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;
27 import java.util.Collection;
28 import java.util.Vector;
30 import org.junit.Assert;
31 import org.testng.annotations.AfterMethod;
32 import org.testng.annotations.BeforeClass;
33 import org.testng.annotations.BeforeMethod;
34 import org.testng.annotations.Test;
36 import jalview.datamodel.DBRefEntry;
37 import jalview.datamodel.PDBEntry;
38 import jalview.datamodel.Sequence;
39 import jalview.datamodel.SequenceI;
40 import jalview.fts.api.FTSData;
41 import jalview.fts.core.FTSRestClient;
42 import jalview.fts.service.pdb.PDBFTSRestClient;
43 import jalview.fts.service.pdb.PDBFTSRestClientTest;
44 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
45 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
46 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
47 import jalview.jbgui.FilterOption;
48 import junit.extensions.PA;
50 @Test(singleThreaded = true)
51 public class StructureChooserTest
54 @BeforeClass(alwaysRun = true)
55 public void setUpJvOptionPane()
57 JvOptionPane.setInteractiveMode(false);
58 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
63 @BeforeMethod(alwaysRun = true)
64 public void setUp() throws Exception
66 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
68 seq.createDatasetSequence();
69 for (int x = 1; x < 5; x++)
71 DBRefEntry dbRef = new DBRefEntry();
72 dbRef.setAccessionId("XYZ_" + x);
76 PDBEntry dbRef = new PDBEntry();
79 Vector<PDBEntry> pdbIds = new Vector<>();
84 // Uniprot sequence for 3D-Beacons mocks
85 upSeq = new Sequence("P38398",
86 "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
87 + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
88 + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
89 + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
90 + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
91 + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
92 + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
93 + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
94 + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
95 + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
96 + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
97 + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
98 + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
99 + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
100 + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
101 + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
102 + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
103 + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
104 + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
105 + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
106 + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
107 + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
108 + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
109 + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
110 + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
111 + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
114 upSeq.createDatasetSequence();
115 upSeq.setDescription("Breast cancer type 1 susceptibility protein");
116 upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
119 @AfterMethod(alwaysRun = true)
120 public void tearDown() throws Exception
126 @Test(groups = { "Functional" })
127 public void populateFilterComboBoxTest() throws InterruptedException
129 TDBeaconsFTSRestClientTest.setMock();
130 PDBFTSRestClientTest.setMock();
132 SequenceI[] selectedSeqs = new SequenceI[] { seq };
133 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
134 ThreadwaitFor(200, sc);
136 // if structures are not discovered then don't
137 // populate filter options
138 sc.populateFilterComboBox(false, false);
139 int optionsSize = sc.getCmbFilterOption().getItemCount();
140 System.out.println("Items (no data, no cache): ");
141 StringBuilder items = new StringBuilder();
142 for (int p=0;p<optionsSize;p++)
145 ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
148 // report items when this fails - seems to be a race condition
149 Assert.assertEquals(items.toString(),optionsSize,2);
151 sc.populateFilterComboBox(true, false);
152 optionsSize = sc.getCmbFilterOption().getItemCount();
153 assertTrue(optionsSize > 3); // if structures are found, filter options
154 // should be populated
156 sc.populateFilterComboBox(true, true);
157 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
158 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
160 assertEquals("Cached Structures", filterOpt.getName());
161 FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
162 FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
166 @Test(groups = { "Network" })
167 public void fetchStructuresInfoTest()
169 FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
170 PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
171 SequenceI[] selectedSeqs = new SequenceI[] { seq };
172 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
173 // not mocked, wait for 2s
174 ThreadwaitFor(2000, sc);
176 sc.fetchStructuresMetaData();
177 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
178 "discoveredStructuresSet");
180 assertTrue(ss.size() > 0);
183 @Test(groups = { "Functional" })
184 public void fetchStructuresInfoMockedTest()
186 TDBeaconsFTSRestClientTest.setMock();
187 PDBFTSRestClientTest.setMock();
188 SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
189 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
190 ThreadwaitFor(500, sc);
192 sc.fetchStructuresMetaData();
193 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
194 "discoveredStructuresSet");
196 assertTrue(ss.size() > 0);
199 private void ThreadwaitFor(int i, StructureChooser sc)
201 long timeout = i+System.currentTimeMillis();
202 while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
206 } catch (InterruptedException x)
215 @Test(groups = { "Functional" })
216 public void sanitizeSeqNameTest()
218 String name = "ab_cdEF|fwxyz012349";
219 assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
221 // remove a [nn] substring
222 name = "abcde12[345]fg";
223 assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
225 // remove characters other than a-zA-Z0-9 | or _
226 name = "ab[cd],.\t£$*!- \\\"@:e";
227 assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
229 name = "abcde12[345a]fg";
230 assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));