2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.AssertJUnit.assertNotNull;
25 import static org.testng.AssertJUnit.assertTrue;
28 import java.util.Collection;
29 import java.util.Vector;
31 import org.junit.Assert;
32 import org.testng.annotations.AfterMethod;
33 import org.testng.annotations.BeforeClass;
34 import org.testng.annotations.BeforeMethod;
35 import org.testng.annotations.Test;
37 import jalview.datamodel.DBRefEntry;
38 import jalview.datamodel.PDBEntry;
39 import jalview.datamodel.Sequence;
40 import jalview.datamodel.SequenceI;
41 import jalview.fts.api.FTSData;
42 import jalview.fts.core.FTSRestClient;
43 import jalview.fts.service.pdb.PDBFTSRestClient;
44 import jalview.fts.service.pdb.PDBFTSRestClientTest;
45 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
46 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
47 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
48 import jalview.jbgui.FilterOption;
49 import junit.extensions.PA;
51 @Test(singleThreaded = true)
52 public class StructureChooserTest
55 @BeforeClass(alwaysRun = true)
56 public void setUpJvOptionPane()
58 JvOptionPane.setInteractiveMode(false);
59 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
62 Sequence seq, upSeq, upSeq_nocanonical;
64 @BeforeMethod(alwaysRun = true)
65 public void setUp() throws Exception
67 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
69 seq.createDatasetSequence();
70 for (int x = 1; x < 5; x++)
72 DBRefEntry dbRef = new DBRefEntry();
73 dbRef.setAccessionId("XYZ_" + x);
77 PDBEntry dbRef = new PDBEntry();
80 Vector<PDBEntry> pdbIds = new Vector<>();
85 // Uniprot sequence for 3D-Beacons mocks
86 upSeq = new Sequence("P38398",
87 "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
88 + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
89 + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
90 + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
91 + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
92 + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
93 + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
94 + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
95 + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
96 + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
97 + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
98 + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
99 + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
100 + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
101 + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
102 + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
103 + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
104 + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
105 + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
106 + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
107 + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
108 + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
109 + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
110 + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
111 + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
112 + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
115 upSeq.setDescription("Breast cancer type 1 susceptibility protein");
116 upSeq_nocanonical = new Sequence(upSeq);
117 upSeq.createDatasetSequence();
118 upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
120 upSeq_nocanonical.createDatasetSequence();
121 // not a canonical reference
122 upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false));
125 @AfterMethod(alwaysRun = true)
126 public void tearDown() throws Exception
130 upSeq_nocanonical = null;
133 @Test(groups = { "Functional" })
134 public void populateFilterComboBoxTest() throws InterruptedException
136 TDBeaconsFTSRestClientTest.setMock();
137 PDBFTSRestClientTest.setMock();
139 SequenceI[] selectedSeqs = new SequenceI[] { seq };
140 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
141 ThreadwaitFor(200, sc);
143 // if structures are not discovered then don't
144 // populate filter options
145 sc.populateFilterComboBox(false, false);
146 int optionsSize = sc.getCmbFilterOption().getItemCount();
147 System.out.println("Items (no data, no cache): ");
148 StringBuilder items = new StringBuilder();
149 for (int p = 0; p < optionsSize; p++)
152 .append(sc.getCmbFilterOption().getItemAt(p).getName())
156 // report items when this fails - seems to be a race condition
157 Assert.assertEquals(items.toString(), optionsSize, 2);
159 sc.populateFilterComboBox(true, false);
160 optionsSize = sc.getCmbFilterOption().getItemCount();
161 assertTrue(optionsSize > 3); // if structures are found, filter options
162 // should be populated
164 sc.populateFilterComboBox(true, true);
165 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
166 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
168 assertEquals("Cached Structures", filterOpt.getName());
170 .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
171 FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
175 @Test(groups = { "Functional" })
176 public void displayTDBQueryTest() throws InterruptedException
178 TDBeaconsFTSRestClientTest.setMock();
179 PDBFTSRestClientTest.setMock();
181 SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
182 StructureChooser sc = new StructureChooser(selectedSeqs,
183 upSeq_nocanonical, null);
184 // mock so should be quick. Exceptions from mocked PDBFTS are expected too
185 ThreadwaitFor(500, sc);
187 assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
190 @Test(groups = { "Network" })
191 public void fetchStructuresInfoTest()
194 .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
195 PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
196 SequenceI[] selectedSeqs = new SequenceI[] { seq };
197 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
198 // not mocked, wait for 2s
199 ThreadwaitFor(2000, sc);
201 sc.fetchStructuresMetaData();
202 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
203 "discoveredStructuresSet");
205 assertTrue(ss.size() > 0);
208 @Test(groups = { "Functional" })
209 public void fetchStructuresInfoMockedTest()
211 TDBeaconsFTSRestClientTest.setMock();
212 PDBFTSRestClientTest.setMock();
213 SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
214 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
215 ThreadwaitFor(500, sc);
217 sc.fetchStructuresMetaData();
218 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
219 "discoveredStructuresSet");
221 assertTrue(ss.size() > 0);
224 private void ThreadwaitFor(int i, StructureChooser sc)
226 long timeout = i + System.currentTimeMillis();
227 while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
232 } catch (InterruptedException x)
238 @Test(groups = { "Functional" })
239 public void sanitizeSeqNameTest()
241 String name = "ab_cdEF|fwxyz012349";
243 PDBStructureChooserQuerySource.sanitizeSeqName(name));
245 // remove a [nn] substring
246 name = "abcde12[345]fg";
247 assertEquals("abcde12fg",
248 PDBStructureChooserQuerySource.sanitizeSeqName(name));
250 // remove characters other than a-zA-Z0-9 | or _
251 name = "ab[cd],.\t£$*!- \\\"@:e";
252 assertEquals("abcde",
253 PDBStructureChooserQuerySource.sanitizeSeqName(name));
255 name = "abcde12[345a]fg";
256 assertEquals("abcde12345afg",
257 PDBStructureChooserQuerySource.sanitizeSeqName(name));