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Coverage Report

  1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.fts.service.threedbeacons

File TDBeaconsFTSRestClient.java

 

Coverage histogram

../../../../img/srcFileCovDistChart8.png
21% of files have more coverage

Code metrics

40
108
12
1
380
273
43
0.4
9
12
3.58

Classes

Class Line # Actions
TDBeaconsFTSRestClient 52 108 43
0.7575%
 

Contributing tests

This file is covered by 45 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.fts.service.threedbeacons;
22   
23    import java.net.URI;
24    import java.util.ArrayList;
25    import java.util.Collection;
26    import java.util.Iterator;
27    import java.util.List;
28    import java.util.Map;
29   
30    import javax.ws.rs.core.MediaType;
31   
32    import org.json.simple.parser.ParseException;
33   
34    import com.sun.jersey.api.client.Client;
35    import com.sun.jersey.api.client.ClientResponse;
36    import com.sun.jersey.api.client.WebResource;
37    import com.sun.jersey.api.client.config.DefaultClientConfig;
38   
39    import jalview.datamodel.SequenceI;
40    import jalview.fts.api.FTSData;
41    import jalview.fts.api.FTSDataColumnI;
42    import jalview.fts.api.FTSRestClientI;
43    import jalview.fts.api.StructureFTSRestClientI;
44    import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
45    import jalview.fts.core.FTSRestClient;
46    import jalview.fts.core.FTSRestRequest;
47    import jalview.fts.core.FTSRestResponse;
48    import jalview.util.JSONUtils;
49    import jalview.util.MessageManager;
50    import jalview.util.Platform;
51   
 
52    public class TDBeaconsFTSRestClient extends FTSRestClient
53    implements StructureFTSRestClientI
54    {
55    /**
56    * production server URI
57    */
58    private static String TDB_PROD_API = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
59   
60    /**
61    * dev server URI
62    */
63    private static String TDB_DEV_API = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
64   
65    private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API;
66   
67    public static FTSRestClientI instance = null;
68   
 
69  5 toggle protected TDBeaconsFTSRestClient()
70    {
71    }
72   
 
73  14 toggle @SuppressWarnings("unchecked")
74    @Override
75    public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
76    throws Exception
77    {
78  14 try
79    {
80  14 String query = tdbRestRequest.getSearchTerm();
81  14 Client client;
82  14 Class<ClientResponse> clientResponseClass;
83  14 if (Platform.isJS())
84    {
85    // JavaScript only
86  0 client = (Client) (Object) new jalview.javascript.web.Client();
87  0 clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
88    }
89    else
90    /**
91    * Java only
92    *
93    * @j2sIgnore
94    */
95    {
96  14 client = Client.create(new DefaultClientConfig());
97  14 clientResponseClass = ClientResponse.class;
98    }
99   
100  14 WebResource webResource;
101  14 webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query);
102   
103  14 URI uri = webResource.getURI();
104  14 jalview.bin.Console.outPrintln(uri.toString());
105   
106    // Execute the REST request
107  14 ClientResponse clientResponse;
108  14 if (isMocked())
109    {
110  14 clientResponse = null;
111    }
112    else
113    {
114  0 clientResponse = webResource.accept(MediaType.APPLICATION_JSON)
115    .get(clientResponseClass);
116    }
117   
118    // Get the JSON string from the response object or directly from the
119    // client (JavaScript)
120  14 Map<String, Object> jsonObj = null;
121  14 String responseString = null;
122   
123    // Check the response status and report exception if one occurs
124  14 int responseStatus = isMocked()
125  14 ? (mockQueries.containsKey(query) ? 200 : 404)
126    : clientResponse.getStatus();
127  14 switch (responseStatus)
128    {
129    // if success
130  13 case 200:
131  13 if (Platform.isJS())
132    {
133  0 jsonObj = clientResponse.getEntity(Map.class);
134    }
135    else
136    {
137  13 responseString = isMocked() ? mockQueries.get(query)
138    : clientResponse.getEntity(String.class);
139    }
140  13 break;
141  0 case 400:
142  0 throw new Exception(parseJsonExceptionString(responseString));
143  1 case 404:
144  1 return emptyTDBeaconsJsonResponse();
145  0 default:
146  0 throw new Exception(
147    getMessageByHTTPStatusCode(responseStatus, "3DBeacons"));
148    }
149    // Process the response and return the result to the caller.
150  13 return parseTDBeaconsJsonResponse(responseString, jsonObj,
151    tdbRestRequest);
152    } catch (Exception e)
153    {
154  0 String exceptionMsg = e.getMessage();
155  0 if (exceptionMsg != null)
156    {
157  0 if (exceptionMsg.contains("SocketException"))
158    {
159    // No internet connection
160  0 throw new Exception(MessageManager.getString(
161    "exception.unable_to_detect_internet_connection"));
162    }
163  0 else if (exceptionMsg.contains("UnknownHostException"))
164    {
165    // The server is unreachable
166  0 throw new Exception(MessageManager.formatMessage(
167    "exception.fts_server_unreachable", "3DB Hub"));
168    }
169    }
170  0 throw e;
171   
172    }
173   
174    }
175   
176    /**
177    * returns response for when the 3D-Beacons service doesn't have a record for
178    * the given query - in 2.11.2 this triggers a failover to the PDBe FTS
179    *
180    * @return null
181    */
 
182  1 toggle private FTSRestResponse emptyTDBeaconsJsonResponse()
183    {
184  1 return null;
185    }
186   
 
187  0 toggle public String setSearchTerm(String term)
188    {
189  0 return term;
190    }
191   
 
192  0 toggle public static FTSRestResponse parseTDBeaconsJsonResponse(
193    String tdbJsonResponseString, FTSRestRequest tdbRestRequest)
194    {
195  0 return parseTDBeaconsJsonResponse(tdbJsonResponseString,
196    (Map<String, Object>) null, tdbRestRequest);
197    }
198   
 
199  13 toggle @SuppressWarnings("unchecked")
200    public static FTSRestResponse parseTDBeaconsJsonResponse(
201    String tdbJsonResponseString, Map<String, Object> jsonObj,
202    FTSRestRequest tdbRestRequest)
203    {
204  13 FTSRestResponse searchResult = new FTSRestResponse();
205  13 List<FTSData> result = null;
206   
207  13 try
208    {
209  13 if (jsonObj == null)
210    {
211  13 jsonObj = (Map<String, Object>) JSONUtils
212    .parse(tdbJsonResponseString);
213    }
214   
215  13 Object uniprot_entry = jsonObj.get("uniprot_entry");
216    // TODO: decide if anything from uniprot_entry needs to be reported via
217    // the FTSRestResponse object
218    // Arnaud added seqLength = (Long) ((Map<String, Object>)
219    // jsonObj.get("uniprot_entry")).get("sequence_length");
220   
221  13 List<Object> structures = (List<Object>) jsonObj.get("structures");
222  13 result = new ArrayList<>();
223   
224  13 int numFound = 0;
225  5106 for (Iterator<Object> strucIter = structures.iterator(); strucIter
226    .hasNext();)
227    {
228  5093 Map<String, Object> structure = (Map<String, Object>) strucIter
229    .next();
230  5093 result.add(getFTSData(structure, tdbRestRequest));
231  5093 numFound++;
232    }
233   
234  13 searchResult.setNumberOfItemsFound(numFound);
235  13 searchResult.setSearchSummary(result);
236   
237    } catch (ParseException e)
238    {
239  0 e.printStackTrace();
240    }
241  13 return searchResult;
242    }
243   
 
244  5093 toggle private static FTSData getFTSData(
245    Map<String, Object> tdbJsonStructureSummary,
246    FTSRestRequest tdbRequest)
247    {
248  5093 String primaryKey = null;
249  5093 Object[] summaryRowData;
250   
251  5093 SequenceI associatedSequence;
252   
253  5093 Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
254  5093 SequenceI associatedSeq = tdbRequest.getAssociatedSequence();
255  5093 int colCounter = 0;
256  5093 summaryRowData = new Object[(associatedSeq != null)
257    ? displayFields.size() + 1
258    : displayFields.size()];
259  5093 if (associatedSeq != null)
260    {
261  5030 associatedSequence = associatedSeq;
262  5030 summaryRowData[0] = associatedSequence;
263  5030 colCounter = 1;
264    }
265  5093 Map<String, Object> tdbJsonStructure = (Map<String, Object>) tdbJsonStructureSummary
266    .get("summary");
267  5093 for (FTSDataColumnI field : displayFields)
268    {
269  75702 String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
270    ? " "
271    : tdbJsonStructure.get(field.getCode()).toString();
272    // jalview.bin.Console.outPrintln("Field : " + field + " Data : " +
273    // fieldData);
274  75702 if (field.isPrimaryKeyColumn())
275    {
276  5093 primaryKey = fieldData;
277  5093 summaryRowData[colCounter++] = primaryKey;
278    }
279  70609 else if (fieldData == null || fieldData.trim().isEmpty())
280    {
281  20088 summaryRowData[colCounter++] = null;
282    }
283    else
284    {
285  50521 try
286    {
287  50521 summaryRowData[colCounter++] = (field.getDataType()
288    .getDataTypeClass() == Integer.class)
289    ? Integer.valueOf(fieldData)
290  40461 : (field.getDataType()
291    .getDataTypeClass() == Double.class)
292    ? Double.valueOf(fieldData)
293    : fieldData;
294    } catch (Exception e)
295    {
296    // e.printStackTrace();
297  0 jalview.bin.Console
298    .outPrintln("offending value:" + fieldData + fieldData);
299    }
300    }
301    }
302  5093 final String primaryKey1 = primaryKey;
303  5093 final Object[] summaryRowData1 = summaryRowData;
304   
305  5093 return new TDB_FTSData(primaryKey, tdbJsonStructure, summaryRowData1);
306    }
307   
308    // private static FTSData getFTSData(Map<String, Object> doc,
309    // FTSRestRequest tdbRestRequest)
310    // {
311    // String primaryKey = null;
312    //
313    // Object[] summaryRowData;
314    //
315    // Collection<FTSDataColumnI> displayFields =
316    // tdbRestRequest.getWantedFields();
317    // int colCounter = 0;
318    // summaryRowData = new Object[displayFields.size() + 1];
319    //
320    // return null;
321    // }
322   
 
323  0 toggle private String parseJsonExceptionString(String jsonErrorString)
324    {
325    // TODO Auto-generated method stub
326  0 return null;
327    }
328   
 
329  5 toggle @Override
330    public String getColumnDataConfigFileName()
331    {
332  5 return "/fts/tdbeacons_data_columns.txt";
333    }
334   
 
335  166 toggle public static FTSRestClientI getInstance()
336    {
337  166 if (instance == null)
338    {
339  5 instance = new TDBeaconsFTSRestClient();
340    }
341  166 return instance;
342    }
343   
344    private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
345   
 
346  70 toggle @Override
347    public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
348    {
349  70 if (allDefaultDisplayedStructureDataColumns == null
350    || allDefaultDisplayedStructureDataColumns.isEmpty())
351    {
352  5 allDefaultDisplayedStructureDataColumns = new ArrayList<>();
353  5 allDefaultDisplayedStructureDataColumns
354    .addAll(super.getAllDefaultDisplayedFTSDataColumns());
355    }
356  70 return allDefaultDisplayedStructureDataColumns;
357    }
358   
 
359  71 toggle @Override
360    public String[] getPreferencesColumnsFor(PreferenceSource source)
361    {
362  71 String[] columnNames = null;
363  71 switch (source)
364    {
365  1 case SEARCH_SUMMARY:
366  1 columnNames = new String[] { "", "Display", "Group" };
367  1 break;
368  70 case STRUCTURE_CHOOSER:
369  70 columnNames = new String[] { "", "Display", "Group" };
370  70 break;
371  0 case PREFERENCES:
372  0 columnNames = new String[] { "3DB Beacons Field",
373    "Show in search summary", "Show in structure summary" };
374  0 break;
375  0 default:
376  0 break;
377    }
378  71 return columnNames;
379    }
380    }
  • Report generated by OpenClover v 4.4.1 on Fri Dec 6 2024 13:54:25 GMT using coverage data from Fri Dec 6 2024 13:54:13 GMT.
  • OpenClover is free and open-source software.