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.bin.Jalview;
24 import jalview.datamodel.SequenceI;
25 import jalview.fts.api.FTSData;
26 import jalview.fts.api.FTSDataColumnI;
27 import jalview.fts.api.FTSRestClientI;
28 import jalview.fts.core.FTSRestClient;
29 import jalview.fts.core.FTSRestRequest;
30 import jalview.fts.core.FTSRestResponse;
31 import jalview.util.JSONUtils;
32 import jalview.util.MessageManager;
33 import jalview.util.Platform;
36 import java.util.ArrayList;
37 import java.util.Collection;
38 import java.util.Iterator;
39 import java.util.List;
41 import java.util.Objects;
43 import javax.ws.rs.core.MediaType;
45 import org.json.simple.parser.ParseException;
47 import com.sun.jersey.api.client.Client;
48 import com.sun.jersey.api.client.ClientResponse;
49 import com.sun.jersey.api.client.WebResource;
50 import com.sun.jersey.api.client.config.DefaultClientConfig;
53 * A rest client for querying the Search endpoint of the PDB API
57 public class PDBFTSRestClient extends FTSRestClient
60 public static FTSRestClientI getInstance()
62 Jalview j = Jalview.getInstance();
63 return (j.pdbFTSRestClient == null
64 ? j.pdbFTSRestClient = new PDBFTSRestClient()
65 : j.pdbFTSRestClient);
68 public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?";
70 protected PDBFTSRestClient()
75 * Takes a PDBRestRequest object and returns a response upon execution
77 * @param pdbRestRequest
78 * the PDBRestRequest instance to be processed
79 * @return the pdbResponse object for the given request
82 @SuppressWarnings({ "unused", "unchecked" })
84 public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
89 String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
90 pdbRestRequest.getWantedFields());
91 int responseSize = (pdbRestRequest.getResponseSize() == 0)
92 ? getDefaultResponsePageSize()
93 : pdbRestRequest.getResponseSize();
94 int offSet = pdbRestRequest.getOffSet();
95 String sortParam = null;
96 if (pdbRestRequest.getFieldToSortBy() == null
97 || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
103 if (pdbRestRequest.getFieldToSortBy()
104 .equalsIgnoreCase("Resolution"))
106 sortParam = pdbRestRequest.getFieldToSortBy()
107 + (pdbRestRequest.isAscending() ? " asc" : " desc");
111 sortParam = pdbRestRequest.getFieldToSortBy()
112 + (pdbRestRequest.isAscending() ? " desc" : " asc");
116 String facetPivot = (pdbRestRequest.getFacetPivot() == null
117 || pdbRestRequest.getFacetPivot().isEmpty()) ? ""
118 : pdbRestRequest.getFacetPivot();
119 String facetPivotMinCount = String
120 .valueOf(pdbRestRequest.getFacetPivotMinCount());
122 String query = pdbRestRequest.getFieldToSearchBy()
123 + pdbRestRequest.getSearchTerm()
124 + (pdbRestRequest.isAllowEmptySeq() ? ""
125 : " AND molecule_sequence:['' TO *]")
126 + (pdbRestRequest.isAllowUnpublishedEntries() ? ""
127 : " AND status:REL");
129 // Build request parameters for the REST Request
131 // BH 2018 the trick here is to coerce the classes in Javascript to be
132 // different from the ones in Java yet still allow this to be correct for Java
134 Class<ClientResponse> clientResponseClass;
137 // JavaScript only -- coerce types to Java types for Java
138 client = (Client) (Object) new jalview.javascript.web.Client();
139 clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
148 client = Client.create(new DefaultClientConfig());
149 clientResponseClass = ClientResponse.class;
152 WebResource webResource;
153 if (pdbRestRequest.isFacet())
155 webResource = client.resource(PDB_SEARCH_ENDPOINT)
156 .queryParam("wt", "json").queryParam("fl", wantedFields)
157 .queryParam("rows", String.valueOf(responseSize))
158 .queryParam("q", query)
159 .queryParam("start", String.valueOf(offSet))
160 .queryParam("sort", sortParam).queryParam("facet", "true")
161 .queryParam("facet.pivot", facetPivot)
162 .queryParam("facet.pivot.mincount", facetPivotMinCount);
166 webResource = client.resource(PDB_SEARCH_ENDPOINT)
167 .queryParam("wt", "json").queryParam("fl", wantedFields)
168 .queryParam("rows", String.valueOf(responseSize))
169 .queryParam("start", String.valueOf(offSet))
170 .queryParam("q", query).queryParam("sort", sortParam);
173 URI uri = webResource.getURI();
175 System.out.println(uri);
177 // Execute the REST request
178 ClientResponse clientResponse = webResource
179 .accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
181 int status = clientResponse.getStatus();
183 // Get the JSON string from the response object or directly from the
184 // client (JavaScript)
185 Map<String, Object> jsonObj = (Platform.isJS() && status == 200
186 ? clientResponse.getEntity(Map.class)
188 String responseString = (jsonObj == null
189 ? clientResponse.getEntity(String.class)
192 // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
194 // Check the response status and report exception if one occurs
200 throw new Exception(parseJsonExceptionString(responseString));
202 throw new Exception(getMessageByHTTPStatusCode(status, "PDB"));
205 // Make redundant objects eligible for garbage collection to conserve
207 clientResponse = null;
210 // Process the response and return the result to the caller.
211 return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
212 } catch (Exception e)
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());
331 result = new ArrayList<>();
332 List<Object> docs = (List<Object>) pdbResponse.get("docs");
333 for (Iterator<Object> docIter = docs.iterator(); docIter
336 Map<String, Object> doc = (Map<String, Object>) docIter.next();
337 result.add(getFTSData(doc, pdbRestRequest));
339 searchResult.setNumberOfItemsFound(numFound);
340 searchResult.setResponseTime(queryTime);
341 searchResult.setSearchSummary(result);
343 } catch (ParseException e)
350 public static FTSData getFTSData(Map<String, Object> pdbJsonDoc,
351 FTSRestRequest request)
354 String primaryKey = null;
356 Object[] summaryRowData;
358 SequenceI associatedSequence;
360 Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
361 SequenceI associatedSeq = request.getAssociatedSequence();
363 summaryRowData = new Object[(associatedSeq != null)
364 ? diplayFields.size() + 1
365 : diplayFields.size()];
366 if (associatedSeq != null)
368 associatedSequence = associatedSeq;
369 summaryRowData[0] = associatedSequence;
373 for (FTSDataColumnI field : diplayFields)
375 String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
376 : pdbJsonDoc.get(field.getCode()).toString();
377 if (field.isPrimaryKeyColumn())
379 primaryKey = fieldData;
380 summaryRowData[colCounter++] = primaryKey;
382 else if (fieldData == null || fieldData.isEmpty())
384 summaryRowData[colCounter++] = null;
390 summaryRowData[colCounter++] = (field.getDataType()
391 .getDataTypeClass() == Integer.class)
392 ? Integer.valueOf(fieldData)
393 : (field.getDataType()
394 .getDataTypeClass() == Double.class)
395 ? Double.valueOf(fieldData)
396 : sanitiseData(fieldData);
397 } catch (Exception e)
400 System.out.println("offending value:" + fieldData);
405 final String primaryKey1 = primaryKey;
407 final Object[] summaryRowData1 = summaryRowData;
411 public Object[] getSummaryData()
413 return summaryRowData1;
417 public Object getPrimaryKey()
423 * Returns a string representation of this object;
426 public String toString()
428 StringBuilder summaryFieldValues = new StringBuilder();
429 for (Object summaryField : summaryRowData1)
431 summaryFieldValues.append(
432 summaryField == null ? " " : summaryField.toString())
435 return summaryFieldValues.toString();
439 * Returns hash code value for this object
442 public int hashCode()
444 return Objects.hash(primaryKey1, this.toString());
448 public boolean equals(Object that)
450 return this.toString().equals(that.toString());
455 private static String sanitiseData(String data)
457 String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
458 .replaceAll("\\[", "").replaceAll("\\]", "")
459 .replaceAll("\",\"", ", ").replaceAll("\"", "");
464 public String getColumnDataConfigFileName()
466 return "/fts/pdb_data_columns.txt";
469 private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
471 public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
473 if (allDefaultDisplayedStructureDataColumns == null
474 || allDefaultDisplayedStructureDataColumns.isEmpty())
476 allDefaultDisplayedStructureDataColumns = new ArrayList<>();
477 allDefaultDisplayedStructureDataColumns
478 .addAll(super.getAllDefaultDisplayedFTSDataColumns());
480 return allDefaultDisplayedStructureDataColumns;