X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniProtFTSRestClient.java;h=57689f9cb2acfaf8f1f9a40c6282e2cc93aa4fba;hb=e1976b4025f648431974e7ddcb2be93115688abd;hp=2930468a367499deda3951d796c3952f94b96877;hpb=007af0c9001900071f6d8e9214143f79e10f4938;p=jalview.git

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 2930468..57689f9 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -1,10 +1,38 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
 package jalview.fts.service.uniprot;
 
+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 java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+
 import javax.ws.rs.core.MediaType;
 
 import com.sun.jersey.api.client.Client;
@@ -13,63 +41,208 @@ import com.sun.jersey.api.client.WebResource;
 import com.sun.jersey.api.client.config.ClientConfig;
 import com.sun.jersey.api.client.config.DefaultClientConfig;
 
-public class UniProtRestClient extends FTSRestClient
+public class UniProtFTSRestClient extends FTSRestClient
 {
   private static FTSRestClientI instance = null;
 
   public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
 
-  private static int DEFAULT_RESPONSE_SIZE = 200;
-
   @Override
   public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
   {
     ClientConfig clientConfig = new DefaultClientConfig();
     Client client = Client.create(clientConfig);
 
-    @SuppressWarnings("unchecked")
-    // String wantedFields =
-    // getUniProtDocFieldsAsCommaDelimitedString((Collection<UniProtDocField>)
-    // uniportRestRequest
-    // .getWantedFields());
-    int responseSize = (uniportRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+    String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
+            .getWantedFields());
+    int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
             : uniportRestRequest.getResponseSize();
 
-    WebResource webResource = null;
+    int offSet = (uniportRestRequest.getOffSet() == 0) ? getDefaultResponsePageSize()
+            : uniportRestRequest.getOffSet();
 
+    String query = uniportRestRequest.getFieldToSearchBy()
+            .equalsIgnoreCase("Search All") ? uniportRestRequest
+            .getSearchTerm()
+            : uniportRestRequest.getFieldToSearchBy() + ":"
+                    + uniportRestRequest.getSearchTerm();
+
+    // + (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("columns", wantedFields)
             .queryParam("limit", String.valueOf(responseSize))
-            .queryParam("query", "name:filaggrin");
+            .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 responseString = clientResponse.getEntity(String.class);
-    String[] results = responseString.split("\n");
-    for (String result : results)
-    {
-      String[] columns = result.split("\t");
-      System.out.println("Entry : " + columns[0]);
-      System.out.println("Entry name : " + columns[1]);
-      System.out.println("Status : " + columns[2]);
-      System.out.println("Protein names : " + columns[3]);
-      System.out.println("Gene name : " + columns[4]);
-      System.out.println("Organism : " + columns[5]);
-      System.out.println("Lenght : " + columns[6]);
-      System.out.println("");
-    }
-
+    String uniProtTabDelimittedResponseString = clientResponse
+            .getEntity(String.class);
     // Make redundant objects eligible for garbage collection to conserve
     // memory
     clientResponse = null;
     client = null;
-    return null;
+    // System.out.println(">>>>> response : "
+    // + uniProtTabDelimittedResponseString);
+    return parseUniprotResponse(uniProtTabDelimittedResponseString,
+            uniportRestRequest);
+
+  }
+
+  public FTSRestResponse parseUniprotResponse(
+          String uniProtTabDelimittedResponseString,
+          FTSRestRequest uniprotRestRequest)
+  {
+    FTSRestResponse searchResult = new FTSRestResponse();
+    List<FTSData> result = null;
+    String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
+    if (foundDataRow != null && foundDataRow.length > 0)
+    {
+      result = new ArrayList<FTSData>();
+      String titleRow = getDataColumnsFieldsAsTabDelimitedString(uniprotRestRequest
+              .getWantedFields());
+      // System.out.println(">>>>Title row : " + titleRow);
+      for (String dataRow : foundDataRow)
+      {
+        if (dataRow.equalsIgnoreCase(titleRow))
+        {
+          // System.out.println(">>>>>>>>>> matched!!!");
+          continue;
+        }
+        // System.out.println(dataRow);
+        result.add(getFTSData(dataRow, uniprotRestRequest));
+      }
+      searchResult.setNumberOfItemsFound(result.size());
+      searchResult.setSearchSummary(result);
+    }
+    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;
+  }
+  public static FTSData getFTSData(String tabDelimittedDataStr,
+          FTSRestRequest request)
+  {
+    String primaryKey = null;
+
+    Object[] summaryRowData;
+
+    Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
+    int colCounter = 0;
+    summaryRowData = new Object[diplayFields.size()];
+    String[] columns = tabDelimittedDataStr.split("\t");
+    for (FTSDataColumnI field : diplayFields)
+    {
+      try
+      {
+        String fieldData = columns[colCounter];
+        if (field.isPrimaryKeyColumn())
+        {
+          primaryKey = fieldData;
+          summaryRowData[colCounter++] = primaryKey;
+        }
+        else if (fieldData == null || fieldData.isEmpty())
+        {
+          summaryRowData[colCounter++] = null;
+        }
+        else
+        {
+          try
+          {
+            summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
+                    .valueOf(fieldData)
+                    : (field.getDataColumnClass() == Double.class) ? Double
+                            .valueOf(fieldData) : fieldData;
+          } catch (Exception e)
+          {
+            e.printStackTrace();
+              System.out.println("offending value:" + fieldData);
+          }
+        }
+      } catch (Exception e)
+      {
+        // e.printStackTrace();
+      }
+    }
+
+    final String primaryKey1 = primaryKey;
+
+    final Object[] summaryRowData1 = summaryRowData;
+    return new FTSData()
+    {
+      @Override
+      public Object[] getSummaryData()
+      {
+        return summaryRowData1;
+      }
+
+      @Override
+      public Object getPrimaryKey()
+      {
+        return primaryKey1;
+      }
 
-    // Process the response and return the result to the caller.
-    // return parsePDBJsonResponse(responseString, pdbRestRequest);
-    // System.out.println(">>>>> " + responseString);
+      /**
+       * Returns a string representation of this object;
+       */
+      @Override
+      public String toString()
+      {
+        StringBuilder summaryFieldValues = new StringBuilder();
+        for (Object summaryField : summaryRowData1)
+        {
+          summaryFieldValues.append(
+                  summaryField == null ? " " : summaryField.toString())
+                  .append("\t");
+        }
+        return summaryFieldValues.toString();
+      }
 
+      /**
+       * Returns hash code value for this object
+       */
+      @Override
+      public int hashCode()
+      {
+        return Objects.hash(primaryKey1, this.toString());
+      }
+    };
   }
 
 
@@ -77,15 +250,15 @@ public class UniProtRestClient extends FTSRestClient
   {
     if (instance == null)
     {
-      instance = new UniProtRestClient();
+      instance = new UniProtFTSRestClient();
     }
     return instance;
   }
 
   @Override
-  public String getColumnDataConfigFile()
+  public String getColumnDataConfigFileName()
   {
-    return "fts/uniprot_data_columns.conf";
+    return "/fts/uniprot_data_columns.txt";
   }
 
 }