From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 8 Mar 2022 18:53:09 +0000 (+0000)
Subject: JAL-3108 updated Ensembl client and model species names
X-Git-Tag: Release_2_11_2_1~22
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ca74027f55fb1f8af9fef0d77348449a07a1b5d5;p=jalview.git

JAL-3108 updated Ensembl client and model species names
---

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 940c08e..2f9c096 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -100,6 +100,11 @@ li:before {
             <!-- JAL-3863 -->Support for Canonical Uniprot IDs
           </li>
           <li>
+            <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
+            to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now
+            rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster)
+          </li>
+          <li>
             <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
             non-alphanumerics when discovering database references with
             'Fetch DB Refs'
diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 59c568b..4a5544e 100644
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -69,9 +69,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
    * @see http://rest.ensembl.org/info/rest?content-type=application/json
    */
-  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "13.0";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "15.2";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "13.0";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "15.2";
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
diff --git a/src/jalview/ext/ensembl/Species.java b/src/jalview/ext/ensembl/Species.java
index cc5465e..3feea05 100644
--- a/src/jalview/ext/ensembl/Species.java
+++ b/src/jalview/ext/ensembl/Species.java
@@ -36,10 +36,10 @@ enum Species
    * valid species parameters to Ensembl REST services where applicable
    */
   human(true), mouse(true), s_cerevisiae(true), cow(false), pig(false),
-  rat(true), celegans(true), sheep(false), horse(false), gorilla(false),
-  rabbit(false), gibbon(false), dog(false), orangutan(false), xenopus(true),
+  rattus_norvegicus(true), celegans(true), sheep(false), horse(false), gorilla(false),
+  rabbit(false), gibbon(false), dog(false), orangutan(false), xenopus_tropicalis(true),
   chimpanzee(false), cat(false), zebrafish(true), chicken(true),
-  dmelanogaster(true);
+  drosophila_melanogaster(true);
 
   static Set<Species> modelOrganisms = new HashSet<>();
 
diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index e16197a..2de08f5 100644
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -317,7 +317,6 @@ public class EnsemblGeneTest
     String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
     EnsemblGene testee = new EnsemblGene();
     List<String> geneIds = testee.getGeneIds(ids);
-    assertEquals(8, geneIds.size());
     assertTrue(geneIds.contains("ENSG00000158828"));
     assertTrue(geneIds.contains("ENSG00000136448"));
     assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
@@ -326,5 +325,7 @@ public class EnsemblGeneTest
     assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
     assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
     assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
+    assertEquals(8, geneIds.size());
+    
   }
 }