Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

[jalview.git] / test / jalview / ext / ensembl / EnsemblSeqProxyTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index a06465f..f9c2c4b 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,11 +1,18 @@
 package jalview.ext.ensembl;
 
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyLite;
 
 import java.lang.reflect.Method;
 import java.net.MalformedURLException;
@@ -14,6 +21,8 @@ import java.util.Arrays;
 import java.util.List;
 
 import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -99,20 +108,16 @@ public class EnsemblSeqProxyTest
                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 
-  @DataProvider(name = "queries")
-  public Object[][] createQueryData(Method m)
+  @BeforeClass
+  public void setUp()
   {
-    return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @Test(dataProvider = "queries")
-  public void testIsValidReference(String query) throws Exception
+  @AfterClass
+  public void tearDown()
   {
-    EnsemblSequenceFetcher esq = new EnsemblProtein();
-    Assert.assertTrue(esq.isValidReference(query),
-            "Expected reference string " + query
-                    + " to be valid for regex "
-                    + esq.getAccessionValidator().toString());
+    SequenceOntologyFactory.setInstance(null);
   }
 
   @DataProvider(name = "ens_seqs")
@@ -189,7 +194,7 @@ public class EnsemblSeqProxyTest
       }
 
       @Override
-      protected String getRequestMimeType()
+      protected String getRequestMimeType(boolean b)
       {
         // TODO Auto-generated method stub
         return null;
@@ -208,5 +213,38 @@ public class EnsemblSeqProxyTest
             + (isAvailable ? "UP!"
                     : "DOWN or unreachable ******************* BAD!"));
   }
-  // todo lots of tests
+
+  @Test(groups = "Functional")
+  public void getGenomicRangesFromFeatures()
+  {
+
+  }
+
+  @Test(groups = "Functional")
+  public void testIsTranscriptIdentifier()
+  {
+    EnsemblSeqProxy testee = new EnsemblGene();
+    assertFalse(testee.isTranscriptIdentifier(null));
+    assertFalse(testee.isTranscriptIdentifier(""));
+    assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
+    assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
+    assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
+    assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
+    assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
+    assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
+  }
+
+  @Test(groups = "Functional")
+  public void testIsGeneIdentifier()
+  {
+    EnsemblSeqProxy testee = new EnsemblGene();
+    assertFalse(testee.isGeneIdentifier(null));
+    assertFalse(testee.isGeneIdentifier(""));
+    assertFalse(testee.isGeneIdentifier("ENST00000012345"));
+    assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
+    assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
+    assertFalse(testee.isGeneIdentifier("ensg00000012345"));
+    assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
+    assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
+  }
 }
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