X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=dd5cd4ccc17b71327f3c4df537194d74692f6d0d;hb=56d72101b0584635cf539d5413db27abc8deb575;hp=dbe0906ae2c2bef04a6bc27400d6e6744e77427a;hpb=8c2df9aa1581b9fdea9ae6708f50e2a81f6efcb2;p=jalview.git diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index dbe0906..dd5cd4c 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -20,37 +20,49 @@ */ 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.io.File; +import java.util.Collection; +import java.util.List; +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.DataProvider; +import org.testng.annotations.Test; + +import jalview.api.AlignViewportI; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; 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.core.FTSRestRequest; +import jalview.fts.core.FTSRestClient; 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.StructureViewer.ViewerType; import jalview.gui.structurechooser.PDBStructureChooserQuerySource; -import jalview.gui.structurechooser.StructureChooserQuerySource; -import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource; +import jalview.io.DataSourceType; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; +import jalview.io.FileLoader; +import jalview.io.IdentifyFile; 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 jalview.structure.StructureImportSettings.TFType; import junit.extensions.PA; +@Test(singleThreaded = true) public class StructureChooserTest { @@ -61,7 +73,7 @@ public class StructureChooserTest JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - Sequence seq,upSeq; + Sequence seq, upSeq, upSeq_nocanonical; @BeforeMethod(alwaysRun = true) public void setUp() throws Exception @@ -83,58 +95,82 @@ 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" }) public void populateFilterComboBoxTest() throws InterruptedException { + TDBeaconsFTSRestClientTest.setMock(); + PDBFTSRestClientTest.setMock(); + 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(); @@ -146,13 +182,38 @@ public class StructureChooserTest FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption() .getSelectedItem(); assertEquals("Cached Structures", filterOpt.getName()); + 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()); + 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"); @@ -164,9 +225,11 @@ public class StructureChooserTest public void fetchStructuresInfoMockedTest() { TDBeaconsFTSRestClientTest.setMock(); - PDBFTSRestClient.setMock(); + 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"); @@ -174,21 +237,184 @@ 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)); + } + + @Test(groups = { "Functional" }, dataProvider = "openStructureFileParams") + public void openStructureFileForSequenceTest(String alfile, String seqid, + String sFilename, TFType tft, String paeFilename, + boolean showRefAnnotations, boolean doXferSettings, + ViewerType viewerType, int seqNum, int annNum, int viewerNum, + String propsFile) + { + Cache.loadProperties( + propsFile == null ? "test/jalview/io/testProps.jvprops" + : propsFile); + + Jalview.main( + propsFile == null ? null : new String[] + { "--props", propsFile }); + if (Desktop.instance != null) + Desktop.instance.closeAll_actionPerformed(null); + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.OK_OPTION); + + FileLoader fileLoader = new FileLoader(true); + FileFormatI format = null; + File alFile = new File(alfile); + try + { + format = new IdentifyFile().identify(alFile, DataSourceType.FILE); + } catch (FileFormatException e1) + { + Assert.fail( + "Unknown file format for '" + alFile.getAbsolutePath() + "'"); + } + + AlignFrame af = fileLoader.LoadFileWaitTillLoaded(alFile, + DataSourceType.FILE, format); + AlignmentPanel ap = af.alignPanel; + Assert.assertNotNull("No alignPanel", ap); + + AlignmentI al = ap.getAlignment(); + Assert.assertNotNull(al); + + SequenceI seq = al.findName(seqid); + Assert.assertNotNull("Sequence '" + seqid + "' not found in alignment", + seq); + + StructureChooser.openStructureFileForSequence(null, null, ap, seq, + false, sFilename, tft, paeFilename, false, showRefAnnotations, + doXferSettings, viewerType); + + List seqs = al.getSequences(); + Assert.assertNotNull(seqs); + + Assert.assertEquals("Wrong number of sequences", seqNum, seqs.size()); + + AlignViewportI av = ap.getAlignViewport(); + Assert.assertNotNull(av); + + AlignmentAnnotation[] aas = al.getAlignmentAnnotation(); + int visibleAnn = 0; + for (AlignmentAnnotation aa : aas) + { + if (aa.visible) + visibleAnn++; + } + Assert.assertEquals("Wrong number of viewed annotations", annNum, + visibleAnn); + + if (viewerNum > -1) + { + try + { + Thread.sleep(100); + } catch (InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + List openViewers = Desktop.instance + .getStructureViewers(ap, null); + Assert.assertNotNull(openViewers); + int count = 0; + for (StructureViewerBase svb : openViewers) + { + if (svb.isVisible()) + count++; + } + Assert.assertEquals("Wrong number of structure viewers opened", + viewerNum, count); + + } + + if (af != null) + { + af.setVisible(false); + af.dispose(); + } } + + @DataProvider(name = "openStructureFileParams") + public Object[][] openStructureFileParams() + { + /* + String alFile, + String seqid, + String structureFilename, + TFType tft, + String paeFilename, + boolean showRefAnnotations, + boolean doXferSettings, // false for Commands + ViewerType viewerType, + int seqNum, + int annNum, + int viewerNum, + String propsFile + */ + return new Object[][] { + /* + */ + { "examples/uniref50.fa", "FER1_SPIOL", + "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT, + "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", + true, false, null, 15, 7, 0, null }, + { "examples/uniref50.fa", "FER1_SPIOL", + "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT, + "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", + true, false, null, 15, 7, 0, null }, + { "examples/uniref50.fa", "FER1_SPIOL", + "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT, + "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", + false, false, null, 15, 4, 0, null }, + { "examples/uniref50.fa", "FER1_SPIOL", + "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT, + "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", + true, false, ViewerType.JMOL, 15, 7, 1, null }, + { "examples/uniref50.fa", "FER1_SPIOL", + "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT, + "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", + true, false, ViewerType.JMOL, 15, 7, 1, null }, + { "examples/uniref50.fa", "FER1_SPIOL", + "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT, + "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", + false, false, ViewerType.JMOL, 15, 4, 1, null }, }; + } + }