From f1ad88cc8d9b26244086e5c24b73fb80b0ff0a38 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 16 Dec 2016 16:04:52 +0000 Subject: [PATCH] JAL-2356 enhanced unit test to verify reuse (or not) of file from cache --- src/jalview/ws/sifts/SiftsClient.java | 4 +- test/jalview/ws/sifts/SiftsClientTest.java | 231 +++++++++++++--------------- 2 files changed, 106 insertions(+), 129 deletions(-) diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index c11302c..8bae5ba 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -281,6 +281,7 @@ public class SiftsClient implements SiftsClientI siftsDownloadDir.mkdirs(); } // System.out.println(">> Download ftp url : " + siftsFileFTPURL); + // long now = System.currentTimeMillis(); URL url = new URL(siftsFileFTPURL); URLConnection conn = url.openConnection(); InputStream inputStream = conn.getInputStream(); @@ -294,7 +295,8 @@ public class SiftsClient implements SiftsClientI } outputStream.close(); inputStream.close(); - // System.out.println(">>> File downloaded : " + downloadedSiftsFile); +// System.out.println(">>> File downloaded : " + downloadedSiftsFile +// + " took " + (System.currentTimeMillis() - now) + "ms"); return new File(downloadedSiftsFile); } diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index 45c5412..d805e47 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -20,6 +20,9 @@ */ 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; @@ -178,7 +181,7 @@ public class SiftsClientTest } @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"); @@ -191,15 +194,9 @@ public class SiftsClientTest 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(); - } + pdbFile = new PDBfile(false, false, false, "test/jalview/io/" + + testPDBId + ".pdb", DataSourceType.FILE); + siftsClient = new SiftsClient(pdbFile); } @AfterTest(alwaysRun = true) @@ -208,44 +205,56 @@ 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); - // test for SIFTs file caching - SiftsSettings.setCacheThresholdInDays("0"); - siftsFile = SiftsClient.getSiftsFile(testPDBId); - FileAssert.assertFile(siftsFile); - SiftsSettings.setCacheThresholdInDays("2"); - } catch (IOException e) + 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) { - 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); @@ -253,7 +262,7 @@ public class SiftsClientTest Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getGreedyMappingTest() { Assert.assertNotNull(siftsClient); @@ -279,7 +288,7 @@ public class SiftsClientTest } } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) private void getAtomIndexTest() { ArrayList atoms = new ArrayList(); @@ -294,21 +303,21 @@ public class SiftsClientTest } @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" }, +groups = { "Network" }, expectedExceptions = SiftsException.class) private void populateAtomPositionsNullTest1() throws IllegalArgumentException, SiftsException @@ -317,7 +326,7 @@ public class SiftsClientTest } @Test( - groups = { "Functional" }, +groups = { "Network" }, expectedExceptions = SiftsException.class) private void populateAtomPositionsNullTest2() throws IllegalArgumentException, SiftsException @@ -325,40 +334,29 @@ public class SiftsClientTest 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" }, +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()); - } + siftsClient.getValidSourceDBRef(invalidTestSeq); } @Test( - groups = { "Functional" }, +groups = { "Network" }, expectedExceptions = SiftsException.class) public void getValidSourceDBRefExceptionXTest() throws SiftsException { @@ -366,17 +364,10 @@ public class SiftsClientTest 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(); @@ -386,38 +377,32 @@ 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 : 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); - Assert.assertEquals(strucMapping.getMapping(), expectedMapping); - } catch (SiftsException e) - { - e.printStackTrace(); - } + 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); + Assert.assertEquals(strucMapping.getMapping(), expectedMapping); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getEntityCountTest() { int actualEntityCount = siftsClient.getEntityCount(); @@ -425,7 +410,7 @@ public class SiftsClientTest Assert.assertEquals(actualEntityCount, 1); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbAccessionIdTest() { String actualDbAccId = siftsClient.getDbAccessionId(); @@ -433,7 +418,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbAccId, "1a70"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbCoordSysTest() { String actualDbCoordSys = siftsClient.getDbCoordSys(); @@ -441,7 +426,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbCoordSys, "PDBe"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbSourceTest() { String actualDbSource = siftsClient.getDbSource(); @@ -449,7 +434,7 @@ public class SiftsClientTest Assert.assertEquals(actualDbSource, "PDBe"); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getDbVersionTest() { String actualDbVersion = siftsClient.getDbVersion(); @@ -457,20 +442,15 @@ public class SiftsClientTest Assert.assertEquals(actualDbVersion, "2.0"); } - @Test(groups = { "Functional" }) - public void getEntityByMostOptimalMatchedIdTest1() + @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", DataSourceType.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"); @@ -482,23 +462,18 @@ public class SiftsClientTest } - @Test(groups = { "Functional" }) - public void getEntityByMostOptimalMatchedIdTest2() + @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; - try - { - pdbFile = new PDBfile(false, false, false, - "test/jalview/io/3ucu.cif", DataSourceType.FILE); - siftsClientX = new SiftsClient(pdbFile); - } catch (Exception e) - { - e.printStackTrace(); - } + 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"); -- 1.7.10.2