X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=685e1bcf3bba3b37f20416c4717158f3b30739d5;hp=4c7df4677f10e2fb7bdcc4303a6126e350539c87;hb=1782673a61778d3aec570fbfc291ab21f99af7a3;hpb=32e495296239f89190828a16d8893c1e143e0a12 diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index 4c7df46..685e1bc 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -21,6 +21,7 @@ package jalview.gui; import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertTrue; import jalview.datamodel.DBRefEntry; @@ -28,23 +29,46 @@ 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.service.pdb.PDBFTSRestClient; +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; + public class StructureChooserTest { - Sequence seq; + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + Sequence seq,upSeq; @BeforeMethod(alwaysRun = true) public void setUp() throws Exception { seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26); - seq.setDatasetSequence(seq); + seq.createDatasetSequence(); for (int x = 1; x < 5; x++) { DBRefEntry dbRef = new DBRefEntry(); @@ -55,53 +79,51 @@ public class StructureChooserTest PDBEntry dbRef = new PDBEntry(); dbRef.setId("1tim"); - Vector pdbIds = new Vector(); + Vector pdbIds = new Vector<>(); 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.createDatasetSequence(); + upSeq.setDescription("Breast cancer type 1 susceptibility protein"); + upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true)); } @AfterMethod(alwaysRun = true) public void tearDown() throws Exception { seq = null; - } - - @Test(groups = { "Functional" }) - public void buildQueryTest() - { - String query = StructureChooser.buildQuery(seq); - assertEquals("pdb_id:1tim", query); - System.out.println("seq >>>> " + seq); - seq.getAllPDBEntries().clear(); - query = StructureChooser.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 = StructureChooser.buildQuery(seq); - 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); - } - query = StructureChooser.buildQuery(seq); - assertEquals( - "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz", - query); + upSeq=null; } @Test(groups = { "Functional" }) @@ -109,43 +131,66 @@ public class StructureChooserTest { SequenceI[] selectedSeqs = new SequenceI[] { seq }; StructureChooser sc = new StructureChooser(selectedSeqs, seq, null); - sc.populateFilterComboBox(false); + sc.populateFilterComboBox(false, false); int optionsSize = sc.getCmbFilterOption().getItemCount(); - assertEquals(3, optionsSize); // if structures are not discovered then don't + assertEquals(2, optionsSize); // if structures are not discovered then don't // populate filter options - sc.populateFilterComboBox(true); + sc.populateFilterComboBox(true, false); optionsSize = sc.getCmbFilterOption().getItemCount(); assertTrue(optionsSize > 3); // if structures are found, filter options // should be populated + + sc.populateFilterComboBox(true, true); + assertTrue(sc.getCmbFilterOption().getSelectedItem() != null); + FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption() + .getSelectedItem(); + assertEquals("Cached Structures", filterOpt.getName()); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void fetchStructuresInfoTest() { SequenceI[] selectedSeqs = new SequenceI[] { seq }; StructureChooser sc = new StructureChooser(selectedSeqs, seq, null); sc.fetchStructuresMetaData(); - assertTrue(sc.getDiscoveredStructuresSet() != null); - assertTrue(sc.getDiscoveredStructuresSet().size() > 0); + Collection ss = (Collection) PA.getValue(sc, + "discoveredStructuresSet"); + assertNotNull(ss); + assertTrue(ss.size() > 0); + } + @Test(groups = { "Functional" }) + public void fetchStructuresInfoMockedTest() + { + Assert.fail("Not yet implemented"); + TDBeaconsFTSRestClientTest.setMock(); + + // PDBFTSRestClient.setMock(); + SequenceI[] selectedSeqs = new SequenceI[] { upSeq }; + StructureChooser sc = new StructureChooser(selectedSeqs, seq, null); + sc.fetchStructuresMetaData(); + Collection ss = (Collection) PA.getValue(sc, + "discoveredStructuresSet"); + assertNotNull(ss); + assertTrue(ss.size() > 0); } @Test(groups = { "Functional" }) public void sanitizeSeqNameTest() { String name = "ab_cdEF|fwxyz012349"; - assertEquals(name, StructureChooser.sanitizeSeqName(name)); + assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name)); // remove a [nn] substring name = "abcde12[345]fg"; - assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name)); + assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name)); // remove characters other than a-zA-Z0-9 | or _ name = "ab[cd],.\t£$*!- \\\"@:e"; - assertEquals("abcde", StructureChooser.sanitizeSeqName(name)); + assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name)); name = "abcde12[345a]fg"; - assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name)); + assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name)); } }