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
  26 import java.util.List;
  27 import java.util.Vector;
  28
  29 import org.junit.Assert;
  30 import org.testng.AssertJUnit;
  31 import org.testng.annotations.AfterMethod;
  32 import org.testng.annotations.BeforeClass;
  33 import org.testng.annotations.BeforeMethod;
  34 import org.testng.annotations.DataProvider;
  35 import org.testng.annotations.Test;
  36
  37 import jalview.datamodel.DBRefEntry;
  38 import jalview.datamodel.DBRefSource;
  39 import jalview.datamodel.PDBEntry;
  40 import jalview.datamodel.Sequence;
  41 import jalview.datamodel.SequenceI;
  42 import jalview.fts.core.FTSRestResponse;
  43 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  44 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  45 import jalview.gui.JvOptionPane;
  46 import jalview.gui.StructureChooser;
  47 import jalview.jbgui.FilterOption;
  48
  49 public class StructureChooserQuerySourceTest
  50 {
  51
  52   @BeforeClass(alwaysRun = true)
  53   public void setUpJvOptionPane()
  54   {
  55     JvOptionPane.setInteractiveMode(false);
  56     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  57   }
  58
  59   Sequence seq, upSeq, upSeq_insulin, upSeq_r1ab;
  60
  61   private Sequence upSeq_fer1_maize;
  62
  63   // same set up as for structurechooser test
  64
  65   @BeforeMethod(alwaysRun = true)
  66   public void setUp() throws Exception
  67   {
  68     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  69             26);
  70     seq.createDatasetSequence();
  71     for (int x = 1; x < 5; x++)
  72     {
  73       DBRefEntry dbRef = new DBRefEntry();
  74       dbRef.setAccessionId("XYZ_" + x);
  75       seq.addDBRef(dbRef);
  76     }
  77
  78     PDBEntry dbRef = new PDBEntry();
  79     dbRef.setId("1tim");
  80
  81     Vector<PDBEntry> pdbIds = new Vector<>();
  82     pdbIds.add(dbRef);
  83
  84     seq.setPDBId(pdbIds);
  85
  86     // Uniprot sequence for 3D-Beacons mocks
  87     upSeq = new Sequence("P38398",
  88             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  89                     + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  90                     + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  91                     + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  92                     + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  93                     + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  94                     + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  95                     + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  96                     + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  97                     + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
  98                     + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
  99                     + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
 100                     + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
 101                     + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 102                     + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 103                     + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 104                     + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 105                     + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 106                     + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 107                     + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 108                     + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 109                     + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 110                     + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 111                     + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 112                     + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 113                     + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 114                     + "",
 115             1, 1863);
 116     upSeq.createDatasetSequence();
 117     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 118     upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
 119
 120     upSeq_insulin = new Sequence("INS_HUMAN",
 121             "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
 122                     + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
 123     upSeq_insulin.createDatasetSequence();
 124     upSeq_insulin.setDescription("Insulin");
 125     upSeq_insulin
 126             .addDBRef(new DBRefEntry("UNIPROT", "0", "P01308", null, true));
 127
 128     upSeq_r1ab = new Sequence("R1AB_SARS2",
 129             "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIK\n"
 130                     + "RSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFD\n"
 131                     + "LGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLS\n"
 132                     + "EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRV\n"
 133                     + "EKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL\n"
 134                     + "PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIG\n"
 135                     + "CNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVE\n"
 136                     + "SCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY\n"
 137                     + "SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI\n"
 138                     + "VKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC\n"
 139                     + "VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLE\n"
 140                     + "IKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVEL\n"
 141                     + "GTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDC\n"
 142                     + "EEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEV\n"
 143                     + "QPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATN\n"
 144                     + "NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAG\n"
 145                     + "IFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQ\n"
 146                     + "RKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVL\n"
 147                     + "TAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEIL\n"
 148                     + "GTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLND\n"
 149                     + "LNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYK\n"
 150                     + "DWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVV\n"
 151                     + "DMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKW\n"
 152                     + "KYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDV\n"
 153                     + "RETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ\n"
 154                     + "ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENS\n"
 155                     + "YTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQL\n"
 156                     + "TGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWST\n"
 157                     + "KPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITE\n"
 158                     + "EVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRC\n"
 159                     + "LNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIW\n"
 160                     + "FLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSL\n"
 161                     + "ETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAP\n"
 162                     + "ISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLH\n"
 163                     + "NWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH\n"
 164                     + "FVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFD\n"
 165                     + "AYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIE\n"
 166                     + "VTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKN\n"
 167                     + "NLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIG\n"
 168                     + "YKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD\n"
 169                     + "FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDT\n"
 170                     + "RYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAV\n"
 171                     + "NLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTP\n"
 172                     + "VYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFN\n"
 173                     + "GVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALND\n"
 174                     + "FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM\n"
 175                     + "LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGS\n"
 176                     + "PSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQA\n"
 177                     + "AGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMC\n"
 178                     + "ASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQW\n"
 179                     + "SLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDT\n"
 180                     + "SLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNY\n"
 181                     + "SGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVS\n"
 182                     + "TQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLW\n"
 183                     + "AQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATA\n"
 184                     + "QEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTM\n"
 185                     + "LFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDA\n"
 186                     + "DSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTK\n"
 187                     + "GGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAA\n"
 188                     + "TVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES\n"
 189                     + "FGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ\n"
 190                     + "SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVV\n"
 191                     + "KRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKE\n"
 192                     + "ILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNW\n"
 193                     + "YDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFK\n"
 194                     + "YWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN\n"
 195                     + "LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEG\n"
 196                     + "SSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGF\n"
 197                     + "PFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLL\n"
 198                     + "KSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL\n"
 199                     + "SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV\n"
 200                     + "RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNV\n"
 201                     + "FMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAI\n"
 202                     + "DAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGA\n"
 203                     + "CVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK\n"
 204                     + "PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLS\n"
 205                     + "YGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLN\n"
 206                     + "VGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFA\n"
 207                     + "IGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALP\n"
 208                     + "ETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM\n"
 209                     + "FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRK\n"
 210                     + "AVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRD\n"
 211                     + "LYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTY\n"
 212                     + "RRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTG\n"
 213                     + "YVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM\n"
 214                     + "KYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNA\n"
 215                     + "HVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIK\n"
 216                     + "CVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNL\n"
 217                     + "PGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAV\n"
 218                     + "CRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN\n"
 219                     + "NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIG\n"
 220                     + "VCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAV\n"
 221                     + "KTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQ\n"
 222                     + "LGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSK\n"
 223                     + "VVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM\n"
 224                     + "NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGD\n"
 225                     + "CATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGH\n"
 226                     + "FAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTA\n"
 227                     + "VMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN");
 228     upSeq_r1ab.setDescription("sars2 r1ab polyprotein");
 229     upSeq_r1ab
 230             .addDBRef(new DBRefEntry("UNIPROT", "0", "P0DTD1", null, true));
 231     upSeq_r1ab.createDatasetSequence();
 232     upSeq_fer1_maize = new Sequence("FER1_MAIZE",
 233             "MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGE"
 234                     + "VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV"
 235                     + "VIETHKEEELTGA");
 236     upSeq_fer1_maize.setDescription("Feredoxin 1 Maize");
 237     upSeq_fer1_maize
 238             .addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true));
 239     upSeq_fer1_maize.createDatasetSequence();
 240
 241   }
 242
 243   @AfterMethod(alwaysRun = true)
 244   public void tearDown() throws Exception
 245   {
 246     seq = null;
 247     upSeq = null;
 248     upSeq_r1ab = null;
 249     upSeq_fer1_maize = null;
 250   }
 251
 252   @SuppressWarnings("deprecation")
 253   @Test(groups =
 254   { "Functional" })
 255   public void buildPDBQueryTest()
 256   {
 257     System.out.println("seq >>>> " + seq);
 258
 259     StructureChooserQuerySource scquery = StructureChooserQuerySource
 260             .getQuerySourceFor(new SequenceI[]
 261             { seq });
 262     AssertJUnit
 263             .assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 264     String query = scquery.buildQuery(seq);
 265     AssertJUnit.assertEquals("pdb_id:1tim", query);
 266     seq.getAllPDBEntries().clear();
 267     query = scquery.buildQuery(seq);
 268     AssertJUnit.assertEquals(
 269             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 270             query);
 271     seq.setDBRefs(null);
 272     query = scquery.buildQuery(seq);
 273     System.out.println(query);
 274     AssertJUnit.assertEquals("text:4kqy", query);
 275
 276     DBRefEntry uniprotDBRef = new DBRefEntry();
 277     uniprotDBRef.setAccessionId("P12345");
 278     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 279     seq.addDBRef(uniprotDBRef);
 280
 281     DBRefEntry pdbDBRef = new DBRefEntry();
 282     pdbDBRef.setAccessionId("1XYZ");
 283     pdbDBRef.setSource(DBRefSource.PDB);
 284     seq.addDBRef(pdbDBRef);
 285
 286     for (int x = 1; x < 5; x++)
 287     {
 288       DBRefEntry dbRef = new DBRefEntry();
 289       dbRef.setAccessionId("XYZ_" + x);
 290       seq.addDBRef(dbRef);
 291     }
 292     System.out.println("");
 293     System.out.println(seq.getDBRefs());
 294     System.out.println(query);
 295     query = scquery.buildQuery(seq);
 296     AssertJUnit.assertEquals(
 297             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 298             query);
 299   }
 300
 301   @SuppressWarnings("deprecation")
 302   @Test(groups =
 303   { "Functional" })
 304   public void buildThreeDBQueryTest()
 305   {
 306     System.out.println("seq >>>> " + upSeq);
 307     TDBeaconsFTSRestClientTest.setMock();
 308     PDBFTSRestClientTest.setMock();
 309     StructureChooserQuerySource scquery = StructureChooserQuerySource
 310             .getQuerySourceFor(new SequenceI[]
 311             { upSeq });
 312     // gets the lightweight proxy rather than the
 313     // ThreeDBStructureChooserQuerySource
 314     AssertJUnit.assertTrue(
 315             scquery instanceof ThreeDBStructureChooserQuerySource);
 316     String query = scquery.buildQuery(upSeq);
 317     AssertJUnit.assertEquals("P38398", query);
 318
 319     // query shouldn't change regardless of additional entries
 320     // because 3DBeacons requires canonical entries.
 321     upSeq.getAllPDBEntries().clear();
 322     query = scquery.buildQuery(upSeq);
 323     AssertJUnit.assertEquals("P38398", query);
 324     upSeq.setDBRefs(null);
 325     query = scquery.buildQuery(upSeq);
 326     /*
 327      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 328      * graceful behaviour would be to
 329      *  - pick one ? not possible
 330      *  - iterate through all until a 200 is obtained ?
 331      *  ---> ideal but could be costly
 332      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 333      *  ----> need a test to check that accessions can be promoted to canonical!
 334      */
 335     // FIXME - need to be able to use ID to query here ?
 336     AssertJUnit.assertEquals(null, query);
 337
 338     // TODO:
 339     /**
 340      * set of sequences: - no protein -> TDB not applicable, query PDBe only
 341      * (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
 342      * -> first consider trying to get uniprot refs (need a mark to say none are
 343      * available) - protein and uniprot - no canonicals -> resolve to uniprot
 344      * automatically to get canonicals - query uniprot against 3DBeacons -->
 345      * decorate experimental structures with additional data from PDBe - query
 346      * remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
 347      * need to query twice Rank by - experimental > AlphaFold -> Model - start >
 348      * end -> filters for -> experimental only -> experimental plus best models
 349      * for other regions -> "best cover" -> need to be able to select correct
 350      * reference (the longest one that covers all) for superposition
 351      */
 352     //
 353     // DBRefEntry uniprotDBRef = new DBRefEntry();
 354     // uniprotDBRef.setAccessionId("P12345");
 355     // uniprotDBRef.setSource(DBRefSource.UNIPROT);
 356     // upSeq.addDBRef(uniprotDBRef);
 357     //
 358     // DBRefEntry pdbDBRef = new DBRefEntry();
 359     // pdbDBRef.setAccessionId("1XYZ");
 360     // pdbDBRef.setSource(DBRefSource.PDB);
 361     // upSeq.addDBRef(pdbDBRef);
 362     //
 363     // for (int x = 1; x < 5; x++)
 364     // {
 365     // DBRefEntry dbRef = new DBRefEntry();
 366     // dbRef.setAccessionId("XYZ_" + x);
 367     // seq.addDBRef(dbRef);
 368     // }
 369     // System.out.println("");
 370     // System.out.println(seq.getDBRefs());
 371     // System.out.println(query);
 372     // query = scquery.buildQuery(seq);
 373     // assertEquals(
 374     // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 375     // query);
 376   }
 377
 378   @Test(groups = { "Functional" }, dataProvider = "testUpSeqs")
 379   public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
 380   {
 381     TDBeaconsFTSRestClientTest.setMock();
 382     PDBFTSRestClientTest.setMock();
 383     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 384     PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
 385
 386     FTSRestResponse upResponse = null;
 387     List<FTSRestResponse> pdbResponse = null;
 388     // TODO test available options
 389     // Best coverage
 390     // Best Alphafold Model
 391     // Best model (by confidence score)
 392     // Will also need to develop a more sophisticated filtering system
 393     List<FilterOption> opts = tdbquery
 394             .getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
 395     FilterOption opt_singlebest = opts.get(0);
 396     FilterOption opt_manybest = opts.get(1);
 397     assertEquals(opt_singlebest.getValue(),
 398             ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
 399     assertEquals(opt_manybest.getValue(),
 400             ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
 401
 402     try
 403     {
 404       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
 405               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 406               opt_singlebest, false);
 407       tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
 408               opts, upResponse.getSearchSummary());
 409       // test ranking without additional PDBe data
 410       FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
 411               testUpSeq, upResponse.getSearchSummary(),
 412               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 413               opt_singlebest.getValue(), false);
 414       assertEquals(firstRanked.getNumberOfItemsFound(), 1);
 415       // many best response
 416       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
 417               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 418               opt_manybest, false);
 419       assertTrue(firstRanked.getSearchSummary().size() < upResponse
 420               .getSearchSummary().size());
 421       // NB Could have race condition here
 422       List<String> pdb_Queries = tdbquery.buildPDBFTSQueryFor(upResponse);
 423       assertTrue(pdb_Queries.size() > 0);
 424       for (String pdb_Query : pdb_Queries)
 425       {
 426         assertTrue(pdb_Query.trim().length() > 0);
 427       }
 428
 429       pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
 430               upResponse);
 431       // check all queries resulted in a response
 432       assertEquals(pdbResponse.size(), pdb_Queries.size());
 433       for (FTSRestResponse pdbr : pdbResponse)
 434       {
 435         assertTrue(pdbr.getNumberOfItemsFound() > 0);
 436       }
 437
 438       // and finally that join works
 439       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
 440               pdbResponse);
 441       assertEquals(upResponse.getNumberOfItemsFound(),
 442               joinedResp.getNumberOfItemsFound());
 443
 444     } catch (
 445
 446     Exception x)
 447     {
 448       x.printStackTrace();
 449       Assert.fail("Unexpected Exception");
 450     }
 451
 452     StructureChooserQuerySource scquery = StructureChooserQuerySource
 453             .getQuerySourceFor(new SequenceI[]
 454             { testUpSeq });
 455
 456   }
 457
 458   @DataProvider(name = "testUpSeqs")
 459   public Object[][] testUpSeqs() throws Exception
 460   {
 461     setUp();
 462     return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab },
 463         { upSeq_fer1_maize } };
 464   }
 465
 466   @Test(groups = { "Functional" })
 467   public void sanitizeSeqNameTest()
 468   {
 469     String name = "ab_cdEF|fwxyz012349";
 470     AssertJUnit.assertEquals(name,
 471             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 472
 473     // remove a [nn] substring
 474     name = "abcde12[345]fg";
 475     AssertJUnit.assertEquals("abcde12fg",
 476             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 477
 478     // remove characters other than a-zA-Z0-9 | or _
 479     name = "ab[cd],.\t£$*!- \\\"@:e";
 480     AssertJUnit.assertEquals("abcde",
 481             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 482
 483     name = "abcde12[345a]fg";
 484     AssertJUnit.assertEquals("abcde12345afg",
 485             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 486   }
 487 }