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JAL-3108 updated Ensembl client and model species names
author
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 8 Mar 2022 18:53:09 +0000
(18:53 +0000)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 8 Mar 2022 18:53:09 +0000
(18:53 +0000)
help/help/html/releases.html
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src/jalview/ext/ensembl/EnsemblRestClient.java
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src/jalview/ext/ensembl/Species.java
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test/jalview/ext/ensembl/EnsemblGeneTest.java
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diff --git
a/help/help/html/releases.html
b/help/help/html/releases.html
index
940c08e
..
2f9c096
100755
(executable)
--- 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-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'
<!-- 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
(file)
--- 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
*/
* @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";
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
(file)
--- 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),
* 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),
chimpanzee(false), cat(false), zebrafish(true), chicken(true),
- dmelanogaster(true);
+ drosophila_melanogaster(true);
static Set<Species> modelOrganisms = new HashSet<>();
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
(file)
--- 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);
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
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
assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
+ assertEquals(8, geneIds.size());
+
}
}
}
}