X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniProtFTSRestClient.java;fp=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniProtFTSRestClient.java;h=5ee518bc26715d6c7f0cc3fc06971c5d96558b27;hb=8c7fd90d480e2671e0fa251ada3c89fa1d18862a;hp=57689f9cb2acfaf8f1f9a40c6282e2cc93aa4fba;hpb=ea7b9666447dea727e9d607de3694cfe27bc811e;p=jalview.git

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 57689f9..5ee518b 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -27,6 +27,7 @@ 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;
@@ -49,58 +50,109 @@ public class UniProtFTSRestClient extends FTSRestClient
 
   @Override
   public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
+          throws Exception
   {
-    ClientConfig clientConfig = new DefaultClientConfig();
-    Client client = Client.create(clientConfig);
+    try
+    {
+      ClientConfig clientConfig = new DefaultClientConfig();
+      Client client = Client.create(clientConfig);
 
-    String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
-            .getWantedFields());
-    int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
-            : uniportRestRequest.getResponseSize();
+      String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
+              .getWantedFields());
+      int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
+              : uniportRestRequest.getResponseSize();
 
-    int offSet = (uniportRestRequest.getOffSet() == 0) ? getDefaultResponsePageSize()
-            : uniportRestRequest.getOffSet();
+      int offSet = uniportRestRequest.getOffSet();
+      String query;
+      if (isAdvancedQuery(uniportRestRequest.getSearchTerm()))
+      {
+        query = uniportRestRequest.getSearchTerm();
+      }
+      else
+      {
+        query = uniportRestRequest.getFieldToSearchBy().equalsIgnoreCase(
+                "Search All") ? uniportRestRequest.getSearchTerm()
+                + " or mnemonic:" + uniportRestRequest.getSearchTerm()
+                : uniportRestRequest.getFieldToSearchBy() + ":"
+                        + uniportRestRequest.getSearchTerm();
+      }
 
-    String query = uniportRestRequest.getFieldToSearchBy()
-            .equalsIgnoreCase("Search All") ? uniportRestRequest
-            .getSearchTerm()
-            : uniportRestRequest.getFieldToSearchBy() + ":"
-                    + uniportRestRequest.getSearchTerm();
+      WebResource webResource = null;
+      webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
+              .queryParam("format", "tab")
+              .queryParam("columns", wantedFields)
+              .queryParam("limit", String.valueOf(responseSize))
+              .queryParam("offset", String.valueOf(offSet))
+              .queryParam("sort", "score").queryParam("query", query);
+      // Execute the REST request
+      ClientResponse clientResponse = webResource.accept(
+              MediaType.TEXT_PLAIN).get(ClientResponse.class);
+      String uniProtTabDelimittedResponseString = clientResponse
+              .getEntity(String.class);
+      // Make redundant objects eligible for garbage collection to conserve
+      // memory
+      // System.out.println(">>>>> response : "
+      // + uniProtTabDelimittedResponseString);
+      if (clientResponse.getStatus() != 200)
+      {
+        String errorMessage = getMessageByHTTPStatusCode(
+                clientResponse.getStatus(), "Uniprot");
+        throw new Exception(errorMessage);
 
-    // + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
-    // : " AND status:REL");
-    // System.out.println(">>>>> Query : " + query);
-    // System.out.println(">>>>> Columns : " + wantedFields);
-    WebResource webResource = null;
-    webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
-            .queryParam("format", "tab")
-            .queryParam("columns", wantedFields)
-            .queryParam("limit", String.valueOf(responseSize))
-            .queryParam("offset", String.valueOf(offSet))
-            .queryParam("sort", "score")
-            .queryParam("query", query);
-    // Execute the REST request
-    ClientResponse clientResponse = webResource
-            .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
-    String uniProtTabDelimittedResponseString = clientResponse
-            .getEntity(String.class);
-    // Make redundant objects eligible for garbage collection to conserve
-    // memory
-    clientResponse = null;
-    client = null;
-    // System.out.println(">>>>> response : "
-    // + uniProtTabDelimittedResponseString);
-    return parseUniprotResponse(uniProtTabDelimittedResponseString,
-            uniportRestRequest);
+      }
+      int xTotalResults = Integer.valueOf(clientResponse.getHeaders()
+              .get("X-Total-Results").get(0));
+      clientResponse = null;
+      client = null;
+      return parseUniprotResponse(uniProtTabDelimittedResponseString,
+              uniportRestRequest, xTotalResults);
+    } catch (Exception e)
+    {
+      String exceptionMsg = e.getMessage();
+      if (exceptionMsg.contains("SocketException"))
+      {
+        // No internet connection
+        throw new Exception(
+                MessageManager
+                        .getString("exception.unable_to_detect_internet_connection"));
+      }
+      else if (exceptionMsg.contains("UnknownHostException"))
+      {
+        // The server 'http://www.uniprot.org' is unreachable
+        throw new Exception(MessageManager.formatMessage(
+                "exception.fts_server_unreachable", "Uniprot"));
+      }
+      else
+      {
+        throw e;
+      }
+    }
+  }
 
+  public boolean isAdvancedQuery(String query)
+  {
+    if (query.contains(" AND ") || query.contains(" OR ")
+            || query.contains(" NOT ") || query.contains(" ! ")
+            || query.contains(" || ") || query.contains(" && ")
+            || query.contains(":") || query.contains("-"))
+    {
+      return true;
+    }
+    return false;
   }
 
   public FTSRestResponse parseUniprotResponse(
           String uniProtTabDelimittedResponseString,
-          FTSRestRequest uniprotRestRequest)
+          FTSRestRequest uniprotRestRequest, int xTotalResults)
   {
     FTSRestResponse searchResult = new FTSRestResponse();
     List<FTSData> result = null;
+    if (uniProtTabDelimittedResponseString == null
+            || uniProtTabDelimittedResponseString.trim().isEmpty())
+    {
+      searchResult.setNumberOfItemsFound(0);
+      return searchResult;
+    }
     String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
     if (foundDataRow != null && foundDataRow.length > 0)
     {
@@ -118,7 +170,7 @@ public class UniProtFTSRestClient extends FTSRestClient
         // System.out.println(dataRow);
         result.add(getFTSData(dataRow, uniprotRestRequest));
       }
-      searchResult.setNumberOfItemsFound(result.size());
+      searchResult.setNumberOfItemsFound(xTotalResults);
       searchResult.setSearchSummary(result);
     }
     return searchResult;
@@ -156,6 +208,7 @@ public class UniProtFTSRestClient extends FTSRestClient
     }
     return result;
   }
+
   public static FTSData getFTSData(String tabDelimittedDataStr,
           FTSRestRequest request)
   {
@@ -185,9 +238,11 @@ public class UniProtFTSRestClient extends FTSRestClient
         {
           try
           {
-            summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
-                    .valueOf(fieldData)
-                    : (field.getDataColumnClass() == Double.class) ? Double
+            summaryRowData[colCounter++] = (field.getDataType()
+                    .getDataTypeClass() == Integer.class) ? Integer
+                    .valueOf(fieldData.replace(",", ""))
+ : (field.getDataType()
+                    .getDataTypeClass() == Double.class) ? Double
                             .valueOf(fieldData) : fieldData;
           } catch (Exception e)
           {
@@ -242,6 +297,12 @@ public class UniProtFTSRestClient extends FTSRestClient
       {
         return Objects.hash(primaryKey1, this.toString());
       }
+
+      @Override
+      public boolean equals(Object that)
+      {
+        return this.toString().equals(that.toString());
+      }
     };
   }