2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
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18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 package jalview.fts.service.uniprot;
24 import jalview.fts.api.FTSData;
25 import jalview.fts.api.FTSDataColumnI;
26 import jalview.fts.api.FTSRestClientI;
27 import jalview.fts.core.FTSRestClient;
28 import jalview.fts.core.FTSRestRequest;
29 import jalview.fts.core.FTSRestResponse;
30 import jalview.util.MessageManager;
32 import java.util.ArrayList;
33 import java.util.Collection;
34 import java.util.List;
35 import java.util.Objects;
37 import javax.ws.rs.core.MediaType;
39 import com.sun.jersey.api.client.Client;
40 import com.sun.jersey.api.client.ClientResponse;
41 import com.sun.jersey.api.client.WebResource;
42 import com.sun.jersey.api.client.config.ClientConfig;
43 import com.sun.jersey.api.client.config.DefaultClientConfig;
45 public class UniProtFTSRestClient extends FTSRestClient
47 private static FTSRestClientI instance = null;
49 public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
52 public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
57 ClientConfig clientConfig = new DefaultClientConfig();
58 Client client = Client.create(clientConfig);
60 String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
62 int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
63 : uniportRestRequest.getResponseSize();
65 int offSet = uniportRestRequest.getOffSet();
67 String query = uniportRestRequest.getFieldToSearchBy()
68 .equalsIgnoreCase("Search All") ? uniportRestRequest
72 .getSearchTerm() : uniportRestRequest.getFieldToSearchBy()
73 + ":" + uniportRestRequest.getSearchTerm();
75 // + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
76 // : " AND status:REL");
77 // System.out.println(">>>>> Query : " + query);
78 // System.out.println(">>>>> Columns : " + wantedFields);
79 // System.out.println(">>>>> Response size: " + responseSize
82 WebResource webResource = null;
83 webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
84 .queryParam("format", "tab")
85 .queryParam("columns", wantedFields)
86 .queryParam("limit", String.valueOf(responseSize))
87 .queryParam("offset", String.valueOf(offSet))
88 .queryParam("sort", "score").queryParam("query", query);
89 // Execute the REST request
90 ClientResponse clientResponse = webResource.accept(
91 MediaType.TEXT_PLAIN).get(ClientResponse.class);
92 String uniProtTabDelimittedResponseString = clientResponse
93 .getEntity(String.class);
94 // Make redundant objects eligible for garbage collection to conserve
96 // System.out.println(">>>>> response : "
97 // + uniProtTabDelimittedResponseString);
98 if (clientResponse.getStatus() != 200)
100 String errorMessage = getMessageByHTTPStatusCode(
101 clientResponse.getStatus(), "Uniprot");
102 throw new Exception(errorMessage);
105 int xTotalResults = Integer.valueOf(clientResponse.getHeaders()
106 .get("X-Total-Results").get(0));
107 clientResponse = null;
109 return parseUniprotResponse(uniProtTabDelimittedResponseString,
110 uniportRestRequest, xTotalResults);
111 } catch (Exception e)
113 String exceptionMsg = e.getMessage();
114 if (exceptionMsg.contains("SocketException"))
116 // No internet connection
119 .getString("exception.unable_to_detect_internet_connection"));
121 else if (exceptionMsg.contains("UnknownHostException"))
123 // The server 'http://www.uniprot.org' is unreachable
124 throw new Exception(MessageManager.formatMessage(
125 "exception.fts_server_unreachable", "Uniprot"));
135 public FTSRestResponse parseUniprotResponse(
136 String uniProtTabDelimittedResponseString,
137 FTSRestRequest uniprotRestRequest, int xTotalResults)
139 FTSRestResponse searchResult = new FTSRestResponse();
140 List<FTSData> result = null;
141 if (uniProtTabDelimittedResponseString == null
142 || uniProtTabDelimittedResponseString.trim().isEmpty())
144 searchResult.setNumberOfItemsFound(0);
147 String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
148 if (foundDataRow != null && foundDataRow.length > 0)
150 result = new ArrayList<FTSData>();
151 String titleRow = getDataColumnsFieldsAsTabDelimitedString(uniprotRestRequest
153 // System.out.println(">>>>Title row : " + titleRow);
154 for (String dataRow : foundDataRow)
156 if (dataRow.equalsIgnoreCase(titleRow))
158 // System.out.println(">>>>>>>>>> matched!!!");
161 // System.out.println(dataRow);
162 result.add(getFTSData(dataRow, uniprotRestRequest));
164 searchResult.setNumberOfItemsFound(xTotalResults);
165 searchResult.setSearchSummary(result);
171 * Takes a collection of FTSDataColumnI and converts its 'code' values into a
172 * tab delimited string.
174 * @param dataColumnFields
175 * the collection of FTSDataColumnI to process
176 * @return the generated comma delimited string from the supplied
177 * FTSDataColumnI collection
179 private String getDataColumnsFieldsAsTabDelimitedString(
180 Collection<FTSDataColumnI> dataColumnFields)
183 if (dataColumnFields != null && !dataColumnFields.isEmpty())
185 StringBuilder returnedFields = new StringBuilder();
186 for (FTSDataColumnI field : dataColumnFields)
188 if (field.getName().equalsIgnoreCase("Uniprot Id"))
190 returnedFields.append("\t").append("Entry");
194 returnedFields.append("\t").append(field.getName());
197 returnedFields.deleteCharAt(0);
198 result = returnedFields.toString();
203 public static FTSData getFTSData(String tabDelimittedDataStr,
204 FTSRestRequest request)
206 String primaryKey = null;
208 Object[] summaryRowData;
210 Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
212 summaryRowData = new Object[diplayFields.size()];
213 String[] columns = tabDelimittedDataStr.split("\t");
214 for (FTSDataColumnI field : diplayFields)
218 String fieldData = columns[colCounter];
219 if (field.isPrimaryKeyColumn())
221 primaryKey = fieldData;
222 summaryRowData[colCounter++] = primaryKey;
224 else if (fieldData == null || fieldData.isEmpty())
226 summaryRowData[colCounter++] = null;
232 summaryRowData[colCounter++] = (field.getDataType()
233 .getDataTypeClass() == Integer.class) ? Integer
235 : (field.getDataType()
236 .getDataTypeClass() == Double.class) ? Double
237 .valueOf(fieldData) : fieldData;
238 } catch (Exception e)
241 System.out.println("offending value:" + fieldData);
244 } catch (Exception e)
246 // e.printStackTrace();
250 final String primaryKey1 = primaryKey;
252 final Object[] summaryRowData1 = summaryRowData;
256 public Object[] getSummaryData()
258 return summaryRowData1;
262 public Object getPrimaryKey()
268 * Returns a string representation of this object;
271 public String toString()
273 StringBuilder summaryFieldValues = new StringBuilder();
274 for (Object summaryField : summaryRowData1)
276 summaryFieldValues.append(
277 summaryField == null ? " " : summaryField.toString())
280 return summaryFieldValues.toString();
284 * Returns hash code value for this object
287 public int hashCode()
289 return Objects.hash(primaryKey1, this.toString());
293 public boolean equals(Object that)
295 return this.toString().equals(that.toString());
301 public static FTSRestClientI getInstance()
303 if (instance == null)
305 instance = new UniProtFTSRestClient();
311 public String getColumnDataConfigFileName()
313 return "/fts/uniprot_data_columns.txt";