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

[jalview.git] / src / jalview / fts / service / uniprot / UniProtFTSRestClient.java

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 250fba0..262ed86 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -21,6 +21,7 @@
 
 package jalview.fts.service.uniprot;
 
+import jalview.bin.Cache;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
@@ -44,9 +45,18 @@ import com.sun.jersey.api.client.config.DefaultClientConfig;
 
 public class UniProtFTSRestClient extends FTSRestClient
 {
+  private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
   private static FTSRestClientI instance = null;
 
-  public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
+  public final String uniprotSearchEndpoint;
+
+  public UniProtFTSRestClient()
+  {
+    super();
+    uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
+            DEFAULT_UNIPROT_DOMAIN) + "/uniprot/?";
+  }
 
   @Override
   public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
@@ -81,7 +91,7 @@ public class UniProtFTSRestClient extends FTSRestClient
       }
 
       WebResource webResource = null;
-      webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
+      webResource = client.resource(uniprotSearchEndpoint)
               .queryParam("format", "tab")
               .queryParam("columns", wantedFields)
               .queryParam("limit", String.valueOf(responseSize))
@@ -158,7 +168,7 @@ public class UniProtFTSRestClient extends FTSRestClient
     String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
     if (foundDataRow != null && foundDataRow.length > 0)
     {
-      result = new ArrayList<FTSData>();
+      result = new ArrayList<>();
       boolean firstRow = true;
       for (String dataRow : foundDataRow)
       {