Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
UrlLinkTest	43	211	9	0	1.0100%	Show methods

Class UrlLinkTest

Class UrlLinkTest	Line # 43	Total Statements 211	Complexity 9	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	0.00	1.0 1.0100%
testUrlLinkCreationNoRegex() : void   testUrlLinkCreationNoRegex() : void	7070	29.029	1.01	0.00	1.0 1.0100%
testUrlLinkCreationWithRegex() : void   testUrlLinkCreationWithRegex() : void	114114	30.030	1.01	0.00	1.0 1.0100%
testMakeUrlNoRegex() : void   testMakeUrlNoRegex() : void	167167	10.010	1.01	0.00	1.0 1.0100%
testMakeUrlWithRegex() : void   testMakeUrlWithRegex() : void	191191	49.049	1.01	0.00	1.0 1.0100%
testCreateLinksFromNullSequence() : void   testCreateLinksFromNullSequence() : void	268268	10.010	1.01	0.00	1.0 1.0100%
testCreateLinksForNonDynamic() : void   testCreateLinksForNonDynamic() : void	289289	10.010	1.01	0.00	1.0 1.0100%
testCreateLinksFromSequence() : void   testCreateLinksFromSequence() : void	309309	61.061	1.01	0.00	1.0 1.0100%
testLinksWithTargets() : void   testLinksWithTargets() : void	414414	10.010	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.28181818	jalview.util.UrlLinkTest.testCreateLinksFromSequencejalview.util.UrlLinkTest.testCreateLinksFromSequence	1PASS
	0.22727273	jalview.util.UrlLinkTest.testMakeUrlWithRegexjalview.util.UrlLinkTest.testMakeUrlWithRegex	1PASS
	0.14090909	jalview.util.UrlLinkTest.testUrlLinkCreationWithRegexjalview.util.UrlLinkTest.testUrlLinkCreationWithRegex	1PASS
	0.13636364	jalview.util.UrlLinkTest.testUrlLinkCreationNoRegexjalview.util.UrlLinkTest.testUrlLinkCreationNoRegex	1PASS
	0.05	jalview.util.UrlLinkTest.testCreateLinksForNonDynamicjalview.util.UrlLinkTest.testCreateLinksForNonDynamic	1PASS
	0.05	jalview.util.UrlLinkTest.testLinksWithTargetsjalview.util.UrlLinkTest.testLinksWithTargets	1PASS
	0.05	jalview.util.UrlLinkTest.testMakeUrlNoRegexjalview.util.UrlLinkTest.testMakeUrlNoRegex	1PASS
	0.05	jalview.util.UrlLinkTest.testCreateLinksFromNullSequencejalview.util.UrlLinkTest.testCreateLinksFromNullSequence	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.util;
22
23		import static jalview.util.UrlConstants.DB_ACCESSION;
24		import static jalview.util.UrlConstants.SEQUENCE_ID;
25		import static org.testng.AssertJUnit.assertEquals;
26		import static org.testng.AssertJUnit.assertFalse;
27		import static org.testng.AssertJUnit.assertNull;
28		import static org.testng.AssertJUnit.assertTrue;
29
30		import jalview.datamodel.DBRefEntry;
31		import jalview.datamodel.DBRefSource;
32		import jalview.datamodel.Sequence;
33		import jalview.gui.JvOptionPane;
34
35		import java.util.ArrayList;
36		import java.util.LinkedHashMap;
37		import java.util.List;
38		import java.util.Map;
39
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.Test;
42
		100% Uncovered Elements: 0 (220) Complexity: 9 Complexity Density: 0.04
43		public class UrlLinkTest
44		{
45
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
46	1	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	1	JvOptionPane.setInteractiveMode(false);
50	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51		}
52
53		final static String DB = "Test";
54
55		final static String URL_PREFIX = "http://www.jalview.org/";
56
57		final static String URL_SUFFIX = "/blah";
58
59		final static String SEP = "|";
60
61		final static String DELIM = "$";
62
63		final static String REGEX_NESTED = "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=";
64
65		final static String REGEX_RUBBISH = "=/[0-9]++/=";
66
67		/**
68		* Test URL link creation when the input string has no regex
69		*/
		100% Uncovered Elements: 0 (29) Complexity: 1 Complexity Density: 0.03 1PASS
70	1	@Test(groups = { "Functional" })...
71		public void testUrlLinkCreationNoRegex()
72		{
73		// SEQUENCE_ID
74	1	UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
75		+ DELIM + URL_SUFFIX);
76	1	assertEquals(DB, ul.getTarget());
77	1	assertEquals(DB, ul.getLabel());
78	1	assertEquals(URL_PREFIX, ul.getUrlPrefix());
79	1	assertEquals(URL_SUFFIX, ul.getUrlSuffix());
80	1	assertTrue(ul.isDynamic());
81	1	assertFalse(ul.usesDBAccession());
82	1	assertNull(ul.getRegexReplace());
83	1	assertTrue(ul.isValid());
84	1	assertNull(ul.getInvalidMessage());
85
86		// DB_ACCESSION
87	1	ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
88		+ URL_SUFFIX);
89	1	assertEquals(DB, ul.getTarget());
90	1	assertEquals(DB, ul.getLabel());
91	1	assertEquals(URL_PREFIX, ul.getUrlPrefix());
92	1	assertEquals(URL_SUFFIX, ul.getUrlSuffix());
93	1	assertTrue(ul.isDynamic());
94	1	assertTrue(ul.usesDBAccession());
95	1	assertNull(ul.getRegexReplace());
96	1	assertTrue(ul.isValid());
97	1	assertNull(ul.getInvalidMessage());
98
99		// Not dynamic
100	1	ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1));
101	1	assertEquals(DB, ul.getTarget());
102	1	assertEquals(DB, ul.getLabel());
103	1	assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrlPrefix());
104	1	assertFalse(ul.isDynamic());
105	1	assertFalse(ul.usesDBAccession());
106	1	assertNull(ul.getRegexReplace());
107	1	assertTrue(ul.isValid());
108	1	assertNull(ul.getInvalidMessage());
109		}
110
111		/**
112		* Test URL link creation when the input string has regex
113		*/
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
114	1	@Test(groups = { "Functional" })...
115		public void testUrlLinkCreationWithRegex()
116		{
117		// SEQUENCE_ID
118	1	UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
119		+ REGEX_NESTED + DELIM + URL_SUFFIX);
120	1	assertEquals(DB, ul.getTarget());
121	1	assertEquals(DB, ul.getLabel());
122	1	assertEquals(URL_PREFIX, ul.getUrlPrefix());
123	1	assertEquals(URL_SUFFIX, ul.getUrlSuffix());
124	1	assertTrue(ul.isDynamic());
125	1	assertFalse(ul.usesDBAccession());
126	1	assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
127		ul.getRegexReplace());
128	1	assertTrue(ul.isValid());
129	1	assertNull(ul.getInvalidMessage());
130
131		// DB_ACCESSION
132	1	ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
133		+ REGEX_NESTED + DELIM + URL_SUFFIX);
134	1	assertEquals(DB, ul.getTarget());
135	1	assertEquals(DB, ul.getLabel());
136	1	assertEquals(URL_PREFIX, ul.getUrlPrefix());
137	1	assertEquals(URL_SUFFIX, ul.getUrlSuffix());
138	1	assertTrue(ul.isDynamic());
139	1	assertTrue(ul.usesDBAccession());
140	1	assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
141		ul.getRegexReplace());
142	1	assertTrue(ul.isValid());
143	1	assertNull(ul.getInvalidMessage());
144
145		// invalid regex
146	1	ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
147		+ REGEX_RUBBISH + DELIM + URL_SUFFIX);
148	1	assertEquals(DB, ul.getTarget());
149	1	assertEquals(DB, ul.getLabel());
150	1	assertEquals(URL_PREFIX, ul.getUrlPrefix());
151	1	assertEquals(URL_SUFFIX, ul.getUrlSuffix());
152	1	assertTrue(ul.isDynamic());
153	1	assertTrue(ul.usesDBAccession());
154	1	assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
155		ul.getRegexReplace());
156	1	assertFalse(ul.isValid());
157	1	assertEquals(
158		"Invalid Regular Expression : '"
159		+ REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2)
160		+ "'\n",
161		ul.getInvalidMessage());
162		}
163
164		/**
165		* Test construction of link by substituting sequence id or name
166		*/
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
167	1	@Test(groups = { "Functional" })...
168		public void testMakeUrlNoRegex()
169		{
170		// Single non-regex
171	1	UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
172		+ DELIM + URL_SUFFIX);
173	1	String idstring = "FER_CAPAA";
174	1	String[] urls = ul.makeUrls(idstring, true);
175
176	1	assertEquals(2, urls.length);
177	1	assertEquals(idstring, urls[0]);
178	1	assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
179
180	1	urls = ul.makeUrls(idstring, false);
181
182	1	assertEquals(2, urls.length);
183	1	assertEquals(idstring, urls[0]);
184	1	assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
185		}
186
187		/**
188		* Test construction of link by substituting sequence id or name using regular
189		* expression
190		*/
		100% Uncovered Elements: 0 (49) Complexity: 1 Complexity Density: 0.02 1PASS
191	1	@Test(groups = { "Functional" })...
192		public void testMakeUrlWithRegex()
193		{
194		// Unused regex
195	1	UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
196		+ REGEX_NESTED + DELIM + URL_SUFFIX);
197	1	String idstring = "FER_CAPAA";
198	1	String[] urls = ul.makeUrls(idstring, true);
199
200	1	assertEquals(2, urls.length);
201	1	assertEquals(idstring, urls[0]);
202	1	assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
203	1	assertTrue(ul.isValid());
204	1	assertNull(ul.getInvalidMessage());
205
206	1	urls = ul.makeUrls(idstring, false);
207
208	1	assertEquals(2, urls.length);
209	1	assertEquals(idstring, urls[0]);
210	1	assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
211	1	assertTrue(ul.isValid());
212	1	assertNull(ul.getInvalidMessage());
213
214		// nested regex
215	1	idstring = "Label:gi|9234|pdb|102L|A";
216	1	urls = ul.makeUrls(idstring, true);
217
218	1	assertEquals(2, urls.length);
219	1	assertEquals("9234", urls[0]);
220	1	assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]);
221	1	assertTrue(ul.isValid());
222	1	assertNull(ul.getInvalidMessage());
223
224	1	urls = ul.makeUrls(idstring, false);
225
226	1	assertEquals(2, urls.length);
227	1	assertEquals("9234", urls[0]);
228	1	assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]);
229	1	assertTrue(ul.isValid());
230	1	assertNull(ul.getInvalidMessage());
231
232		// unmatched regex
233	1	idstring = "this does not match";
234	1	urls = ul.makeUrls(idstring, true);
235
236	1	assertEquals(2, urls.length);
237	1	assertEquals(idstring, urls[0]);
238	1	assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
239	1	assertTrue(ul.isValid());
240	1	assertNull(ul.getInvalidMessage());
241
242	1	urls = ul.makeUrls(idstring, false);
243
244	1	assertEquals(2, urls.length);
245	1	assertEquals(idstring, urls[0]);
246	1	assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
247	1	assertTrue(ul.isValid());
248	1	assertNull(ul.getInvalidMessage());
249
250		// empty idstring
251	1	idstring = "";
252	1	urls = ul.makeUrls(idstring, true);
253
254	1	assertNull(urls);
255
256	1	urls = ul.makeUrls(idstring, false);
257
258	1	assertEquals(2, urls.length);
259	1	assertEquals("", urls[0]);
260	1	assertEquals(URL_PREFIX + URL_SUFFIX, urls[1]);
261	1	assertTrue(ul.isValid());
262	1	assertNull(ul.getInvalidMessage());
263		}
264
265		/**
266		* Test creating links with null sequence
267		*/
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
268	1	@Test(groups = { "Functional" })...
269		public void testCreateLinksFromNullSequence()
270		{
271	1	UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
272		+ DELIM + URL_SUFFIX);
273
274	1	Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
275	1	ul.createLinksFromSeq(null, linkset);
276
277	1	String key = DB + SEP + URL_PREFIX;
278	1	assertEquals(1, linkset.size());
279	1	assertTrue(linkset.containsKey(key));
280	1	assertEquals(DB, linkset.get(key).get(0));
281	1	assertEquals(DB, linkset.get(key).get(1));
282	1	assertEquals(null, linkset.get(key).get(2));
283	1	assertEquals(URL_PREFIX, linkset.get(key).get(3));
284		}
285
286		/**
287		* Test creating links with non-dynamic urlLink
288		*/
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
289	1	@Test(groups = { "Functional" })...
290		public void testCreateLinksForNonDynamic()
291		{
292	1	UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX);
293
294	1	Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
295	1	ul.createLinksFromSeq(null, linkset);
296
297	1	String key = DB + SEP + URL_PREFIX + URL_SUFFIX;
298	1	assertEquals(1, linkset.size());
299	1	assertTrue(linkset.containsKey(key));
300	1	assertEquals(DB, linkset.get(key).get(0));
301	1	assertEquals(DB, linkset.get(key).get(1));
302	1	assertEquals(null, linkset.get(key).get(2));
303	1	assertEquals(URL_PREFIX + URL_SUFFIX, linkset.get(key).get(3));
304		}
305
306		/**
307		* Test creating links
308		*/
		100% Uncovered Elements: 0 (61) Complexity: 1 Complexity Density: 0.02 1PASS
309	1	@Test(groups = { "Functional" })...
310		public void testCreateLinksFromSequence()
311		{
312
313		// create list of links and list of DBRefs
314	1	List<String> links = new ArrayList<String>();
315	1	List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
316
317		// links as might be added into Preferences | Connections dialog
318	1	links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
319		+ SEQUENCE_ID + "$");
320	1	links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
321		+ "$");
322	1	links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
323		+ DB_ACCESSION + "$");
324
325		// make seq0 dbrefs
326	1	refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
327	1	refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
328	1	refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
329	1	refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
330
331	1	Sequence seq0 = new Sequence("FER1", "AKPNGVL");
332
333		// add all the dbrefs to the sequence
334	1	seq0.addDBRef(refs.get(0));
335	1	seq0.addDBRef(refs.get(1));
336	1	seq0.addDBRef(refs.get(2));
337	1	seq0.addDBRef(refs.get(3));
338	1	seq0.createDatasetSequence();
339
340		// Test where link takes a sequence id as replacement
341	1	UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
342		+ DELIM + URL_SUFFIX);
343
344	1	Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
345	1	ul.createLinksFromSeq(seq0, linkset);
346
347	1	String key = seq0.getName() + SEP + URL_PREFIX + seq0.getName()
348		+ URL_SUFFIX;
349	1	assertEquals(1, linkset.size());
350	1	assertTrue(linkset.containsKey(key));
351	1	assertEquals(DB, linkset.get(key).get(0));
352	1	assertEquals(DB, linkset.get(key).get(1));
353	1	assertEquals(seq0.getName(), linkset.get(key).get(2));
354	1	assertEquals(URL_PREFIX + seq0.getName() + URL_SUFFIX, linkset.get(key)
355		.get(3));
356
357		// Test where link takes a db annotation id and only has one dbref
358	1	ul = new UrlLink(links.get(1));
359	1	linkset = new LinkedHashMap<String, List<String>>();
360	1	ul.createLinksFromSeq(seq0, linkset);
361
362	1	key = "P83527|http://www.uniprot.org/uniprot/P83527";
363	1	assertEquals(linkset.size(), 1);
364	1	assertTrue(linkset.containsKey(key));
365	1	assertEquals(DBRefSource.UNIPROT, linkset.get(key).get(0));
366	1	assertEquals(DBRefSource.UNIPROT + SEP + "P83527", linkset.get(key)
367		.get(1));
368	1	assertEquals("P83527", linkset.get(key).get(2));
369	1	assertEquals("http://www.uniprot.org/uniprot/P83527", linkset.get(key)
370		.get(3));
371
372		// Test where link takes a db annotation id and has multiple dbrefs
373	1	ul = new UrlLink(links.get(2));
374	1	linkset = new LinkedHashMap<String, List<String>>();
375	1	ul.createLinksFromSeq(seq0, linkset);
376	1	assertEquals(3, linkset.size());
377
378		// check each link made it in correctly
379	1	key = "IPR001041|http://www.ebi.ac.uk/interpro/entry/IPR001041";
380	1	assertTrue(linkset.containsKey(key));
381	1	assertEquals("INTERPRO", linkset.get(key).get(0));
382	1	assertEquals("INTERPRO" + SEP + "IPR001041", linkset.get(key).get(1));
383	1	assertEquals("IPR001041", linkset.get(key).get(2));
384	1	assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR001041", linkset
385		.get(key).get(3));
386
387	1	key = "IPR006058|http://www.ebi.ac.uk/interpro/entry/IPR006058";
388	1	assertTrue(linkset.containsKey(key));
389	1	assertEquals("INTERPRO", linkset.get(key).get(0));
390	1	assertEquals("INTERPRO" + SEP + "IPR006058", linkset.get(key).get(1));
391	1	assertEquals("IPR006058", linkset.get(key).get(2));
392	1	assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR006058", linkset
393		.get(key).get(3));
394
395	1	key = "IPR012675|http://www.ebi.ac.uk/interpro/entry/IPR012675";
396	1	assertTrue(linkset.containsKey(key));
397	1	assertEquals("INTERPRO", linkset.get(key).get(0));
398	1	assertEquals("INTERPRO" + SEP + "IPR012675", linkset.get(key).get(1));
399	1	assertEquals("IPR012675", linkset.get(key).get(2));
400	1	assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR012675", linkset
401		.get(key).get(3));
402
403		// Test where there are no matching dbrefs for the link
404	1	ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
405		+ URL_SUFFIX);
406	1	linkset = new LinkedHashMap<String, List<String>>();
407	1	ul.createLinksFromSeq(seq0, linkset);
408	1	assertTrue(linkset.isEmpty());
409		}
410
411		/**
412		* Test links where label and target are both included
413		*/
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
414	1	@Test(groups = { "Functional" })...
415		public void testLinksWithTargets()
416		{
417	1	UrlLink ul = new UrlLink(
418		"Protein Data Bank | http://www.identifiers.org/pdb/$"
419		+ DB_ACCESSION + "$" + " | pdb");
420
421	1	assertEquals("Protein Data Bank", ul.getLabel());
422	1	assertEquals("pdb", ul.getTarget());
423	1	assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$",
424		ul.getUrlWithToken());
425
426	1	assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$"
427		+ DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget());
428
429	1	ul = new UrlLink("Protein Data Bank",
430		"http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", "pdb");
431
432	1	assertEquals("Protein Data Bank", ul.getLabel());
433	1	assertEquals("pdb", ul.getTarget());
434	1	assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$",
435		ul.getUrlWithToken());
436
437	1	assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$"
438		+ DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget());
439
440		}
441
442		}