From 61484f9c89a866cc5c9a22499653a1c17b938ffb Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 3 Oct 2019 14:36:10 +0100
Subject: [PATCH] JAL-3253 one global singleton instance of EnsemblInfo
 suffices

---
 src/jalview/ext/ensembl/EnsemblInfo.java |  109 +++++++++++++++---------------
 src/jalview/ext/ensembl/EnsemblMap.java  |    2 +-
 src/jalview/gui/CrossRefAction.java      |    2 +-
 3 files changed, 58 insertions(+), 55 deletions(-)

diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index a59a64d..71730de 100644
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -1,7 +1,5 @@
 package jalview.ext.ensembl;
 
-import jalview.bin.ApplicationSingletonProvider;
-import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 
@@ -16,64 +14,27 @@ import java.util.Set;
 
 import org.json.simple.parser.ParseException;
 
-public class EnsemblInfo extends EnsemblRestClient implements ApplicationSingletonI
+public class EnsemblInfo extends EnsemblRestClient
 {
 
   /**
-   * On first request only, populate the lookup map by fetching the list of
-   * divisions known to EnsemblGenomes
-   * 
-   */
-  private static EnsemblInfo getInstance()
-  {
-    return (EnsemblInfo) ApplicationSingletonProvider.getInstance(EnsemblInfo.class);
-  }
-
-  private EnsemblInfo()
-  {
-    // use getInstance()
-
-    /*
-     * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
-     */
-    divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
-    try
-    {
-      @SuppressWarnings("unchecked")
-      Iterator<Object> rvals = (Iterator<Object>) getJSON(
-              getDivisionsUrl(ensemblGenomesDomain), null, -1,
-              MODE_ITERATOR, null);
-      if (rvals == null)
-      {
-        return;
-      }
-      while (rvals.hasNext())
-      {
-        String division = rvals.next().toString();
-        divisions.put(division.toUpperCase(), ensemblGenomesDomain);
-      }
-    } catch (IOException | ParseException | NumberFormatException e)
-    {
-      // ignore
-    }
-  }
-
-  /*
    * cached results of REST /info/divisions service, currently
+   * 
    * <pre>
    * { 
-   *  { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBL", "http://rest.ensembl.org" }
+   *  "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
+   *  "ENSEMBL", "http://rest.ensembl.org"
    *  }
    * </pre>
+   * 
    * The values for EnsemblGenomes are retrieved by a REST call, that for
    * Ensembl is added programmatically for convenience of lookup
    */
-  private Map<String, String> divisions = new HashMap<>();
+  private static Map<String, String> divisions;
 
   @Override
   public String getDbName()
@@ -107,9 +68,46 @@ public class EnsemblInfo extends EnsemblRestClient implements ApplicationSinglet
    * @param division
    * @return
    */
-  public static String getDomain(String division)
+  public String getDomain(String division)
   {
-    return getInstance().divisions.get(division.toUpperCase());
+    if (divisions == null)
+    {
+      fetchDivisions();
+    }
+    return divisions.get(division.toUpperCase());
+  }
+
+  /**
+   * On first request only, populate the lookup map by fetching the list of
+   * divisions known to EnsemblGenomes.
+   */
+  void fetchDivisions()
+  {
+    divisions = new HashMap<>();
+
+    /*
+     * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
+     */
+    divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
+    try
+    {
+      @SuppressWarnings("unchecked")
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(
+              getDivisionsUrl(ensemblGenomesDomain), null, -1,
+              MODE_ITERATOR, null);
+      if (rvals == null)
+      {
+        return;
+      }
+      while (rvals.hasNext())
+      {
+        String division = rvals.next().toString();
+        divisions.put(division.toUpperCase(), ensemblGenomesDomain);
+      }
+    } catch (IOException | ParseException | NumberFormatException e)
+    {
+      // ignore
+    }
   }
 
   /**
@@ -130,8 +128,13 @@ public class EnsemblInfo extends EnsemblRestClient implements ApplicationSinglet
    * 
    * @return
    */
-  public static Set<String> getDivisions()
+  public Set<String> getDivisions()
   {
-    return getInstance().divisions.keySet();
+    if (divisions == null)
+    {
+      fetchDivisions();
+    }
+
+    return divisions.keySet();
   }
 }
diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
index 9789819..ae36749 100644
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -221,7 +221,7 @@ public class EnsemblMap extends EnsemblRestClient
     URL url = null;
     try
     {
-      String domain = EnsemblInfo.getDomain(division);
+      String domain = new EnsemblInfo().getDomain(division);
       if (domain != null)
       {
         url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index f607686..d37cb29 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -276,7 +276,7 @@ public class CrossRefAction implements Runnable
       return;
     }
     
-    Set<String> ensemblDivisions = EnsemblInfo.getDivisions();
+    Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
     
     /*
      * first look for direct dbrefs from sequence to Ensembl
-- 
1.7.10.2