Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
UniProtFTSRestClient	46	88	44	0.00%	Show methods

Class UniProtFTSRestClient

Class UniProtFTSRestClient	Line # 46	Total Statements 88	Complexity 44	TOTAL Coverage 0.00%
<clinit>, line 50()   <clinit>, line 50()	5050	1.01	1.01	0.0 0.00%
UniProtFTSRestClient()   UniProtFTSRestClient()	5959	2.02	1.01	0.0 0.00%
executeRequest(FTSRestRequest) : FTSRestResponse   executeRequest(FTSRestRequest) : FTSRestResponse	6666	32.032	10.010	0.0 0.00%
isAdvancedQuery(String) : boolean   isAdvancedQuery(String) : boolean	171171	3.03	9.09	0.0 0.00%
parseUniprotResponse(String,FTSRestRequest,int) : FTSRestResponse   parseUniprotResponse(String,FTSRestRequest,int) : FTSRestResponse	183183	17.017	6.06	0.0 0.00%
getSummaryData() : Object[]   getSummaryData() : Object[]	305305	1.01	1.01	0.0 0.00%
getPrimaryKey() : Object   getPrimaryKey() : Object	311311	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	320320	4.04	2.02	0.0 0.00%
hashCode() : int   hashCode() : int	336336	1.01	1.01	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	342342	1.01	1.01	0.0 0.00%
getFTSData(String,FTSRestRequest) : FTSData   getFTSData(String,FTSRestRequest) : FTSData	252252	21.021	8.08	0.0 0.00%
getInstance() : FTSRestClientI   getInstance() : FTSRestClientI	350350	3.03	2.02	0.0 0.00%
getColumnDataConfigFileName() : String   getColumnDataConfigFileName() : String	359359	1.01	1.01	0.0 0.00%

 

Contributing tests

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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
22		package jalview.fts.service.uniprot;
23
24		import jalview.bin.Cache;
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.MessageManager;
32		import jalview.util.Platform;
33
34		import java.util.ArrayList;
35		import java.util.Collection;
36		import java.util.List;
37		import java.util.Objects;
38
39		import javax.ws.rs.core.MediaType;
40
41		import com.sun.jersey.api.client.Client;
42		import com.sun.jersey.api.client.ClientResponse;
43		import com.sun.jersey.api.client.WebResource;
44		import com.sun.jersey.api.client.config.DefaultClientConfig;
45
		0% Uncovered Elements: 137 (137) Complexity: 44 Complexity Density: 0.5
46		public class UniProtFTSRestClient extends FTSRestClient
47		{
48		private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
49
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	static...
51		{
52	0	Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
53		}
54
55		private static FTSRestClientI instance = null;
56
57		public final String uniprotSearchEndpoint;
58
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
59	0	public UniProtFTSRestClient()...
60		{
61	0	super();
62	0	uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
63		DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";
64		}
65
		0% Uncovered Elements: 48 (48) Complexity: 10 Complexity Density: 0.31
66	0	@SuppressWarnings("unchecked")...
67		@Override
68		public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest)
69		throws Exception
70		{
71	0	try
72		{
73	0	String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
74		uniprotRestRequest.getWantedFields());
75	0	int responseSize = (uniprotRestRequest.getResponseSize() == 0)
76		? getDefaultResponsePageSize()
77		: uniprotRestRequest.getResponseSize();
78
79	0	int offSet = uniprotRestRequest.getOffSet();
80	0	String query;
81	0	if (isAdvancedQuery(uniprotRestRequest.getSearchTerm()))
82		{
83	0	query = uniprotRestRequest.getSearchTerm();
84		}
85		else
86		{
87	0	query = uniprotRestRequest.getFieldToSearchBy()
88		.equalsIgnoreCase("Search All")
89		? uniprotRestRequest.getSearchTerm()
90		+ " or mnemonic:"
91		+ uniprotRestRequest.getSearchTerm()
92		: uniprotRestRequest.getFieldToSearchBy() + ":"
93		+ uniprotRestRequest.getSearchTerm();
94		}
95
96		// BH 2018 the trick here is to coerce the classes in Javascript to be
97		// different from the ones in Java yet still allow this to be correct for
98		// Java
99	0	Client client;
100	0	Class<ClientResponse> clientResponseClass;
101	0	if (Platform.isJS())
102		{
103		// JavaScript only -- coerce types to Java types for Java
104	0	client = (Client) (Object) new jalview.javascript.web.Client();
105	0	clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
106		}
107		else
108		/**
109		* Java only
110		*
111		* @j2sIgnore
112		*/
113		{
114		// Java only
115	0	client = Client.create(new DefaultClientConfig());
116	0	clientResponseClass = ClientResponse.class;
117		}
118
119	0	WebResource webResource = null;
120	0	webResource = client.resource(uniprotSearchEndpoint)
121		.queryParam("format", "tab")
122		.queryParam("columns", wantedFields)
123		.queryParam("limit", String.valueOf(responseSize))
124		.queryParam("offset", String.valueOf(offSet))
125		.queryParam("sort", "score").queryParam("query", query);
126		// Execute the REST request
127	0	ClientResponse clientResponse = webResource
128		.accept(MediaType.TEXT_PLAIN).get(clientResponseClass);
129	0	String uniProtTabDelimittedResponseString = clientResponse
130		.getEntity(String.class);
131		// Make redundant objects eligible for garbage collection to conserve
132		// memory
133		// System.out.println(">>>>> response : "
134		// + uniProtTabDelimittedResponseString);
135	0	if (clientResponse.getStatus() != 200)
136		{
137	0	String errorMessage = getMessageByHTTPStatusCode(
138		clientResponse.getStatus(), "Uniprot");
139	0	throw new Exception(errorMessage);
140
141		}
142	0	int xTotalResults = Platform.isJS() ? 1
143		: Integer.valueOf(clientResponse.getHeaders()
144		.get("X-Total-Results").get(0));
145	0	clientResponse = null;
146	0	client = null;
147	0	return parseUniprotResponse(uniProtTabDelimittedResponseString,
148		uniprotRestRequest, xTotalResults);
149		} catch (Exception e)
150		{
151	0	String exceptionMsg = e.getMessage();
152	0	if (exceptionMsg.contains("SocketException"))
153		{
154		// No internet connection
155	0	throw new Exception(MessageManager.getString(
156		"exception.unable_to_detect_internet_connection"));
157		}
158	0	else if (exceptionMsg.contains("UnknownHostException"))
159		{
160		// The server 'http://www.uniprot.org' is unreachable
161	0	throw new Exception(MessageManager.formatMessage(
162		"exception.fts_server_unreachable", "Uniprot"));
163		}
164		else
165		{
166	0	throw e;
167		}
168		}
169		}
170
		0% Uncovered Elements: 5 (5) Complexity: 9 Complexity Density: 3
171	0	public boolean isAdvancedQuery(String query)...
172		{
173	0	if (query.contains(" AND ") || query.contains(" OR ")
174		|| query.contains(" NOT ") || query.contains(" ! ")
175		|| query.contains(" || ") || query.contains(" && ")
176		|| query.contains(":") || query.contains("-"))
177		{
178	0	return true;
179		}
180	0	return false;
181		}
182
		0% Uncovered Elements: 23 (23) Complexity: 6 Complexity Density: 0.35
183	0	public FTSRestResponse parseUniprotResponse(...
184		String uniProtTabDelimittedResponseString,
185		FTSRestRequest uniprotRestRequest, int xTotalResults)
186		{
187	0	FTSRestResponse searchResult = new FTSRestResponse();
188	0	List<FTSData> result = null;
189	0	if (uniProtTabDelimittedResponseString == null
190		|| uniProtTabDelimittedResponseString.trim().isEmpty())
191		{
192	0	searchResult.setNumberOfItemsFound(0);
193	0	return searchResult;
194		}
195	0	String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
196	0	if (foundDataRow != null && foundDataRow.length > 0)
197		{
198	0	result = new ArrayList<>();
199	0	boolean firstRow = true;
200	0	for (String dataRow : foundDataRow)
201		{
202		// The first data row is usually the header data. This should be
203		// filtered out from the rest of the data See: JAL-2485
204	0	if (firstRow)
205		{
206	0	firstRow = false;
207	0	continue;
208		}
209		// System.out.println(dataRow);
210	0	result.add(getFTSData(dataRow, uniprotRestRequest));
211		}
212	0	searchResult.setNumberOfItemsFound(xTotalResults);
213	0	searchResult.setSearchSummary(result);
214		}
215	0	return searchResult;
216		}
217
218		// /**
219		// * Takes a collection of FTSDataColumnI and converts its 'code' values into
220		// a
221		// * tab delimited string.
222		// *
223		// * @param dataColumnFields
224		// * the collection of FTSDataColumnI to process
225		// * @return the generated comma delimited string from the supplied
226		// * FTSDataColumnI collection
227		// */
228		// private String getDataColumnsFieldsAsTabDelimitedString(
229		// Collection<FTSDataColumnI> dataColumnFields)
230		// {
231		// String result = "";
232		// if (dataColumnFields != null && !dataColumnFields.isEmpty())
233		// {
234		// StringBuilder returnedFields = new StringBuilder();
235		// for (FTSDataColumnI field : dataColumnFields)
236		// {
237		// if (field.getName().equalsIgnoreCase("Uniprot Id"))
238		// {
239		// returnedFields.append("\t").append("Entry");
240		// }
241		// else
242		// {
243		// returnedFields.append("\t").append(field.getName());
244		// }
245		// }
246		// returnedFields.deleteCharAt(0);
247		// result = returnedFields.toString();
248		// }
249		// return result;
250		// }
251
		0% Uncovered Elements: 29 (29) Complexity: 8 Complexity Density: 0.38
252	0	public static FTSData getFTSData(String tabDelimittedDataStr,...
253		FTSRestRequest request)
254		{
255	0	String primaryKey = null;
256
257	0	Object[] summaryRowData;
258
259	0	Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
260	0	int colCounter = 0;
261	0	summaryRowData = new Object[diplayFields.size()];
262	0	String[] columns = tabDelimittedDataStr.split("\t");
263	0	for (FTSDataColumnI field : diplayFields)
264		{
265	0	try
266		{
267	0	String fieldData = columns[colCounter];
268	0	if (field.isPrimaryKeyColumn())
269		{
270	0	primaryKey = fieldData;
271	0	summaryRowData[colCounter++] = primaryKey;
272		}
273	0	else if (fieldData == null || fieldData.isEmpty())
274		{
275	0	summaryRowData[colCounter++] = null;
276		}
277		else
278		{
279	0	try
280		{
281	0	summaryRowData[colCounter++] = (field.getDataType()
282		.getDataTypeClass() == Integer.class)
283		? Integer.valueOf(fieldData.replace(",", ""))
284	0	: (field.getDataType()
285		.getDataTypeClass() == Double.class)
286		? Double.valueOf(fieldData)
287		: fieldData;
288		} catch (Exception e)
289		{
290	0	e.printStackTrace();
291	0	System.out.println("offending value:" + fieldData);
292		}
293		}
294		} catch (Exception e)
295		{
296		// e.printStackTrace();
297		}
298		}
299
300	0	final String primaryKey1 = primaryKey;
301
302	0	final Object[] summaryRowData1 = summaryRowData;
303	0	return new FTSData()
304		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
305	0	@Override...
306		public Object[] getSummaryData()
307		{
308	0	return summaryRowData1;
309		}
310
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
311	0	@Override...
312		public Object getPrimaryKey()
313		{
314	0	return primaryKey1;
315		}
316
317		/**
318		* Returns a string representation of this object;
319		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
320	0	@Override...
321		public String toString()
322		{
323	0	StringBuilder summaryFieldValues = new StringBuilder();
324	0	for (Object summaryField : summaryRowData1)
325		{
326	0	summaryFieldValues.append(
327	0	summaryField == null ? " " : summaryField.toString())
328		.append("\t");
329		}
330	0	return summaryFieldValues.toString();
331		}
332
333		/**
334		* Returns hash code value for this object
335		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
336	0	@Override...
337		public int hashCode()
338		{
339	0	return Objects.hash(primaryKey1, this.toString());
340		}
341
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
342	0	@Override...
343		public boolean equals(Object that)
344		{
345	0	return this.toString().equals(that.toString());
346		}
347		};
348		}
349
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
350	0	public static FTSRestClientI getInstance()...
351		{
352	0	if (instance == null)
353		{
354	0	instance = new UniProtFTSRestClient();
355		}
356	0	return instance;
357		}
358
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
359	0	@Override...
360		public String getColumnDataConfigFileName()
361		{
362	0	return "/fts/uniprot_data_columns.txt";
363		}
364
365		}