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.
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.JSONUtils;
31 import jalview.util.MessageManager;
32 import jalview.util.Platform;
35 import java.util.ArrayList;
36 import java.util.Collection;
37 import java.util.Iterator;
38 import java.util.List;
40 import java.util.Objects;
42 import javax.ws.rs.core.MediaType;
44 import org.json.simple.parser.ParseException;
46 import com.sun.jersey.api.client.Client;
47 import com.sun.jersey.api.client.ClientResponse;
48 import com.sun.jersey.api.client.WebResource;
49 import com.sun.jersey.api.client.config.DefaultClientConfig;
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 int status = clientResponse.getStatus();
176 // Get the JSON string from the response object or directly from the
177 // client (JavaScript)
178 Map<String, Object> jsonObj = (Platform.isJS() && status == 200
179 ? clientResponse.getEntity(Map.class)
181 String responseString = (jsonObj == null
182 ? clientResponse.getEntity(String.class)
185 // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
187 // Check the response status and report exception if one occurs
193 throw new Exception(parseJsonExceptionString(responseString));
195 throw new Exception(getMessageByHTTPStatusCode(status, "PDB"));
198 // Make redundant objects eligible for garbage collection to conserve
200 clientResponse = null;
203 // Process the response and return the result to the caller.
204 return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
205 } catch (Exception e)
207 String exceptionMsg = e.getMessage();
208 if (exceptionMsg.contains("SocketException"))
210 // No internet connection
211 throw new Exception(MessageManager.getString(
212 "exception.unable_to_detect_internet_connection"));
214 else if (exceptionMsg.contains("UnknownHostException"))
216 // The server 'www.ebi.ac.uk' is unreachable
217 throw new Exception(MessageManager.formatMessage(
218 "exception.fts_server_unreachable", "PDB Solr"));
228 * Process error response from PDB server if/when one occurs.
230 * @param jsonResponse
231 * the JSON string containing error message from the server
232 * @return the processed error message from the JSON string
234 @SuppressWarnings("unchecked")
235 public static String parseJsonExceptionString(String jsonErrorResponse)
237 StringBuilder errorMessage = new StringBuilder(
238 "\n============= PDB Rest Client RunTime error =============\n");
242 // "responseHeader":{
246 // "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
247 // "fl":"pdb_id,title,experimental_method,resolution",
249 // "sort":"overall_quality desc",
252 // "response":{"numFound":1,"start":0,"docs":[
254 // "experimental_method":["X-ray diffraction"],
256 // "resolution":2.46,
257 // "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}]
262 Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(jsonErrorResponse);
263 Map<String, Object> errorResponse = (Map<String, Object>) jsonObj.get("error");
265 Map<String, Object> responseHeader = (Map<String, Object>) jsonObj
266 .get("responseHeader");
267 Map<String, Object> paramsObj = (Map<String, Object>) responseHeader.get("params");
268 String status = responseHeader.get("status").toString();
269 String message = errorResponse.get("msg").toString();
270 String query = paramsObj.get("q").toString();
271 String fl = paramsObj.get("fl").toString();
273 errorMessage.append("Status: ").append(status).append("\n");
274 errorMessage.append("Message: ").append(message).append("\n");
275 errorMessage.append("query: ").append(query).append("\n");
276 errorMessage.append("fl: ").append(fl).append("\n");
278 } catch (ParseException e)
282 return errorMessage.toString();
286 * Parses the JSON response string from PDB REST API. The response is dynamic
287 * hence, only fields specifically requested for in the 'wantedFields'
288 * parameter is fetched/processed
290 * @param pdbJsonResponseString
291 * the JSON string to be parsed
292 * @param pdbRestRequest
293 * the request object which contains parameters used to process the
297 public static FTSRestResponse parsePDBJsonResponse(
298 String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
300 return parsePDBJsonResponse(pdbJsonResponseString,
301 (Map<String, Object>) null, pdbRestRequest);
304 @SuppressWarnings("unchecked")
305 public static FTSRestResponse parsePDBJsonResponse(
306 String pdbJsonResponseString, Map<String, Object> jsonObj,
307 FTSRestRequest pdbRestRequest)
309 FTSRestResponse searchResult = new FTSRestResponse();
310 List<FTSData> result = null;
315 jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
317 Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj.get("response");
318 String queryTime = ((Map<String, Object>) jsonObj.get("responseHeader"))
319 .get("QTime").toString();
320 int numFound = Integer
321 .valueOf(pdbResponse.get("numFound").toString());
324 result = new ArrayList<>();
325 List<Object> docs = (List<Object>) pdbResponse.get("docs");
326 for (Iterator<Object> docIter = docs.iterator(); docIter
329 Map<String, Object> doc = (Map<String, Object>) docIter.next();
330 result.add(getFTSData(doc, pdbRestRequest));
332 searchResult.setNumberOfItemsFound(numFound);
333 searchResult.setResponseTime(queryTime);
334 searchResult.setSearchSummary(result);
336 } catch (ParseException e)
343 public static FTSData getFTSData(Map<String, Object> pdbJsonDoc,
344 FTSRestRequest request)
347 String primaryKey = null;
349 Object[] summaryRowData;
351 SequenceI associatedSequence;
353 Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
354 SequenceI associatedSeq = request.getAssociatedSequence();
356 summaryRowData = new Object[(associatedSeq != null)
357 ? diplayFields.size() + 1
358 : diplayFields.size()];
359 if (associatedSeq != null)
361 associatedSequence = associatedSeq;
362 summaryRowData[0] = associatedSequence;
366 for (FTSDataColumnI field : diplayFields)
368 String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
369 : pdbJsonDoc.get(field.getCode()).toString();
370 if (field.isPrimaryKeyColumn())
372 primaryKey = fieldData;
373 summaryRowData[colCounter++] = primaryKey;
375 else if (fieldData == null || fieldData.isEmpty())
377 summaryRowData[colCounter++] = null;
383 summaryRowData[colCounter++] = (field.getDataType()
384 .getDataTypeClass() == Integer.class)
385 ? Integer.valueOf(fieldData)
386 : (field.getDataType()
387 .getDataTypeClass() == Double.class)
388 ? Double.valueOf(fieldData)
389 : sanitiseData(fieldData);
390 } catch (Exception e)
393 System.out.println("offending value:" + fieldData);
398 final String primaryKey1 = primaryKey;
400 final Object[] summaryRowData1 = summaryRowData;
404 public Object[] getSummaryData()
406 return summaryRowData1;
410 public Object getPrimaryKey()
416 * Returns a string representation of this object;
419 public String toString()
421 StringBuilder summaryFieldValues = new StringBuilder();
422 for (Object summaryField : summaryRowData1)
424 summaryFieldValues.append(
425 summaryField == null ? " " : summaryField.toString())
428 return summaryFieldValues.toString();
432 * Returns hash code value for this object
435 public int hashCode()
437 return Objects.hash(primaryKey1, this.toString());
441 public boolean equals(Object that)
443 return this.toString().equals(that.toString());
448 private static String sanitiseData(String data)
450 String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
451 .replaceAll("\\[", "").replaceAll("\\]", "")
452 .replaceAll("\",\"", ", ").replaceAll("\"", "");
457 public String getColumnDataConfigFileName()
459 return "/fts/pdb_data_columns.txt";
462 public static FTSRestClientI getInstance()
464 if (instance == null)
466 instance = new PDBFTSRestClient();
471 private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
473 public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
475 if (allDefaultDisplayedStructureDataColumns == null
476 || allDefaultDisplayedStructureDataColumns.isEmpty())
478 allDefaultDisplayedStructureDataColumns = new ArrayList<>();
479 allDefaultDisplayedStructureDataColumns
480 .addAll(super.getAllDefaultDisplayedFTSDataColumns());
482 return allDefaultDisplayedStructureDataColumns;