/*
* 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 .
* 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 result = null;
String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
if (foundDataRow != null && foundDataRow.length > 0)
{
result = new ArrayList();
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 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 "/fts/uniprot_data_columns.txt";
}
}