X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=54b4d719a1d382dc3fe9d9ddbcb50bf6fd64c54d;hb=c0501eaa85c0594f9275766f64de8ea44a59c368;hp=31f5f8b03aff269303f3f3e60c8de0d4ed1c874f;hpb=55ea4d59b2f4ce51f8310047dd1f8898697dde0c;p=jalview.git diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index 31f5f8b..54b4d71 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -20,31 +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 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.gui.structurechooser.PDBStructureChooserQuerySource; -import jalview.gui.structurechooser.StructureChooserQuerySource; -import jalview.jbgui.GStructureChooser.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.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.fts.api.FTSData; +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.structurechooser.PDBStructureChooserQuerySource; +import jalview.jbgui.FilterOption; import junit.extensions.PA; +@Test(singleThreaded = true) public class StructureChooserTest { @@ -55,7 +59,7 @@ public class StructureChooserTest JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - Sequence seq; + Sequence seq, upSeq, upSeq_nocanonical; @BeforeMethod(alwaysRun = true) public void setUp() throws Exception @@ -77,66 +81,80 @@ public class StructureChooserTest pdbIds.add(dbRef); seq.setPDBId(pdbIds); + + // Uniprot sequence for 3D-Beacons mocks + 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.setDescription("Breast cancer type 1 susceptibility protein"); + 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; - } - - @SuppressWarnings("deprecation") - @Test(groups = { "Functional" }) - public void buildQueryTest() - { - System.out.println("seq >>>> " + seq); - StructureChooserQuerySource scquery = StructureChooserQuerySource.getPDBfts(); - String query = scquery.buildQuery(seq); - assertEquals("pdb_id:1tim", query); - seq.getAllPDBEntries().clear(); - query = scquery.buildQuery(seq); - assertEquals( - "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy", - query); - seq.setDBRefs(null); - query = scquery.buildQuery(seq); - System.out.println(query); - assertEquals("text:4kqy", query); - - DBRefEntry uniprotDBRef = new DBRefEntry(); - uniprotDBRef.setAccessionId("P12345"); - uniprotDBRef.setSource(DBRefSource.UNIPROT); - seq.addDBRef(uniprotDBRef); - - DBRefEntry pdbDBRef = new DBRefEntry(); - pdbDBRef.setAccessionId("1XYZ"); - pdbDBRef.setSource(DBRefSource.PDB); - seq.addDBRef(pdbDBRef); - - for (int x = 1; x < 5; x++) - { - DBRefEntry dbRef = new DBRefEntry(); - dbRef.setAccessionId("XYZ_" + x); - seq.addDBRef(dbRef); - } - System.out.println(""); - System.out.println(seq.getDBRefs()); - System.out.println(query); - query = scquery.buildQuery(seq); - assertEquals( - "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz", - query); + 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(); @@ -148,36 +166,94 @@ 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"); assertNotNull(ss); assertTrue(ss.size() > 0); + } + + @Test(groups = { "Functional" }) + public void fetchStructuresInfoMockedTest() + { + TDBeaconsFTSRestClientTest.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"); + assertNotNull(ss); + 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)); } }