/*
 * 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.structurechooser;


import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;

import java.util.Collection;
import java.util.List;
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.gui.StructureChooser;
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<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(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;
    // TODO test available options
    // Best coverage
    // Best Alphafold Model
    // Best model (by confidence score)
    // Will also need to develop a more sophisticated filtering system
    List<FilterOption> opts = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
    FilterOption opt_singlebest = opts.get(0);
    FilterOption opt_manybest = opts.get(1);
    assertEquals(opt_singlebest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
    assertEquals(opt_manybest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
    
    try {
      upResponse = tdbquery.fetchStructuresMetaData(upSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt_singlebest, false);
      tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,opts,upResponse.getSearchSummary());
      // test ranking without additional PDBe data
      FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(upSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest.getValue(), false);
      assertEquals(firstRanked.getNumberOfItemsFound(),1);
      // many best response
      upResponse = tdbquery.fetchStructuresMetaData(upSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt_manybest, false);
      assertTrue(firstRanked.getNumberOfItemsFound()<upResponse.getNumberOfItemsFound());
      // NB Could have race condition here 
      String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
      assertTrue(pdb_Query.trim().length()>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));
  }
}