X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniProtFTSRestClient.java;h=2606b628b01a694d7347c3a1d3144480c0cf0de0;hp=262ed863e441eafea977b9917137f91f57ffe57c;hb=8879d902c46cd33cfe201fcbd96e87d33b89259f;hpb=f87f3bc59e76f6112821e01ed88cf4c3ed853379

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 262ed86..2606b62 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -21,15 +21,6 @@
 
 package jalview.fts.service.uniprot;
 
-import jalview.bin.Cache;
-import jalview.fts.api.FTSData;
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
-import jalview.fts.core.FTSRestClient;
-import jalview.fts.core.FTSRestRequest;
-import jalview.fts.core.FTSRestResponse;
-import jalview.util.MessageManager;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
@@ -40,12 +31,27 @@ import javax.ws.rs.core.MediaType;
 import com.sun.jersey.api.client.Client;
 import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
-import com.sun.jersey.api.client.config.ClientConfig;
 import com.sun.jersey.api.client.config.DefaultClientConfig;
 
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestClient;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 public class UniProtFTSRestClient extends FTSRestClient
 {
-  private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+  private static final String DEFAULT_UNIPROT_DOMAIN = "https://legacy.uniprot.org";
+
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
+  }
 
   private static FTSRestClientI instance = null;
 
@@ -55,39 +61,60 @@ public class UniProtFTSRestClient extends FTSRestClient
   {
     super();
     uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
-            DEFAULT_UNIPROT_DOMAIN) + "/uniprot/?";
+            DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";
   }
 
+  @SuppressWarnings("unchecked")
   @Override
-  public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
+  public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest)
           throws Exception
   {
     try
     {
-      ClientConfig clientConfig = new DefaultClientConfig();
-      Client client = Client.create(clientConfig);
-
       String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
-              uniportRestRequest.getWantedFields());
-      int responseSize = (uniportRestRequest.getResponseSize() == 0)
+              uniprotRestRequest.getWantedFields());
+      int responseSize = (uniprotRestRequest.getResponseSize() == 0)
               ? getDefaultResponsePageSize()
-              : uniportRestRequest.getResponseSize();
+              : uniprotRestRequest.getResponseSize();
 
-      int offSet = uniportRestRequest.getOffSet();
+      int offSet = uniprotRestRequest.getOffSet();
       String query;
-      if (isAdvancedQuery(uniportRestRequest.getSearchTerm()))
+      if (isAdvancedQuery(uniprotRestRequest.getSearchTerm()))
       {
-        query = uniportRestRequest.getSearchTerm();
+        query = uniprotRestRequest.getSearchTerm();
       }
       else
       {
-        query = uniportRestRequest.getFieldToSearchBy()
+        query = uniprotRestRequest.getFieldToSearchBy()
                 .equalsIgnoreCase("Search All")
-                        ? uniportRestRequest.getSearchTerm()
+                        ? uniprotRestRequest.getSearchTerm()
                                 + " or mnemonic:"
-                                + uniportRestRequest.getSearchTerm()
-                        : uniportRestRequest.getFieldToSearchBy() + ":"
-                                + uniportRestRequest.getSearchTerm();
+                                + uniprotRestRequest.getSearchTerm()
+                        : uniprotRestRequest.getFieldToSearchBy() + ":"
+                                + uniprotRestRequest.getSearchTerm();
+      }
+
+      // BH 2018 the trick here is to coerce the classes in Javascript to be
+      // different from the ones in Java yet still allow this to be correct for
+      // Java
+      Client client;
+      Class<ClientResponse> clientResponseClass;
+      if (Platform.isJS())
+      {
+        // JavaScript only -- coerce types to Java types for Java
+        client = (Client) (Object) new jalview.javascript.web.Client();
+        clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
+      }
+      else
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
+      {
+        // Java only
+        client = Client.create(new DefaultClientConfig());
+        clientResponseClass = ClientResponse.class;
       }
 
       WebResource webResource = null;
@@ -97,9 +124,13 @@ public class UniProtFTSRestClient extends FTSRestClient
               .queryParam("limit", String.valueOf(responseSize))
               .queryParam("offset", String.valueOf(offSet))
               .queryParam("sort", "score").queryParam("query", query);
+      if (Console.isDebugEnabled())
+      {
+        Console.debug("Uniprot FTS Request: " + webResource.toString());
+      }
       // Execute the REST request
       ClientResponse clientResponse = webResource
-              .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
+              .accept(MediaType.TEXT_PLAIN).get(clientResponseClass);
       String uniProtTabDelimittedResponseString = clientResponse
               .getEntity(String.class);
       // Make redundant objects eligible for garbage collection to conserve
@@ -113,12 +144,13 @@ public class UniProtFTSRestClient extends FTSRestClient
         throw new Exception(errorMessage);
 
       }
-      int xTotalResults = Integer.valueOf(
-              clientResponse.getHeaders().get("X-Total-Results").get(0));
+      int xTotalResults = Platform.isJS() ? 1
+              : Integer.valueOf(clientResponse.getHeaders()
+                      .get("X-Total-Results").get(0));
       clientResponse = null;
       client = null;
       return parseUniprotResponse(uniProtTabDelimittedResponseString,
-              uniportRestRequest, xTotalResults);
+              uniprotRestRequest, xTotalResults);
     } catch (Exception e)
     {
       String exceptionMsg = e.getMessage();
@@ -188,38 +220,39 @@ public class UniProtFTSRestClient extends FTSRestClient
     return searchResult;
   }
 
-  /**
-   * Takes a collection of FTSDataColumnI and converts its 'code' values into a
-   * tab delimited string.
-   * 
-   * @param dataColumnFields
-   *          the collection of FTSDataColumnI to process
-   * @return the generated comma delimited string from the supplied
-   *         FTSDataColumnI collection
-   */
-  private String getDataColumnsFieldsAsTabDelimitedString(
-          Collection<FTSDataColumnI> dataColumnFields)
-  {
-    String result = "";
-    if (dataColumnFields != null && !dataColumnFields.isEmpty())
-    {
-      StringBuilder returnedFields = new StringBuilder();
-      for (FTSDataColumnI field : dataColumnFields)
-      {
-        if (field.getName().equalsIgnoreCase("Uniprot Id"))
-        {
-          returnedFields.append("\t").append("Entry");
-        }
-        else
-        {
-          returnedFields.append("\t").append(field.getName());
-        }
-      }
-      returnedFields.deleteCharAt(0);
-      result = returnedFields.toString();
-    }
-    return result;
-  }
+  // /**
+  // * Takes a collection of FTSDataColumnI and converts its 'code' values into
+  // a
+  // * tab delimited string.
+  // *
+  // * @param dataColumnFields
+  // * the collection of FTSDataColumnI to process
+  // * @return the generated comma delimited string from the supplied
+  // * FTSDataColumnI collection
+  // */
+  // private String getDataColumnsFieldsAsTabDelimitedString(
+  // Collection<FTSDataColumnI> dataColumnFields)
+  // {
+  // String result = "";
+  // if (dataColumnFields != null && !dataColumnFields.isEmpty())
+  // {
+  // StringBuilder returnedFields = new StringBuilder();
+  // for (FTSDataColumnI field : dataColumnFields)
+  // {
+  // if (field.getName().equalsIgnoreCase("Uniprot Id"))
+  // {
+  // returnedFields.append("\t").append("Entry");
+  // }
+  // else
+  // {
+  // returnedFields.append("\t").append(field.getName());
+  // }
+  // }
+  // returnedFields.deleteCharAt(0);
+  // result = returnedFields.toString();
+  // }
+  // return result;
+  // }
 
   public static FTSData getFTSData(String tabDelimittedDataStr,
           FTSRestRequest request)