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.api.StructureFTSRestClientI;
45 import jalview.fts.core.FTSDataColumnPreferences;
46 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
47 import jalview.fts.core.FTSRestClient;
48 import jalview.fts.core.FTSRestRequest;
49 import jalview.fts.core.FTSRestResponse;
50 import jalview.fts.service.alphafold.AlphafoldRestClient;
51 import jalview.util.JSONUtils;
52 import jalview.util.MessageManager;
53 import jalview.util.Platform;
56 * A rest client for querying the Search endpoint of the PDB API
60 public class PDBFTSRestClient extends FTSRestClient implements StructureFTSRestClientI
63 private static FTSRestClientI instance = null;
65 public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?";
67 protected PDBFTSRestClient()
72 * Takes a PDBRestRequest object and returns a response upon execution
74 * @param pdbRestRequest
75 * the PDBRestRequest instance to be processed
76 * @return the pdbResponse object for the given request
79 @SuppressWarnings({ "unused", "unchecked" })
81 public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
86 String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
87 pdbRestRequest.getWantedFields());
88 int responseSize = (pdbRestRequest.getResponseSize() == 0)
89 ? getDefaultResponsePageSize()
90 : pdbRestRequest.getResponseSize();
91 int offSet = pdbRestRequest.getOffSet();
92 String sortParam = null;
93 if (pdbRestRequest.getFieldToSortBy() == null
94 || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
100 if (pdbRestRequest.getFieldToSortBy()
101 .equalsIgnoreCase("Resolution"))
103 sortParam = pdbRestRequest.getFieldToSortBy()
104 + (pdbRestRequest.isAscending() ? " asc" : " desc");
108 sortParam = pdbRestRequest.getFieldToSortBy()
109 + (pdbRestRequest.isAscending() ? " desc" : " asc");
113 String facetPivot = (pdbRestRequest.getFacetPivot() == null
114 || pdbRestRequest.getFacetPivot().isEmpty()) ? ""
115 : pdbRestRequest.getFacetPivot();
116 String facetPivotMinCount = String
117 .valueOf(pdbRestRequest.getFacetPivotMinCount());
119 String query = pdbRestRequest.getFieldToSearchBy()
120 + pdbRestRequest.getSearchTerm()
121 + (pdbRestRequest.isAllowEmptySeq() ? ""
122 : " AND molecule_sequence:['' TO *]")
123 + (pdbRestRequest.isAllowUnpublishedEntries() ? ""
124 : " AND status:REL");
126 // Build request parameters for the REST Request
128 // BH 2018 the trick here is to coerce the classes in Javascript to be
129 // different from the ones in Java yet still allow this to be correct for Java
131 Class<ClientResponse> clientResponseClass;
134 // JavaScript only -- coerce types to Java types for Java
135 client = (Client) (Object) new jalview.javascript.web.Client();
136 clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
145 client = Client.create(new DefaultClientConfig());
146 clientResponseClass = ClientResponse.class;
149 WebResource webResource;
150 if (pdbRestRequest.isFacet())
152 webResource = client.resource(PDB_SEARCH_ENDPOINT)
153 .queryParam("wt", "json").queryParam("fl", wantedFields)
154 .queryParam("rows", String.valueOf(responseSize))
155 .queryParam("q", query)
156 .queryParam("start", String.valueOf(offSet))
157 .queryParam("sort", sortParam).queryParam("facet", "true")
158 .queryParam("facet.pivot", facetPivot)
159 .queryParam("facet.pivot.mincount", facetPivotMinCount);
163 webResource = client.resource(PDB_SEARCH_ENDPOINT)
164 .queryParam("wt", "json").queryParam("fl", wantedFields)
165 .queryParam("rows", String.valueOf(responseSize))
166 .queryParam("start", String.valueOf(offSet))
167 .queryParam("q", query).queryParam("sort", sortParam);
170 URI uri = webResource.getURI();
172 System.out.println(uri);
174 // Execute the REST request
175 ClientResponse clientResponse = webResource
176 .accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
178 // Get the JSON string from the response object or directly from the
179 // client (JavaScript)
180 Map<String, Object> jsonObj = null;
181 String responseString = null;
183 System.out.println("query >>>>>>> " + pdbRestRequest.toString());
185 // Check the response status and report exception if one occurs
186 int responseStatus = clientResponse.getStatus();
187 switch (responseStatus)
192 jsonObj = clientResponse.getEntity(Map.class);
196 responseString = clientResponse.getEntity(String.class);
200 throw new Exception(parseJsonExceptionString(responseString));
203 getMessageByHTTPStatusCode(responseStatus, "PDB"));
206 // Process the response and return the result to the caller.
207 return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
208 } catch (Exception e)
210 if (e.getMessage()==null)
214 String exceptionMsg = e.getMessage();
215 if (exceptionMsg.contains("SocketException"))
217 // No internet connection
218 throw new Exception(MessageManager.getString(
219 "exception.unable_to_detect_internet_connection"));
221 else if (exceptionMsg.contains("UnknownHostException"))
223 // The server 'www.ebi.ac.uk' is unreachable
224 throw new Exception(MessageManager.formatMessage(
225 "exception.fts_server_unreachable", "PDB Solr"));
235 * Process error response from PDB server if/when one occurs.
237 * @param jsonResponse
238 * the JSON string containing error message from the server
239 * @return the processed error message from the JSON string
241 @SuppressWarnings("unchecked")
242 public static String parseJsonExceptionString(String jsonErrorResponse)
244 StringBuilder errorMessage = new StringBuilder(
245 "\n============= PDB Rest Client RunTime error =============\n");
249 // "responseHeader":{
253 // "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
254 // "fl":"pdb_id,title,experimental_method,resolution",
256 // "sort":"overall_quality desc",
259 // "response":{"numFound":1,"start":0,"docs":[
261 // "experimental_method":["X-ray diffraction"],
263 // "resolution":2.46,
264 // "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}]
269 Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(jsonErrorResponse);
270 Map<String, Object> errorResponse = (Map<String, Object>) jsonObj.get("error");
272 Map<String, Object> responseHeader = (Map<String, Object>) jsonObj
273 .get("responseHeader");
274 Map<String, Object> paramsObj = (Map<String, Object>) responseHeader.get("params");
275 String status = responseHeader.get("status").toString();
276 String message = errorResponse.get("msg").toString();
277 String query = paramsObj.get("q").toString();
278 String fl = paramsObj.get("fl").toString();
280 errorMessage.append("Status: ").append(status).append("\n");
281 errorMessage.append("Message: ").append(message).append("\n");
282 errorMessage.append("query: ").append(query).append("\n");
283 errorMessage.append("fl: ").append(fl).append("\n");
285 } catch (ParseException e)
289 return errorMessage.toString();
293 * Parses the JSON response string from PDB REST API. The response is dynamic
294 * hence, only fields specifically requested for in the 'wantedFields'
295 * parameter is fetched/processed
297 * @param pdbJsonResponseString
298 * the JSON string to be parsed
299 * @param pdbRestRequest
300 * the request object which contains parameters used to process the
304 public static FTSRestResponse parsePDBJsonResponse(
305 String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
307 return parsePDBJsonResponse(pdbJsonResponseString,
308 (Map<String, Object>) null, pdbRestRequest);
311 @SuppressWarnings("unchecked")
312 public static FTSRestResponse parsePDBJsonResponse(
313 String pdbJsonResponseString, Map<String, Object> jsonObj,
314 FTSRestRequest pdbRestRequest)
316 FTSRestResponse searchResult = new FTSRestResponse();
317 List<FTSData> result = null;
322 jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
324 Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj.get("response");
325 String queryTime = ((Map<String, Object>) jsonObj.get("responseHeader"))
326 .get("QTime").toString();
327 int numFound = Integer
328 .valueOf(pdbResponse.get("numFound").toString());
329 List<Object> docs = (List<Object>) pdbResponse.get("docs");
331 result = new ArrayList<FTSData>();
335 for (Iterator<Object> docIter = docs.iterator(); docIter
338 Map<String, Object> doc = (Map<String, Object>) docIter.next();
339 result.add(getFTSData(doc, pdbRestRequest));
342 searchResult.setNumberOfItemsFound(result.size());
343 searchResult.setResponseTime(queryTime);
344 searchResult.setSearchSummary(result);
346 } catch (ParseException e)
353 public static FTSData getFTSData(Map<String, Object> pdbJsonDoc,
354 FTSRestRequest request)
357 String primaryKey = null;
359 Object[] summaryRowData;
361 SequenceI associatedSequence;
363 Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
364 SequenceI associatedSeq = request.getAssociatedSequence();
366 summaryRowData = new Object[(associatedSeq != null)
367 ? diplayFields.size() + 1
368 : diplayFields.size()];
369 if (associatedSeq != null)
371 associatedSequence = associatedSeq;
372 summaryRowData[0] = associatedSequence;
376 for (FTSDataColumnI field : diplayFields)
378 //System.out.println("Field " + field);
379 String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
380 : pdbJsonDoc.get(field.getCode()).toString();
381 //System.out.println("Field Data : " + fieldData);
382 if (field.isPrimaryKeyColumn())
384 primaryKey = fieldData;
385 summaryRowData[colCounter++] = primaryKey;
387 else if (fieldData == null || fieldData.isEmpty())
389 summaryRowData[colCounter++] = null;
395 summaryRowData[colCounter++] = (field.getDataType()
396 .getDataTypeClass() == Integer.class)
397 ? Integer.valueOf(fieldData)
398 : (field.getDataType()
399 .getDataTypeClass() == Double.class)
400 ? Double.valueOf(fieldData)
401 : sanitiseData(fieldData);
402 } catch (Exception e)
405 System.out.println("offending value:" + fieldData);
410 final String primaryKey1 = primaryKey;
412 final Object[] summaryRowData1 = summaryRowData;
416 public Object[] getSummaryData()
418 return summaryRowData1;
422 public Object getPrimaryKey()
428 * Returns a string representation of this object;
431 public String toString()
433 StringBuilder summaryFieldValues = new StringBuilder();
434 for (Object summaryField : summaryRowData1)
436 summaryFieldValues.append(
437 summaryField == null ? " " : summaryField.toString())
440 return summaryFieldValues.toString();
444 * Returns hash code value for this object
447 public int hashCode()
449 return Objects.hash(primaryKey1, this.toString());
453 public boolean equals(Object that)
455 return this.toString().equals(that.toString());
460 private static String sanitiseData(String data)
462 String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
463 .replaceAll("\\[", "").replaceAll("\\]", "")
464 .replaceAll("\",\"", ", ").replaceAll("\"", "");
469 public String getColumnDataConfigFileName()
471 return "/fts/pdb_data_columns.txt";
474 public static FTSRestClientI getInstance()
476 if (instance == null)
478 instance = new PDBFTSRestClient();
483 private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
485 public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
487 if (allDefaultDisplayedStructureDataColumns == null
488 || allDefaultDisplayedStructureDataColumns.isEmpty())
490 allDefaultDisplayedStructureDataColumns = new ArrayList<>();
491 allDefaultDisplayedStructureDataColumns
492 .addAll(super.getAllDefaultDisplayedFTSDataColumns());
494 return allDefaultDisplayedStructureDataColumns;
497 public String[] getPreferencesColumnsFor(PreferenceSource source) {
498 String[] columnNames = null;
502 columnNames = new String[] { "", "Display", "Group" };
504 case STRUCTURE_CHOOSER:
505 columnNames = new String[] { "", "Display", "Group" };
508 columnNames = new String[] { "PDB Field", "Show in search summary",
509 "Show in structure summary" };