From ca74027f55fb1f8af9fef0d77348449a07a1b5d5 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 8 Mar 2022 18:53:09 +0000 Subject: [PATCH] JAL-3108 updated Ensembl client and model species names --- help/help/html/releases.html | 5 +++++ src/jalview/ext/ensembl/EnsemblRestClient.java | 4 ++-- src/jalview/ext/ensembl/Species.java | 6 +++--- test/jalview/ext/ensembl/EnsemblGeneTest.java | 3 ++- 4 files changed, 12 insertions(+), 6 deletions(-) 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 { Support for Canonical Uniprot IDs
  • + Updated Ensembl REST Client compatibility + to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now + rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster) +
    • +
  • 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 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 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()); + } } -- 1.7.10.2