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=f92016631cdba330a1ff01662277ad7b1790144e;hb=659cdd6d20a562ff4a856f2325399f2dbb398126;hp=0000000000000000000000000000000000000000;hpb=49a16230c3aa7081afe8a6c502bac36b46b25eee;p=jalview.git

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
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+/*
+ * 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;
+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;
+
+public class UniProtFTSRestClient extends FTSRestClient
+{
+  private static FTSRestClientI instance = null;
+
+  public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
+
+  @Override
+  public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
+  {
+    ClientConfig clientConfig = new DefaultClientConfig();
+    Client client = Client.create(clientConfig);
+
+    String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
+            .getWantedFields());
+    int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
+            : uniportRestRequest.getResponseSize();
+
+    String query = 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("limit", String.valueOf(responseSize))
+            .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);
+
+  }
+
+  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;
+  }
+
+  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;
+      }
+
+      /**
+       * 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());
+      }
+    };
+  }
+
+
+  public static FTSRestClientI getInstance()
+  {
+    if (instance == null)
+    {
+      instance = new UniProtFTSRestClient();
+    }
+    return instance;
+  }
+
+  @Override
+  public String getColumnDataConfigFileName()
+  {
+    return getResourceFile("/fts/uniprot_data_columns.conf");
+  }
+
+}