+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
+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.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.StructureViewer.ViewerType;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+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.structure.StructureImportSettings.TFType;
+import junit.extensions.PA;
+
+@Test(singleThreaded = true)
public class StructureChooserTest
{
- Sequence seq;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ Sequence seq, upSeq, upSeq_nocanonical;
@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();
PDBEntry dbRef = new PDBEntry();
dbRef.setId("1tim");
- Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+ Vector<PDBEntry> 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.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
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
+ upSeq = null;
+ upSeq_nocanonical = null;
}
@Test(groups = { "Functional" })
- public void buildQueryTest()
+ public void populateFilterComboBoxTest() throws InterruptedException
{
- String query = StructureChooser.buildQuery(seq);
- System.out.println(">>>>>>>>>> query : " + query);
- assertEquals(
- "4kqy OR text:1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
- query);
- }
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
- @Test(groups = { "Functional" })
- public void populateFilterComboBoxTest()
- {
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
- sc.populateFilterComboBox();
+ ThreadwaitFor(200, sc);
+
+ // if structures are not discovered then don't
+ // populate filter options
+ sc.populateFilterComboBox(false, false);
int optionsSize = sc.getCmbFilterOption().getItemCount();
- assertEquals(3, 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");
- sc.setStructuresDiscovered(true);
- sc.populateFilterComboBox();
+ }
+ // 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();
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());
+ 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<FTSData> ss = (Collection<FTSData>) 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();
- assertTrue(sc.getDiscoveredStructuresSet() != null);
- assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
+ Collection<FTSData> ss = (Collection<FTSData>) 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));
+
+ // remove a [nn] substring
+ name = "abcde12[345]fg";
+ assertEquals("abcde12fg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
+
+ // remove characters other than a-zA-Z0-9 | or _
+ name = "ab[cd],.\t£$*!- \\\"@:e";
+ assertEquals("abcde",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
+
+ name = "abcde12[345a]fg";
+ 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<SequenceI> 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<StructureViewerBase> openViewers = Desktop.instance
+ .getStructureViewers(ap, null);
+ Assert.assertNotNull(openViewers);
+ Assert.assertEquals("Wrong number of structure viewers opened",
+ viewerNum, openViewers.size());
+ }
+
+ 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 }, };
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff