowEmptySeq(false);
+    request.setResponseSize(100);
+    request.setFieldToSearchBy("Search All");
+    request.setSearchTerm("metanephrops"); // lobster!
+    request.setWantedFields(wantedFields);
+  
+    FTSRestResponse response;
+    response = client.executeRequest(request);
+    assertTrue(response.getNumberOfItemsFound() > 20);
+    assertTrue(response.getSearchSummary() != null);
+    assertTrue(response.getSearchSummary().size() > 20);
+    // verify we successfully filtered out the header row (JAL-2485)
+    FTSData header = response.getSearchSummary().iterator().next();
+    assertFalse(
+            header.getSummaryData()[0].toString().equalsIgnoreCase("Entry"),
+            "Failed to filter out summary header row");
+  }
+}