From 94814d1d6b542c2a4f4e75787f30562716269fdb Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 23 Feb 2018 11:33:41 +0000 Subject: [PATCH] JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL --- src/jalview/ext/ensembl/EnsemblGenomes.java | 4 ++-- src/jalview/ext/ensembl/EnsemblRestClient.java | 9 +++++---- src/jalview/ext/ensembl/EnsemblSequenceFetcher.java | 17 ++++++++++------- 3 files changed, 17 insertions(+), 13 deletions(-) diff --git a/src/jalview/ext/ensembl/EnsemblGenomes.java b/src/jalview/ext/ensembl/EnsemblGenomes.java index 6af6d44..6dd69a8 100644 --- a/src/jalview/ext/ensembl/EnsemblGenomes.java +++ b/src/jalview/ext/ensembl/EnsemblGenomes.java @@ -38,8 +38,8 @@ public class EnsemblGenomes extends EnsemblGene public EnsemblGenomes() { super(); - setDomain(Cache.getDefault(ENSEMBL_GENOMES_DOMAIN, - DEFAULT_ENSEMBL_GENOMES_DOMAIN)); + setDomain(Cache.getDefault(ENSEMBL_GENOMES_BASEURL, + DEFAULT_ENSEMBL_GENOMES_BASEURL)); } @Override diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index d457668..b19f557 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -82,10 +82,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher static { - domainData.put(DEFAULT_ENSEMBL_DOMAIN, - new EnsemblInfo(DEFAULT_ENSEMBL_DOMAIN, LATEST_ENSEMBL_REST_VERSION)); - domainData.put(DEFAULT_ENSEMBL_GENOMES_DOMAIN, new EnsemblInfo( - DEFAULT_ENSEMBL_GENOMES_DOMAIN, LATEST_ENSEMBLGENOMES_REST_VERSION)); + domainData.put(DEFAULT_ENSEMBL_BASEURL, + new EnsemblInfo(DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION)); + domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL, + new EnsemblInfo( + DEFAULT_ENSEMBL_GENOMES_BASEURL, LATEST_ENSEMBLGENOMES_REST_VERSION)); } protected volatile boolean inProgress = false; diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java index 2f642b5..f16dda6 100644 --- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java +++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java @@ -34,12 +34,14 @@ import com.stevesoft.pat.Regex; abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl { // domain properties lookup keys: - protected static final String ENSEMBL_DOMAIN = "ENSEMBL_DOMAIN"; - protected static final String ENSEMBL_GENOMES_DOMAIN = "ENSEMBL_GENOMES_DOMAIN"; + protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL"; + + protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL"; // domain properties default values: - protected static final String DEFAULT_ENSEMBL_DOMAIN = "http://rest.ensembl.org"; - protected static final String DEFAULT_ENSEMBL_GENOMES_DOMAIN = "http://rest.ensemblgenomes.org"; + protected static final String DEFAULT_ENSEMBL_BASEURL = "http://rest.ensembl.org"; + + protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = "http://rest.ensemblgenomes.org"; /* * accepts ENSG/T/E/P with 11 digits @@ -76,9 +78,10 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl * the default domain names may be overridden in .jalview_properties; * this allows an easy change from http to https in future if needed */ - ensemblDomain = Cache.getDefault(ENSEMBL_DOMAIN, DEFAULT_ENSEMBL_DOMAIN); - ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_DOMAIN, - DEFAULT_ENSEMBL_GENOMES_DOMAIN); + ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL, + DEFAULT_ENSEMBL_BASEURL); + ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL, + DEFAULT_ENSEMBL_GENOMES_BASEURL); domain = ensemblDomain; } -- 1.7.10.2