JAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)

[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 924b061..2606b62 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -21,16 +21,6 @@
 
 package jalview.fts.service.uniprot;
 
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-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;
@@ -43,9 +33,25 @@ 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.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;
 
@@ -55,36 +61,37 @@ 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
     {
       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
@@ -92,14 +99,18 @@ public class UniProtFTSRestClient extends FTSRestClient
       // Java
       Client client;
       Class<ClientResponse> clientResponseClass;
-      if (/** @j2sNative true || */
-      false)
+      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());
@@ -113,6 +124,10 @@ 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(clientResponseClass);
@@ -129,13 +144,13 @@ public class UniProtFTSRestClient extends FTSRestClient
         throw new Exception(errorMessage);
 
       }
-      int xTotalResults = Jalview.isJS() ? 1
+      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();
@@ -205,38 +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)