JAL-4059 Added some more Platform.addJ2SDirectDatabaseCall web service URLs in static...

[jalview.git] / src / jalview / fts / service / pdb / PDBFTSRestClient.java

diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index b4bb66e..53a0415 100644 (file)
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -20,11 +20,7 @@
  */
 package jalview.fts.service.pdb;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
 import java.net.URI;
-import java.nio.CharBuffer;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Iterator;
@@ -41,17 +37,16 @@ import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
 import com.sun.jersey.api.client.config.DefaultClientConfig;
 
+import jalview.bin.Console;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
 import jalview.fts.api.StructureFTSRestClientI;
-import jalview.fts.core.FTSDataColumnPreferences;
 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.core.FTSRestClient;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
-import jalview.fts.service.alphafold.AlphafoldRestClient;
 import jalview.util.JSONUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -69,6 +64,11 @@ public class PDBFTSRestClient extends FTSRestClient
 
   public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?";
 
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall(PDB_SEARCH_ENDPOINT);
+  }
+
   protected PDBFTSRestClient()
   {
   }
@@ -175,7 +175,6 @@ public class PDBFTSRestClient extends FTSRestClient
 
       URI uri = webResource.getURI();
 
-      jalview.bin.Console.outPrintln(uri);
       ClientResponse clientResponse = null;
       int responseStatus = -1;
       // Get the JSON string from the response object or directly from the
@@ -183,8 +182,7 @@ public class PDBFTSRestClient extends FTSRestClient
       Map<String, Object> jsonObj = null;
       String responseString = null;
 
-      jalview.bin.Console
-              .outPrintln("query >>>>>>> " + pdbRestRequest.toString());
+      Console.info("REST request: " + uri.toString());
 
       if (!isMocked())
       {
@@ -414,10 +412,10 @@ public class PDBFTSRestClient extends FTSRestClient
 
     for (FTSDataColumnI field : diplayFields)
     {
-      // jalview.bin.Console.outPrintln("Field " + field);
+      // Console.outPrintln("Field " + field);
       String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
               : pdbJsonDoc.get(field.getCode()).toString();
-      // jalview.bin.Console.outPrintln("Field Data : " + fieldData);
+      // Console.outPrintln("Field Data : " + fieldData);
       if (field.isPrimaryKeyColumn())
       {
         primaryKey = fieldData;
@@ -441,7 +439,7 @@ public class PDBFTSRestClient extends FTSRestClient
         } catch (Exception e)
         {
           e.printStackTrace();
-          jalview.bin.Console.outPrintln("offending value:" + fieldData);
+          Console.warn("offending value:" + fieldData);
         }
       }
     }