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   private Sequence noUpSeq_fer1_maize;
  64
  65   // same set up as for structurechooser test
  66
  67   @BeforeMethod(alwaysRun = true)
  68   public void setUp() throws Exception
  69   {
  70     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  71             26);
  72     seq.createDatasetSequence();
  73     for (int x = 1; x < 5; x++)
  74     {
  75       DBRefEntry dbRef = new DBRefEntry();
  76       dbRef.setAccessionId("XYZ_" + x);
  77       seq.addDBRef(dbRef);
  78     }
  79
  80     PDBEntry dbRef = new PDBEntry();
  81     dbRef.setId("1tim");
  82
  83     Vector<PDBEntry> pdbIds = new Vector<>();
  84     pdbIds.add(dbRef);
  85
  86     seq.setPDBId(pdbIds);
  87
  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"
 116                     + "",
 117             1, 1863);
 118     upSeq.createDatasetSequence();
 119     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 120     upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
 121
 122     upSeq_insulin = new Sequence("INS_HUMAN",
 123             "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
 124                     + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
 125     upSeq_insulin.createDatasetSequence();
 126     upSeq_insulin.setDescription("Insulin");
 127     upSeq_insulin
 128             .addDBRef(new DBRefEntry("UNIPROT", "0", "P01308", null, true));
 129
 130     upSeq_r1ab = new Sequence("R1AB_SARS2",
 131             "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIK\n"
 132                     + "RSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFD\n"
 133                     + "LGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLS\n"
 134                     + "EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRV\n"
 135                     + "EKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL\n"
 136                     + "PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIG\n"
 137                     + "CNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVE\n"
 138                     + "SCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY\n"
 139                     + "SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI\n"
 140                     + "VKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC\n"
 141                     + "VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLE\n"
 142                     + "IKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVEL\n"
 143                     + "GTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDC\n"
 144                     + "EEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEV\n"
 145                     + "QPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATN\n"
 146                     + "NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAG\n"
 147                     + "IFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQ\n"
 148                     + "RKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVL\n"
 149                     + "TAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEIL\n"
 150                     + "GTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLND\n"
 151                     + "LNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYK\n"
 152                     + "DWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVV\n"
 153                     + "DMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKW\n"
 154                     + "KYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDV\n"
 155                     + "RETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ\n"
 156                     + "ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENS\n"
 157                     + "YTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQL\n"
 158                     + "TGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWST\n"
 159                     + "KPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITE\n"
 160                     + "EVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRC\n"
 161                     + "LNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIW\n"
 162                     + "FLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSL\n"
 163                     + "ETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAP\n"
 164                     + "ISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLH\n"
 165                     + "NWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH\n"
 166                     + "FVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFD\n"
 167                     + "AYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIE\n"
 168                     + "VTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKN\n"
 169                     + "NLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIG\n"
 170                     + "YKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD\n"
 171                     + "FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDT\n"
 172                     + "RYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAV\n"
 173                     + "NLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTP\n"
 174                     + "VYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFN\n"
 175                     + "GVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALND\n"
 176                     + "FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM\n"
 177                     + "LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGS\n"
 178                     + "PSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQA\n"
 179                     + "AGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMC\n"
 180                     + "ASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQW\n"
 181                     + "SLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDT\n"
 182                     + "SLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNY\n"
 183                     + "SGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVS\n"
 184                     + "TQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLW\n"
 185                     + "AQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATA\n"
 186                     + "QEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTM\n"
 187                     + "LFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDA\n"
 188                     + "DSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTK\n"
 189                     + "GGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAA\n"
 190                     + "TVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES\n"
 191                     + "FGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ\n"
 192                     + "SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVV\n"
 193                     + "KRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKE\n"
 194                     + "ILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNW\n"
 195                     + "YDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFK\n"
 196                     + "YWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN\n"
 197                     + "LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEG\n"
 198                     + "SSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGF\n"
 199                     + "PFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLL\n"
 200                     + "KSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL\n"
 201                     + "SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV\n"
 202                     + "RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNV\n"
 203                     + "FMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAI\n"
 204                     + "DAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGA\n"
 205                     + "CVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK\n"
 206                     + "PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLS\n"
 207                     + "YGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLN\n"
 208                     + "VGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFA\n"
 209                     + "IGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALP\n"
 210                     + "ETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM\n"
 211                     + "FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRK\n"
 212                     + "AVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRD\n"
 213                     + "LYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTY\n"
 214                     + "RRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTG\n"
 215                     + "YVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM\n"
 216                     + "KYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNA\n"
 217                     + "HVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIK\n"
 218                     + "CVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNL\n"
 219                     + "PGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAV\n"
 220                     + "CRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN\n"
 221                     + "NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIG\n"
 222                     + "VCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAV\n"
 223                     + "KTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQ\n"
 224                     + "LGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSK\n"
 225                     + "VVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM\n"
 226                     + "NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGD\n"
 227                     + "CATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGH\n"
 228                     + "FAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTA\n"
 229                     + "VMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN");
 230     upSeq_r1ab.setDescription("sars2 r1ab polyprotein");
 231     upSeq_r1ab
 232             .addDBRef(new DBRefEntry("UNIPROT", "0", "P0DTD1", null, true));
 233     upSeq_r1ab.createDatasetSequence();
 234     upSeq_fer1_maize = new Sequence("FER1_MAIZE",
 235             "MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGE"
 236                     + "VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV"
 237                     + "VIETHKEEELTGA");
 238     upSeq_fer1_maize.setDescription("Feredoxin 1 Maize");
 239     upSeq_fer1_maize
 240             .addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true));
 241     upSeq_fer1_maize.createDatasetSequence();
 242     noUpSeq_fer1_maize = new Sequence("O80429_MAIZE","MAATALSMSILRAPPPCFSSPLRLRVAVAKPLAAPMRRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL");
 243     noUpSeq_fer1_maize.setDescription("Feredoxin from a Maize");
 244     noUpSeq_fer1_maize.createDatasetSequence();
 245
 246   }
 247
 248   @AfterMethod(alwaysRun = true)
 249   public void tearDown() throws Exception
 250   {
 251     seq = null;
 252     upSeq = null;
 253     upSeq_r1ab = null;
 254     upSeq_fer1_maize = null;
 255     noUpSeq_fer1_maize = null;
 256
 257   }
 258
 259   @SuppressWarnings("deprecation")
 260   @Test(groups = { "Functional" })
 261   public void buildPDBQueryTest()
 262   {
 263     System.out.println("seq >>>> " + seq);
 264
 265     StructureChooserQuerySource scquery = StructureChooserQuerySource
 266             .getQuerySourceFor(new SequenceI[]
 267             { seq });
 268     AssertJUnit
 269             .assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 270     String query = scquery.buildQuery(seq);
 271     AssertJUnit.assertEquals("pdb_id:1tim", query);
 272     seq.getAllPDBEntries().clear();
 273     query = scquery.buildQuery(seq);
 274     AssertJUnit.assertEquals(
 275             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 276             query);
 277     seq.setDBRefs(null);
 278     query = scquery.buildQuery(seq);
 279     System.out.println(query);
 280     AssertJUnit.assertEquals("text:4kqy", query);
 281
 282     DBRefEntry uniprotDBRef = new DBRefEntry();
 283     uniprotDBRef.setAccessionId("P12345");
 284     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 285     seq.addDBRef(uniprotDBRef);
 286
 287     DBRefEntry pdbDBRef = new DBRefEntry();
 288     pdbDBRef.setAccessionId("1XYZ");
 289     pdbDBRef.setSource(DBRefSource.PDB);
 290     seq.addDBRef(pdbDBRef);
 291
 292     for (int x = 1; x < 5; x++)
 293     {
 294       DBRefEntry dbRef = new DBRefEntry();
 295       dbRef.setAccessionId("XYZ_" + x);
 296       seq.addDBRef(dbRef);
 297     }
 298     System.out.println("");
 299     System.out.println(seq.getDBRefs());
 300     System.out.println(query);
 301     query = scquery.buildQuery(seq);
 302     AssertJUnit.assertEquals(
 303             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 304             query);
 305   }
 306
 307   @SuppressWarnings("deprecation")
 308   @Test(groups = { "Functional" })
 309   public void buildThreeDBQueryTest()
 310   {
 311     System.out.println("seq >>>> " + upSeq);
 312     TDBeaconsFTSRestClientTest.setMock();
 313     PDBFTSRestClientTest.setMock();
 314     StructureChooserQuerySource scquery = StructureChooserQuerySource
 315             .getQuerySourceFor(new SequenceI[]
 316             { upSeq });
 317     // gets the lightweight proxy rather than the
 318     // ThreeDBStructureChooserQuerySource
 319     AssertJUnit.assertTrue(
 320             scquery instanceof ThreeDBStructureChooserQuerySource);
 321     String query = scquery.buildQuery(upSeq);
 322     AssertJUnit.assertEquals("P38398", query);
 323
 324     // query shouldn't change regardless of additional entries
 325     // because 3DBeacons requires canonical entries.
 326     upSeq.getAllPDBEntries().clear();
 327     query = scquery.buildQuery(upSeq);
 328     AssertJUnit.assertEquals("P38398", query);
 329     upSeq.setDBRefs(null);
 330     query = scquery.buildQuery(upSeq);
 331     /*
 332      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 333      * graceful behaviour would be to
 334      *  - pick one ? not possible
 335      *  - iterate through all until a 200 is obtained ?
 336      *  ---> ideal but could be costly
 337      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 338      *  ----> need a test to check that accessions can be promoted to canonical!
 339      */
 340     // FIXME - need to be able to use ID to query here ?
 341     AssertJUnit.assertEquals(null, query);
 342
 343     // TODO:
 344     /**
 345      * set of sequences: - no protein -> TDB not applicable, query PDBe only
 346      * (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
 347      * -> first consider trying to get uniprot refs (need a mark to say none are
 348      * available) - protein and uniprot - no canonicals -> resolve to uniprot
 349      * automatically to get canonicals - query uniprot against 3DBeacons -->
 350      * decorate experimental structures with additional data from PDBe - query
 351      * remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
 352      * need to query twice Rank by - experimental > AlphaFold -> Model - start >
 353      * end -> filters for -> experimental only -> experimental plus best models
 354      * for other regions -> "best cover" -> need to be able to select correct
 355      * reference (the longest one that covers all) for superposition
 356      */
 357     //
 358     // DBRefEntry uniprotDBRef = new DBRefEntry();
 359     // uniprotDBRef.setAccessionId("P12345");
 360     // uniprotDBRef.setSource(DBRefSource.UNIPROT);
 361     // upSeq.addDBRef(uniprotDBRef);
 362     //
 363     // DBRefEntry pdbDBRef = new DBRefEntry();
 364     // pdbDBRef.setAccessionId("1XYZ");
 365     // pdbDBRef.setSource(DBRefSource.PDB);
 366     // upSeq.addDBRef(pdbDBRef);
 367     //
 368     // for (int x = 1; x < 5; x++)
 369     // {
 370     // DBRefEntry dbRef = new DBRefEntry();
 371     // dbRef.setAccessionId("XYZ_" + x);
 372     // seq.addDBRef(dbRef);
 373     // }
 374     // System.out.println("");
 375     // System.out.println(seq.getDBRefs());
 376     // System.out.println(query);
 377     // query = scquery.buildQuery(seq);
 378     // assertEquals(
 379     // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 380     // query);
 381   }
 382
 383   @Test(groups = { "Functional" }, dataProvider = "testUpSeqs")
 384   public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
 385   {
 386     TDBeaconsFTSRestClientTest.setMock();
 387     PDBFTSRestClientTest.setMock();
 388     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 389     PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
 390
 391     FTSRestResponse upResponse = null;
 392     List<FTSRestResponse> pdbResponse = null;
 393     // TODO test available options
 394     // Best coverage
 395     // Best Alphafold Model
 396     // Best model (by confidence score)
 397     // Will also need to develop a more sophisticated filtering system
 398     List<FilterOption> opts = tdbquery
 399             .getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
 400     FilterOption opt_singlebest = opts.get(0);
 401     FilterOption opt_manybest = opts.get(1);
 402     assertEquals(opt_singlebest.getValue(),
 403             ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
 404     assertEquals(opt_manybest.getValue(),
 405             ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
 406
 407     try
 408     {
 409       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
 410               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 411               opt_singlebest, false);
 412       tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
 413               opts, upResponse.getSearchSummary());
 414       // test ranking without additional PDBe data
 415       FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
 416               testUpSeq, upResponse.getSearchSummary(),
 417               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 418               opt_singlebest.getValue(), false);
 419       assertEquals(firstRanked.getNumberOfItemsFound(), 1);
 420       // many best response
 421       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
 422               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 423               opt_manybest, false);
 424       assertTrue(firstRanked.getSearchSummary().size() < upResponse
 425               .getSearchSummary().size());
 426       // NB Could have race condition here
 427       List<String> pdb_Queries = tdbquery.buildPDBFTSQueryFor(upResponse);
 428       assertTrue(pdb_Queries.size() > 0);
 429       for (String pdb_Query : pdb_Queries)
 430       {
 431         assertTrue(pdb_Query.trim().length() > 0);
 432       }
 433
 434       pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
 435               upResponse);
 436       // check all queries resulted in a response
 437       assertEquals(pdbResponse.size(), pdb_Queries.size());
 438       for (FTSRestResponse pdbr : pdbResponse)
 439       {
 440         assertTrue(pdbr.getNumberOfItemsFound() > 0);
 441       }
 442
 443       // and finally that join works
 444       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
 445               pdbResponse);
 446       assertEquals(upResponse.getNumberOfItemsFound(),
 447               joinedResp.getNumberOfItemsFound());
 448
 449     } catch (
 450
 451     Exception x)
 452     {
 453       x.printStackTrace();
 454       Assert.fail("Unexpected Exception");
 455     }
 456
 457     StructureChooserQuerySource scquery = StructureChooserQuerySource
 458             .getQuerySourceFor(new SequenceI[]
 459             { testUpSeq });
 460
 461   }
 462
 463   @Test
 464   public void testTdbWithNoUpSeq()
 465   {
 466     // verify that a
 467     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 468
 469     Assert.fail("Not yet implemented.");
 470   }
 471
 472   @DataProvider(name = "testUpSeqs")
 473   public Object[][] testUpSeqs() throws Exception
 474   {
 475     setUp();
 476     return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab },
 477         { upSeq_fer1_maize }, {noUpSeq_fer1_maize }};
 478   }
 479
 480   @Test(groups = { "Functional" })
 481   public void sanitizeSeqNameTest()
 482   {
 483     String name = "ab_cdEF|fwxyz012349";
 484     AssertJUnit.assertEquals(name,
 485             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 486
 487     // remove a [nn] substring
 488     name = "abcde12[345]fg";
 489     AssertJUnit.assertEquals("abcde12fg",
 490             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 491
 492     // remove characters other than a-zA-Z0-9 | or _
 493     name = "ab[cd],.\t£$*!- \\\"@:e";
 494     AssertJUnit.assertEquals("abcde",
 495             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 496
 497     name = "abcde12[345a]fg";
 498     AssertJUnit.assertEquals("abcde12345afg",
 499             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 500   }
 501 }