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.
12 * Jalview is distributed in the hope that it will be useful, but
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.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.fts.service.pdb;
23 import jalview.datamodel.SequenceI;
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.Iterator;
35 import java.util.List;
36 import java.util.Objects;
38 import javax.ws.rs.core.MediaType;
40 import org.json.simple.JSONArray;
41 import org.json.simple.JSONObject;
42 import org.json.simple.parser.JSONParser;
43 import org.json.simple.parser.ParseException;
45 import com.sun.jersey.api.client.Client;
46 import com.sun.jersey.api.client.ClientResponse;
47 import com.sun.jersey.api.client.WebResource;
48 import com.sun.jersey.api.client.config.ClientConfig;
49 import com.sun.jersey.api.client.config.DefaultClientConfig;
52 * A rest client for querying the Search endpoint of the PDB API
57 public class PDBFTSRestClient extends FTSRestClient
60 private static FTSRestClientI instance = null;
62 public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?";
64 protected PDBFTSRestClient()
69 * Takes a PDBRestRequest object and returns a response upon execution
71 * @param pdbRestRequest
72 * the PDBRestRequest instance to be processed
73 * @return the pdbResponse object for the given request
77 public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
82 ClientConfig clientConfig = new DefaultClientConfig();
83 Client client = Client.create(clientConfig);
85 String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
86 pdbRestRequest.getWantedFields());
87 int responseSize = (pdbRestRequest.getResponseSize() == 0)
88 ? getDefaultResponsePageSize()
89 : pdbRestRequest.getResponseSize();
90 int offSet = pdbRestRequest.getOffSet();
91 String sortParam = null;
92 if (pdbRestRequest.getFieldToSortBy() == null
93 || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
99 if (pdbRestRequest.getFieldToSortBy()
100 .equalsIgnoreCase("Resolution"))
102 sortParam = pdbRestRequest.getFieldToSortBy()
103 + (pdbRestRequest.isAscending() ? " asc" : " desc");
107 sortParam = pdbRestRequest.getFieldToSortBy()
108 + (pdbRestRequest.isAscending() ? " desc" : " asc");
112 String facetPivot = (pdbRestRequest.getFacetPivot() == null
113 || pdbRestRequest.getFacetPivot().isEmpty()) ? ""
114 : pdbRestRequest.getFacetPivot();
115 String facetPivotMinCount = String
116 .valueOf(pdbRestRequest.getFacetPivotMinCount());
118 String query = pdbRestRequest.getFieldToSearchBy()
119 + pdbRestRequest.getSearchTerm()
120 + (pdbRestRequest.isAllowEmptySeq() ? ""
121 : " AND molecule_sequence:['' TO *]")
122 + (pdbRestRequest.isAllowUnpublishedEntries() ? ""
123 : " AND status:REL");
125 // Build request parameters for the REST Request
126 WebResource webResource = null;
127 if (pdbRestRequest.isFacet())
129 webResource = client.resource(PDB_SEARCH_ENDPOINT)
130 .queryParam("wt", "json").queryParam("fl", wantedFields)
131 .queryParam("rows", String.valueOf(responseSize))
132 .queryParam("q", query)
133 .queryParam("start", String.valueOf(offSet))
134 .queryParam("sort", sortParam).queryParam("facet", "true")
135 .queryParam("facet.pivot", facetPivot)
136 .queryParam("facet.pivot.mincount", facetPivotMinCount);
140 webResource = client.resource(PDB_SEARCH_ENDPOINT)
141 .queryParam("wt", "json").queryParam("fl", wantedFields)
142 .queryParam("rows", String.valueOf(responseSize))
143 .queryParam("start", String.valueOf(offSet))
144 .queryParam("q", query).queryParam("sort", sortParam);
146 // Execute the REST request
147 ClientResponse clientResponse = webResource
148 .accept(MediaType.APPLICATION_JSON).get(ClientResponse.class);
150 // Get the JSON string from the response object
151 String responseString = clientResponse.getEntity(String.class);
152 // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
154 // Check the response status and report exception if one occurs
155 if (clientResponse.getStatus() != 200)
157 String errorMessage = "";
158 if (clientResponse.getStatus() == 400)
160 errorMessage = parseJsonExceptionString(responseString);
161 throw new Exception(errorMessage);
165 errorMessage = getMessageByHTTPStatusCode(
166 clientResponse.getStatus(), "PDB");
167 throw new Exception(errorMessage);
171 // Make redundant objects eligible for garbage collection to conserve
173 clientResponse = null;
176 // Process the response and return the result to the caller.
177 return parsePDBJsonResponse(responseString, pdbRestRequest);
178 } catch (Exception e)
180 String exceptionMsg = e.getMessage();
181 if (exceptionMsg.contains("SocketException"))
183 // No internet connection
184 throw new Exception(MessageManager.getString(
185 "exception.unable_to_detect_internet_connection"));
187 else if (exceptionMsg.contains("UnknownHostException"))
189 // The server 'www.ebi.ac.uk' is unreachable
190 throw new Exception(MessageManager.formatMessage(
191 "exception.fts_server_unreachable", "PDB Solr"));
201 * Process error response from PDB server if/when one occurs.
203 * @param jsonResponse
204 * the JSON string containing error message from the server
205 * @return the processed error message from the JSON string
207 public static String parseJsonExceptionString(String jsonErrorResponse)
209 StringBuilder errorMessage = new StringBuilder(
210 "\n============= PDB Rest Client RunTime error =============\n");
214 JSONParser jsonParser = new JSONParser();
215 JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
216 JSONObject errorResponse = (JSONObject) jsonObj.get("error");
218 JSONObject responseHeader = (JSONObject) jsonObj
219 .get("responseHeader");
220 JSONObject paramsObj = (JSONObject) responseHeader.get("params");
221 String status = responseHeader.get("status").toString();
222 String message = errorResponse.get("msg").toString();
223 String query = paramsObj.get("q").toString();
224 String fl = paramsObj.get("fl").toString();
226 errorMessage.append("Status: ").append(status).append("\n");
227 errorMessage.append("Message: ").append(message).append("\n");
228 errorMessage.append("query: ").append(query).append("\n");
229 errorMessage.append("fl: ").append(fl).append("\n");
231 } catch (ParseException e)
235 return errorMessage.toString();
239 * Parses the JSON response string from PDB REST API. The response is dynamic
240 * hence, only fields specifically requested for in the 'wantedFields'
241 * parameter is fetched/processed
243 * @param pdbJsonResponseString
244 * the JSON string to be parsed
245 * @param pdbRestRequest
246 * the request object which contains parameters used to process the
250 @SuppressWarnings("unchecked")
251 public static FTSRestResponse parsePDBJsonResponse(
252 String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
254 FTSRestResponse searchResult = new FTSRestResponse();
255 List<FTSData> result = null;
258 JSONParser jsonParser = new JSONParser();
259 JSONObject jsonObj = (JSONObject) jsonParser
260 .parse(pdbJsonResponseString);
262 JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
263 String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
264 .get("QTime").toString();
265 int numFound = Integer
266 .valueOf(pdbResponse.get("numFound").toString());
269 result = new ArrayList<FTSData>();
270 JSONArray docs = (JSONArray) pdbResponse.get("docs");
271 for (Iterator<JSONObject> docIter = docs.iterator(); docIter
274 JSONObject doc = docIter.next();
275 result.add(getFTSData(doc, pdbRestRequest));
277 searchResult.setNumberOfItemsFound(numFound);
278 searchResult.setResponseTime(queryTime);
279 searchResult.setSearchSummary(result);
281 } catch (ParseException e)
288 public static FTSData getFTSData(JSONObject pdbJsonDoc,
289 FTSRestRequest request)
292 String primaryKey = null;
294 Object[] summaryRowData;
296 SequenceI associatedSequence;
298 Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
299 SequenceI associatedSeq = request.getAssociatedSequence();
301 summaryRowData = new Object[(associatedSeq != null)
302 ? diplayFields.size() + 1
303 : diplayFields.size()];
304 if (associatedSeq != null)
306 associatedSequence = associatedSeq;
307 summaryRowData[0] = associatedSequence;
311 for (FTSDataColumnI field : diplayFields)
313 String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
314 : pdbJsonDoc.get(field.getCode()).toString();
315 if (field.isPrimaryKeyColumn())
317 primaryKey = fieldData;
318 summaryRowData[colCounter++] = primaryKey;
320 else if (fieldData == null || fieldData.isEmpty())
322 summaryRowData[colCounter++] = null;
328 summaryRowData[colCounter++] = (field.getDataType()
329 .getDataTypeClass() == Integer.class)
330 ? Integer.valueOf(fieldData)
331 : (field.getDataType()
332 .getDataTypeClass() == Double.class)
333 ? Double.valueOf(fieldData)
334 : sanitiseData(fieldData);
335 } catch (Exception e)
338 System.out.println("offending value:" + fieldData);
343 final String primaryKey1 = primaryKey;
345 final Object[] summaryRowData1 = summaryRowData;
349 public Object[] getSummaryData()
351 return summaryRowData1;
355 public Object getPrimaryKey()
361 * Returns a string representation of this object;
364 public String toString()
366 StringBuilder summaryFieldValues = new StringBuilder();
367 for (Object summaryField : summaryRowData1)
369 summaryFieldValues.append(
370 summaryField == null ? " " : summaryField.toString())
373 return summaryFieldValues.toString();
377 * Returns hash code value for this object
380 public int hashCode()
382 return Objects.hash(primaryKey1, this.toString());
386 public boolean equals(Object that)
388 return this.toString().equals(that.toString());
393 private static String sanitiseData(String data)
395 String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
396 .replaceAll("\\[", "").replaceAll("\\]", "")
397 .replaceAll("\",\"", ", ").replaceAll("\"", "");
402 public String getColumnDataConfigFileName()
404 return "/fts/pdb_data_columns.txt";
407 public static FTSRestClientI getInstance()
409 if (instance == null)
411 instance = new PDBFTSRestClient();
416 private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
418 public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
420 if (allDefaultDisplayedStructureDataColumns == null
421 || allDefaultDisplayedStructureDataColumns.isEmpty())
423 allDefaultDisplayedStructureDataColumns = new ArrayList<FTSDataColumnI>();
424 allDefaultDisplayedStructureDataColumns
425 .addAll(super.getAllDefaultDisplayedFTSDataColumns());
427 return allDefaultDisplayedStructureDataColumns;