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;
24 import java.util.ArrayList;
25 import java.util.Collection;
26 import java.util.Iterator;
27 import java.util.List;
29 import java.util.Objects;
31 import javax.ws.rs.core.MediaType;
33 import org.json.simple.parser.ParseException;
35 import com.sun.jersey.api.client.Client;
36 import com.sun.jersey.api.client.ClientResponse;
37 import com.sun.jersey.api.client.WebResource;
38 import com.sun.jersey.api.client.config.DefaultClientConfig;
40 import jalview.datamodel.SequenceI;
41 import jalview.fts.api.FTSData;
42 import jalview.fts.api.FTSDataColumnI;
43 import jalview.fts.api.FTSRestClientI;
44 import jalview.fts.core.FTSRestClient;
45 import jalview.fts.core.FTSRestRequest;
46 import jalview.fts.core.FTSRestResponse;
47 import jalview.util.JSONUtils;
48 import jalview.util.MessageManager;
49 import jalview.util.Platform;
52 * A rest client for querying the Search endpoint of the PDB API
56 public class PDBFTSRestClient extends FTSRestClient
59 private static FTSRestClientI instance = null;
61 public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?";
63 protected PDBFTSRestClient()
68 * Takes a PDBRestRequest object and returns a response upon execution
70 * @param pdbRestRequest
71 * the PDBRestRequest instance to be processed
72 * @return the pdbResponse object for the given request
75 @SuppressWarnings({ "unused", "unchecked" })
77 public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
82 String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
83 pdbRestRequest.getWantedFields());
84 int responseSize = (pdbRestRequest.getResponseSize() == 0)
85 ? getDefaultResponsePageSize()
86 : pdbRestRequest.getResponseSize();
87 int offSet = pdbRestRequest.getOffSet();
88 String sortParam = null;
89 if (pdbRestRequest.getFieldToSortBy() == null
90 || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
96 if (pdbRestRequest.getFieldToSortBy()
97 .equalsIgnoreCase("Resolution"))
99 sortParam = pdbRestRequest.getFieldToSortBy()
100 + (pdbRestRequest.isAscending() ? " asc" : " desc");
104 sortParam = pdbRestRequest.getFieldToSortBy()
105 + (pdbRestRequest.isAscending() ? " desc" : " asc");
109 String facetPivot = (pdbRestRequest.getFacetPivot() == null
110 || pdbRestRequest.getFacetPivot().isEmpty()) ? ""
111 : pdbRestRequest.getFacetPivot();
112 String facetPivotMinCount = String
113 .valueOf(pdbRestRequest.getFacetPivotMinCount());
115 String query = pdbRestRequest.getFieldToSearchBy()
116 + pdbRestRequest.getSearchTerm()
117 + (pdbRestRequest.isAllowEmptySeq() ? ""
118 : " AND molecule_sequence:['' TO *]")
119 + (pdbRestRequest.isAllowUnpublishedEntries() ? ""
120 : " AND status:REL");
122 // Build request parameters for the REST Request
124 // BH 2018 the trick here is to coerce the classes in Javascript to be
125 // different from the ones in Java yet still allow this to be correct for Java
127 Class<ClientResponse> clientResponseClass;
130 // JavaScript only -- coerce types to Java types for Java
131 client = (Client) (Object) new jalview.javascript.web.Client();
132 clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
141 client = Client.create(new DefaultClientConfig());
142 clientResponseClass = ClientResponse.class;
145 WebResource webResource;
146 if (pdbRestRequest.isFacet())
148 webResource = client.resource(PDB_SEARCH_ENDPOINT)
149 .queryParam("wt", "json").queryParam("fl", wantedFields)
150 .queryParam("rows", String.valueOf(responseSize))
151 .queryParam("q", query)
152 .queryParam("start", String.valueOf(offSet))
153 .queryParam("sort", sortParam).queryParam("facet", "true")
154 .queryParam("facet.pivot", facetPivot)
155 .queryParam("facet.pivot.mincount", facetPivotMinCount);
159 webResource = client.resource(PDB_SEARCH_ENDPOINT)
160 .queryParam("wt", "json").queryParam("fl", wantedFields)
161 .queryParam("rows", String.valueOf(responseSize))
162 .queryParam("start", String.valueOf(offSet))
163 .queryParam("q", query).queryParam("sort", sortParam);
166 URI uri = webResource.getURI();
168 // System.out.println(uri);
170 // Execute the REST request
171 ClientResponse clientResponse = webResource
172 .accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
174 // Get the JSON string from the response object or directly from the
175 // client (JavaScript)
176 Map<String, Object> jsonObj = null;
177 String responseString = null;
179 // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
181 // Check the response status and report exception if one occurs
182 int responseStatus = clientResponse.getStatus();
183 switch (responseStatus)
188 jsonObj = clientResponse.getEntity(Map.class);
192 responseString = clientResponse.getEntity(String.class);
196 throw new Exception(parseJsonExceptionString(responseString));
199 getMessageByHTTPStatusCode(responseStatus, "PDB"));
202 // Process the response and return the result to the caller.
203 return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
204 } catch (Exception e)
206 String exceptionMsg = e.getMessage();
207 if (exceptionMsg.contains("SocketException"))
209 // No internet connection
210 throw new Exception(MessageManager.getString(
211 "exception.unable_to_detect_internet_connection"));
213 else if (exceptionMsg.contains("UnknownHostException"))
215 // The server 'www.ebi.ac.uk' is unreachable
216 throw new Exception(MessageManager.formatMessage(
217 "exception.fts_server_unreachable", "PDB Solr"));
227 * Process error response from PDB server if/when one occurs.
229 * @param jsonResponse
230 * the JSON string containing error message from the server
231 * @return the processed error message from the JSON string
233 @SuppressWarnings("unchecked")
234 public static String parseJsonExceptionString(String jsonErrorResponse)
236 StringBuilder errorMessage = new StringBuilder(
237 "\n============= PDB Rest Client RunTime error =============\n");
241 // "responseHeader":{
245 // "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
246 // "fl":"pdb_id,title,experimental_method,resolution",
248 // "sort":"overall_quality desc",
251 // "response":{"numFound":1,"start":0,"docs":[
253 // "experimental_method":["X-ray diffraction"],
255 // "resolution":2.46,
256 // "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}]
261 Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(jsonErrorResponse);
262 Map<String, Object> errorResponse = (Map<String, Object>) jsonObj.get("error");
264 Map<String, Object> responseHeader = (Map<String, Object>) jsonObj
265 .get("responseHeader");
266 Map<String, Object> paramsObj = (Map<String, Object>) responseHeader.get("params");
267 String status = responseHeader.get("status").toString();
268 String message = errorResponse.get("msg").toString();
269 String query = paramsObj.get("q").toString();
270 String fl = paramsObj.get("fl").toString();
272 errorMessage.append("Status: ").append(status).append("\n");
273 errorMessage.append("Message: ").append(message).append("\n");
274 errorMessage.append("query: ").append(query).append("\n");
275 errorMessage.append("fl: ").append(fl).append("\n");
277 } catch (ParseException e)
281 return errorMessage.toString();
285 * Parses the JSON response string from PDB REST API. The response is dynamic
286 * hence, only fields specifically requested for in the 'wantedFields'
287 * parameter is fetched/processed
289 * @param pdbJsonResponseString
290 * the JSON string to be parsed
291 * @param pdbRestRequest
292 * the request object which contains parameters used to process the
296 public static FTSRestResponse parsePDBJsonResponse(
297 String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
299 return parsePDBJsonResponse(pdbJsonResponseString,
300 (Map<String, Object>) null, pdbRestRequest);
303 @SuppressWarnings("unchecked")
304 public static FTSRestResponse parsePDBJsonResponse(
305 String pdbJsonResponseString, Map<String, Object> jsonObj,
306 FTSRestRequest pdbRestRequest)
308 FTSRestResponse searchResult = new FTSRestResponse();
309 List<FTSData> result = null;
314 jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
316 Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj.get("response");
317 String queryTime = ((Map<String, Object>) jsonObj.get("responseHeader"))
318 .get("QTime").toString();
319 int numFound = Integer
320 .valueOf(pdbResponse.get("numFound").toString());
323 result = new ArrayList<>();
324 List<Object> docs = (List<Object>) pdbResponse.get("docs");
325 for (Iterator<Object> docIter = docs.iterator(); docIter
328 Map<String, Object> doc = (Map<String, Object>) docIter.next();
329 result.add(getFTSData(doc, pdbRestRequest));
331 searchResult.setNumberOfItemsFound(numFound);
332 searchResult.setResponseTime(queryTime);
333 searchResult.setSearchSummary(result);
335 } catch (ParseException e)
342 public static FTSData getFTSData(Map<String, Object> pdbJsonDoc,
343 FTSRestRequest request)
346 String primaryKey = null;
348 Object[] summaryRowData;
350 SequenceI associatedSequence;
352 Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
353 SequenceI associatedSeq = request.getAssociatedSequence();
355 summaryRowData = new Object[(associatedSeq != null)
356 ? diplayFields.size() + 1
357 : diplayFields.size()];
358 if (associatedSeq != null)
360 associatedSequence = associatedSeq;
361 summaryRowData[0] = associatedSequence;
365 for (FTSDataColumnI field : diplayFields)
367 String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
368 : pdbJsonDoc.get(field.getCode()).toString();
369 if (field.isPrimaryKeyColumn())
371 primaryKey = fieldData;
372 summaryRowData[colCounter++] = primaryKey;
374 else if (fieldData == null || fieldData.isEmpty())
376 summaryRowData[colCounter++] = null;
382 summaryRowData[colCounter++] = (field.getDataType()
383 .getDataTypeClass() == Integer.class)
384 ? Integer.valueOf(fieldData)
385 : (field.getDataType()
386 .getDataTypeClass() == Double.class)
387 ? Double.valueOf(fieldData)
388 : sanitiseData(fieldData);
389 } catch (Exception e)
392 System.out.println("offending value:" + fieldData);
397 final String primaryKey1 = primaryKey;
399 final Object[] summaryRowData1 = summaryRowData;
403 public Object[] getSummaryData()
405 return summaryRowData1;
409 public Object getPrimaryKey()
415 * Returns a string representation of this object;
418 public String toString()
420 StringBuilder summaryFieldValues = new StringBuilder();
421 for (Object summaryField : summaryRowData1)
423 summaryFieldValues.append(
424 summaryField == null ? " " : summaryField.toString())
427 return summaryFieldValues.toString();
431 * Returns hash code value for this object
434 public int hashCode()
436 return Objects.hash(primaryKey1, this.toString());
440 public boolean equals(Object that)
442 return this.toString().equals(that.toString());
447 private static String sanitiseData(String data)
449 String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
450 .replaceAll("\\[", "").replaceAll("\\]", "")
451 .replaceAll("\",\"", ", ").replaceAll("\"", "");
456 public String getColumnDataConfigFileName()
458 return "/fts/pdb_data_columns.txt";
461 public static FTSRestClientI getInstance()
463 if (instance == null)
465 instance = new PDBFTSRestClient();
470 private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
472 public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
474 if (allDefaultDisplayedStructureDataColumns == null
475 || allDefaultDisplayedStructureDataColumns.isEmpty())
477 allDefaultDisplayedStructureDataColumns = new ArrayList<>();
478 allDefaultDisplayedStructureDataColumns
479 .addAll(super.getAllDefaultDisplayedFTSDataColumns());
481 return allDefaultDisplayedStructureDataColumns;