X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=b50bafff15ac7fbcd2440dbb1c4df602b1d49d35;hb=207b06de28859536277608ad94897eaa526b1279;hp=28b44e128725cd000e1f325b1eed2e8da4e0c765;hpb=6971cef43ca33a794aef8e8493ba7301d921444e;p=jalview.git diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index 28b44e1..b50baff 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -20,26 +20,48 @@ */ package jalview.ws.sifts; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; + +import jalview.api.DBRefEntryI; +import jalview.bin.Cache; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; +import jalview.io.DataSourceType; +import jalview.structure.StructureMapping; +import jalview.structure.StructureMappingClient.StructureMappingException; +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.Arrays; import java.util.HashMap; +import java.util.Iterator; +import java.util.Map; import org.testng.Assert; import org.testng.FileAssert; import org.testng.annotations.AfterTest; +import org.testng.annotations.BeforeClass; 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(); + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System .getProperty("user.home") @@ -62,26 +84,123 @@ public class SiftsClientTest @BeforeTest(alwaysRun = true) public void populateExpectedMapping() throws SiftsException - { - for (int x = 1; x <= 97; x++) - { - expectedMapping.put(50 + x, new int[] { x, u }); - } - } - + { + 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() throws SiftsException + public void setUpSiftsClient() throws SiftsException, IOException { + // read test props before manipulating config + Cache.loadProperties("test/jalview/io/testProps.jvprops"); // SIFTs entries are updated weekly - so use saved SIFTs file to enforce // test reproducibility + new SiftsSettings(); SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault( "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); - - File testSiftsFile = new File("test/jalview/io/" + testPDBId - + ".xml.gz"); - PDBfile pdbFile = new PDBfile(false, false, false); - pdbFile.id = testPDBId; - siftsClient = new SiftsClient(pdbFile, testSiftsFile); + SiftsSettings.setMapWithSifts(true); + SiftsSettings.setCacheThresholdInDays("2"); + SiftsSettings.setFailSafePIDThreshold("70"); + PDBfile pdbFile; + pdbFile = new PDBfile(false, false, false, "test/jalview/io/" + + testPDBId + ".pdb", DataSourceType.FILE); + siftsClient = new SiftsClient(pdbFile); } @AfterTest(alwaysRun = true) @@ -90,44 +209,56 @@ public class SiftsClientTest siftsClient = null; } - @BeforeTest(alwaysRun = true) - public void setUpStreams() - { - System.setOut(new PrintStream(outContent)); - } - - @AfterTest(alwaysRun = true) - public void cleanUpStreams() + @Test(groups = { "Network" }) + public void getSIFTsFileTest() throws SiftsException, IOException { - System.setOut(null); - } + File siftsFile; + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + long t1 = siftsFile.lastModified(); - @Test(groups = { "Functional" }) - public void getSIFTsFileTest() throws SiftsException - { - Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId)); - SiftsClient.getSiftsFile(testPDBId); - Assert.assertFalse(outContent.toString().contains( - ">>> SIFTS File already downloaded for " + testPDBId)); + // re-read file should be returned from cache + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + long t2 = siftsFile.lastModified(); + assertEquals(t1, t2); + + /* + * force fetch by having 0 expiry of cache + * also wait one second, because file timestamp does not + * give millisecond resolution :-( + */ + synchronized (this) + { + try + { + wait(1000); + } catch (InterruptedException e) + { + } + } + SiftsSettings.setCacheThresholdInDays("0"); + siftsFile = SiftsClient.getSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + long t3 = siftsFile.lastModified(); + assertTrue(t3 > t2, "file timestamp unchanged at " + t3); - // test for SIFTs file caching - SiftsClient.getSiftsFile(testPDBId); - Assert.assertTrue(outContent.toString().contains( - ">>> SIFTS File already downloaded for " + testPDBId)); + SiftsSettings.setCacheThresholdInDays("2"); } - @Test(groups = { "Functional" }) - public void downloadSiftsFileTest() throws SiftsException + @Test(groups = { "Network" }) + public void downloadSiftsFileTest() throws SiftsException, IOException { // Assert that file isn't yet downloaded - if already downloaded, assert it // is deleted Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId)); - File siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + File siftsFile; + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); FileAssert.assertFile(siftsFile); SiftsClient.downloadSiftsFile(testPDBId); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getAllMappingAccessionTest() { Assert.assertNotNull(siftsClient); @@ -135,7 +266,7 @@ public class SiftsClientTest Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getGreedyMappingTest() { Assert.assertNotNull(siftsClient); @@ -144,19 +275,41 @@ public class SiftsClientTest // TODO delete when auto-fetching of DBRefEntry is implemented DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221"); - dbRef.setStartRes(1); - dbRef.setEndRes(147); testSeq.addDBRef(dbRef); // testSeq.setSourceDBRef(dbRef); try { HashMap actualMapping = siftsClient.getGreedyMapping( - "A", testSeq, - null); - Assert.assertEquals(actualMapping, expectedMapping); + "A", testSeq, null); Assert.assertEquals(testSeq.getStart(), 1); Assert.assertEquals(testSeq.getEnd(), 147); +<<<<<<< HEAD + // Can't do Assert.assertEquals(actualMapping, expectedMapping); + // because this fails in our version of TestNG + Assert.assertEquals(actualMapping.size(), expectedMapping.size()); + Iterator> it = expectedMapping.entrySet() + .iterator(); + while (it.hasNext()) + { + Map.Entry pair = it.next(); + Assert.assertTrue(actualMapping.containsKey(pair.getKey())); + Assert.assertEquals(actualMapping.get(pair.getKey()), + pair.getValue()); + } + +======= + // Assert.assertEquals(actualMapping, expectedMapping); + Assert.assertEquals(actualMapping.size(), expectedMapping.size()); + // Test key set + Assert.assertEquals(actualMapping.keySet(), expectedMapping.keySet()); + // Test entry set + for (int key : expectedMapping.keySet()) + { + Assert.assertTrue(Arrays.equals(expectedMapping.get(key), + actualMapping.get(key))); + } +>>>>>>> f80180a53bf16dc72ecdd4ace0f70c83cb0d274a } catch (Exception e) { e.printStackTrace(); @@ -164,42 +317,231 @@ public class SiftsClientTest } } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) private void getAtomIndexTest() { - // siftsClient.getAtomIndex(1, null); - // Assert.assertTrue(true); + 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" }, + groups = { "Network" }, expectedExceptions = IllegalArgumentException.class) private void getAtomIndexNullTest() { siftsClient.getAtomIndex(1, null); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) private void padWithGapsTest() { } - @Test(groups = { "Functional" }) - private void populateAtomPositionsTest() + @Test( +groups = { "Network" }, + expectedExceptions = StructureMappingException.class) + private void populateAtomPositionsNullTest1() + throws IllegalArgumentException, StructureMappingException { + siftsClient.populateAtomPositions(null, null); + } + @Test( +groups = { "Network" }, + expectedExceptions = StructureMappingException.class) + private void populateAtomPositionsNullTest2() + throws IllegalArgumentException, StructureMappingException + { + siftsClient.populateAtomPositions("A", null); } - @Test(groups = { "Functional" }) - public void getValidSourceDBRefTest() + @Test(groups = { "Network" }) + public void getValidSourceDBRefTest() throws SiftsException + { + DBRefEntryI actualValidSrcDBRef = siftsClient + .getValidSourceDBRef(testSeq); + DBRefEntryI expectedDBRef = new DBRefEntry(); + expectedDBRef.setSource(DBRefSource.UNIPROT); + expectedDBRef.setAccessionId("P00221"); + expectedDBRef.setVersion(""); + Assert.assertEquals(actualValidSrcDBRef, expectedDBRef); + } + + @Test( +groups = { "Network" }, + expectedExceptions = SiftsException.class) + public void getValidSourceDBRefExceptionTest() throws SiftsException { + SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH"); + siftsClient.getValidSourceDBRef(invalidTestSeq); + } + @Test( +groups = { "Network" }, + expectedExceptions = SiftsException.class) + public void getValidSourceDBRefExceptionXTest() throws SiftsException + { + SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH"); + DBRefEntry invalidDBRef = new DBRefEntry(); + invalidDBRef.setAccessionId("BLAR"); + invalidTestSeq.addDBRef(invalidDBRef); + siftsClient.getValidSourceDBRef(invalidTestSeq); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void isValidDBRefEntryTest() { + DBRefEntryI validDBRef = new DBRefEntry(); + validDBRef.setSource(DBRefSource.UNIPROT); + validDBRef.setAccessionId("P00221"); + validDBRef.setVersion(""); + Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef)); + } + + @Test(groups = { "Network" }) + public void getSiftsStructureMappingTest() + throws StructureMappingException, Exception + { + Assert.assertTrue(SiftsSettings.isMapWithSifts()); + StructureMapping strucMapping = siftsClient.getStructureMapping( + testSeq, testPDBId, "A"); + String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n" + + "Method: SIFTS\n\n" + + "P00221 : 51 - 147 Maps to \n" + + "1A70|A : 1 - 97\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); + +<<<<<<< HEAD + // Can't do Assert.assertEquals(strucMapping.getMapping(), expectedMapping); + // because this fails in our version of TestNG + Assert.assertEquals(strucMapping.getMapping().size(), + expectedMapping.size()); + Iterator> it = expectedMapping.entrySet() + .iterator(); + while (it.hasNext()) + { + Map.Entry pair = it.next(); + Assert.assertTrue(strucMapping.getMapping() + .containsKey(pair.getKey())); + Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()), + pair.getValue()); +======= + // Assert.assertEquals(strucMapping.getMapping(), expectedMapping); + Assert.assertEquals(strucMapping.getMapping().size(), + expectedMapping.size()); + // Test key set + Assert.assertEquals(strucMapping.getMapping().keySet(), + expectedMapping.keySet()); + // Test entry set + for (int key : expectedMapping.keySet()) + { + Assert.assertTrue(Arrays.equals(expectedMapping.get(key), + strucMapping.getMapping().get(key))); +>>>>>>> f80180a53bf16dc72ecdd4ace0f70c83cb0d274a + } + } + + @Test(groups = { "Network" }) + public void getEntityCountTest() + { + int actualEntityCount = siftsClient.getEntityCount(); + System.out.println("actual entity count : " + actualEntityCount); + Assert.assertEquals(actualEntityCount, 1); + } + + @Test(groups = { "Network" }) + public void getDbAccessionIdTest() + { + String actualDbAccId = siftsClient.getDbAccessionId(); + System.out.println("Actual Db Accession Id: " + actualDbAccId); + Assert.assertEquals(actualDbAccId, "1a70"); + } + + @Test(groups = { "Network" }) + public void getDbCoordSysTest() + { + String actualDbCoordSys = siftsClient.getDbCoordSys(); + System.out.println("Actual DbCoordSys: " + actualDbCoordSys); + Assert.assertEquals(actualDbCoordSys, "PDBe"); + } + + @Test(groups = { "Network" }) + public void getDbSourceTest() + { + String actualDbSource = siftsClient.getDbSource(); + System.out.println("Actual DbSource: " + actualDbSource); + Assert.assertEquals(actualDbSource, "PDBe"); + } + + @Test(groups = { "Network" }) + public void getDbVersionTest() + { + String actualDbVersion = siftsClient.getDbVersion(); + System.out.println("Actual DbVersion: " + actualDbVersion); + Assert.assertEquals(actualDbVersion, "2.0"); + } + + @Test(groups = { "Network" }) + public void getEntityByMostOptimalMatchedIdTest1() throws IOException, + SiftsException + { + SiftsClient siftsClientX = null; + PDBfile pdbFile; + pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2" + + ".pdb", DataSourceType.FILE); + siftsClientX = new SiftsClient(pdbFile); + 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"); + + } + + @Test(groups = { "Network" }) + public void getEntityByMostOptimalMatchedIdTest2() throws IOException, + SiftsException + { + // This test is for a SIFTS file in which entity A should map to chain P for + // the given PDB Id. All the other chains shouldn't be mapped as there are + // no SIFTS entity records for them. + SiftsClient siftsClientX = null; + PDBfile pdbFile; + pdbFile = new PDBfile(false, false, false, "test/jalview/io/3ucu.cif", + DataSourceType.FILE); + siftsClientX = new SiftsClient(pdbFile); + Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P"); + Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A"); + Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R"); + Assert.assertEquals(entityA.getEntityId(), "A"); + Assert.assertNotEquals(entityR, "A"); + Assert.assertNotEquals(entityP, "A"); + Assert.assertNotEquals(entityR, "R"); + Assert.assertNotEquals(entityP, "P"); + Assert.assertNull(entityR); + Assert.assertNull(entityP); } }