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;
28 import java.io.IOException;
29 import java.util.ArrayList;
30 import java.util.HashMap;
31 import java.util.Iterator;
34 import org.testng.Assert;
35 import org.testng.FileAssert;
36 import org.testng.annotations.AfterTest;
37 import org.testng.annotations.BeforeClass;
38 import org.testng.annotations.BeforeTest;
39 import org.testng.annotations.Test;
41 import jalview.api.DBRefEntryI;
42 import jalview.bin.Cache;
43 import jalview.datamodel.DBRefEntry;
44 import jalview.datamodel.DBRefSource;
45 import jalview.datamodel.Sequence;
46 import jalview.datamodel.SequenceI;
47 import jalview.gui.JvOptionPane;
48 import jalview.io.DataSourceType;
49 import jalview.structure.StructureMapping;
50 import jalview.xml.binding.sifts.Entry.Entity;
52 import mc_view.PDBfile;
55 public class SiftsClientTest
58 @BeforeClass(alwaysRun = true)
59 public void setUpJvOptionPane()
61 JvOptionPane.setInteractiveMode(false);
62 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
65 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
66 .getProperty("user.home")
68 + ".sifts_downloads" + File.separatorChar;
70 // FIXME 1a70 has no sifts mapping any more !!! all tests fail
71 private String testPDBId = "1a70";
73 private SiftsClient siftsClient = null;
75 SequenceI testSeq = new Sequence(
77 "MAAT..TTTMMG..MATTFVPKPQAPPMMAALPSNTGR..SLFGLKT.GSR..GGRMTMA"
78 + "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD"
79 + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", 1, 147);
81 int u = SiftsClient.UNASSIGNED;
83 HashMap<Integer, int[]> expectedMapping = new HashMap<Integer, int[]>();
85 @BeforeTest(alwaysRun = true)
86 public void populateExpectedMapping() throws SiftsException
88 expectedMapping.put(51, new int[] { 1, 2, 1 });
89 expectedMapping.put(52, new int[] { 2, 7, 2 });
90 expectedMapping.put(53, new int[] { 3, 12, 3 });
91 expectedMapping.put(54, new int[] { 4, 24, 4 });
92 expectedMapping.put(55, new int[] { 5, 33, 5 });
93 expectedMapping.put(56, new int[] { 6, 40, 6 });
94 expectedMapping.put(57, new int[] { 7, 47, 7 });
95 expectedMapping.put(58, new int[] { 8, 55, 8 });
96 expectedMapping.put(59, new int[] { 9, 62, 9 });
97 expectedMapping.put(60, new int[] { 10, 69, 10 });
98 expectedMapping.put(61, new int[] { 11, 76, 11 });
99 expectedMapping.put(62, new int[] { 12, 83, 12 });
100 expectedMapping.put(63, new int[] { 13, 87, 13 });
101 expectedMapping.put(64, new int[] { 14, 95, 14 });
102 expectedMapping.put(65, new int[] { 15, 102, 15 });
103 expectedMapping.put(66, new int[] { 16, 111, 16 });
104 expectedMapping.put(67, new int[] { 17, 122, 17 });
105 expectedMapping.put(68, new int[] { 18, 131, 18 });
106 expectedMapping.put(69, new int[] { 19, 137, 19 });
107 expectedMapping.put(70, new int[] { 20, 144, 20 });
108 expectedMapping.put(71, new int[] { 21, 152, 21 });
109 expectedMapping.put(72, new int[] { 22, 160, 22 });
110 expectedMapping.put(73, new int[] { 23, 167, 23 });
111 expectedMapping.put(74, new int[] { 24, 179, 24 });
112 expectedMapping.put(75, new int[] { 25, 187, 25 });
113 expectedMapping.put(76, new int[] { 26, 195, 26 });
114 expectedMapping.put(77, new int[] { 27, 203, 27 });
115 expectedMapping.put(78, new int[] { 28, 208, 28 });
116 expectedMapping.put(79, new int[] { 29, 213, 29 });
117 expectedMapping.put(80, new int[] { 30, 222, 30 });
118 expectedMapping.put(81, new int[] { 31, 231, 31 });
119 expectedMapping.put(82, new int[] { 32, 240, 32 });
120 expectedMapping.put(83, new int[] { 33, 244, 33 });
121 expectedMapping.put(84, new int[] { 34, 252, 34 });
122 expectedMapping.put(85, new int[] { 35, 260, 35 });
123 expectedMapping.put(86, new int[] { 36, 268, 36 });
124 expectedMapping.put(87, new int[] { 37, 275, 37 });
125 expectedMapping.put(88, new int[] { 38, 287, 38 });
126 expectedMapping.put(89, new int[] { 39, 293, 39 });
127 expectedMapping.put(90, new int[] { 40, 299, 40 });
128 expectedMapping.put(91, new int[] { 41, 310, 41 });
129 expectedMapping.put(92, new int[] { 42, 315, 42 });
130 expectedMapping.put(93, new int[] { 43, 319, 43 });
131 expectedMapping.put(94, new int[] { 44, 325, 44 });
132 expectedMapping.put(95, new int[] { 45, 331, 45 });
133 expectedMapping.put(96, new int[] { 46, 337, 46 });
134 expectedMapping.put(97, new int[] { 47, 343, 47 });
135 expectedMapping.put(98, new int[] { 48, 349, 48 });
136 expectedMapping.put(99, new int[] { 49, 354, 49 });
137 expectedMapping.put(100, new int[] { 50, 358, 50 });
138 expectedMapping.put(101, new int[] { 51, 367, 51 });
139 expectedMapping.put(102, new int[] { 52, 375, 52 });
140 expectedMapping.put(103, new int[] { 53, 384, 53 });
141 expectedMapping.put(104, new int[] { 54, 391, 54 });
142 expectedMapping.put(105, new int[] { 55, 395, 55 });
143 expectedMapping.put(106, new int[] { 56, 401, 56 });
144 expectedMapping.put(107, new int[] { 57, 409, 57 });
145 expectedMapping.put(108, new int[] { 58, 417, 58 });
146 expectedMapping.put(109, new int[] { 59, 426, 59 });
147 expectedMapping.put(110, new int[] { 60, 434, 60 });
148 expectedMapping.put(111, new int[] { 61, 442, 61 });
149 expectedMapping.put(112, new int[] { 62, 451, 62 });
150 expectedMapping.put(113, new int[] { 63, 457, 63 });
151 expectedMapping.put(114, new int[] { 64, 468, 64 });
152 expectedMapping.put(115, new int[] { 65, 476, 65 });
153 expectedMapping.put(116, new int[] { 66, 484, 66 });
154 expectedMapping.put(117, new int[] { 67, 492, 67 });
155 expectedMapping.put(118, new int[] { 68, 500, 68 });
156 expectedMapping.put(119, new int[] { 69, 509, 69 });
157 expectedMapping.put(120, new int[] { 70, 517, 70 });
158 expectedMapping.put(121, new int[] { 71, 525, 71 });
159 expectedMapping.put(122, new int[] { 72, 534, 72 });
160 expectedMapping.put(123, new int[] { 73, 538, 73 });
161 expectedMapping.put(124, new int[] { 74, 552, 74 });
162 expectedMapping.put(125, new int[] { 75, 559, 75 });
163 expectedMapping.put(126, new int[] { 76, 567, 76 });
164 expectedMapping.put(127, new int[] { 77, 574, 77 });
165 expectedMapping.put(128, new int[] { 78, 580, 78 });
166 expectedMapping.put(129, new int[] { 79, 585, 79 });
167 expectedMapping.put(130, new int[] { 80, 590, 80 });
168 expectedMapping.put(131, new int[] { 81, 602, 81 });
169 expectedMapping.put(132, new int[] { 82, 609, 82 });
170 expectedMapping.put(133, new int[] { 83, 616, 83 });
171 expectedMapping.put(134, new int[] { 84, 622, 84 });
172 expectedMapping.put(135, new int[] { 85, 630, 85 });
173 expectedMapping.put(136, new int[] { 86, 637, 86 });
174 expectedMapping.put(137, new int[] { 87, 644, 87 });
175 expectedMapping.put(138, new int[] { 88, 652, 88 });
176 expectedMapping.put(139, new int[] { 89, 661, 89 });
177 expectedMapping.put(140, new int[] { 90, 668, 90 });
178 expectedMapping.put(141, new int[] { 91, 678, 91 });
179 expectedMapping.put(142, new int[] { 92, 687, 92 });
180 expectedMapping.put(143, new int[] { 93, 696, 93 });
181 expectedMapping.put(144, new int[] { 94, 705, 94 });
182 expectedMapping.put(145, new int[] { 95, 714, 95 });
183 expectedMapping.put(146, new int[] { 96, 722, 96 });
184 expectedMapping.put(147, new int[] { 97, 729, 97 });
187 @BeforeTest(alwaysRun = true)
188 public void setUpSiftsClient() throws SiftsException, IOException
190 // read test props before manipulating config
191 Cache.loadProperties("test/jalview/io/testProps.jvprops");
192 // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
193 // test reproducibility
194 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
195 "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
196 SiftsSettings.setMapWithSifts(true);
197 SiftsSettings.setCacheThresholdInDays("2");
198 SiftsSettings.setFailSafePIDThreshold("70");
200 pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
201 + testPDBId + ".pdb", DataSourceType.FILE);
203 siftsClient = new SiftsClient(pdbFile);
207 System.err.println("SiftsClientTest setupSiftsClient failed.");
211 @AfterTest(alwaysRun = true)
212 public void cleanUpSiftsClient()
217 @Test(groups = { "Network" })
218 public void getSIFTsFileTest() throws SiftsException, IOException
221 siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
222 FileAssert.assertFile(siftsFile);
223 long t1 = siftsFile.lastModified();
225 // re-read file should be returned from cache
226 siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
227 FileAssert.assertFile(siftsFile);
228 long t2 = siftsFile.lastModified();
229 assertEquals(t1, t2);
232 * force fetch by having 0 expiry of cache
233 * also wait one second, because file timestamp does not
234 * give millisecond resolution :-(
241 } catch (InterruptedException e)
245 SiftsSettings.setCacheThresholdInDays("0");
246 siftsFile = SiftsClient.getSiftsFile(testPDBId);
247 FileAssert.assertFile(siftsFile);
248 long t3 = siftsFile.lastModified();
249 assertTrue(t3 > t2, "file timestamp unchanged at " + t3);
251 SiftsSettings.setCacheThresholdInDays("2");
254 @Test(groups = { "Network" })
255 public void downloadSiftsFileTest() throws SiftsException, IOException
257 // Assert that file isn't yet downloaded - if already downloaded, assert it
259 Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
261 siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
262 FileAssert.assertFile(siftsFile);
263 SiftsClient.downloadSiftsFile(testPDBId);
266 @Test(groups = { "Network" })
267 public void getAllMappingAccessionTest()
269 Assert.assertNotNull(siftsClient);
270 Assert.assertNotNull(siftsClient.getAllMappingAccession());
271 Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1);
274 @Test(groups = { "Network" })
275 public void getGreedyMappingTest()
277 Assert.assertNotNull(siftsClient);
278 Assert.assertNotNull(testSeq);
279 Assert.assertNotNull(expectedMapping);
281 // TODO delete when auto-fetching of DBRefEntry is implemented
282 DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
283 testSeq.addDBRef(dbRef);
284 // testSeq.setSourceDBRef(dbRef);
288 HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
290 Assert.assertEquals(testSeq.getStart(), 1);
291 Assert.assertEquals(testSeq.getEnd(), 147);
292 // Can't do Assert.assertEquals(actualMapping, expectedMapping);
293 // because this fails in our version of TestNG
294 Assert.assertEquals(actualMapping.size(), expectedMapping.size());
295 Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
299 Map.Entry<Integer, int[]> pair = it.next();
300 Assert.assertTrue(actualMapping.containsKey(pair.getKey()));
301 Assert.assertEquals(actualMapping.get(pair.getKey()),
305 } catch (Exception e)
308 Assert.fail("Exception thrown while generating mapping...");
312 @Test(groups = { "Network" })
313 private void getAtomIndexTest()
315 ArrayList<Atom> atoms = new ArrayList<Atom>();
316 Atom atom = new Atom(u, u, u);
320 int actualAtomIndex = siftsClient.getAtomIndex(1, atoms);
321 Assert.assertEquals(actualAtomIndex, SiftsClient.UNASSIGNED);
322 actualAtomIndex = siftsClient.getAtomIndex(43, atoms);
323 Assert.assertEquals(actualAtomIndex, 7);
327 groups = { "Network" },
328 expectedExceptions = IllegalArgumentException.class)
329 private void getAtomIndexNullTest()
331 siftsClient.getAtomIndex(1, null);
334 @Test(groups = { "Network" })
335 private void padWithGapsTest()
341 groups = { "Network" },
342 expectedExceptions = SiftsException.class)
343 private void populateAtomPositionsNullTest1()
344 throws IllegalArgumentException, SiftsException
346 siftsClient.populateAtomPositions(null, null);
350 groups = { "Network" },
351 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);
371 groups = { "Network" },
372 expectedExceptions = SiftsException.class)
373 public void getValidSourceDBRefExceptionTest() throws SiftsException
375 SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
376 siftsClient.getValidSourceDBRef(invalidTestSeq);
380 groups = { "Network" },
381 expectedExceptions = SiftsException.class)
382 public void getValidSourceDBRefExceptionXTest() throws SiftsException
384 SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
385 DBRefEntry invalidDBRef = new DBRefEntry();
386 invalidDBRef.setAccessionId("BLAR");
387 invalidTestSeq.addDBRef(invalidDBRef);
388 siftsClient.getValidSourceDBRef(invalidTestSeq);
391 @Test(groups = { "Network" })
392 public void isValidDBRefEntryTest()
394 DBRefEntryI validDBRef = new DBRefEntry();
395 validDBRef.setSource(DBRefSource.UNIPROT);
396 validDBRef.setAccessionId("P00221");
397 validDBRef.setVersion("");
398 Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
401 @Test(groups = { "Network" })
402 public void getSiftsStructureMappingTest() throws SiftsException
404 Assert.assertTrue(SiftsSettings.isMapWithSifts());
405 StructureMapping strucMapping = siftsClient.getSiftsStructureMapping(
406 testSeq, testPDBId, "A");
407 String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
408 + "Method: SIFTS\n\n"
409 + "P00221 : 51 - 147 Maps to \n"
410 + "1A70|A : 1 - 97\n\n"
411 + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
412 + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
413 + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"
415 + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n"
416 + " |||||||||||||||||||||||||| |||||\n"
417 + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" +
419 "Length of alignment = 97\n" + "Percentage ID = 98.97\n";
421 Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
422 expectedMappingOutput);
424 // Can't do Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
425 // because this fails in our version of TestNG
426 Assert.assertEquals(strucMapping.getMapping().size(),
427 expectedMapping.size());
428 Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
432 Map.Entry<Integer, int[]> pair = it.next();
433 Assert.assertTrue(strucMapping.getMapping()
434 .containsKey(pair.getKey()));
435 Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
440 @Test(groups = { "Network" })
441 public void getEntityCountTest()
443 int actualEntityCount = siftsClient.getEntityCount();
444 System.out.println("actual entity count : " + actualEntityCount);
445 Assert.assertEquals(actualEntityCount, 1);
448 @Test(groups = { "Network" })
449 public void getDbAccessionIdTest()
451 String actualDbAccId = siftsClient.getDbAccessionId();
452 System.out.println("Actual Db Accession Id: " + actualDbAccId);
453 Assert.assertEquals(actualDbAccId, "1a70");
456 @Test(groups = { "Network" })
457 public void getDbCoordSysTest()
459 String actualDbCoordSys = siftsClient.getDbCoordSys();
460 System.out.println("Actual DbCoordSys: " + actualDbCoordSys);
461 Assert.assertEquals(actualDbCoordSys, "PDBe");
464 @Test(groups = { "Network" })
465 public void getDbSourceTest()
467 String actualDbSource = siftsClient.getDbSource();
468 System.out.println("Actual DbSource: " + actualDbSource);
469 Assert.assertEquals(actualDbSource, "PDBe");
472 @Test(groups = { "Network" })
473 public void getDbVersionTest()
475 String actualDbVersion = siftsClient.getDbVersion();
476 System.out.println("Actual DbVersion: " + actualDbVersion);
477 Assert.assertEquals(actualDbVersion, "2.0");
480 @Test(groups = { "Network" })
481 public void getEntityByMostOptimalMatchedIdTest1() throws IOException,
484 SiftsClient siftsClientX = null;
486 pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
487 + ".pdb", DataSourceType.FILE);
488 siftsClientX = new SiftsClient(pdbFile);
489 Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
490 Assert.assertEquals(entityA.getEntityId(), "A");
491 Entity entityB = siftsClientX.getEntityByMostOptimalMatchedId("B");
492 Assert.assertEquals(entityB.getEntityId(), "C");
493 Entity entityC = siftsClientX.getEntityByMostOptimalMatchedId("C");
494 Assert.assertEquals(entityC.getEntityId(), "B");
495 Entity entityD = siftsClientX.getEntityByMostOptimalMatchedId("D");
496 Assert.assertEquals(entityD.getEntityId(), "D");
500 @Test(groups = { "Network" })
501 public void getEntityByMostOptimalMatchedIdTest2() throws IOException,
504 // This test is for a SIFTS file in which entity A should map to chain P for
505 // the given PDB Id. All the other chains shouldn't be mapped as there are
506 // no SIFTS entity records for them.
507 SiftsClient siftsClientX = null;
509 pdbFile = new PDBfile(false, false, false, "test/jalview/io/3ucu.cif",
510 DataSourceType.FILE);
511 siftsClientX = new SiftsClient(pdbFile);
512 Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P");
513 Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A");
514 Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");
515 Assert.assertEquals(entityA.getEntityId(), "A");
516 Assert.assertNotEquals(entityR, "A");
517 Assert.assertNotEquals(entityP, "A");
518 Assert.assertNotEquals(entityR, "R");
519 Assert.assertNotEquals(entityP, "P");
520 Assert.assertNull(entityR);
521 Assert.assertNull(entityP);