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.
21 package jalview.gui.structurechooser;
24 import static org.testng.Assert.assertEquals;
25 import static org.testng.Assert.assertTrue;
27 import java.util.Collection;
28 import java.util.List;
29 import java.util.Vector;
31 import org.junit.Assert;
32 import org.testng.AssertJUnit;
33 import org.testng.annotations.AfterMethod;
34 import org.testng.annotations.BeforeClass;
35 import org.testng.annotations.BeforeMethod;
36 import org.testng.annotations.DataProvider;
37 import org.testng.annotations.Test;
39 import jalview.datamodel.DBRefEntry;
40 import jalview.datamodel.DBRefSource;
41 import jalview.datamodel.PDBEntry;
42 import jalview.datamodel.Sequence;
43 import jalview.datamodel.SequenceI;
44 import jalview.fts.api.FTSData;
45 import jalview.fts.core.FTSRestRequest;
46 import jalview.fts.core.FTSRestResponse;
47 import jalview.fts.service.pdb.PDBFTSRestClient;
48 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
49 import jalview.gui.JvOptionPane;
50 import jalview.gui.StructureChooser;
51 import jalview.jbgui.FilterOption;
53 public class StructureChooserQuerySourceTest
56 @BeforeClass(alwaysRun = true)
57 public void setUpJvOptionPane()
59 JvOptionPane.setInteractiveMode(false);
60 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
63 Sequence seq,upSeq,upSeq_insulin;
65 // same set up as for structurechooser test
67 @BeforeMethod(alwaysRun = true)
68 public void setUp() throws Exception
70 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
72 seq.createDatasetSequence();
73 for (int x = 1; x < 5; x++)
75 DBRefEntry dbRef = new DBRefEntry();
76 dbRef.setAccessionId("XYZ_" + x);
80 PDBEntry dbRef = new PDBEntry();
83 Vector<PDBEntry> pdbIds = new Vector<>();
88 // Uniprot sequence for 3D-Beacons mocks
89 upSeq = new Sequence("P38398",
90 "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
91 + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
92 + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
93 + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
94 + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
95 + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
96 + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
97 + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
98 + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
99 + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
100 + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
101 + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
102 + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
103 + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
104 + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
105 + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
106 + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
107 + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
108 + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
109 + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
110 + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
111 + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
112 + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
113 + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
114 + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
115 + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
118 upSeq.createDatasetSequence();
119 upSeq.setDescription("Breast cancer type 1 susceptibility protein");
120 upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
122 upSeq_insulin=new Sequence("INS_HUMAN",
123 "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
124 + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
125 upSeq_insulin.createDatasetSequence();
126 upSeq_insulin.setDescription("Insulin");
127 upSeq_insulin.addDBRef(new DBRefEntry("UNIPROT","0","P01308",null,true));
130 @AfterMethod(alwaysRun = true)
131 public void tearDown() throws Exception
137 @SuppressWarnings("deprecation")
138 @Test(groups = { "Functional" })
139 public void buildPDBQueryTest()
141 System.out.println("seq >>>> " + seq);
143 StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
144 AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
145 String query = scquery.buildQuery(seq);
146 AssertJUnit.assertEquals("pdb_id:1tim", query);
147 seq.getAllPDBEntries().clear();
148 query = scquery.buildQuery(seq);
149 AssertJUnit.assertEquals(
150 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
153 query = scquery.buildQuery(seq);
154 System.out.println(query);
155 AssertJUnit.assertEquals("text:4kqy", query);
157 DBRefEntry uniprotDBRef = new DBRefEntry();
158 uniprotDBRef.setAccessionId("P12345");
159 uniprotDBRef.setSource(DBRefSource.UNIPROT);
160 seq.addDBRef(uniprotDBRef);
162 DBRefEntry pdbDBRef = new DBRefEntry();
163 pdbDBRef.setAccessionId("1XYZ");
164 pdbDBRef.setSource(DBRefSource.PDB);
165 seq.addDBRef(pdbDBRef);
167 for (int x = 1; x < 5; x++)
169 DBRefEntry dbRef = new DBRefEntry();
170 dbRef.setAccessionId("XYZ_" + x);
173 System.out.println("");
174 System.out.println(seq.getDBRefs());
175 System.out.println(query);
176 query = scquery.buildQuery(seq);
177 AssertJUnit.assertEquals(
178 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
182 @SuppressWarnings("deprecation")
183 @Test(groups = { "Functional" })
184 public void buildThreeDBQueryTest()
186 System.out.println("seq >>>> " + upSeq);
187 TDBeaconsFTSRestClientTest.setMock();
188 PDBFTSRestClient.setMock();
189 StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
190 // gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
191 AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
192 String query = scquery.buildQuery(upSeq);
193 AssertJUnit.assertEquals("P38398", query);
195 // query shouldn't change regardless of additional entries
196 // because 3DBeacons requires canonical entries.
197 upSeq.getAllPDBEntries().clear();
198 query = scquery.buildQuery(upSeq);
199 AssertJUnit.assertEquals("P38398", query);
200 upSeq.setDBRefs(null);
201 query = scquery.buildQuery(upSeq);
203 * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
204 * graceful behaviour would be to
205 * - pick one ? not possible
206 * - iterate through all until a 200 is obtained ?
207 * ---> ideal but could be costly
208 * ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
209 * ----> need a test to check that accessions can be promoted to canonical!
211 //FIXME - need to be able to use ID to query here ?
212 AssertJUnit.assertEquals(null, query);
219 * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
220 * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
221 * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
222 * - query uniprot against 3DBeacons
223 * --> decorate experimental structures with additional data from PDBe
224 * - query remaining against PDBe
227 * --> in memory ranking - no need to query twice
229 * - experimental > AlphaFold -> Model
232 * -> experimental only
233 * -> experimental plus best models for other regions
235 * -> need to be able to select correct reference (the longest one that covers all) for superposition
238 // DBRefEntry uniprotDBRef = new DBRefEntry();
239 // uniprotDBRef.setAccessionId("P12345");
240 // uniprotDBRef.setSource(DBRefSource.UNIPROT);
241 // upSeq.addDBRef(uniprotDBRef);
243 // DBRefEntry pdbDBRef = new DBRefEntry();
244 // pdbDBRef.setAccessionId("1XYZ");
245 // pdbDBRef.setSource(DBRefSource.PDB);
246 // upSeq.addDBRef(pdbDBRef);
248 // for (int x = 1; x < 5; x++)
250 // DBRefEntry dbRef = new DBRefEntry();
251 // dbRef.setAccessionId("XYZ_" + x);
252 // seq.addDBRef(dbRef);
254 // System.out.println("");
255 // System.out.println(seq.getDBRefs());
256 // System.out.println(query);
257 // query = scquery.buildQuery(seq);
259 // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
262 @Test(groups= {"Functional"},dataProvider = "testUpSeqs")
263 public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
265 TDBeaconsFTSRestClientTest.setMock();
266 PDBFTSRestClient.setMock();
267 ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
268 PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
272 FTSRestResponse upResponse = null;
273 FTSRestResponse pdbResponse = null;
274 // TODO test available options
276 // Best Alphafold Model
277 // Best model (by confidence score)
278 // Will also need to develop a more sophisticated filtering system
279 List<FilterOption> opts = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
280 FilterOption opt_singlebest = opts.get(0);
281 FilterOption opt_manybest = opts.get(1);
282 assertEquals(opt_singlebest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
283 assertEquals(opt_manybest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
286 upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest, false);
287 tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,opts,upResponse.getSearchSummary());
288 // test ranking without additional PDBe data
289 FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(testUpSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest.getValue(), false);
290 assertEquals(firstRanked.getNumberOfItemsFound(),1);
291 // many best response
292 upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_manybest, false);
293 assertTrue(firstRanked.getSearchSummary().size()<upResponse.getSearchSummary().size());
294 // NB Could have race condition here
295 String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
296 assertTrue(pdb_Query.trim().length()>0);
297 pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
298 assertTrue(pdbResponse.getNumberOfItemsFound()>0);
299 FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
300 assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
303 } catch (Exception x)
306 Assert.fail("Unexpected Exception");
308 StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { testUpSeq});
312 @DataProvider(name = "testUpSeqs")
313 public Object[][] testUpSeqs() throws Exception
316 return new Object[][] { {upSeq},{upSeq_insulin}};
319 @Test(groups = { "Functional" })
320 public void sanitizeSeqNameTest()
322 String name = "ab_cdEF|fwxyz012349";
323 AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
325 // remove a [nn] substring
326 name = "abcde12[345]fg";
327 AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
329 // remove characters other than a-zA-Z0-9 | or _
330 name = "ab[cd],.\t£$*!- \\\"@:e";
331 AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
333 name = "abcde12[345a]fg";
334 AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));