Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PDBFTSRestClient	56	125	51	0.3020833430.2%	Show methods

Class PDBFTSRestClient

Class PDBFTSRestClient	Line # 56	Total Statements 125	Complexity 51	TOTAL Coverage 0.3020833430.2%
PDBFTSRestClient()   PDBFTSRestClient()	6363	0.00	1.01	-1.0 -1.0 -
executeRequest(FTSRestRequest) : FTSRestResponse   executeRequest(FTSRestRequest) : FTSRestResponse	7575	46.046	19.019	0.5277778 0.527777852.8%
parseJsonExceptionString(String) : String   parseJsonExceptionString(String) : String	233233	16.016	2.02	0.1875 0.187518.8%
parsePDBJsonResponse(String,FTSRestRequest) : FTSRestResponse   parsePDBJsonResponse(String,FTSRestRequest) : FTSRestResponse	296296	1.01	1.01	0.0 0.00%
parsePDBJsonResponse(String,Map<String, Object>,FTSRestRequest) : FTSRestResponse   parsePDBJsonResponse(String,Map<String, Object>,FTSRestRequest) : FTSRestResponse	303303	19.019	5.05	0.0 0.00%
getSummaryData() : Object[]   getSummaryData() : Object[]	402402	1.01	1.01	0.0 0.00%
getPrimaryKey() : Object   getPrimaryKey() : Object	408408	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	417417	4.04	2.02	0.0 0.00%
hashCode() : int   hashCode() : int	433433	1.01	1.01	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	439439	1.01	1.01	0.0 0.00%
getFTSData(Map<String, Object>,FTSRestRequest) : FTSData   getFTSData(Map<String, Object>,FTSRestRequest) : FTSData	342342	25.025	10.010	0.0 0.00%
sanitiseData(String) : String   sanitiseData(String) : String	447447	2.02	1.01	0.0 0.00%
getColumnDataConfigFileName() : String   getColumnDataConfigFileName() : String	455455	1.01	1.01	1.0 1.0100%
getInstance() : FTSRestClientI   getInstance() : FTSRestClientI	461461	3.03	2.02	1.0 1.0100%
getAllDefaultDisplayedStructureDataColumns() : Collection<FTSDataColumnI>   getAllDefaultDisplayedStructureDataColumns() : Collection<FTSDataColumnI>	472472	4.04	3.03	0.8333333 0.833333383.3%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.078125	jalview.gui.StructureChooserTest.populateFilterComboBoxTestjalview.gui.StructureChooserTest.populateFilterComboBoxTest	1PASS
	0.020833334	jalview.fts.service.pdb.PDBFTSRestClientTest.getPDBIdColumIndexTestjalview.fts.service.pdb.PDBFTSRestClientTest.getPDBIdColumIndexTest	1PASS
	0.020833334	jalview.fts.service.pdb.PDBFTSRestClientTest.getPDBDocFieldsAsCommaDelimitedStringTestjalview.fts.service.pdb.PDBFTSRestClientTest.getPDBDocFieldsAsCommaDelimitedStringTest	1PASS
	0.020833334	jalview.fts.service.pdb.PDBFTSPanelTest.populateCmbSearchTargetOptionsTestjalview.fts.service.pdb.PDBFTSPanelTest.populateCmbSearchTargetOptionsTest	1PASS

 

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.pdb;
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		import java.util.Objects;
30
31		import javax.ws.rs.core.MediaType;
32
33		import org.json.simple.parser.ParseException;
34
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;
39
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;
50
51		/**
52		* A rest client for querying the Search endpoint of the PDB API
53		*
54		* @author tcnofoegbu
55		*/
		30.2% Uncovered Elements: 134 (192) Complexity: 51 Complexity Density: 0.41
56		public class PDBFTSRestClient extends FTSRestClient
57		{
58
59		private static FTSRestClientI instance = null;
60
61		public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?";
62
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
63	1	protected PDBFTSRestClient()...
64		{
65		}
66
67		/**
68		* Takes a PDBRestRequest object and returns a response upon execution
69		*
70		* @param pdbRestRequest
71		* the PDBRestRequest instance to be processed
72		* @return the pdbResponse object for the given request
73		* @throws Exception
74		*/
		52.8% Uncovered Elements: 34 (72) Complexity: 19 Complexity Density: 0.41
75	1	@SuppressWarnings({ "unused", "unchecked" })...
76		@Override
77		public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
78		throws Exception
79		{
80	1	try
81		{
82	1	String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
83		pdbRestRequest.getWantedFields());
84	1	int responseSize = (pdbRestRequest.getResponseSize() == 0)
85		? getDefaultResponsePageSize()
86		: pdbRestRequest.getResponseSize();
87	1	int offSet = pdbRestRequest.getOffSet();
88	1	String sortParam = null;
89	1	if (pdbRestRequest.getFieldToSortBy() == null
90		|| pdbRestRequest.getFieldToSortBy().trim().isEmpty())
91		{
92	0	sortParam = "";
93		}
94		else
95		{
96	1	if (pdbRestRequest.getFieldToSortBy()
97		.equalsIgnoreCase("Resolution"))
98		{
99	0	sortParam = pdbRestRequest.getFieldToSortBy()
100	0	+ (pdbRestRequest.isAscending() ? " asc" : " desc");
101		}
102		else
103		{
104	1	sortParam = pdbRestRequest.getFieldToSortBy()
105	1	+ (pdbRestRequest.isAscending() ? " desc" : " asc");
106		}
107		}
108
109	1	String facetPivot = (pdbRestRequest.getFacetPivot() == null
110		|| pdbRestRequest.getFacetPivot().isEmpty()) ? ""
111		: pdbRestRequest.getFacetPivot();
112	1	String facetPivotMinCount = String
113		.valueOf(pdbRestRequest.getFacetPivotMinCount());
114
115	1	String query = pdbRestRequest.getFieldToSearchBy()
116		+ pdbRestRequest.getSearchTerm()
117	1	+ (pdbRestRequest.isAllowEmptySeq() ? ""
118		: " AND molecule_sequence:['' TO *]")
119	1	+ (pdbRestRequest.isAllowUnpublishedEntries() ? ""
120		: " AND status:REL");
121
122		// Build request parameters for the REST Request
123
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
126	1	Client client;
127	1	Class<ClientResponse> clientResponseClass;
128	1	if (Platform.isJS())
129		{
130		// JavaScript only -- coerce types to Java types for Java
131	0	client = (Client) (Object) new jalview.javascript.web.Client();
132	0	clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
133		}
134		else
135		/**
136		* Java only
137		*
138		* @j2sIgnore
139		*/
140		{
141	1	client = Client.create(new DefaultClientConfig());
142	1	clientResponseClass = ClientResponse.class;
143		}
144
145	1	WebResource webResource;
146	1	if (pdbRestRequest.isFacet())
147		{
148	0	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);
156		}
157		else
158		{
159	1	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);
164		}
165
166	1	URI uri = webResource.getURI();
167
168		// System.out.println(uri);
169
170		// Execute the REST request
171	1	ClientResponse clientResponse = webResource
172		.accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
173
174		// Get the JSON string from the response object or directly from the
175		// client (JavaScript)
176	1	Map<String, Object> jsonObj = null;
177	1	String responseString = null;
178
179		// System.out.println("query >>>>>>> " + pdbRestRequest.toString());
180
181		// Check the response status and report exception if one occurs
182	1	int responseStatus = clientResponse.getStatus();
183	1	switch (responseStatus)
184		{
185	0	case 200:
186	0	if (Platform.isJS())
187		{
188	0	jsonObj = clientResponse.getEntity(Map.class);
189		}
190		else
191		{
192	0	responseString = clientResponse.getEntity(String.class);
193		}
194	0	break;
195	1	case 400:
196	1	throw new Exception(parseJsonExceptionString(responseString));
197	0	default:
198	0	throw new Exception(
199		getMessageByHTTPStatusCode(responseStatus, "PDB"));
200		}
201
202		// Process the response and return the result to the caller.
203	0	return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
204		} catch (Exception e)
205		{
206	1	String exceptionMsg = e.getMessage();
207	0	if (exceptionMsg.contains("SocketException"))
208		{
209		// No internet connection
210	0	throw new Exception(MessageManager.getString(
211		"exception.unable_to_detect_internet_connection"));
212		}
213	0	else if (exceptionMsg.contains("UnknownHostException"))
214		{
215		// The server 'www.ebi.ac.uk' is unreachable
216	0	throw new Exception(MessageManager.formatMessage(
217		"exception.fts_server_unreachable", "PDB Solr"));
218		}
219		else
220		{
221	0	throw e;
222		}
223		}
224		}
225
226		/**
227		* Process error response from PDB server if/when one occurs.
228		*
229		* @param jsonResponse
230		* the JSON string containing error message from the server
231		* @return the processed error message from the JSON string
232		*/
		18.8% Uncovered Elements: 13 (16) Complexity: 2 Complexity Density: 0.12
233	1	@SuppressWarnings("unchecked")...
234		public static String parseJsonExceptionString(String jsonErrorResponse)
235		{
236	1	StringBuilder errorMessage = new StringBuilder(
237		"\n============= PDB Rest Client RunTime error =============\n");
238
239
240		// {
241		// "responseHeader":{
242		// "status":0,
243		// "QTime":0,
244		// "params":{
245		// "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
246		// "fl":"pdb_id,title,experimental_method,resolution",
247		// "start":"0",
248		// "sort":"overall_quality desc",
249		// "rows":"500",
250		// "wt":"json"}},
251		// "response":{"numFound":1,"start":0,"docs":[
252		// {
253		// "experimental_method":["X-ray diffraction"],
254		// "pdb_id":"4zhp",
255		// "resolution":2.46,
256		// "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}]
257		// }}
258		//
259	1	try
260		{
261	1	Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(jsonErrorResponse);
262	0	Map<String, Object> errorResponse = (Map<String, Object>) jsonObj.get("error");
263
264	0	Map<String, Object> responseHeader = (Map<String, Object>) jsonObj
265		.get("responseHeader");
266	0	Map<String, Object> paramsObj = (Map<String, Object>) responseHeader.get("params");
267	0	String status = responseHeader.get("status").toString();
268	0	String message = errorResponse.get("msg").toString();
269	0	String query = paramsObj.get("q").toString();
270	0	String fl = paramsObj.get("fl").toString();
271
272	0	errorMessage.append("Status: ").append(status).append("\n");
273	0	errorMessage.append("Message: ").append(message).append("\n");
274	0	errorMessage.append("query: ").append(query).append("\n");
275	0	errorMessage.append("fl: ").append(fl).append("\n");
276
277		} catch (ParseException e)
278		{
279	0	e.printStackTrace();
280		}
281	0	return errorMessage.toString();
282		}
283
284		/**
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
288		*
289		* @param pdbJsonResponseString
290		* the JSON string to be parsed
291		* @param pdbRestRequest
292		* the request object which contains parameters used to process the
293		* JSON string
294		* @return
295		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
296	0	public static FTSRestResponse parsePDBJsonResponse(...
297		String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
298		{
299	0	return parsePDBJsonResponse(pdbJsonResponseString,
300		(Map<String, Object>) null, pdbRestRequest);
301		}
302
		0% Uncovered Elements: 25 (25) Complexity: 5 Complexity Density: 0.26
303	0	@SuppressWarnings("unchecked")...
304		public static FTSRestResponse parsePDBJsonResponse(
305		String pdbJsonResponseString, Map<String, Object> jsonObj,
306		FTSRestRequest pdbRestRequest)
307		{
308	0	FTSRestResponse searchResult = new FTSRestResponse();
309	0	List<FTSData> result = null;
310	0	try
311		{
312	0	if (jsonObj == null)
313		{
314	0	jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
315		}
316	0	Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj.get("response");
317	0	String queryTime = ((Map<String, Object>) jsonObj.get("responseHeader"))
318		.get("QTime").toString();
319	0	int numFound = Integer
320		.valueOf(pdbResponse.get("numFound").toString());
321	0	if (numFound > 0)
322		{
323	0	result = new ArrayList<>();
324	0	List<Object> docs = (List<Object>) pdbResponse.get("docs");
325	0	for (Iterator<Object> docIter = docs.iterator(); docIter
326		.hasNext();)
327		{
328	0	Map<String, Object> doc = (Map<String, Object>) docIter.next();
329	0	result.add(getFTSData(doc, pdbRestRequest));
330		}
331	0	searchResult.setNumberOfItemsFound(numFound);
332	0	searchResult.setResponseTime(queryTime);
333	0	searchResult.setSearchSummary(result);
334		}
335		} catch (ParseException e)
336		{
337	0	e.printStackTrace();
338		}
339	0	return searchResult;
340		}
341
		0% Uncovered Elements: 39 (39) Complexity: 10 Complexity Density: 0.4
342	0	public static FTSData getFTSData(Map<String, Object> pdbJsonDoc,...
343		FTSRestRequest request)
344		{
345
346	0	String primaryKey = null;
347
348	0	Object[] summaryRowData;
349
350	0	SequenceI associatedSequence;
351
352	0	Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
353	0	SequenceI associatedSeq = request.getAssociatedSequence();
354	0	int colCounter = 0;
355	0	summaryRowData = new Object[(associatedSeq != null)
356		? diplayFields.size() + 1
357		: diplayFields.size()];
358	0	if (associatedSeq != null)
359		{
360	0	associatedSequence = associatedSeq;
361	0	summaryRowData[0] = associatedSequence;
362	0	colCounter = 1;
363		}
364
365	0	for (FTSDataColumnI field : diplayFields)
366		{
367	0	String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
368		: pdbJsonDoc.get(field.getCode()).toString();
369	0	if (field.isPrimaryKeyColumn())
370		{
371	0	primaryKey = fieldData;
372	0	summaryRowData[colCounter++] = primaryKey;
373		}
374	0	else if (fieldData == null || fieldData.isEmpty())
375		{
376	0	summaryRowData[colCounter++] = null;
377		}
378		else
379		{
380	0	try
381		{
382	0	summaryRowData[colCounter++] = (field.getDataType()
383		.getDataTypeClass() == Integer.class)
384		? Integer.valueOf(fieldData)
385	0	: (field.getDataType()
386		.getDataTypeClass() == Double.class)
387		? Double.valueOf(fieldData)
388		: sanitiseData(fieldData);
389		} catch (Exception e)
390		{
391	0	e.printStackTrace();
392	0	System.out.println("offending value:" + fieldData);
393		}
394		}
395		}
396
397	0	final String primaryKey1 = primaryKey;
398
399	0	final Object[] summaryRowData1 = summaryRowData;
400	0	return new FTSData()
401		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
402	0	@Override...
403		public Object[] getSummaryData()
404		{
405	0	return summaryRowData1;
406		}
407
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
408	0	@Override...
409		public Object getPrimaryKey()
410		{
411	0	return primaryKey1;
412		}
413
414		/**
415		* Returns a string representation of this object;
416		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
417	0	@Override...
418		public String toString()
419		{
420	0	StringBuilder summaryFieldValues = new StringBuilder();
421	0	for (Object summaryField : summaryRowData1)
422		{
423	0	summaryFieldValues.append(
424	0	summaryField == null ? " " : summaryField.toString())
425		.append("\t");
426		}
427	0	return summaryFieldValues.toString();
428		}
429
430		/**
431		* Returns hash code value for this object
432		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
433	0	@Override...
434		public int hashCode()
435		{
436	0	return Objects.hash(primaryKey1, this.toString());
437		}
438
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
439	0	@Override...
440		public boolean equals(Object that)
441		{
442	0	return this.toString().equals(that.toString());
443		}
444		};
445		}
446
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
447	0	private static String sanitiseData(String data)...
448		{
449	0	String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
450		.replaceAll("\\[", "").replaceAll("\\]", "")
451		.replaceAll("\",\"", ", ").replaceAll("\"", "");
452	0	return cleanData;
453		}
454
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
455	1	@Override...
456		public String getColumnDataConfigFileName()
457		{
458	1	return "/fts/pdb_data_columns.txt";
459		}
460
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
461	19	public static FTSRestClientI getInstance()...
462		{
463	19	if (instance == null)
464		{
465	1	instance = new PDBFTSRestClient();
466		}
467	19	return instance;
468		}
469
470		private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
471
		83.3% Uncovered Elements: 1 (6) Complexity: 3 Complexity Density: 0.75
472	1	public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()...
473		{
474	1	if (allDefaultDisplayedStructureDataColumns == null
475		|| allDefaultDisplayedStructureDataColumns.isEmpty())
476		{
477	1	allDefaultDisplayedStructureDataColumns = new ArrayList<>();
478	1	allDefaultDisplayedStructureDataColumns
479		.addAll(super.getAllDefaultDisplayedFTSDataColumns());
480		}
481	1	return allDefaultDisplayedStructureDataColumns;
482		}
483
484
485		}