GenbankProxySequenceReader throws error if GI is for not protein sequence sequence whereas AminoAcidCompoundSet is declared

jgrzebyta · jgrzebyta · commit 4bcab7df77d0 · 2015-02-24T18:12:17.000Z
added additional test
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -88,7 +88,7 @@ public GenbankProxySequenceReader(
         header = genbankParser.getHeader();
         features = genbankParser.getFeatures();
 
-        if (compoundSet.equals(AminoAcidCompoundSet.class)) {
+        if (compoundSet.getClass().equals(AminoAcidCompoundSet.class)) {
             if (!genbankParser.getCompoundType().equals(compoundSet)) {
                 logger.error("Declared compount type {} does not mach the real: {}", genbankParser.getCompoundType().toString(), compoundSet.toString());
                 throw new IOException("Wrong declared compound type for: " + accessionID); 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
@@ -62,12 +62,10 @@ public static Collection<String[]> getExamples() {
         String[][] out = new String[][]{
             {"399235158"},
             {"7525057"},
-            {"34567"},
             {"379015144"},
             {"381353147"},
             {"381353148"},
             {"152970917"},
-            {"7856885"},
             {"381353149"},
             {"254839678"}
         };
@@ -87,24 +85,25 @@ public void testFeatures() throws IOException, InterruptedException, CompoundNot
         ProteinSequence seq = new ProteinSequence(genbankReader);
 
         Assert.assertNotNull("protein sequence is null", seq);
-        
+
         /*
-        parse description from header. There is no separate interface/abstract class for method getHeader()
-        so it should be done here (manualy).
-        */
+         parse description from header. There is no separate interface/abstract class for method getHeader()
+         so it should be done here (manualy).
+         */
         genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
-        
+
         // test description
         Assert.assertTrue(seq.getDescription() != null);
-        
+
         // test accession Id
         logger.info("accession id: {}", seq.getAccession().getID());
         Assert.assertNotNull(seq.getAccession().getID());
 
         // test taxonomy id
         logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
         Assert.assertNotNull(seq.getTaxonomy().getID());
-        
+        Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));
+
         // test taxonomy name
         String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").getValue();
         logger.info("taxonomy name '{}'", taxonName);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
@@ -0,0 +1,57 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ */
+package org.biojava.nbio.core.sequence.loader;
+
+import java.io.IOException;
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+
+/**
+ * Testing example for issue #834
+ *
+ * @author Jacek Grzebyta
+ * @author Paolo Pavan
+ * @see InfoTask
+ */
+public class SimpleGenbankProxySequenceReaderTest {
+
+
+    private final static Logger logger = LoggerFactory.getLogger(SimpleGenbankProxySequenceReaderTest.class);
+    
+    @Test(expected = IOException.class)
+    public void testWrongSequence() throws Exception {
+        logger.info("test wrong sequence");
+        
+        String wrongGi = "34567";
+        
+        GenbankProxySequenceReader<AminoAcidCompound> genbankReader
+                = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
+                        wrongGi,
+                        AminoAcidCompoundSet.getAminoAcidCompoundSet());
+
+        ProteinSequence seq = new ProteinSequence(genbankReader);
+    }
+}
