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 7e8745e..f9c2c4b 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,53 +1,37 @@
 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.ext.ensembl.SeqFetcher.EnsemblSeqType;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
-import jalview.util.DBRefUtils;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyLite;
 
 import java.lang.reflect.Method;
+import java.net.MalformedURLException;
+import java.net.URL;
 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;
 
+
 public class EnsemblSeqProxyTest
 {
-  @Test
-  public void testCheckEnsembl()
-  {
-    SeqFetcher sf = new SeqFetcher();
-    sf.setTestEnsemblStatus(true);
-    sf.setTesting(true);
-    Assert.assertTrue(sf.isEnsemblAvailable());
-    sf.setTestEnsemblStatus(false);
-    Assert.assertFalse(sf.isEnsemblAvailable());
-  }
-
-  @Test(suiteName = "live")
-  public void testLiveCheckEnsembl()
-  {
-    SeqFetcher sf = new SeqFetcher();
-    boolean isAvailable = sf.isEnsemblAvailable();
-    System.out.println("Ensembl is "
-            + (isAvailable ? "UP!" : "DOWN ******************* BAD!"));
-  }
-
-  @DataProvider(name = "ens_seqs")
-  public Object[][] createData(Method m)
-  {
-    System.out.println(m.getName());
-    return allSeqs;
-  }
-
-  public static Object[][] allSeqs = new Object[][]
-  {
+  private static final Object[][] allSeqs = new Object[][] {
       {
-          EnsemblSeqType.PROTEIN,
+          new EnsemblProtein(),
           "CCDS5863.1",
           ">CCDS5863.1\n"
                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
@@ -64,7 +48,7 @@ public class EnsemblSeqProxyTest
                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
       {
-          EnsemblSeqType.TRANSCRIPT,
+          new EnsemblCdna(),
           "CCDS5863.1",
           ">CCDS5863.1\n"
                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
@@ -107,7 +91,7 @@ public class EnsemblSeqProxyTest
                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
                   + "GGTGCGTTTCCTGTCCACTGA\n" },
       {
-          EnsemblSeqType.PROTEIN,
+          new EnsemblProtein(),
           "ENSP00000288602",
           ">ENSP00000288602\n"
                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
@@ -124,12 +108,31 @@ public class EnsemblSeqProxyTest
                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 
+  @BeforeClass
+  public void setUp()
+  {
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+  }
+
+  @AfterClass
+  public void tearDown()
+  {
+    SequenceOntologyFactory.setInstance(null);
+  }
+
+  @DataProvider(name = "ens_seqs")
+  public Object[][] createData(Method m)
+  {
+    System.out.println(m.getName());
+    return allSeqs;
+  }
+
   @Test(dataProvider = "ens_seqs", suiteName = "live")
-  public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
+  public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
           throws Exception
   {
-    SeqFetcher sf = new SeqFetcher();
-    FileParse fp = sf.getSequenceReader(type, Arrays.asList(new String[]
+    FileParse fp = proxy.getSequenceReader(Arrays
+            .asList(new String[]
     { sq }));
     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
@@ -152,7 +155,96 @@ public class EnsemblSeqProxyTest
               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                       + tr.getSequenceAsString() + "\n" + "Got:"
                       + rseq[0].getSequenceAsString());
-
+  
     }
   }
+
+  @Test(suiteName = "live")
+  public void testLiveCheckEnsembl()
+  {
+    EnsemblRestClient sf = new EnsemblRestClient()
+    {
+
+      @Override
+      public String getDbName()
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      public AlignmentI getSequenceRecords(String queries) throws Exception
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      protected URL getUrl(List<String> ids) throws MalformedURLException
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      protected boolean useGetRequest()
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      protected String getRequestMimeType(boolean b)
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      protected String getResponseMimeType()
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+    };
+    boolean isAvailable = sf.isEnsemblAvailable();
+    System.out.println("Ensembl is "
+            + (isAvailable ? "UP!"
+                    : "DOWN or unreachable ******************* BAD!"));
+  }
+
+  @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"));
+  }
 }
\ No newline at end of file