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

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 709136c..3fe219c 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -49,8 +49,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   static
   {
-    Platform.addJ2SDirectDatabaseCall("http://rest.ensembl");
-    Platform.addJ2SDirectDatabaseCall("https://rest.ensembl");
+    Platform.addJ2SDirectDatabaseCall("http://rest.ensembl.org");
+    Platform.addJ2SDirectDatabaseCall("https://rest.ensembl.org");
   }
 
   private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes

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);
         }
       }
     }

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index 67ed7e6..d9a5ed8 100644 (file)
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -36,6 +36,7 @@ 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;
@@ -66,6 +67,11 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
 
   public static FTSRestClientI instance = null;
 
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_THREEDBEACONS_DOMAIN);
+  }
+
   protected TDBeaconsFTSRestClient()
   {
   }
@@ -101,7 +107,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query);
 
       URI uri = webResource.getURI();
-      jalview.bin.Console.outPrintln(uri.toString());
+      Console.info("3DBeacons URL: " + uri.toString());
 
       // Execute the REST request
       ClientResponse clientResponse;
@@ -269,8 +275,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
               ? " "
               : tdbJsonStructure.get(field.getCode()).toString();
-      // jalview.bin.Console.outPrintln("Field : " + field + " Data : " +
-      // fieldData);
+      // Console.outPrintln("Field : " + field + " Data : " + fieldData);
       if (field.isPrimaryKeyColumn())
       {
         primaryKey = fieldData;
@@ -294,8 +299,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
         } catch (Exception e)
         {
           // e.printStackTrace();
-          jalview.bin.Console
-                  .outPrintln("offending value:" + fieldData + fieldData);
+          Console.warn("offending value:" + fieldData + fieldData);
         }
       }
     }

diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index daaed77..fdddd32 100644 (file)
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -30,6 +30,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
+import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Properties;
 
@@ -38,6 +39,7 @@ import javax.swing.SwingUtilities;
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
+import jalview.bin.Console;
 import jalview.javascript.json.JSON;
 
 /**
@@ -309,7 +311,7 @@ public class Platform
       time = mark = t;
       if (msg != null)
       {
-        jalview.bin.Console.errPrintln("Platform: timer reset\t\t\t" + msg);
+        Console.errPrintln("Platform: timer reset\t\t\t" + msg);
       }
       break;
     case TIME_MARK:
@@ -325,9 +327,8 @@ public class Platform
         }
         if (msg != null)
         {
-          jalview.bin.Console.errPrintln(
-                  "Platform: timer mark\t" + ((t - time) / 1000f) + "\t"
-                          + ((t - mark) / 1000f) + "\t" + msg);
+          Console.errPrintln("Platform: timer mark\t" + ((t - time) / 1000f)
+                  + "\t" + ((t - mark) / 1000f) + "\t" + msg);
         }
         mark = t;
       }
@@ -338,9 +339,8 @@ public class Platform
     case TIME_GET:
       if (msg != null)
       {
-        jalview.bin.Console
-                .errPrintln("Platform: timer dur\t" + ((t - time) / 1000f)
-                        + "\t" + ((duration) / 1000f) + "\t" + msg);
+        Console.errPrintln("Platform: timer dur\t" + ((t - time) / 1000f)
+                + "\t" + ((duration) / 1000f) + "\t" + msg);
       }
       set = 0;
       break;
@@ -496,7 +496,7 @@ public class Platform
      *            info[key];
      */
 
-    jalview.bin.Console.outPrintln(
+    Console.outPrintln(
             "Platform id=" + id + " reading Info." + key + " = " + value);
     p.put(id + "_" + key, value);
 
@@ -617,18 +617,31 @@ public class Platform
    * @author hansonr@stolaf.edu
    * 
    */
-  public static void addJ2SDirectDatabaseCall(String domain)
+  public static void addJ2SDirectDatabaseCall(String urlString)
   {
 
     if (isJS())
     {
-      jalview.bin.Console.outPrintln(
+      String domainString = urlString;
+      try
+      {
+        URL url = new URL(urlString);
+        URL domain = new URL(url.getProtocol(), url.getHost(),
+                url.getPort(), "");
+        domainString = domain.toString();
+      } catch (MalformedURLException e)
+      {
+        Console.warn("Could not add '" + urlString
+                + "' in J2SDirectDatabase -- not a recognised URL");
+      }
+      Console.outPrintln(
               "Platform adding known access-control-allow-origin * for domain "
-                      + domain);/**
-                                 * @j2sNative
-                                 * 
-                                 *            J2S.addDirectDatabaseCall(domain);
-                                 */
+                      + domainString);
+      /**
+       * @j2sNative
+       * 
+       *            J2S.addDirectDatabaseCall(domain);
+       */
     }
 
   }

diff --git a/src/jalview/ws/dbsources/TDBeacons.java b/src/jalview/ws/dbsources/TDBeacons.java
index 7326c6e..66190ca 100644 (file)
--- a/src/jalview/ws/dbsources/TDBeacons.java
+++ b/src/jalview/ws/dbsources/TDBeacons.java
@@ -20,7 +20,23 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.InputStream;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Locale;
+import java.util.Vector;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
 
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -32,9 +48,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.uniprot.DbReferenceType;
 import jalview.xml.binding.uniprot.Entry;
 import jalview.xml.binding.uniprot.FeatureType;
@@ -42,23 +58,6 @@ import jalview.xml.binding.uniprot.LocationType;
 import jalview.xml.binding.uniprot.PositionType;
 import jalview.xml.binding.uniprot.PropertyType;
 
-import java.io.InputStream;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * This class queries the Uniprot database for sequence data, unmarshals the
  * returned XML, and converts it to Jalview Sequence records (including attached
@@ -75,6 +74,12 @@ public class TDBeacons extends DbSourceProxyImpl
 
   private static final String DEFAULT_THREEDBEACONS_DOMAIN = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/summary/";
 
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_THREEDBEACONS_DOMAIN);
+  }
+
   /**
    * Constructor
    */

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 69ee379..b5b3ca2 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -49,6 +49,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 import jalview.xml.binding.uniprot.DbReferenceType;
@@ -72,6 +73,11 @@ public class Uniprot extends DbSourceProxyImpl
 
   private static final String BAR_DELIMITER = "|";
 
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
+  }
+
   /**
    * Constructor
    */

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 8aca9a2..0d3d54f 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -20,12 +20,6 @@
  */
 package jalview.ws.ebi;
 
-import java.util.Locale;
-
-import jalview.datamodel.DBRefSource;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
@@ -35,8 +29,13 @@ import java.net.HttpURLConnection;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
+import jalview.datamodel.DBRefSource;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /**
  * DOCUMENT ME!
  * 
@@ -45,6 +44,10 @@ import java.util.StringTokenizer;
  */
 public class EBIFetchClient
 {
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall("https://www.ebi.ac.uk/");
+  }
 
   /**
    * Creates a new EBIFetchClient object.
@@ -270,11 +273,6 @@ public class EBIFetchClient
     return null;
   }
 
-  static
-  {
-    Platform.addJ2SDirectDatabaseCall("https://www.ebi.ac.uk/");
-  }
-
   /**
    * Constructs the URL to fetch from
    *