+/*
+ * 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.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.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.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;
- @BeforeMethod
+ @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();
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.createDatasetSequence();
+ upSeq.setDescription("Breast cancer type 1 susceptibility protein");
+ upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
+ upSeq=null;
}
-
-
- @Test
+ @SuppressWarnings("deprecation")
+ @Test(groups = { "Functional" })
public void buildQueryTest()
{
- String query = StructureChooser.buildQuery(seq);
- System.out.println(">>>>>>>>>> query : " + query);
+ System.out.println("seq >>>> " + seq);
+
+ StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
+ assertTrue(scquery instanceof PDBStructureChooserQuerySource);
+ 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(
- "4kqy OR text:1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
+ "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
query);
}
- @Test
- public void populateFilterComboBoxTest()
+ @SuppressWarnings("deprecation")
+ @Test(groups = { "Functional" })
+ public void buildThreeDBQueryTest()
+ {
+ System.out.println("seq >>>> " + upSeq);
+ TDBeaconsFTSRestClientTest.setMock();
+ StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
+ assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
+ String query = scquery.buildQuery(upSeq);
+ assertEquals("P38398", query);
+
+ // query shouldn't change regardless of additional entries
+ // because 3DBeacons requires canonical entries.
+ upSeq.getAllPDBEntries().clear();
+ query = scquery.buildQuery(upSeq);
+ assertEquals("P38398", query);
+ upSeq.setDBRefs(null);
+ query = scquery.buildQuery(upSeq);
+ /*
+ * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
+ * graceful behaviour would be to
+ * - pick one ? not possible
+ * - iterate through all until a 200 is obtained ?
+ * ---> ideal but could be costly
+ * ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
+ * ----> need a test to check that accessions can be promoted to canonical!
+ */
+ assertEquals(null, query);
+
+ // TODO:
+//
+// DBRefEntry uniprotDBRef = new DBRefEntry();
+// uniprotDBRef.setAccessionId("P12345");
+// uniprotDBRef.setSource(DBRefSource.UNIPROT);
+// upSeq.addDBRef(uniprotDBRef);
+//
+// DBRefEntry pdbDBRef = new DBRefEntry();
+// pdbDBRef.setAccessionId("1XYZ");
+// pdbDBRef.setSource(DBRefSource.PDB);
+// upSeq.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);
+ }
+
+
+ @Test(groups = { "Functional" })
+ public void populateFilterComboBoxTest() throws InterruptedException
{
- SequenceI[] selectedSeqs = new SequenceI[]
- { seq };
- StructureChooser sc = new StructureChooser(selectedSeqs, seq,
- null);
- sc.populateFilterComboBox();
+ SequenceI[] selectedSeqs = new SequenceI[] { seq };
+ StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+ 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.setStructuresDiscovered(true);
- sc.populateFilterComboBox();
+ 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
+ @Test(groups = { "Network" })
public void fetchStructuresInfoTest()
{
- SequenceI[] selectedSeqs = new SequenceI[]
- { seq };
+ SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
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);
+
+ }
+
+ @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));
}
}
git://source.jalview.org / jalview.git / blobdiff