JAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam configurable

[jalview.git] / src / jalview / ext / ensembl / EnsemblRestClient.java

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index b1bc8e5..d457668 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -72,10 +72,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
-  private static Map<String, EnsemblInfo> domainData;
-
-  // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
-  private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
+  private static Map<String, EnsemblInfo> domainData = new HashMap<>();
 
   private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
 
@@ -85,11 +82,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   static
   {
-    domainData = new HashMap<>();
-    domainData.put(ENSEMBL_REST,
-            new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
-    domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
-            ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
+    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));
   }
 
   protected volatile boolean inProgress = false;
@@ -99,7 +95,21 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    */
   public EnsemblRestClient()
   {
-    this(ENSEMBL_REST);
+    super();
+
+    /*
+     * initialise domain info lazily
+     */
+    if (!domainData.containsKey(ensemblDomain))
+    {
+      domainData.put(ensemblDomain,
+              new EnsemblInfo(ensemblDomain, LATEST_ENSEMBL_REST_VERSION));
+    }
+    if (!domainData.containsKey(ensemblGenomesDomain))
+    {
+      domainData.put(ensemblGenomesDomain, new EnsemblInfo(
+              ensemblGenomesDomain, LATEST_ENSEMBLGENOMES_REST_VERSION));
+    }
   }
 
   /**
@@ -169,11 +179,12 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   boolean checkEnsembl()
   {
     BufferedReader br = null;
+    String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
     try
     {
       // note this format works for both ensembl and ensemblgenomes
       // info/ping.json works for ensembl only (March 2016)
-      URL ping = new URL(getDomain() + "/info/ping" + CONTENT_TYPE_JSON);
+      URL ping = new URL(pingUrl);
 
       /*
        * expect {"ping":1} if ok
@@ -192,7 +203,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     } catch (Throwable t)
     {
       System.err.println(
-              "Error connecting to " + PING_URL + ": " + t.getMessage());
+              "Error connecting to " + pingUrl + ": " + t.getMessage());
     } finally
     {
       if (br != null)