Fix #596. Remove test for GenBank identifier parsing

sbliven · sbliven · commit 837dc63f9ece · 2016-11-09T12:25:08.000+01:00
Starting Nov 2016, Entrez stopped including the GI identifier in
GenBank files. In such cases, getAccession().getIdentifier() will
return null.

This updates the tests to reflect that null identifiers are acceptable.

Users who need the GI identifier should store it manually after fetching
the sequence.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
@@ -133,6 +133,8 @@ public void setVersion(Integer version) {
 
 	/**
 	 * In case if {@link #getID() } in not unique keeps the alternative id, eg. NCBI GI number.
+	 * 
+	 * This may null.
 	 *
 	 * @return
 	 */
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
@@ -99,9 +99,10 @@ so it should be done here (manualy).
 		logger.info("accession id: {}", seq.getAccession().getID());
 		Assert.assertNotNull(seq.getAccession().getID());
 		// test GID number
-		Assert.assertEquals(gi, seq.getAccession().getIdentifier());
-		logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
-
+		if( seq.getAccession().getIdentifier() != null) { // GI: in header now optional. See #596
+			Assert.assertEquals(gi, seq.getAccession().getIdentifier());
+			logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
+		}
 		// test taxonomy id
 		logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
 		Assert.assertNotNull(seq.getTaxonomy().getID());

Original file line number	Diff line number	Diff line change
`@@ -133,6 +133,8 @@ public void setVersion(Integer version) {`
`133`	`133`
`134`	`134`	`/**`
`135`	`135`	`* In case if {@link #getID() } in not unique keeps the alternative id, eg. NCBI GI number.`
	`136`	`+ *`
	`137`	`+ * This may null.`
`136`	`138`	`*`
`137`	`139`	`* @return`
`138`	`140`	`*/`