Clover icon

Coverage Report

  1. Project Clover database Thu Nov 7 2024 17:01:39 GMT
  2. Package jalview.util

File UrlLinkTest.java

 

Code metrics

0
223
10
1
463
324
10
0.04
22.3
10
1

Classes

Class Line # Actions
UrlLinkTest 44 223 10
0.00%
 

Contributing tests

No tests hitting this source file were found.

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.Comparator;
37    import java.util.LinkedHashMap;
38    import java.util.List;
39    import java.util.Map;
40   
41    import org.testng.annotations.BeforeClass;
42    import org.testng.annotations.Test;
43   
 
44    public class UrlLinkTest
45    {
46   
 
47  0 toggle @BeforeClass(alwaysRun = true)
48    public void setUpJvOptionPane()
49    {
50  0 JvOptionPane.setInteractiveMode(false);
51  0 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52    }
53   
54    final static String DB = "Test";
55   
56    final static String URL_PREFIX = "http://www.jalview.org/";
57   
58    final static String URL_SUFFIX = "/blah";
59   
60    final static String SEP = "|";
61   
62    final static String DELIM = "$";
63   
64    final static String REGEX_NESTED = "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=";
65   
66    final static String REGEX_RUBBISH = "=/[0-9]++/=";
67   
68    /**
69    * Test URL link creation when the input string has no regex
70    */
 
71  0 toggle @Test(groups = { "Functional" })
72    public void testUrlLinkCreationNoRegex()
73    {
74    // SEQUENCE_ID
75  0 UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
76    + DELIM + URL_SUFFIX);
77  0 assertEquals(DB, ul.getTarget());
78  0 assertEquals(DB, ul.getLabel());
79  0 assertEquals(URL_PREFIX, ul.getUrlPrefix());
80  0 assertEquals(URL_SUFFIX, ul.getUrlSuffix());
81  0 assertTrue(ul.isDynamic());
82  0 assertFalse(ul.usesDBAccession());
83  0 assertNull(ul.getRegexReplace());
84  0 assertTrue(ul.isValid());
85  0 assertNull(ul.getInvalidMessage());
86   
87    // DB_ACCESSION
88  0 ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
89    + URL_SUFFIX);
90  0 assertEquals(DB, ul.getTarget());
91  0 assertEquals(DB, ul.getLabel());
92  0 assertEquals(URL_PREFIX, ul.getUrlPrefix());
93  0 assertEquals(URL_SUFFIX, ul.getUrlSuffix());
94  0 assertTrue(ul.isDynamic());
95  0 assertTrue(ul.usesDBAccession());
96  0 assertNull(ul.getRegexReplace());
97  0 assertTrue(ul.isValid());
98  0 assertNull(ul.getInvalidMessage());
99   
100    // Not dynamic
101  0 ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1));
102  0 assertEquals(DB, ul.getTarget());
103  0 assertEquals(DB, ul.getLabel());
104  0 assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrlPrefix());
105  0 assertFalse(ul.isDynamic());
106  0 assertFalse(ul.usesDBAccession());
107  0 assertNull(ul.getRegexReplace());
108  0 assertTrue(ul.isValid());
109  0 assertNull(ul.getInvalidMessage());
110    }
111   
112    /**
113    * Test URL link creation when the input string has regex
114    */
 
115  0 toggle @Test(groups = { "Functional" })
116    public void testUrlLinkCreationWithRegex()
117    {
118    // SEQUENCE_ID
119  0 UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
120    + REGEX_NESTED + DELIM + URL_SUFFIX);
121  0 assertEquals(DB, ul.getTarget());
122  0 assertEquals(DB, ul.getLabel());
123  0 assertEquals(URL_PREFIX, ul.getUrlPrefix());
124  0 assertEquals(URL_SUFFIX, ul.getUrlSuffix());
125  0 assertTrue(ul.isDynamic());
126  0 assertFalse(ul.usesDBAccession());
127  0 assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
128    ul.getRegexReplace());
129  0 assertTrue(ul.isValid());
130  0 assertNull(ul.getInvalidMessage());
131   
132    // DB_ACCESSION
133  0 ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
134    + REGEX_NESTED + DELIM + URL_SUFFIX);
135  0 assertEquals(DB, ul.getTarget());
136  0 assertEquals(DB, ul.getLabel());
137  0 assertEquals(URL_PREFIX, ul.getUrlPrefix());
138  0 assertEquals(URL_SUFFIX, ul.getUrlSuffix());
139  0 assertTrue(ul.isDynamic());
140  0 assertTrue(ul.usesDBAccession());
141  0 assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
142    ul.getRegexReplace());
143  0 assertTrue(ul.isValid());
144  0 assertNull(ul.getInvalidMessage());
145   
146    // invalid regex
147  0 ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
148    + REGEX_RUBBISH + DELIM + URL_SUFFIX);
149  0 assertEquals(DB, ul.getTarget());
150  0 assertEquals(DB, ul.getLabel());
151  0 assertEquals(URL_PREFIX, ul.getUrlPrefix());
152  0 assertEquals(URL_SUFFIX, ul.getUrlSuffix());
153  0 assertTrue(ul.isDynamic());
154  0 assertTrue(ul.usesDBAccession());
155  0 assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
156    ul.getRegexReplace());
157  0 assertFalse(ul.isValid());
158  0 assertEquals("Invalid Regular Expression : '"
159    + REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2)
160    + "'\n", ul.getInvalidMessage());
161    }
162   
163    /**
164    * Test construction of link by substituting sequence id or name
165    */
 
166  0 toggle @Test(groups = { "Functional" })
167    public void testMakeUrlNoRegex()
168    {
169    // Single non-regex
170  0 UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
171    + DELIM + URL_SUFFIX);
172  0 String idstring = "FER_CAPAA";
173  0 String[] urls = ul.makeUrls(idstring, true);
174   
175  0 assertEquals(2, urls.length);
176  0 assertEquals(idstring, urls[0]);
177  0 assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
178   
179  0 urls = ul.makeUrls(idstring, false);
180   
181  0 assertEquals(2, urls.length);
182  0 assertEquals(idstring, urls[0]);
183  0 assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
184    }
185   
186    /**
187    * Test construction of link by substituting sequence id or name using regular
188    * expression
189    */
 
190  0 toggle @Test(groups = { "Functional" })
191    public void testMakeUrlWithRegex()
192    {
193    // Unused regex
194  0 UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
195    + REGEX_NESTED + DELIM + URL_SUFFIX);
196  0 String idstring = "FER_CAPAA";
197  0 String[] urls = ul.makeUrls(idstring, true);
198   
199  0 assertEquals(2, urls.length);
200  0 assertEquals(idstring, urls[0]);
201  0 assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
202  0 assertTrue(ul.isValid());
203  0 assertNull(ul.getInvalidMessage());
204   
205  0 urls = ul.makeUrls(idstring, false);
206   
207  0 assertEquals(2, urls.length);
208  0 assertEquals(idstring, urls[0]);
209  0 assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
210  0 assertTrue(ul.isValid());
211  0 assertNull(ul.getInvalidMessage());
212   
213    // nested regex
214  0 idstring = "Label:gi|9234|pdb|102L|A";
215  0 urls = ul.makeUrls(idstring, true);
216   
217  0 assertEquals(2, urls.length);
218  0 assertEquals("9234", urls[0]);
219  0 assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]);
220  0 assertTrue(ul.isValid());
221  0 assertNull(ul.getInvalidMessage());
222   
223  0 urls = ul.makeUrls(idstring, false);
224   
225  0 assertEquals(2, urls.length);
226  0 assertEquals("9234", urls[0]);
227  0 assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]);
228  0 assertTrue(ul.isValid());
229  0 assertNull(ul.getInvalidMessage());
230   
231    // unmatched regex
232  0 idstring = "this does not match";
233  0 urls = ul.makeUrls(idstring, true);
234   
235  0 assertEquals(2, urls.length);
236  0 assertEquals(idstring, urls[0]);
237  0 assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
238  0 assertTrue(ul.isValid());
239  0 assertNull(ul.getInvalidMessage());
240   
241  0 urls = ul.makeUrls(idstring, false);
242   
243  0 assertEquals(2, urls.length);
244  0 assertEquals(idstring, urls[0]);
245  0 assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
246  0 assertTrue(ul.isValid());
247  0 assertNull(ul.getInvalidMessage());
248   
249    // empty idstring
250  0 idstring = "";
251  0 urls = ul.makeUrls(idstring, true);
252   
253  0 assertNull(urls);
254   
255  0 urls = ul.makeUrls(idstring, false);
256   
257  0 assertEquals(2, urls.length);
258  0 assertEquals("", urls[0]);
259  0 assertEquals(URL_PREFIX + URL_SUFFIX, urls[1]);
260  0 assertTrue(ul.isValid());
261  0 assertNull(ul.getInvalidMessage());
262    }
263   
264    /**
265    * Test creating links with null sequence
266    */
 
267  0 toggle @Test(groups = { "Functional" })
268    public void testCreateLinksFromNullSequence()
269    {
270  0 UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
271    + DELIM + URL_SUFFIX);
272   
273  0 Map<String, List<String>> linkset = new LinkedHashMap<>();
274  0 ul.createLinksFromSeq(null, linkset);
275   
276  0 String key = DB + SEP + URL_PREFIX;
277  0 assertEquals(1, linkset.size());
278  0 assertTrue(linkset.containsKey(key));
279  0 assertEquals(DB, linkset.get(key).get(0));
280  0 assertEquals(DB, linkset.get(key).get(1));
281  0 assertEquals(null, linkset.get(key).get(2));
282  0 assertEquals(URL_PREFIX, linkset.get(key).get(3));
283    }
284   
285    /**
286    * Test creating links with non-dynamic urlLink
287    */
 
288  0 toggle @Test(groups = { "Functional" })
289    public void testCreateLinksForNonDynamic()
290    {
291  0 UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX);
292   
293  0 Map<String, List<String>> linkset = new LinkedHashMap<>();
294  0 ul.createLinksFromSeq(null, linkset);
295   
296  0 String key = DB + SEP + URL_PREFIX + URL_SUFFIX;
297  0 assertEquals(1, linkset.size());
298  0 assertTrue(linkset.containsKey(key));
299  0 assertEquals(DB, linkset.get(key).get(0));
300  0 assertEquals(DB, linkset.get(key).get(1));
301  0 assertEquals(null, linkset.get(key).get(2));
302  0 assertEquals(URL_PREFIX + URL_SUFFIX, linkset.get(key).get(3));
303    }
304   
305    /**
306    * Test creating links
307    */
 
308  0 toggle @Test(groups = { "Functional" })
309    public void testCreateLinksFromSequence()
310    {
311   
312    // create list of links and list of DBRefs
313  0 List<String> links = new ArrayList<>();
314  0 List<DBRefEntry> refs = new ArrayList<>();
315   
316    // links as might be added into Preferences | Connections dialog
317  0 links.add(
318    "EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
319    + SEQUENCE_ID + "$");
320  0 links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
321    + "$");
322  0 links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
323    + DB_ACCESSION + "$");
324   
325    // make seq0 dbrefs
326  0 refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
327  0 refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
328  0 refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
329  0 refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
330   
331  0 Sequence seq0 = new Sequence("FER1", "AKPNGVL");
332   
333    // add all the dbrefs to the sequence
334  0 seq0.addDBRef(refs.get(0));
335  0 seq0.addDBRef(refs.get(1));
336  0 seq0.addDBRef(refs.get(2));
337  0 seq0.addDBRef(refs.get(3));
338  0 seq0.createDatasetSequence();
339   
340    // Test where link takes a sequence id as replacement
341  0 UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
342    + DELIM + URL_SUFFIX);
343   
344  0 Map<String, List<String>> linkset = new LinkedHashMap<>();
345  0 ul.createLinksFromSeq(seq0, linkset);
346   
347  0 String key = seq0.getName() + SEP + URL_PREFIX + seq0.getName()
348    + URL_SUFFIX;
349  0 assertEquals(1, linkset.size());
350  0 assertTrue(linkset.containsKey(key));
351  0 assertEquals(DB, linkset.get(key).get(0));
352  0 assertEquals(DB, linkset.get(key).get(1));
353  0 assertEquals(seq0.getName(), linkset.get(key).get(2));
354  0 assertEquals(URL_PREFIX + seq0.getName() + URL_SUFFIX,
355    linkset.get(key).get(3));
356   
357    // Test where link takes a db annotation id and only has one dbref
358  0 ul = new UrlLink(links.get(1));
359  0 linkset = new LinkedHashMap<>();
360  0 ul.createLinksFromSeq(seq0, linkset);
361   
362  0 key = "P83527|http://www.uniprot.org/uniprot/P83527";
363  0 assertEquals(linkset.size(), 1);
364  0 assertTrue(linkset.containsKey(key));
365  0 assertEquals(DBRefSource.UNIPROT, linkset.get(key).get(0));
366  0 assertEquals(DBRefSource.UNIPROT + SEP + "P83527",
367    linkset.get(key).get(1));
368  0 assertEquals("P83527", linkset.get(key).get(2));
369  0 assertEquals("http://www.uniprot.org/uniprot/P83527",
370    linkset.get(key).get(3));
371   
372    // Test where link takes a db annotation id and has multiple dbrefs
373  0 ul = new UrlLink(links.get(2));
374  0 linkset = new LinkedHashMap<>();
375  0 ul.createLinksFromSeq(seq0, linkset);
376  0 assertEquals(3, linkset.size());
377   
378    // check each link made it in correctly
379  0 key = "IPR001041|http://www.ebi.ac.uk/interpro/entry/IPR001041";
380  0 assertTrue(linkset.containsKey(key));
381  0 assertEquals("INTERPRO", linkset.get(key).get(0));
382  0 assertEquals("INTERPRO" + SEP + "IPR001041", linkset.get(key).get(1));
383  0 assertEquals("IPR001041", linkset.get(key).get(2));
384  0 assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR001041",
385    linkset.get(key).get(3));
386   
387  0 key = "IPR006058|http://www.ebi.ac.uk/interpro/entry/IPR006058";
388  0 assertTrue(linkset.containsKey(key));
389  0 assertEquals("INTERPRO", linkset.get(key).get(0));
390  0 assertEquals("INTERPRO" + SEP + "IPR006058", linkset.get(key).get(1));
391  0 assertEquals("IPR006058", linkset.get(key).get(2));
392  0 assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR006058",
393    linkset.get(key).get(3));
394   
395  0 key = "IPR012675|http://www.ebi.ac.uk/interpro/entry/IPR012675";
396  0 assertTrue(linkset.containsKey(key));
397  0 assertEquals("INTERPRO", linkset.get(key).get(0));
398  0 assertEquals("INTERPRO" + SEP + "IPR012675", linkset.get(key).get(1));
399  0 assertEquals("IPR012675", linkset.get(key).get(2));
400  0 assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR012675",
401    linkset.get(key).get(3));
402   
403    // Test where there are no matching dbrefs for the link
404  0 ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
405    + URL_SUFFIX);
406  0 linkset = new LinkedHashMap<>();
407  0 ul.createLinksFromSeq(seq0, linkset);
408  0 assertTrue(linkset.isEmpty());
409    }
410   
411    /**
412    * Test links where label and target are both included
413    */
 
414  0 toggle @Test(groups = { "Functional" })
415    public void testLinksWithTargets()
416    {
417  0 UrlLink ul = new UrlLink(
418    "Protein Data Bank | http://www.identifiers.org/pdb/$"
419    + DB_ACCESSION + "$" + " | pdb");
420   
421  0 assertEquals("Protein Data Bank", ul.getLabel());
422  0 assertEquals("pdb", ul.getTarget());
423  0 assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$",
424    ul.getUrlWithToken());
425   
426  0 assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$"
427    + DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget());
428   
429  0 ul = new UrlLink("Protein Data Bank",
430    "http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", "pdb");
431   
432  0 assertEquals("Protein Data Bank", ul.getLabel());
433  0 assertEquals("pdb", ul.getTarget());
434  0 assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$",
435    ul.getUrlWithToken());
436   
437  0 assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$"
438    + DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget());
439   
440    }
441   
 
442  0 toggle @Test(groups = { "Functional" })
443    public void testLinkComparator()
444    {
445  0 Comparator<String> c = UrlLink.LINK_COMPARATOR;
446  0 assertEquals(0, c.compare(null, null));
447  0 assertEquals(0, c.compare(null, "x"));
448  0 assertEquals(0, c.compare("y", null));
449   
450    /*
451    * SEQUENCE_ID templates should come before DB_ACCESSION templates
452    */
453  0 String dbRefUrl = "Cath|http://www.cathdb.info/version/v4_2_0/superfamily/$DB_ACCESSION$";
454  0 String seqIdUrl = "EBI|https://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
455  0 assertTrue(c.compare(seqIdUrl, dbRefUrl) < 0);
456  0 assertTrue(c.compare(dbRefUrl, seqIdUrl) > 0);
457   
458  0 String interpro = "Interpro|https://www.ebi.ac.uk/interpro/entry/$DB_ACCESSION$";
459  0 String prosite = "ProSite|https://prosite.expasy.org/PS00197";
460  0 assertTrue(c.compare(interpro, prosite) < 0);
461  0 assertTrue(c.compare(prosite, interpro) > 0);
462    }
463    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 7 2024 17:02:19 GMT using coverage data from Thu Jan 1 1970 01:00:00 GMT.
  • OpenClover is free and open-source software.