X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=27e500416a4b69225427439b914a5c8d8af29cfb;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=dab7f1231d19beb93195ee23398f62672588c02d;hpb=9b6d2ddd33ba5e479953700040e1129847e47a06;p=jalview.git diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index dab7f12..27e5004 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -20,13 +20,19 @@ */ package jalview.ws.sifts; +import jalview.api.DBRefEntryI; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.structure.StructureMapping; +import jalview.xml.binding.sifts.Entry.Entity; -import java.io.ByteArrayOutputStream; import java.io.File; -import java.io.PrintStream; +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashMap; import org.testng.Assert; import org.testng.FileAssert; @@ -34,9 +40,16 @@ import org.testng.annotations.AfterTest; import org.testng.annotations.BeforeTest; import org.testng.annotations.Test; +import MCview.Atom; +import MCview.PDBfile; + public class SiftsClientTest { - private final ByteArrayOutputStream outContent = new ByteArrayOutputStream(); + + public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System + .getProperty("user.home") + + File.separatorChar + + ".sifts_downloads" + File.separatorChar; private String testPDBId = "1a70"; @@ -48,45 +61,133 @@ public class SiftsClientTest + "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD" + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", 1, 147); - int[][] expectedMapping = { { -1, 0 }, { -1, 1 }, { -1, 2 }, { -1, 3 }, - { -1, 4 }, { -1, 5 }, { -1, 6 }, { -1, 7 }, { -1, 8 }, { -1, 9 }, - { -1, 10 }, { -1, 11 }, { -1, 12 }, { -1, 13 }, { -1, 14 }, - { -1, 15 }, { -1, 16 }, { -1, 17 }, { -1, 18 }, { -1, 19 }, - { -1, 20 }, { -1, 21 }, { -1, 22 }, { -1, 23 }, { -1, 24 }, - { -1, 25 }, { -1, 26 }, { -1, 27 }, { -1, 28 }, { -1, 29 }, - { -1, 30 }, { -1, 31 }, { -1, 32 }, { -1, 33 }, { -1, 34 }, - { -1, 35 }, { -1, 36 }, { -1, 37 }, { -1, 38 }, { -1, 39 }, - { -1, 40 }, { -1, 41 }, { -1, 42 }, { -1, 43 }, { -1, 44 }, - { -1, 45 }, { -1, 46 }, { -1, 47 }, { -1, 48 }, { -1, 49 }, - { -1, 50 }, { 1, 51 }, { 2, 52 }, { 3, 53 }, { 4, 54 }, { 5, 55 }, - { 6, 56 }, { 7, 57 }, { 8, 58 }, { 9, 59 }, { 10, 60 }, { 11, 61 }, - { 12, 62 }, { 13, 63 }, { 14, 64 }, { 15, 65 }, { 16, 66 }, - { 17, 67 }, { 18, 68 }, { 19, 69 }, { 20, 70 }, { 21, 71 }, - { 22, 72 }, { 23, 73 }, { 24, 74 }, { 25, 75 }, { 26, 76 }, - { 27, 77 }, { 28, 78 }, { 29, 79 }, { 30, 80 }, { 31, 81 }, - { 32, 82 }, { 33, 83 }, { 34, 84 }, { 35, 85 }, { 36, 86 }, - { 37, 87 }, { 38, 88 }, { 39, 89 }, { 40, 90 }, { 41, 91 }, - { 42, 92 }, { 43, 93 }, { 44, 94 }, { 45, 95 }, { 46, 96 }, - { 47, 97 }, { 48, 98 }, { 49, 99 }, { 50, 100 }, { 51, 101 }, - { 52, 102 }, { 53, 103 }, { 54, 104 }, { 55, 105 }, { 56, 106 }, - { 57, 107 }, { 58, 108 }, { 59, 109 }, { 60, 110 }, { 61, 111 }, - { 62, 112 }, { 63, 113 }, { 64, 114 }, { 65, 115 }, { 66, 116 }, - { 67, 117 }, { 68, 118 }, { 69, 119 }, { 70, 120 }, { 71, 121 }, - { 72, 122 }, { 73, 123 }, { 74, 124 }, { 75, 125 }, { 76, 126 }, - { 77, 127 }, { 78, 128 }, { 79, 129 }, { 80, 130 }, { 81, 131 }, - { 82, 132 }, { 83, 133 }, { 84, 134 }, { 85, 135 }, { 86, 136 }, - { 87, 137 }, { 88, 138 }, { 89, 139 }, { 90, 140 }, { 91, 141 }, - { 92, 142 }, { 93, 143 }, { 94, 144 }, { 95, 145 }, { 96, 146 }, - { 97, 147 } }; + int u = SiftsClient.UNASSIGNED; + HashMap expectedMapping = new HashMap(); + + @BeforeTest(alwaysRun = true) + public void populateExpectedMapping() throws SiftsException + { + expectedMapping.put(51, new int[] { 1, 2 }); + expectedMapping.put(52, new int[] { 2, 7 }); + expectedMapping.put(53, new int[] { 3, 12 }); + expectedMapping.put(54, new int[] { 4, 24 }); + expectedMapping.put(55, new int[] { 5, 33 }); + expectedMapping.put(56, new int[] { 6, 40 }); + expectedMapping.put(57, new int[] { 7, 47 }); + expectedMapping.put(58, new int[] { 8, 55 }); + expectedMapping.put(59, new int[] { 9, 62 }); + expectedMapping.put(60, new int[] { 10, 69 }); + expectedMapping.put(61, new int[] { 11, 76 }); + expectedMapping.put(62, new int[] { 12, 83 }); + expectedMapping.put(63, new int[] { 13, 87 }); + expectedMapping.put(64, new int[] { 14, 95 }); + expectedMapping.put(65, new int[] { 15, 102 }); + expectedMapping.put(66, new int[] { 16, 111 }); + expectedMapping.put(67, new int[] { 17, 122 }); + expectedMapping.put(68, new int[] { 18, 131 }); + expectedMapping.put(69, new int[] { 19, 137 }); + expectedMapping.put(70, new int[] { 20, 144 }); + expectedMapping.put(71, new int[] { 21, 152 }); + expectedMapping.put(72, new int[] { 22, 160 }); + expectedMapping.put(73, new int[] { 23, 167 }); + expectedMapping.put(74, new int[] { 24, 179 }); + expectedMapping.put(75, new int[] { 25, 187 }); + expectedMapping.put(76, new int[] { 26, 195 }); + expectedMapping.put(77, new int[] { 27, 203 }); + expectedMapping.put(78, new int[] { 28, 208 }); + expectedMapping.put(79, new int[] { 29, 213 }); + expectedMapping.put(80, new int[] { 30, 222 }); + expectedMapping.put(81, new int[] { 31, 231 }); + expectedMapping.put(82, new int[] { 32, 240 }); + expectedMapping.put(83, new int[] { 33, 244 }); + expectedMapping.put(84, new int[] { 34, 252 }); + expectedMapping.put(85, new int[] { 35, 260 }); + expectedMapping.put(86, new int[] { 36, 268 }); + expectedMapping.put(87, new int[] { 37, 275 }); + expectedMapping.put(88, new int[] { 38, 287 }); + expectedMapping.put(89, new int[] { 39, 293 }); + expectedMapping.put(90, new int[] { 40, 299 }); + expectedMapping.put(91, new int[] { 41, 310 }); + expectedMapping.put(92, new int[] { 42, 315 }); + expectedMapping.put(93, new int[] { 43, 319 }); + expectedMapping.put(94, new int[] { 44, 325 }); + expectedMapping.put(95, new int[] { 45, 331 }); + expectedMapping.put(96, new int[] { 46, 337 }); + expectedMapping.put(97, new int[] { 47, 343 }); + expectedMapping.put(98, new int[] { 48, 349 }); + expectedMapping.put(99, new int[] { 49, 354 }); + expectedMapping.put(100, new int[] { 50, 358 }); + expectedMapping.put(101, new int[] { 51, 367 }); + expectedMapping.put(102, new int[] { 52, 375 }); + expectedMapping.put(103, new int[] { 53, 384 }); + expectedMapping.put(104, new int[] { 54, 391 }); + expectedMapping.put(105, new int[] { 55, 395 }); + expectedMapping.put(106, new int[] { 56, 401 }); + expectedMapping.put(107, new int[] { 57, 409 }); + expectedMapping.put(108, new int[] { 58, 417 }); + expectedMapping.put(109, new int[] { 59, 426 }); + expectedMapping.put(110, new int[] { 60, 434 }); + expectedMapping.put(111, new int[] { 61, 442 }); + expectedMapping.put(112, new int[] { 62, 451 }); + expectedMapping.put(113, new int[] { 63, 457 }); + expectedMapping.put(114, new int[] { 64, 468 }); + expectedMapping.put(115, new int[] { 65, 476 }); + expectedMapping.put(116, new int[] { 66, 484 }); + expectedMapping.put(117, new int[] { 67, 492 }); + expectedMapping.put(118, new int[] { 68, 500 }); + expectedMapping.put(119, new int[] { 69, 509 }); + expectedMapping.put(120, new int[] { 70, 517 }); + expectedMapping.put(121, new int[] { 71, 525 }); + expectedMapping.put(122, new int[] { 72, 534 }); + expectedMapping.put(123, new int[] { 73, 538 }); + expectedMapping.put(124, new int[] { 74, 552 }); + expectedMapping.put(125, new int[] { 75, 559 }); + expectedMapping.put(126, new int[] { 76, 567 }); + expectedMapping.put(127, new int[] { 77, 574 }); + expectedMapping.put(128, new int[] { 78, 580 }); + expectedMapping.put(129, new int[] { 79, 585 }); + expectedMapping.put(130, new int[] { 80, 590 }); + expectedMapping.put(131, new int[] { 81, 602 }); + expectedMapping.put(132, new int[] { 82, 609 }); + expectedMapping.put(133, new int[] { 83, 616 }); + expectedMapping.put(134, new int[] { 84, 622 }); + expectedMapping.put(135, new int[] { 85, 630 }); + expectedMapping.put(136, new int[] { 86, 637 }); + expectedMapping.put(137, new int[] { 87, 644 }); + expectedMapping.put(138, new int[] { 88, 652 }); + expectedMapping.put(139, new int[] { 89, 661 }); + expectedMapping.put(140, new int[] { 90, 668 }); + expectedMapping.put(141, new int[] { 91, 678 }); + expectedMapping.put(142, new int[] { 92, 687 }); + expectedMapping.put(143, new int[] { 93, 696 }); + expectedMapping.put(144, new int[] { 94, 705 }); + expectedMapping.put(145, new int[] { 95, 714 }); + expectedMapping.put(146, new int[] { 96, 722 }); + expectedMapping.put(147, new int[] { 97, 729 }); + } + @BeforeTest(alwaysRun = true) - public void setUpSiftsClient() + public void setUpSiftsClient() throws SiftsException { // SIFTs entries are updated weekly - so use saved SIFTs file to enforce // test reproducibility - File testSiftsFile = new File("test/jalview/io/" + testPDBId - + ".xml.gz"); - siftsClient = new SiftsClient(testPDBId, testSiftsFile); + new SiftsSettings(); + SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault( + "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); + SiftsSettings.setMapWithSifts(true); + SiftsSettings.setCacheThresholdInDays("2"); + SiftsSettings.setFailSafePIDThreshold("70"); + PDBfile pdbFile; + try + { + pdbFile = new PDBfile(false, false, false, "test/jalview/io/" + + testPDBId + ".pdb", DataSourceType.FILE); + siftsClient = new SiftsClient(pdbFile); + } catch (Exception e) + { + e.printStackTrace(); + } } @AfterTest(alwaysRun = true) @@ -95,43 +196,44 @@ public class SiftsClientTest siftsClient = null; } - @BeforeTest(alwaysRun = true) - public void setUpStreams() - { - System.setOut(new PrintStream(outContent)); - } - - @AfterTest(alwaysRun = true) - public void cleanUpStreams() - { - System.setOut(null); - } - @Test(groups = { "Functional" }) - public void getSIFTsFileTest() + public void getSIFTsFileTest() throws SiftsException { - Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId)); - SiftsClient.getSiftsFile(testPDBId); - Assert.assertFalse(outContent.toString().contains( - ">>> SIFTS File already downloaded for " + testPDBId)); - - // test for SIFTs file caching - SiftsClient.getSiftsFile(testPDBId); - Assert.assertTrue(outContent.toString().contains( - ">>> SIFTS File already downloaded for " + testPDBId)); + File siftsFile; + try + { + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + // test for SIFTs file caching + SiftsSettings.setCacheThresholdInDays("0"); + siftsFile = SiftsClient.getSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + SiftsSettings.setCacheThresholdInDays("2"); + } catch (IOException e) + { + e.printStackTrace(); + } } @Test(groups = { "Functional" }) - public void downloadSiftsFileTest() + public void downloadSiftsFileTest() throws SiftsException { // Assert that file isn't yet downloaded - if already downloaded, assert it // is deleted Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId)); - File siftsFile = SiftsClient.downloadSiftsFile(testPDBId); - FileAssert.assertFile(siftsFile); - SiftsClient.downloadSiftsFile(testPDBId); + File siftsFile; + try + { + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + SiftsClient.downloadSiftsFile(testPDBId); + } catch (IOException e) + { + e.printStackTrace(); + } } + @Test(groups = { "Functional" }) public void getAllMappingAccessionTest() { @@ -156,11 +258,12 @@ public class SiftsClientTest try { - int[][] actualMapping = siftsClient.getGreedyMapping("A", testSeq, + HashMap actualMapping = siftsClient.getGreedyMapping( + "A", testSeq, null); - Assert.assertEquals(actualMapping, expectedMapping); Assert.assertEquals(testSeq.getStart(), 1); Assert.assertEquals(testSeq.getEnd(), 147); + Assert.assertEquals(actualMapping, expectedMapping); } catch (Exception e) { e.printStackTrace(); @@ -169,14 +272,209 @@ public class SiftsClientTest } @Test(groups = { "Functional" }) + private void getAtomIndexTest() + { + ArrayList atoms = new ArrayList(); + Atom atom = new Atom(u, u, u); + atom.resNumber = 43; + atom.atomIndex = 7; + atoms.add(atom); + int actualAtomIndex = siftsClient.getAtomIndex(1, atoms); + Assert.assertEquals(actualAtomIndex, -1); + actualAtomIndex = siftsClient.getAtomIndex(43, atoms); + Assert.assertEquals(actualAtomIndex, 7); + } + + @Test( + groups = { "Functional" }, + expectedExceptions = IllegalArgumentException.class) + private void getAtomIndexNullTest() + { + siftsClient.getAtomIndex(1, null); + } + + @Test(groups = { "Functional" }) + private void padWithGapsTest() + { + + } + + @Test( + groups = { "Functional" }, + expectedExceptions = SiftsException.class) + private void populateAtomPositionsNullTest1() + throws IllegalArgumentException, SiftsException + { + siftsClient.populateAtomPositions(null, null); + } + + @Test( + groups = { "Functional" }, + expectedExceptions = SiftsException.class) + private void populateAtomPositionsNullTest2() + throws IllegalArgumentException, SiftsException + { + siftsClient.populateAtomPositions("A", null); + } + + @Test(groups = { "Functional" }) public void getValidSourceDBRefTest() { + try + { + DBRefEntryI actualValidSrcDBRef = siftsClient + .getValidSourceDBRef(testSeq); + DBRefEntryI expectedDBRef = new DBRefEntry(); + expectedDBRef.setSource(DBRefSource.UNIPROT); + expectedDBRef.setAccessionId("P00221"); + expectedDBRef.setStartRes(1); + expectedDBRef.setEndRes(147); + expectedDBRef.setVersion(""); + Assert.assertEquals(actualValidSrcDBRef, expectedDBRef); + } catch (Exception e) + { + } + } + + @Test( + groups = { "Functional" }, + expectedExceptions = SiftsException.class) + public void getValidSourceDBRefExceptionTest() throws SiftsException + { + SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH"); + try + { + siftsClient.getValidSourceDBRef(invalidTestSeq); + } catch (SiftsException e) + { + throw new SiftsException(e.getMessage()); + } + } + + @Test( + groups = { "Functional" }, + expectedExceptions = SiftsException.class) + public void getValidSourceDBRefExceptionXTest() throws SiftsException + { + SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH"); + DBRefEntry invalidDBRef = new DBRefEntry(); + invalidDBRef.setAccessionId("BLAR"); + invalidTestSeq.addDBRef(invalidDBRef); + try + { + siftsClient.getValidSourceDBRef(invalidTestSeq); + } catch (SiftsException e) + { + throw new SiftsException(e.getMessage()); + } } @Test(groups = { "Functional" }) public void isValidDBRefEntryTest() { + DBRefEntryI validDBRef = new DBRefEntry(); + validDBRef.setSource(DBRefSource.UNIPROT); + validDBRef.setAccessionId("P00221"); + validDBRef.setStartRes(1); + validDBRef.setEndRes(147); + validDBRef.setVersion(""); + Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef)); + } + + @Test(groups = { "Functional" }) + public void getSiftsStructureMappingTest() + { + try + { + Assert.assertTrue(SiftsSettings.isMapWithSifts()); + StructureMapping strucMapping = siftsClient.getSiftsStructureMapping( + testSeq, testPDBId, "A"); + String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n" + + "Method: SIFTS\n\n" + + "P00221 : 1 - 97 Maps to \n" + + "1A70|A : 51 - 147\n\n" + + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n" + + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n" + + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n" + + + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n" + + " |||||||||||||||||||||||||| |||||\n" + + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" + + + "Length of alignment = 97\n" + "Percentage ID = 98.97\n"; + + Assert.assertEquals(strucMapping.getMappingDetailsOutput(), + expectedMappingOutput); + Assert.assertEquals(strucMapping.getMapping(), expectedMapping); + } catch (SiftsException e) + { + e.printStackTrace(); + } + } + + @Test(groups = { "Functional" }) + public void getEntityCountTest() + { + int actualEntityCount = siftsClient.getEntityCount(); + System.out.println("actual entity count : " + actualEntityCount); + Assert.assertEquals(actualEntityCount, 1); + } + + @Test(groups = { "Functional" }) + public void getDbAccessionIdTest() + { + String actualDbAccId = siftsClient.getDbAccessionId(); + System.out.println("Actual Db Accession Id: " + actualDbAccId); + Assert.assertEquals(actualDbAccId, "1a70"); + } + + @Test(groups = { "Functional" }) + public void getDbCoordSysTest() + { + String actualDbCoordSys = siftsClient.getDbCoordSys(); + System.out.println("Actual DbCoordSys: " + actualDbCoordSys); + Assert.assertEquals(actualDbCoordSys, "PDBe"); + } + + @Test(groups = { "Functional" }) + public void getDbSourceTest() + { + String actualDbSource = siftsClient.getDbSource(); + System.out.println("Actual DbSource: " + actualDbSource); + Assert.assertEquals(actualDbSource, "PDBe"); + } + + @Test(groups = { "Functional" }) + public void getDbVersionTest() + { + String actualDbVersion = siftsClient.getDbVersion(); + System.out.println("Actual DbVersion: " + actualDbVersion); + Assert.assertEquals(actualDbVersion, "2.0"); + } + + @Test(groups = { "Functional" }) + public void getEntityByMostOptimalMatchedIdTest() + { + SiftsClient siftsClientX = null; + PDBfile pdbFile; + try + { + pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2" + + ".pdb", DataSourceType.FILE); + siftsClientX = new SiftsClient(pdbFile); + } catch (Exception e) + { + e.printStackTrace(); + } + Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A"); + Assert.assertEquals(entityA.getEntityId(), "A"); + Entity entityB = siftsClientX.getEntityByMostOptimalMatchedId("B"); + Assert.assertEquals(entityB.getEntityId(), "C"); + Entity entityC = siftsClientX.getEntityByMostOptimalMatchedId("C"); + Assert.assertEquals(entityC.getEntityId(), "B"); + Entity entityD = siftsClientX.getEntityByMostOptimalMatchedId("D"); + Assert.assertEquals(entityD.getEntityId(), "D"); } }