2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ws.sifts;
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertTrue;
26 import jalview.api.DBRefEntryI;
27 import jalview.bin.Cache;
28 import jalview.datamodel.DBRefEntry;
29 import jalview.datamodel.DBRefSource;
30 import jalview.datamodel.Sequence;
31 import jalview.datamodel.SequenceI;
32 import jalview.gui.JvOptionPane;
33 import jalview.io.DataSourceType;
34 import jalview.structure.StructureMapping;
35 import jalview.xml.binding.sifts.Entry.Entity;
38 import java.io.IOException;
39 import java.util.ArrayList;
40 import java.util.HashMap;
41 import java.util.Iterator;
44 import org.testng.Assert;
45 import org.testng.FileAssert;
46 import org.testng.annotations.AfterTest;
47 import org.testng.annotations.BeforeClass;
48 import org.testng.annotations.BeforeTest;
49 import org.testng.annotations.Test;
52 import mc_view.PDBfile;
54 public class SiftsClientTest
57 @BeforeClass(alwaysRun = true)
58 public void setUpJvOptionPane()
60 JvOptionPane.setInteractiveMode(false);
61 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
64 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
65 .getProperty("user.home") + File.separatorChar
66 + ".sifts_downloads" + File.separatorChar;
68 private String testPDBId = "1a70";
70 private SiftsClient siftsClient = null;
72 SequenceI testSeq = new Sequence("P00221",
73 "MAAT..TTTMMG..MATTFVPKPQAPPMMAALPSNTGR..SLFGLKT.GSR..GGRMTMA"
74 + "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD"
75 + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.",
78 int u = SiftsClient.UNASSIGNED;
80 HashMap<Integer, int[]> expectedMapping = new HashMap<Integer, int[]>();
82 @BeforeTest(alwaysRun = true)
83 public void populateExpectedMapping() throws SiftsException
85 expectedMapping.put(51, new int[] { 1, 2, 1 });
86 expectedMapping.put(52, new int[] { 2, 7, 2 });
87 expectedMapping.put(53, new int[] { 3, 12, 3 });
88 expectedMapping.put(54, new int[] { 4, 24, 4 });
89 expectedMapping.put(55, new int[] { 5, 33, 5 });
90 expectedMapping.put(56, new int[] { 6, 40, 6 });
91 expectedMapping.put(57, new int[] { 7, 47, 7 });
92 expectedMapping.put(58, new int[] { 8, 55, 8 });
93 expectedMapping.put(59, new int[] { 9, 62, 9 });
94 expectedMapping.put(60, new int[] { 10, 69, 10 });
95 expectedMapping.put(61, new int[] { 11, 76, 11 });
96 expectedMapping.put(62, new int[] { 12, 83, 12 });
97 expectedMapping.put(63, new int[] { 13, 87, 13 });
98 expectedMapping.put(64, new int[] { 14, 95, 14 });
99 expectedMapping.put(65, new int[] { 15, 102, 15 });
100 expectedMapping.put(66, new int[] { 16, 111, 16 });
101 expectedMapping.put(67, new int[] { 17, 122, 17 });
102 expectedMapping.put(68, new int[] { 18, 131, 18 });
103 expectedMapping.put(69, new int[] { 19, 137, 19 });
104 expectedMapping.put(70, new int[] { 20, 144, 20 });
105 expectedMapping.put(71, new int[] { 21, 152, 21 });
106 expectedMapping.put(72, new int[] { 22, 160, 22 });
107 expectedMapping.put(73, new int[] { 23, 167, 23 });
108 expectedMapping.put(74, new int[] { 24, 179, 24 });
109 expectedMapping.put(75, new int[] { 25, 187, 25 });
110 expectedMapping.put(76, new int[] { 26, 195, 26 });
111 expectedMapping.put(77, new int[] { 27, 203, 27 });
112 expectedMapping.put(78, new int[] { 28, 208, 28 });
113 expectedMapping.put(79, new int[] { 29, 213, 29 });
114 expectedMapping.put(80, new int[] { 30, 222, 30 });
115 expectedMapping.put(81, new int[] { 31, 231, 31 });
116 expectedMapping.put(82, new int[] { 32, 240, 32 });
117 expectedMapping.put(83, new int[] { 33, 244, 33 });
118 expectedMapping.put(84, new int[] { 34, 252, 34 });
119 expectedMapping.put(85, new int[] { 35, 260, 35 });
120 expectedMapping.put(86, new int[] { 36, 268, 36 });
121 expectedMapping.put(87, new int[] { 37, 275, 37 });
122 expectedMapping.put(88, new int[] { 38, 287, 38 });
123 expectedMapping.put(89, new int[] { 39, 293, 39 });
124 expectedMapping.put(90, new int[] { 40, 299, 40 });
125 expectedMapping.put(91, new int[] { 41, 310, 41 });
126 expectedMapping.put(92, new int[] { 42, 315, 42 });
127 expectedMapping.put(93, new int[] { 43, 319, 43 });
128 expectedMapping.put(94, new int[] { 44, 325, 44 });
129 expectedMapping.put(95, new int[] { 45, 331, 45 });
130 expectedMapping.put(96, new int[] { 46, 337, 46 });
131 expectedMapping.put(97, new int[] { 47, 343, 47 });
132 expectedMapping.put(98, new int[] { 48, 349, 48 });
133 expectedMapping.put(99, new int[] { 49, 354, 49 });
134 expectedMapping.put(100, new int[] { 50, 358, 50 });
135 expectedMapping.put(101, new int[] { 51, 367, 51 });
136 expectedMapping.put(102, new int[] { 52, 375, 52 });
137 expectedMapping.put(103, new int[] { 53, 384, 53 });
138 expectedMapping.put(104, new int[] { 54, 391, 54 });
139 expectedMapping.put(105, new int[] { 55, 395, 55 });
140 expectedMapping.put(106, new int[] { 56, 401, 56 });
141 expectedMapping.put(107, new int[] { 57, 409, 57 });
142 expectedMapping.put(108, new int[] { 58, 417, 58 });
143 expectedMapping.put(109, new int[] { 59, 426, 59 });
144 expectedMapping.put(110, new int[] { 60, 434, 60 });
145 expectedMapping.put(111, new int[] { 61, 442, 61 });
146 expectedMapping.put(112, new int[] { 62, 451, 62 });
147 expectedMapping.put(113, new int[] { 63, 457, 63 });
148 expectedMapping.put(114, new int[] { 64, 468, 64 });
149 expectedMapping.put(115, new int[] { 65, 476, 65 });
150 expectedMapping.put(116, new int[] { 66, 484, 66 });
151 expectedMapping.put(117, new int[] { 67, 492, 67 });
152 expectedMapping.put(118, new int[] { 68, 500, 68 });
153 expectedMapping.put(119, new int[] { 69, 509, 69 });
154 expectedMapping.put(120, new int[] { 70, 517, 70 });
155 expectedMapping.put(121, new int[] { 71, 525, 71 });
156 expectedMapping.put(122, new int[] { 72, 534, 72 });
157 expectedMapping.put(123, new int[] { 73, 538, 73 });
158 expectedMapping.put(124, new int[] { 74, 552, 74 });
159 expectedMapping.put(125, new int[] { 75, 559, 75 });
160 expectedMapping.put(126, new int[] { 76, 567, 76 });
161 expectedMapping.put(127, new int[] { 77, 574, 77 });
162 expectedMapping.put(128, new int[] { 78, 580, 78 });
163 expectedMapping.put(129, new int[] { 79, 585, 79 });
164 expectedMapping.put(130, new int[] { 80, 590, 80 });
165 expectedMapping.put(131, new int[] { 81, 602, 81 });
166 expectedMapping.put(132, new int[] { 82, 609, 82 });
167 expectedMapping.put(133, new int[] { 83, 616, 83 });
168 expectedMapping.put(134, new int[] { 84, 622, 84 });
169 expectedMapping.put(135, new int[] { 85, 630, 85 });
170 expectedMapping.put(136, new int[] { 86, 637, 86 });
171 expectedMapping.put(137, new int[] { 87, 644, 87 });
172 expectedMapping.put(138, new int[] { 88, 652, 88 });
173 expectedMapping.put(139, new int[] { 89, 661, 89 });
174 expectedMapping.put(140, new int[] { 90, 668, 90 });
175 expectedMapping.put(141, new int[] { 91, 678, 91 });
176 expectedMapping.put(142, new int[] { 92, 687, 92 });
177 expectedMapping.put(143, new int[] { 93, 696, 93 });
178 expectedMapping.put(144, new int[] { 94, 705, 94 });
179 expectedMapping.put(145, new int[] { 95, 714, 95 });
180 expectedMapping.put(146, new int[] { 96, 722, 96 });
181 expectedMapping.put(147, new int[] { 97, 729, 97 });
184 @BeforeTest(alwaysRun = true)
185 public void setUpSiftsClient() throws SiftsException, IOException
187 // read test props before manipulating config
188 Cache.loadProperties("test/jalview/io/testProps.jvprops");
189 // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
190 // test reproducibility
192 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
193 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
194 SiftsSettings.setMapWithSifts(true);
195 SiftsSettings.setCacheThresholdInDays("2");
196 SiftsSettings.setFailSafePIDThreshold("70");
199 pdbFile = new PDBfile(false, false, false,
200 "test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
201 // TODO: this uses a network connection - we should mock the sifts
203 siftsClient = new SiftsClient(pdbFile);
206 @AfterTest(alwaysRun = true)
207 public void cleanUpSiftsClient()
212 @Test(groups = { "Functional" })
213 public void testSIFTsDownloadURL()
215 String expectedUrl = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/xy/1xyz.sifts.xml.gz";
216 Assert.assertEquals(SiftsClient.getDownloadUrlFor("1xyz.sifts.xml.gz"),
220 @Test(groups = { "Network" })
221 public void getSIFTsFileTest() throws SiftsException, IOException
224 siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
225 FileAssert.assertFile(siftsFile);
226 long t1 = siftsFile.lastModified();
228 // re-read file should be returned from cache
229 siftsFile = SiftsClient.getSiftsFile(testPDBId);
230 FileAssert.assertFile(siftsFile);
231 long t2 = siftsFile.lastModified();
232 assertEquals(t1, t2);
235 * force fetch by having 0 expiry of cache
236 * also wait one second, because file timestamp does not
237 * give millisecond resolution :-(
244 } catch (InterruptedException e)
248 SiftsSettings.setCacheThresholdInDays("0");
249 siftsFile = SiftsClient.getSiftsFile(testPDBId);
250 FileAssert.assertFile(siftsFile);
251 long t3 = siftsFile.lastModified();
252 assertTrue(t3 > t2, "file timestamp unchanged at " + t3);
254 SiftsSettings.setCacheThresholdInDays("2");
257 @Test(groups = { "Network" })
258 public void downloadSiftsFileTest() throws SiftsException, IOException
260 // Assert that file isn't yet downloaded - if already downloaded, assert it
262 Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
264 siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
265 FileAssert.assertFile(siftsFile);
266 SiftsClient.downloadSiftsFile(testPDBId);
269 @Test(groups = { "Network" })
270 public void getAllMappingAccessionTest()
272 Assert.assertNotNull(siftsClient);
273 Assert.assertNotNull(siftsClient.getAllMappingAccession());
274 Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1);
277 @Test(groups = { "Network" })
278 public void getGreedyMappingTest()
280 Assert.assertNotNull(siftsClient);
281 Assert.assertNotNull(testSeq);
282 Assert.assertNotNull(expectedMapping);
284 // TODO delete when auto-fetching of DBRefEntry is implemented
285 DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
286 testSeq.addDBRef(dbRef);
287 // testSeq.setSourceDBRef(dbRef);
291 HashMap<Integer, int[]> actualMapping = siftsClient
292 .getGreedyMapping("A", testSeq, null);
293 Assert.assertEquals(testSeq.getStart(), 1);
294 Assert.assertEquals(testSeq.getEnd(), 147);
295 // Can't do Assert.assertEquals(actualMapping, expectedMapping);
296 // because this fails in our version of TestNG
297 Assert.assertEquals(actualMapping.size(), expectedMapping.size());
298 Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
302 Map.Entry<Integer, int[]> pair = it.next();
303 Assert.assertTrue(actualMapping.containsKey(pair.getKey()));
304 Assert.assertEquals(actualMapping.get(pair.getKey()),
308 } catch (Exception e)
311 Assert.fail("Exception thrown while generating mapping...");
315 @Test(groups = { "Network" })
316 private void getAtomIndexTest()
318 ArrayList<Atom> atoms = new ArrayList<Atom>();
319 Atom atom = new Atom(u, u, u);
323 int actualAtomIndex = siftsClient.getAtomIndex(1, atoms);
324 Assert.assertEquals(actualAtomIndex, siftsClient.UNASSIGNED);
325 actualAtomIndex = siftsClient.getAtomIndex(43, atoms);
326 Assert.assertEquals(actualAtomIndex, 7);
332 expectedExceptions = IllegalArgumentException.class)
333 private void getAtomIndexNullTest()
335 siftsClient.getAtomIndex(1, null);
338 @Test(groups = { "Network" })
339 private void padWithGapsTest()
344 @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
345 private void populateAtomPositionsNullTest1()
346 throws IllegalArgumentException, SiftsException
348 siftsClient.populateAtomPositions(null, null);
351 @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
352 private void populateAtomPositionsNullTest2()
353 throws IllegalArgumentException, SiftsException
355 siftsClient.populateAtomPositions("A", null);
358 @Test(groups = { "Network" })
359 public void getValidSourceDBRefTest() throws SiftsException
361 DBRefEntryI actualValidSrcDBRef = siftsClient
362 .getValidSourceDBRef(testSeq);
363 DBRefEntryI expectedDBRef = new DBRefEntry();
364 expectedDBRef.setSource(DBRefSource.UNIPROT);
365 expectedDBRef.setAccessionId("P00221");
366 expectedDBRef.setVersion("");
367 Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
370 @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
371 public void getValidSourceDBRefExceptionTest() throws SiftsException
373 SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
374 siftsClient.getValidSourceDBRef(invalidTestSeq);
377 @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
378 public void getValidSourceDBRefExceptionXTest() throws SiftsException
380 SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
381 DBRefEntry invalidDBRef = new DBRefEntry();
382 invalidDBRef.setAccessionId("BLAR"); // note no version is set, so also
384 invalidTestSeq.addDBRef(invalidDBRef);
385 siftsClient.getValidSourceDBRef(invalidTestSeq);
388 @Test(groups = { "Network" })
389 public void isValidDBRefEntryTest()
391 DBRefEntryI validDBRef = new DBRefEntry();
392 validDBRef.setSource(DBRefSource.UNIPROT);
393 validDBRef.setAccessionId("P00221");
394 validDBRef.setVersion("");
395 Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
398 @Test(groups = { "Network" })
399 public void getSiftsStructureMappingTest() throws SiftsException
401 Assert.assertTrue(SiftsSettings.isMapWithSifts());
402 StructureMapping strucMapping = siftsClient
403 .getSiftsStructureMapping(testSeq, testPDBId, "A");
404 String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
405 + "Method: SIFTS\n\n" + "P00221 : 51 - 147 Maps to \n"
406 + "1A70|A : 1 - 97\n\n"
407 + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
408 + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
409 + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"
411 + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n"
412 + " |||||||||||||||||||||||||| |||||\n"
413 + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" +
415 "Length of alignment = 97\n" + "Percentage ID = 98.97\n";
417 Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
418 expectedMappingOutput);
420 // Can't do Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
421 // because this fails in our version of TestNG
422 Assert.assertEquals(strucMapping.getMapping().size(),
423 expectedMapping.size());
424 Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
428 Map.Entry<Integer, int[]> pair = it.next();
430 strucMapping.getMapping().containsKey(pair.getKey()));
431 Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
436 @Test(groups = { "Network" })
437 public void getEntityCountTest()
439 int actualEntityCount = siftsClient.getEntityCount();
440 System.out.println("actual entity count : " + actualEntityCount);
441 Assert.assertEquals(actualEntityCount, 1);
444 @Test(groups = { "Network" })
445 public void getDbAccessionIdTest()
447 String actualDbAccId = siftsClient.getDbAccessionId();
448 System.out.println("Actual Db Accession Id: " + actualDbAccId);
449 Assert.assertEquals(actualDbAccId, "1a70");
452 @Test(groups = { "Network" })
453 public void getDbCoordSysTest()
455 String actualDbCoordSys = siftsClient.getDbCoordSys();
456 System.out.println("Actual DbCoordSys: " + actualDbCoordSys);
457 Assert.assertEquals(actualDbCoordSys, "PDBe");
460 @Test(groups = { "Network" })
461 public void getDbSourceTest()
463 String actualDbSource = siftsClient.getDbSource();
464 System.out.println("Actual DbSource: " + actualDbSource);
465 Assert.assertEquals(actualDbSource, "PDBe");
468 @Test(groups = { "Network" })
469 public void getDbVersionTest()
471 String actualDbVersion = siftsClient.getDbVersion();
472 System.out.println("Actual DbVersion: " + actualDbVersion);
473 Assert.assertEquals(actualDbVersion, "2.0");
476 @Test(groups = { "Network" })
477 public void getEntityByMostOptimalMatchedIdTest1()
478 throws IOException, SiftsException
480 SiftsClient siftsClientX = null;
482 pdbFile = new PDBfile(false, false, false,
483 "test/jalview/io/2nq2" + ".pdb", DataSourceType.FILE);
484 siftsClientX = new SiftsClient(pdbFile);
485 Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
486 Assert.assertEquals(entityA.getEntityId(), "A");
487 Entity entityB = siftsClientX.getEntityByMostOptimalMatchedId("B");
488 Assert.assertEquals(entityB.getEntityId(), "C");
489 Entity entityC = siftsClientX.getEntityByMostOptimalMatchedId("C");
490 Assert.assertEquals(entityC.getEntityId(), "B");
491 Entity entityD = siftsClientX.getEntityByMostOptimalMatchedId("D");
492 Assert.assertEquals(entityD.getEntityId(), "D");
496 @Test(groups = { "Network" })
497 public void getEntityByMostOptimalMatchedIdTest2()
498 throws IOException, SiftsException
500 // This test is for a SIFTS file in which entity A should map to chain P for
501 // the given PDB Id. All the other chains shouldn't be mapped as there are
502 // no SIFTS entity records for them.
503 SiftsClient siftsClientX = null;
505 pdbFile = new PDBfile(false, false, false, "test/jalview/io/3ucu.cif",
506 DataSourceType.FILE);
507 siftsClientX = new SiftsClient(pdbFile);
508 Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P");
509 Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A");
510 Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");
511 Assert.assertEquals(entityA.getEntityId(), "A");
512 Assert.assertNotEquals(entityR, "A");
513 Assert.assertNotEquals(entityP, "A");
514 Assert.assertNotEquals(entityR, "R");
515 Assert.assertNotEquals(entityP, "P");
516 Assert.assertNull(entityR);
517 Assert.assertNull(entityP);
521 @Test(groups = { "Network" })
522 public void getLeadingIntegerFromString()
524 Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234abcd", -1),
526 Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234", -1),
528 Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
529 Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd1234", -1),
531 Assert.assertEquals(SiftsClient.getLeadingIntegerValue("None", -1), -1);
532 Assert.assertEquals(SiftsClient.getLeadingIntegerValue("Null", -1), -1);