test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21 package jalview.gui.structurechooser;
  22
  23 import static org.testng.Assert.assertEquals;
  24 import static org.testng.Assert.assertTrue;
  25 import static org.testng.Assert.fail;
  26
  27 import java.util.ArrayList;
  28 import java.util.List;
  29 import java.util.Vector;
  30
  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;
  38
  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.api.FTSDataColumnI;
  46 import jalview.fts.core.FTSRestRequest;
  47 import jalview.fts.core.FTSRestResponse;
  48 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  49 import jalview.fts.service.threedbeacons.TDB_FTSData;
  50 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  51 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  52 import jalview.gui.JvOptionPane;
  53 import jalview.gui.StructureChooser;
  54 import jalview.jbgui.FilterOption;
  55
  56 public class StructureChooserQuerySourceTest
  57 {
  58
  59   @BeforeClass(alwaysRun = true)
  60   public void setUpJvOptionPane()
  61   {
  62     JvOptionPane.setInteractiveMode(false);
  63     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  64   }
  65
  66   Sequence seq, upSeq, upSeq_insulin, upSeq_r1ab;
  67
  68   private Sequence upSeq_fer1_maize;
  69
  70   private Sequence upSeq_epas1_human;
  71
  72   // same set up as for structurechooser test
  73
  74   @BeforeMethod(alwaysRun = true)
  75   public void setUp() throws Exception
  76   {
  77     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  78             26);
  79     seq.createDatasetSequence();
  80     for (int x = 1; x < 5; x++)
  81     {
  82       DBRefEntry dbRef = new DBRefEntry();
  83       dbRef.setAccessionId("XYZ_" + x);
  84       seq.addDBRef(dbRef);
  85     }
  86
  87     PDBEntry dbRef = new PDBEntry();
  88     dbRef.setId("1tim");
  89
  90     Vector<PDBEntry> pdbIds = new Vector<>();
  91     pdbIds.add(dbRef);
  92
  93     seq.setPDBId(pdbIds);
  94
  95     // Uniprot sequence for 3D-Beacons mocks
  96     upSeq = new Sequence("P38398",
  97             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  98                     + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  99                     + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
 100                     + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
 101                     + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
 102                     + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
 103                     + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
 104                     + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
 105                     + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
 106                     + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
 107                     + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
 108                     + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
 109                     + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
 110                     + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 111                     + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 112                     + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 113                     + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 114                     + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 115                     + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 116                     + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 117                     + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 118                     + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 119                     + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 120                     + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 121                     + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 122                     + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 123                     + "",
 124             1, 1863);
 125     upSeq.createDatasetSequence();
 126     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 127     upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
 128
 129     upSeq_insulin = new Sequence("INS_HUMAN",
 130             "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
 131                     + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
 132     upSeq_insulin.createDatasetSequence();
 133     upSeq_insulin.setDescription("Insulin");
 134     upSeq_insulin
 135             .addDBRef(new DBRefEntry("UNIPROT", "0", "P01308", null, true));
 136
 137     upSeq_r1ab = new Sequence("R1AB_SARS2",
 138             "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIK\n"
 139                     + "RSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFD\n"
 140                     + "LGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLS\n"
 141                     + "EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRV\n"
 142                     + "EKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL\n"
 143                     + "PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIG\n"
 144                     + "CNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVE\n"
 145                     + "SCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY\n"
 146                     + "SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI\n"
 147                     + "VKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC\n"
 148                     + "VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLE\n"
 149                     + "IKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVEL\n"
 150                     + "GTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDC\n"
 151                     + "EEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEV\n"
 152                     + "QPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATN\n"
 153                     + "NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAG\n"
 154                     + "IFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQ\n"
 155                     + "RKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVL\n"
 156                     + "TAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEIL\n"
 157                     + "GTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLND\n"
 158                     + "LNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYK\n"
 159                     + "DWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVV\n"
 160                     + "DMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKW\n"
 161                     + "KYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDV\n"
 162                     + "RETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ\n"
 163                     + "ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENS\n"
 164                     + "YTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQL\n"
 165                     + "TGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWST\n"
 166                     + "KPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITE\n"
 167                     + "EVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRC\n"
 168                     + "LNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIW\n"
 169                     + "FLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSL\n"
 170                     + "ETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAP\n"
 171                     + "ISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLH\n"
 172                     + "NWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH\n"
 173                     + "FVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFD\n"
 174                     + "AYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIE\n"
 175                     + "VTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKN\n"
 176                     + "NLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIG\n"
 177                     + "YKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD\n"
 178                     + "FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDT\n"
 179                     + "RYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAV\n"
 180                     + "NLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTP\n"
 181                     + "VYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFN\n"
 182                     + "GVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALND\n"
 183                     + "FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM\n"
 184                     + "LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGS\n"
 185                     + "PSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQA\n"
 186                     + "AGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMC\n"
 187                     + "ASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQW\n"
 188                     + "SLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDT\n"
 189                     + "SLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNY\n"
 190                     + "SGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVS\n"
 191                     + "TQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLW\n"
 192                     + "AQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATA\n"
 193                     + "QEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTM\n"
 194                     + "LFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDA\n"
 195                     + "DSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTK\n"
 196                     + "GGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAA\n"
 197                     + "TVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES\n"
 198                     + "FGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ\n"
 199                     + "SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVV\n"
 200                     + "KRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKE\n"
 201                     + "ILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNW\n"
 202                     + "YDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFK\n"
 203                     + "YWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN\n"
 204                     + "LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEG\n"
 205                     + "SSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGF\n"
 206                     + "PFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLL\n"
 207                     + "KSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL\n"
 208                     + "SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV\n"
 209                     + "RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNV\n"
 210                     + "FMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAI\n"
 211                     + "DAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGA\n"
 212                     + "CVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK\n"
 213                     + "PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLS\n"
 214                     + "YGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLN\n"
 215                     + "VGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFA\n"
 216                     + "IGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALP\n"
 217                     + "ETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM\n"
 218                     + "FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRK\n"
 219                     + "AVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRD\n"
 220                     + "LYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTY\n"
 221                     + "RRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTG\n"
 222                     + "YVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM\n"
 223                     + "KYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNA\n"
 224                     + "HVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIK\n"
 225                     + "CVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNL\n"
 226                     + "PGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAV\n"
 227                     + "CRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN\n"
 228                     + "NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIG\n"
 229                     + "VCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAV\n"
 230                     + "KTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQ\n"
 231                     + "LGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSK\n"
 232                     + "VVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM\n"
 233                     + "NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGD\n"
 234                     + "CATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGH\n"
 235                     + "FAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTA\n"
 236                     + "VMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN");
 237     upSeq_r1ab.setDescription("sars2 r1ab polyprotein");
 238     upSeq_r1ab
 239             .addDBRef(new DBRefEntry("UNIPROT", "0", "P0DTD1", null, true));
 240     upSeq_r1ab.createDatasetSequence();
 241     upSeq_fer1_maize = new Sequence("FER1_MAIZE",
 242             "MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGE"
 243                     + "VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV"
 244                     + "VIETHKEEELTGA");
 245     upSeq_fer1_maize.setDescription("Feredoxin 1 Maize");
 246     upSeq_fer1_maize
 247             .addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true));
 248     upSeq_fer1_maize.createDatasetSequence();
 249
 250     upSeq_epas1_human = new Sequence("EPAS1_HUMAN",
 251             "MTADKEKKRSSSERRKEKSRDAARCRRSKETEVFYELAHELPLPHSVSSHLDKASIMRLAISFLRTHKLLSS\n"
 252                     + "VCSENESEAEADQQMDNLYLKALEGFIAVVTQDGDMIFLSENISKFMGLTQVELTGHSIFDFTHPCDHEEIR\n"
 253                     + "ENLSLKNGSGFGKKSKDMSTERDFFMRMKCTVTNRGRTVNLKSATWKVLHCTGQVKVYNNCPPHNSLCGYKE\n"
 254                     + "PLLSCLIIMCEPIQHPSHMDIPLDSKTFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSEN\n"
 255                     + "MTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKNDVVFSMDQTE\n"
 256                     + "SLFKPHLMAMNSIFDSSGKGAVSEKSNFLFTKLKEEPEELAQLAPTPGDAIISLDFGNQNFEESSAYGKAIL\n"
 257                     + "PPSQPWATELRSHSTQSEAGSLPAFTVPQAAAPGSTTPSATSSSSSCSTPNSPEDYYTSLDNDLKIEVIEKL\n"
 258                     + "FAMDTEAKDQCSTQTDFNELDLETLAPYIPMDGEDFQLSPICPEERLLAENPQSTPQHCFSAMTNIFQPLAP\n"
 259                     + "VAPHSPFLLDKFQQQLESKKTEPEHRPMSSIFFDAGSKASLPPCCGQASTPLSSMGGRSNTQWPPDPPLHFG\n"
 260                     + "PTKWAVGDQRTEFLGAAPLGPPVSPPHVSTFKTRSAKGFGARGPDVLSPAMVALSNKLKLKRQLEYEEQAFQ\n"
 261                     + "DLSGGDPPGGSTSHLMWKRMKNLRGGSCPLMPDKPLSANVPNDKFTQNPMRGLGHPLRHLPLPQPPSAISPG\n"
 262                     + "ENSKSRFPPQCYATQYQDYSLSSAHKVSGMASRLLGPSFESYLLPELTRYDCEVNVPVLGSSTLLQGGDLLR\n"
 263                     + "ALDQAT");
 264     upSeq_epas1_human
 265             .setDescription("Endothelial PAS domain-containing protein 1");
 266     upSeq_epas1_human
 267             .addDBRef(new DBRefEntry("UNIPROT", "0", "Q99814", null, true));
 268     upSeq_epas1_human.createDatasetSequence();
 269   }
 270
 271   @AfterMethod(alwaysRun = true)
 272   public void tearDown() throws Exception
 273   {
 274     seq = null;
 275     upSeq = null;
 276     upSeq_r1ab = null;
 277     upSeq_fer1_maize = null;
 278     upSeq_epas1_human = null;
 279   }
 280
 281   @SuppressWarnings("deprecation")
 282   @Test(groups = { "Functional" })
 283   public void buildPDBQueryTest()
 284   {
 285     System.out.println("seq >>>> " + seq);
 286
 287     StructureChooserQuerySource scquery = StructureChooserQuerySource
 288             .getQuerySourceFor(new SequenceI[]
 289             { seq });
 290     AssertJUnit
 291             .assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 292     String query = scquery.buildQuery(seq);
 293     AssertJUnit.assertEquals("pdb_id:1tim", query);
 294     seq.getAllPDBEntries().clear();
 295     query = scquery.buildQuery(seq);
 296     AssertJUnit.assertEquals(
 297             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 298             query);
 299     seq.setDBRefs(null);
 300     query = scquery.buildQuery(seq);
 301     System.out.println(query);
 302     AssertJUnit.assertEquals("text:4kqy", query);
 303
 304     DBRefEntry uniprotDBRef = new DBRefEntry();
 305     uniprotDBRef.setAccessionId("P12345");
 306     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 307     seq.addDBRef(uniprotDBRef);
 308
 309     DBRefEntry pdbDBRef = new DBRefEntry();
 310     pdbDBRef.setAccessionId("1XYZ");
 311     pdbDBRef.setSource(DBRefSource.PDB);
 312     seq.addDBRef(pdbDBRef);
 313
 314     for (int x = 1; x < 5; x++)
 315     {
 316       DBRefEntry dbRef = new DBRefEntry();
 317       dbRef.setAccessionId("XYZ_" + x);
 318       seq.addDBRef(dbRef);
 319     }
 320     System.out.println("");
 321     System.out.println(seq.getDBRefs());
 322     System.out.println(query);
 323     query = scquery.buildQuery(seq);
 324     AssertJUnit.assertEquals(
 325             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 326             query);
 327   }
 328
 329   @SuppressWarnings("deprecation")
 330   @Test(groups = { "Functional" })
 331   public void buildThreeDBQueryTest()
 332   {
 333     System.out.println("seq >>>> " + upSeq);
 334     TDBeaconsFTSRestClientTest.setMock();
 335     PDBFTSRestClientTest.setMock();
 336     StructureChooserQuerySource scquery = StructureChooserQuerySource
 337             .getQuerySourceFor(new SequenceI[]
 338             { upSeq });
 339     // gets the lightweight proxy rather than the
 340     // ThreeDBStructureChooserQuerySource
 341     AssertJUnit.assertTrue(
 342             scquery instanceof ThreeDBStructureChooserQuerySource);
 343     String query = scquery.buildQuery(upSeq);
 344     AssertJUnit.assertEquals("P38398", query);
 345
 346     // query shouldn't change regardless of additional entries
 347     // because 3DBeacons requires canonical entries.
 348     upSeq.getAllPDBEntries().clear();
 349     query = scquery.buildQuery(upSeq);
 350     AssertJUnit.assertEquals("P38398", query);
 351     upSeq.setDBRefs(null);
 352     query = scquery.buildQuery(upSeq);
 353     /*
 354      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 355      * graceful behaviour would be to
 356      *  - pick one ? not possible
 357      *  - iterate through all until a 200 is obtained ?
 358      *  ---> ideal but could be costly
 359      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 360      *  ----> need a test to check that accessions can be promoted to canonical!
 361      */
 362     // FIXME - need to be able to use ID to query here ?
 363     AssertJUnit.assertEquals(null, query);
 364
 365     // TODO:
 366     /**
 367      * set of sequences: - no protein -> TDB not applicable, query PDBe only
 368      * (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
 369      * -> first consider trying to get uniprot refs (need a mark to say none are
 370      * available) - protein and uniprot - no canonicals -> resolve to uniprot
 371      * automatically to get canonicals - query uniprot against 3DBeacons -->
 372      * decorate experimental structures with additional data from PDBe - query
 373      * remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
 374      * need to query twice Rank by - experimental > AlphaFold -> Model - start >
 375      * end -> filters for -> experimental only -> experimental plus best models
 376      * for other regions -> "best cover" -> need to be able to select correct
 377      * reference (the longest one that covers all) for superposition
 378      */
 379     //
 380     // DBRefEntry uniprotDBRef = new DBRefEntry();
 381     // uniprotDBRef.setAccessionId("P12345");
 382     // uniprotDBRef.setSource(DBRefSource.UNIPROT);
 383     // upSeq.addDBRef(uniprotDBRef);
 384     //
 385     // DBRefEntry pdbDBRef = new DBRefEntry();
 386     // pdbDBRef.setAccessionId("1XYZ");
 387     // pdbDBRef.setSource(DBRefSource.PDB);
 388     // upSeq.addDBRef(pdbDBRef);
 389     //
 390     // for (int x = 1; x < 5; x++)
 391     // {
 392     // DBRefEntry dbRef = new DBRefEntry();
 393     // dbRef.setAccessionId("XYZ_" + x);
 394     // seq.addDBRef(dbRef);
 395     // }
 396     // System.out.println("");
 397     // System.out.println(seq.getDBRefs());
 398     // System.out.println(query);
 399     // query = scquery.buildQuery(seq);
 400     // assertEquals(
 401     // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 402     // query);
 403   }
 404
 405   @Test(groups = { "Functional" }, dataProvider = "testUpSeqs")
 406   public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
 407   {
 408     TDBeaconsFTSRestClientTest.setMock();
 409     PDBFTSRestClientTest.setMock();
 410     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 411     PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
 412
 413     FTSRestResponse upResponse = null;
 414     List<FTSRestResponse> pdbResponse = null;
 415     // TODO test available options
 416     // Best coverage
 417     // Best Alphafold Model
 418     // Best model (by confidence score)
 419     // Will also need to develop a more sophisticated filtering system
 420     List<FilterOption> opts = tdbquery
 421             .getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
 422     FilterOption opt_singlebest = opts.get(0);
 423     FilterOption opt_manybest = opts.get(1);
 424     assertEquals(opt_singlebest.getValue(),
 425             ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
 426     assertEquals(opt_manybest.getValue(),
 427             ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
 428
 429     try
 430     {
 431       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
 432               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 433               opt_singlebest, false);
 434       tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
 435               opts, upResponse.getSearchSummary());
 436       // test ranking without additional PDBe data
 437       FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
 438               testUpSeq, upResponse.getSearchSummary(),
 439               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 440               opt_singlebest.getValue(), false);
 441       assertEquals(firstRanked.getNumberOfItemsFound(), 1);
 442       // many best response
 443       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
 444               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 445               opt_manybest, false);
 446       assertTrue(firstRanked.getSearchSummary().size() < upResponse
 447               .getSearchSummary().size());
 448       // NB Could have race condition here
 449       List<String> pdb_Queries = tdbquery.buildPDBFTSQueryFor(upResponse);
 450       assertTrue(pdb_Queries.size() > 0);
 451       for (String pdb_Query : pdb_Queries)
 452       {
 453         assertTrue(pdb_Query.trim().length() > 0);
 454       }
 455
 456       pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
 457               upResponse);
 458       // check all queries resulted in a response
 459       assertEquals(pdbResponse.size(), pdb_Queries.size());
 460       for (FTSRestResponse pdbr : pdbResponse)
 461       {
 462         assertTrue(pdbr.getNumberOfItemsFound() > 0);
 463       }
 464
 465       // and finally that join works
 466       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
 467               pdbResponse);
 468       assertEquals(upResponse.getNumberOfItemsFound(),
 469               joinedResp.getNumberOfItemsFound());
 470
 471       // Special data test case
 472       if (testUpSeq.getDisplayId(true)
 473               .equals(upSeq_epas1_human.getDisplayId(true)))
 474       {
 475
 476         TDBResultAnalyser tDBResultAnalyz = new TDBResultAnalyser(testUpSeq,
 477                 joinedResp.getSearchSummary(), tdbquery.lastTdbRequest,
 478                 ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE,
 479                 tdbquery.remove_prefix(
 480                         ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE));
 481         List<FTSData> ordered = tDBResultAnalyz.getFilteredResponse();
 482         List<FTSData> selected = tDBResultAnalyz.selectStructures(ordered);
 483         assertEquals(((TDB_FTSData) selected.get(0)).getProvider(),
 484                 "AlphaFold DB");
 485         // to be sufficient, should also
 486         // test that adjacent ordered structure in ordered is levyLab
 487         // TDB_FTSData first = (TDB_FTSData) ordered.get(0),
 488         // second = (TDB_FTSData) ordered.get(1),
 489         // third = (TDB_FTSData) ordered.get(2);
 490         // Assert.assertEquals("pLDDT", first.getConfidenceScoreType());
 491         // Assert.assertTrue(first.getConfidenceScoreType()
 492         // .equals(second.getConfidenceScoreType())); // pLDDT first and
 493         // // second
 494       }
 495
 496     } catch (
 497
 498     Exception x)
 499     {
 500       x.printStackTrace();
 501       Assert.fail("Unexpected Exception");
 502     }
 503
 504     StructureChooserQuerySource scquery = StructureChooserQuerySource
 505             .getQuerySourceFor(new SequenceI[]
 506             { testUpSeq });
 507
 508   }
 509
 510   @DataProvider(name = "testUpSeqs")
 511   public Object[][] testUpSeqs() throws Exception
 512   {
 513     setUp();
 514     return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab },
 515         { upSeq_fer1_maize },
 516         { upSeq_epas1_human } };
 517   }
 518
 519   @Test(groups = { "Functional" })
 520   public void sanitizeSeqNameTest()
 521   {
 522     String name = "ab_cdEF|fwxyz012349";
 523     AssertJUnit.assertEquals(name,
 524             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 525
 526     // remove a [nn] substring
 527     name = "abcde12[345]fg";
 528     AssertJUnit.assertEquals("abcde12fg",
 529             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 530
 531     // remove characters other than a-zA-Z0-9 | or _
 532     name = "ab[cd],.\t£$*!- \\\"@:e";
 533     AssertJUnit.assertEquals("abcde",
 534             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 535
 536     name = "abcde12[345a]fg";
 537     AssertJUnit.assertEquals("abcde12345afg",
 538             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 539   }
 540 }