X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=44a6a0258fc378e6ae26f313ad4da00f5d7a8663;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=d3b485e867292fd684304d9f12e590a2bac25f0e;hpb=4bdfd889545ff56e3b697f7b59b0c5320cf6028f;p=jalview.git diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index d3b485e..44a6a02 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -20,13 +20,17 @@ */ 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.io.AppletFormatAdapter; +import jalview.gui.JvOptionPane; +import jalview.io.DataSourceType; import jalview.structure.StructureMapping; import jalview.xml.binding.sifts.Entry.Entity; @@ -34,33 +38,42 @@ import java.io.File; import java.io.IOException; import java.util.ArrayList; 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; +import mc_view.Atom; +import mc_view.PDBfile; public class SiftsClientTest { + @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") - + File.separatorChar + .getProperty("user.home") + File.separatorChar + ".sifts_downloads" + File.separatorChar; private String testPDBId = "1a70"; private SiftsClient siftsClient = null; - SequenceI testSeq = new Sequence( - "P00221", + SequenceI testSeq = new Sequence("P00221", "MAAT..TTTMMG..MATTFVPKPQAPPMMAALPSNTGR..SLFGLKT.GSR..GGRMTMA" + "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD" - + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", 1, 147); + + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", + 1, 147); int u = SiftsClient.UNASSIGNED; @@ -68,129 +81,123 @@ public class SiftsClientTest @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 }); - } - + { + expectedMapping.put(51, new int[] { 1, 2, 1 }); + expectedMapping.put(52, new int[] { 2, 7, 2 }); + expectedMapping.put(53, new int[] { 3, 12, 3 }); + expectedMapping.put(54, new int[] { 4, 24, 4 }); + expectedMapping.put(55, new int[] { 5, 33, 5 }); + expectedMapping.put(56, new int[] { 6, 40, 6 }); + expectedMapping.put(57, new int[] { 7, 47, 7 }); + expectedMapping.put(58, new int[] { 8, 55, 8 }); + expectedMapping.put(59, new int[] { 9, 62, 9 }); + expectedMapping.put(60, new int[] { 10, 69, 10 }); + expectedMapping.put(61, new int[] { 11, 76, 11 }); + expectedMapping.put(62, new int[] { 12, 83, 12 }); + expectedMapping.put(63, new int[] { 13, 87, 13 }); + expectedMapping.put(64, new int[] { 14, 95, 14 }); + expectedMapping.put(65, new int[] { 15, 102, 15 }); + expectedMapping.put(66, new int[] { 16, 111, 16 }); + expectedMapping.put(67, new int[] { 17, 122, 17 }); + expectedMapping.put(68, new int[] { 18, 131, 18 }); + expectedMapping.put(69, new int[] { 19, 137, 19 }); + expectedMapping.put(70, new int[] { 20, 144, 20 }); + expectedMapping.put(71, new int[] { 21, 152, 21 }); + expectedMapping.put(72, new int[] { 22, 160, 22 }); + expectedMapping.put(73, new int[] { 23, 167, 23 }); + expectedMapping.put(74, new int[] { 24, 179, 24 }); + expectedMapping.put(75, new int[] { 25, 187, 25 }); + expectedMapping.put(76, new int[] { 26, 195, 26 }); + expectedMapping.put(77, new int[] { 27, 203, 27 }); + expectedMapping.put(78, new int[] { 28, 208, 28 }); + expectedMapping.put(79, new int[] { 29, 213, 29 }); + expectedMapping.put(80, new int[] { 30, 222, 30 }); + expectedMapping.put(81, new int[] { 31, 231, 31 }); + expectedMapping.put(82, new int[] { 32, 240, 32 }); + expectedMapping.put(83, new int[] { 33, 244, 33 }); + expectedMapping.put(84, new int[] { 34, 252, 34 }); + expectedMapping.put(85, new int[] { 35, 260, 35 }); + expectedMapping.put(86, new int[] { 36, 268, 36 }); + expectedMapping.put(87, new int[] { 37, 275, 37 }); + expectedMapping.put(88, new int[] { 38, 287, 38 }); + expectedMapping.put(89, new int[] { 39, 293, 39 }); + expectedMapping.put(90, new int[] { 40, 299, 40 }); + expectedMapping.put(91, new int[] { 41, 310, 41 }); + expectedMapping.put(92, new int[] { 42, 315, 42 }); + expectedMapping.put(93, new int[] { 43, 319, 43 }); + expectedMapping.put(94, new int[] { 44, 325, 44 }); + expectedMapping.put(95, new int[] { 45, 331, 45 }); + expectedMapping.put(96, new int[] { 46, 337, 46 }); + expectedMapping.put(97, new int[] { 47, 343, 47 }); + expectedMapping.put(98, new int[] { 48, 349, 48 }); + expectedMapping.put(99, new int[] { 49, 354, 49 }); + expectedMapping.put(100, new int[] { 50, 358, 50 }); + expectedMapping.put(101, new int[] { 51, 367, 51 }); + expectedMapping.put(102, new int[] { 52, 375, 52 }); + expectedMapping.put(103, new int[] { 53, 384, 53 }); + expectedMapping.put(104, new int[] { 54, 391, 54 }); + expectedMapping.put(105, new int[] { 55, 395, 55 }); + expectedMapping.put(106, new int[] { 56, 401, 56 }); + expectedMapping.put(107, new int[] { 57, 409, 57 }); + expectedMapping.put(108, new int[] { 58, 417, 58 }); + expectedMapping.put(109, new int[] { 59, 426, 59 }); + expectedMapping.put(110, new int[] { 60, 434, 60 }); + expectedMapping.put(111, new int[] { 61, 442, 61 }); + expectedMapping.put(112, new int[] { 62, 451, 62 }); + expectedMapping.put(113, new int[] { 63, 457, 63 }); + expectedMapping.put(114, new int[] { 64, 468, 64 }); + expectedMapping.put(115, new int[] { 65, 476, 65 }); + expectedMapping.put(116, new int[] { 66, 484, 66 }); + expectedMapping.put(117, new int[] { 67, 492, 67 }); + expectedMapping.put(118, new int[] { 68, 500, 68 }); + expectedMapping.put(119, new int[] { 69, 509, 69 }); + expectedMapping.put(120, new int[] { 70, 517, 70 }); + expectedMapping.put(121, new int[] { 71, 525, 71 }); + expectedMapping.put(122, new int[] { 72, 534, 72 }); + expectedMapping.put(123, new int[] { 73, 538, 73 }); + expectedMapping.put(124, new int[] { 74, 552, 74 }); + expectedMapping.put(125, new int[] { 75, 559, 75 }); + expectedMapping.put(126, new int[] { 76, 567, 76 }); + expectedMapping.put(127, new int[] { 77, 574, 77 }); + expectedMapping.put(128, new int[] { 78, 580, 78 }); + expectedMapping.put(129, new int[] { 79, 585, 79 }); + expectedMapping.put(130, new int[] { 80, 590, 80 }); + expectedMapping.put(131, new int[] { 81, 602, 81 }); + expectedMapping.put(132, new int[] { 82, 609, 82 }); + expectedMapping.put(133, new int[] { 83, 616, 83 }); + expectedMapping.put(134, new int[] { 84, 622, 84 }); + expectedMapping.put(135, new int[] { 85, 630, 85 }); + expectedMapping.put(136, new int[] { 86, 637, 86 }); + expectedMapping.put(137, new int[] { 87, 644, 87 }); + expectedMapping.put(138, new int[] { 88, 652, 88 }); + expectedMapping.put(139, new int[] { 89, 661, 89 }); + expectedMapping.put(140, new int[] { 90, 668, 90 }); + expectedMapping.put(141, new int[] { 91, 678, 91 }); + expectedMapping.put(142, new int[] { 92, 687, 92 }); + expectedMapping.put(143, new int[] { 93, 696, 93 }); + expectedMapping.put(144, new int[] { 94, 705, 94 }); + expectedMapping.put(145, new int[] { 95, 714, 95 }); + expectedMapping.put(146, new int[] { 96, 722, 96 }); + expectedMapping.put(147, new int[] { 97, 729, 97 }); + } + @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)); + 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", AppletFormatAdapter.FILE); - siftsClient = new SiftsClient(pdbFile); - } catch (Exception e) - { - e.printStackTrace(); - } + pdbFile = new PDBfile(false, false, false, + "test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE); + siftsClient = new SiftsClient(pdbFile); } @AfterTest(alwaysRun = true) @@ -199,45 +206,56 @@ public class SiftsClientTest siftsClient = null; } - @Test(groups = { "Functional" }) - public void getSIFTsFileTest() throws SiftsException + @Test(groups = { "Network" }) + public void getSIFTsFileTest() throws SiftsException, IOException { File siftsFile; - try + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + long t1 = siftsFile.lastModified(); + + // 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) { - 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(); + 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); + + 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; - try - { - siftsFile = SiftsClient.downloadSiftsFile(testPDBId); - FileAssert.assertFile(siftsFile); - SiftsClient.downloadSiftsFile(testPDBId); - } catch (IOException e) - { - e.printStackTrace(); - } + siftsFile = SiftsClient.downloadSiftsFile(testPDBId); + FileAssert.assertFile(siftsFile); + SiftsClient.downloadSiftsFile(testPDBId); } - - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getAllMappingAccessionTest() { Assert.assertNotNull(siftsClient); @@ -245,7 +263,7 @@ public class SiftsClientTest Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getGreedyMappingTest() { Assert.assertNotNull(siftsClient); @@ -259,12 +277,23 @@ public class SiftsClientTest try { - HashMap actualMapping = siftsClient.getGreedyMapping( - "A", testSeq, - null); + HashMap actualMapping = siftsClient + .getGreedyMapping("A", testSeq, null); Assert.assertEquals(testSeq.getStart(), 1); Assert.assertEquals(testSeq.getEnd(), 147); - Assert.assertEquals(actualMapping, expectedMapping); + // 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()); + } + } catch (Exception e) { e.printStackTrace(); @@ -272,7 +301,7 @@ public class SiftsClientTest } } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) private void getAtomIndexTest() { ArrayList atoms = new ArrayList(); @@ -281,95 +310,70 @@ public class SiftsClientTest atom.atomIndex = 7; atoms.add(atom); int actualAtomIndex = siftsClient.getAtomIndex(1, atoms); - Assert.assertEquals(actualAtomIndex, -1); + Assert.assertEquals(actualAtomIndex, siftsClient.UNASSIGNED); 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" }, - expectedExceptions = SiftsException.class) + @Test(groups = { "Network" }, expectedExceptions = SiftsException.class) private void populateAtomPositionsNullTest1() throws IllegalArgumentException, SiftsException { - siftsClient.populateAtomPositions(null, null); + siftsClient.populateAtomPositions(null, null); } - @Test( - groups = { "Functional" }, - expectedExceptions = SiftsException.class) + @Test(groups = { "Network" }, expectedExceptions = SiftsException.class) private void populateAtomPositionsNullTest2() throws IllegalArgumentException, SiftsException { siftsClient.populateAtomPositions("A", null); } - @Test(groups = { "Functional" }) - public void getValidSourceDBRefTest() + @Test(groups = { "Network" }) + public void getValidSourceDBRefTest() throws SiftsException { - try - { - DBRefEntryI actualValidSrcDBRef = siftsClient - .getValidSourceDBRef(testSeq); - DBRefEntryI expectedDBRef = new DBRefEntry(); - expectedDBRef.setSource(DBRefSource.UNIPROT); - expectedDBRef.setAccessionId("P00221"); - expectedDBRef.setVersion(""); - Assert.assertEquals(actualValidSrcDBRef, expectedDBRef); - } catch (Exception e) - { - } + DBRefEntryI actualValidSrcDBRef = siftsClient + .getValidSourceDBRef(testSeq); + DBRefEntryI expectedDBRef = new DBRefEntry(); + expectedDBRef.setSource(DBRefSource.UNIPROT); + expectedDBRef.setAccessionId("P00221"); + expectedDBRef.setVersion(""); + Assert.assertEquals(actualValidSrcDBRef, expectedDBRef); } - @Test( - groups = { "Functional" }, - expectedExceptions = SiftsException.class) + @Test(groups = { "Network" }, 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()); - } + SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH"); + siftsClient.getValidSourceDBRef(invalidTestSeq); } - @Test( - groups = { "Functional" }, - expectedExceptions = SiftsException.class) + @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); - try - { - siftsClient.getValidSourceDBRef(invalidTestSeq); - } catch (SiftsException e) - { - throw new SiftsException(e.getMessage()); - } - + siftsClient.getValidSourceDBRef(invalidTestSeq); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void isValidDBRefEntryTest() { DBRefEntryI validDBRef = new DBRefEntry(); @@ -379,38 +383,45 @@ public class SiftsClientTest Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef)); } - @Test(groups = { "Functional" }) - public void getSiftsStructureMappingTest() + @Test(groups = { "Network" }) + public void getSiftsStructureMappingTest() throws SiftsException { - 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) + Assert.assertTrue(SiftsSettings.isMapWithSifts()); + StructureMapping strucMapping = siftsClient + .getSiftsStructureMapping(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); + + // 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()) { - e.printStackTrace(); + Map.Entry pair = it.next(); + Assert.assertTrue( + strucMapping.getMapping().containsKey(pair.getKey())); + Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()), + pair.getValue()); } } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getEntityCountTest() { int actualEntityCount = siftsClient.getEntityCount(); @@ -418,7 +429,7 @@ public class SiftsClientTest Assert.assertEquals(actualEntityCount, 1); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbAccessionIdTest() { String actualDbAccId = siftsClient.getDbAccessionId(); @@ -426,7 +437,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbAccId, "1a70"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbCoordSysTest() { String actualDbCoordSys = siftsClient.getDbCoordSys(); @@ -434,7 +445,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbCoordSys, "PDBe"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbSourceTest() { String actualDbSource = siftsClient.getDbSource(); @@ -442,7 +453,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbSource, "PDBe"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbVersionTest() { String actualDbVersion = siftsClient.getDbVersion(); @@ -450,20 +461,15 @@ public class SiftsClientTest Assert.assertEquals(actualDbVersion, "2.0"); } - @Test(groups = { "Functional" }) - public void getEntityByMostOptimalMatchedIdTest() + @Test(groups = { "Network" }) + public void getEntityByMostOptimalMatchedIdTest1() + throws IOException, SiftsException { SiftsClient siftsClientX = null; PDBfile pdbFile; - try - { - pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2" - + ".pdb", AppletFormatAdapter.FILE); - siftsClientX = new SiftsClient(pdbFile); - } catch (Exception e) - { - e.printStackTrace(); - } + 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"); @@ -474,4 +480,43 @@ public class SiftsClientTest 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); + + } + + @Test(groups = { "Network" }) + public void getLeadingIntegerFromString() + { + Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234abcd", -1), + 1234); + Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234", -1), + 1234); + Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd", -1), -1); + Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd1234", -1), + -1); + Assert.assertEquals(SiftsClient.getLeadingIntegerValue("None", -1), -1); + Assert.assertEquals(SiftsClient.getLeadingIntegerValue("Null", -1), -1); + } }