X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=54b4d719a1d382dc3fe9d9ddbcb50bf6fd64c54d;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=ad3cfc1decd19f9ff0ae31929db378f1aabe7a21;hpb=392e8fadb91582afd4c2626d1aec845b1280122a;p=jalview.git diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index ad3cfc1..54b4d71 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -20,40 +20,35 @@ */ package jalview.gui; -import static org.testng.AssertJUnit.assertEquals; +import static org.testng.Assert.assertEquals; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertTrue; + +import java.util.Collection; +import java.util.Vector; + +import org.junit.Assert; +import org.testng.annotations.AfterMethod; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.BeforeMethod; +import org.testng.annotations.Test; + import jalview.datamodel.DBRefEntry; -import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.fts.api.FTSData; -import jalview.fts.api.FTSRestClientI; import jalview.fts.core.FTSRestClient; -import jalview.fts.core.FTSRestRequest; import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.fts.service.pdb.PDBFTSRestClientTest; import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient; import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest; import jalview.gui.structurechooser.PDBStructureChooserQuerySource; -import jalview.gui.structurechooser.StructureChooserQuerySource; -import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource; import jalview.jbgui.FilterOption; -import jalview.ws.params.InvalidArgumentException; - -import java.util.Collection; -import java.util.Vector; - -import org.junit.Assert; -import org.testng.annotations.AfterMethod; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; - import junit.extensions.PA; +@Test(singleThreaded = true) public class StructureChooserTest { @@ -64,7 +59,7 @@ public class StructureChooserTest JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - Sequence seq,upSeq; + Sequence seq, upSeq, upSeq_nocanonical; @BeforeMethod(alwaysRun = true) public void setUp() throws Exception @@ -86,47 +81,53 @@ public class StructureChooserTest pdbIds.add(dbRef); seq.setPDBId(pdbIds); - + // Uniprot sequence for 3D-Beacons mocks - upSeq = new Sequence("P38398", + upSeq = new Sequence("P38398", "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n" - + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n" - + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n" - + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n" - + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n" - + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n" - + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n" - + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n" - + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n" - + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n" - + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n" - + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n" - + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n" - + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n" - + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n" - + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n" - + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n" - + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n" - + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n" - + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n" - + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n" - + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n" - + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n" - + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n" - + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n" - + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n" - + "", 1, -1863); - upSeq.createDatasetSequence(); + + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n" + + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n" + + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n" + + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n" + + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n" + + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n" + + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n" + + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n" + + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n" + + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n" + + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n" + + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n" + + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n" + + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n" + + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n" + + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n" + + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n" + + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n" + + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n" + + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n" + + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n" + + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n" + + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n" + + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n" + + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n" + + "", + 1, 1863); upSeq.setDescription("Breast cancer type 1 susceptibility protein"); - upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true)); + upSeq_nocanonical = new Sequence(upSeq); + upSeq.createDatasetSequence(); + upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true)); + + upSeq_nocanonical.createDatasetSequence(); + // not a canonical reference + upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false)); } @AfterMethod(alwaysRun = true) public void tearDown() throws Exception { seq = null; - upSeq=null; + upSeq = null; + upSeq_nocanonical = null; } @Test(groups = { "Functional" }) @@ -137,10 +138,23 @@ public class StructureChooserTest SequenceI[] selectedSeqs = new SequenceI[] { seq }; StructureChooser sc = new StructureChooser(selectedSeqs, seq, null); + ThreadwaitFor(200, sc); + + // if structures are not discovered then don't + // populate filter options sc.populateFilterComboBox(false, false); int optionsSize = sc.getCmbFilterOption().getItemCount(); - assertEquals(2, optionsSize); // if structures are not discovered then don't - // populate filter options + System.out.println("Items (no data, no cache): "); + StringBuilder items = new StringBuilder(); + for (int p = 0; p < optionsSize; p++) + { + items.append("- ") + .append(sc.getCmbFilterOption().getItemAt(p).getName()) + .append("\n"); + + } + // report items when this fails - seems to be a race condition + Assert.assertEquals(items.toString(), optionsSize, 2); sc.populateFilterComboBox(true, false); optionsSize = sc.getCmbFilterOption().getItemCount(); @@ -152,18 +166,38 @@ public class StructureChooserTest FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption() .getSelectedItem(); assertEquals("Cached Structures", filterOpt.getName()); - FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance()); + FTSRestClient + .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance()); FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance()); } + @Test(groups = { "Functional" }) + public void displayTDBQueryTest() throws InterruptedException + { + TDBeaconsFTSRestClientTest.setMock(); + PDBFTSRestClientTest.setMock(); + + SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical }; + StructureChooser sc = new StructureChooser(selectedSeqs, + upSeq_nocanonical, null); + // mock so should be quick. Exceptions from mocked PDBFTS are expected too + ThreadwaitFor(500, sc); + + assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet()); + } + @Test(groups = { "Network" }) public void fetchStructuresInfoTest() { - FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance()); + FTSRestClient + .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance()); PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance()); SequenceI[] selectedSeqs = new SequenceI[] { seq }; StructureChooser sc = new StructureChooser(selectedSeqs, seq, null); + // not mocked, wait for 2s + ThreadwaitFor(2000, sc); + sc.fetchStructuresMetaData(); Collection ss = (Collection) PA.getValue(sc, "discoveredStructuresSet"); @@ -178,6 +212,8 @@ public class StructureChooserTest PDBFTSRestClientTest.setMock(); SequenceI[] selectedSeqs = new SequenceI[] { upSeq }; StructureChooser sc = new StructureChooser(selectedSeqs, seq, null); + ThreadwaitFor(500, sc); + sc.fetchStructuresMetaData(); Collection ss = (Collection) PA.getValue(sc, "discoveredStructuresSet"); @@ -185,21 +221,39 @@ public class StructureChooserTest assertTrue(ss.size() > 0); } + private void ThreadwaitFor(int i, StructureChooser sc) + { + long timeout = i + System.currentTimeMillis(); + while (!sc.isDialogVisible() && timeout > System.currentTimeMillis()) + { + try + { + Thread.sleep(50); + } catch (InterruptedException x) + { + + } + } + } @Test(groups = { "Functional" }) public void sanitizeSeqNameTest() { String name = "ab_cdEF|fwxyz012349"; - assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name)); + assertEquals(name, + PDBStructureChooserQuerySource.sanitizeSeqName(name)); // remove a [nn] substring name = "abcde12[345]fg"; - assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name)); + assertEquals("abcde12fg", + PDBStructureChooserQuerySource.sanitizeSeqName(name)); // remove characters other than a-zA-Z0-9 | or _ name = "ab[cd],.\t£$*!- \\\"@:e"; - assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name)); + assertEquals("abcde", + PDBStructureChooserQuerySource.sanitizeSeqName(name)); name = "abcde12[345a]fg"; - assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name)); + assertEquals("abcde12345afg", + PDBStructureChooserQuerySource.sanitizeSeqName(name)); } }