/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui.structurechooser;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import java.util.Collection;
import java.util.Vector;
import org.junit.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
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.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
import jalview.gui.JvOptionPane;
import jalview.jbgui.FilterOption;
public class StructureChooserQuerySourceTest
{
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
Sequence seq,upSeq;
// same set up as for structurechooser test
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
26);
seq.createDatasetSequence();
for (int x = 1; x < 5; x++)
{
DBRefEntry dbRef = new DBRefEntry();
dbRef.setAccessionId("XYZ_" + x);
seq.addDBRef(dbRef);
}
PDBEntry dbRef = new PDBEntry();
dbRef.setId("1tim");
Vector 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(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
upSeq=null;
}
@SuppressWarnings("deprecation")
@Test(groups = { "Functional" })
public void buildPDBQueryTest()
{
System.out.println("seq >>>> " + seq);
StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
String query = scquery.buildQuery(seq);
AssertJUnit.assertEquals("pdb_id:1tim", query);
seq.getAllPDBEntries().clear();
query = scquery.buildQuery(seq);
AssertJUnit.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);
AssertJUnit.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);
AssertJUnit.assertEquals(
"uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
query);
}
@SuppressWarnings("deprecation")
@Test(groups = { "Functional" })
public void buildThreeDBQueryTest()
{
System.out.println("seq >>>> " + upSeq);
TDBeaconsFTSRestClientTest.setMock();
PDBFTSRestClient.setMock();
StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
// gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
String query = scquery.buildQuery(upSeq);
AssertJUnit.assertEquals("P38398", query);
// query shouldn't change regardless of additional entries
// because 3DBeacons requires canonical entries.
upSeq.getAllPDBEntries().clear();
query = scquery.buildQuery(upSeq);
AssertJUnit.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!
*/
//FIXME - need to be able to use ID to query here ?
AssertJUnit.assertEquals(null, query);
// TODO:
/**
* set of sequences:
* - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
* - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
* - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
* - query uniprot against 3DBeacons
* --> decorate experimental structures with additional data from PDBe
* - query remaining against PDBe
* Ranking
* - 3D Beacons
* --> in memory ranking - no need to query twice
* Rank by
* - experimental > AlphaFold -> Model
* - start > end
* -> filters for
* -> experimental only
* -> experimental plus best models for other regions
* -> "best cover"
* -> need to be able to select correct reference (the longest one that covers all) for superposition
*/
//
// 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 cascadingThreeDBandPDBQuerys()
{
TDBeaconsFTSRestClientTest.setMock();
PDBFTSRestClient.setMock();
ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
FTSRestResponse upResponse = null;
FTSRestResponse pdbResponse = null;
try {
upResponse = tdbquery.fetchStructuresMetaData(upSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), null, false);
// test ranking without additional PDBe data
FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(upSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), "", false);
assertTrue(firstRanked.getNumberOfItemsFound()0);
pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
assertTrue(pdbResponse.getNumberOfItemsFound()>0);
FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
} catch (Exception x)
{
x.printStackTrace();
Assert.fail("Unexpected Exception");
}
StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
}
@Test(groups = { "Functional" })
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}