t/unit_mech/Controller/Project/Secretom/Secretary.t

   1 use strict;
   2 use warnings;
   3 use Test::More;
   4
   5 use HTTP::Request::Common;
   6
   7 use lib 't/lib';
   8 use SGN::Test qw/ request /;
   9 BEGIN { use_ok 'SGN::Controller::Project::Secretom::SecreTary' }
  10
  11 ok( request('/secretom/secretary')->is_success, 'Request should succeed' );
  12
  13 my $test_data = <<'';
  14 >AT1G73440.1 AI22=4.545 Gravy22=-1.4545 nR=2 nS=10 nT=0 nDRQPEN=7 Nitrogen=28 Oxygen=42
  15 MARGESEGESSGSERESSSSSSGNESEPTKGTISKYEKQRLSRIAENKARLDALGISKAAKALLSPSPVSKKRRVKRNSGEEDDDYTPVIADGDGDEDDDEVEEIDEDEEFLCKRKNKSSASKRKVSSRKILNTSVSLGEDDDDLDKAIALSLQGSVAGSDKEAATMKKKRPELMSKTQMTQDELVMYFCQFDEGGKGFITLRDVAKMATVHDFTWTEEELQDMIRCFDMDKDGKLSLDEFRKIVSRCRMLKGS*
  16 >AT1G75120.1 AI22=119.545 Gravy22=0.5864 nR=2 nS=0 nT=0 nDRQPEN=6 Nitrogen=31 Oxygen=27
  17 MAVRKEKVQPFRECGIAIAVLVGIFIGCVCTILIPNDFVNFRSSKVASASCESPERVKMFKAEFAIISEKNGELRKQVSDLTEKVRLAEQKEVIKAGPFGTVTGLQTNPTVAPDESANPRLAKLLEKVAVNKEIIVVLANNNVKPMLEVQIASVKRVGIQNYLVVPLDDSLESFCKSNEVAYYKRDPDNAIDVVGKSRRSSDVSGLKFRVLREFLQLGYGVLLSDVDIVFLQNPFGHLYRDSDVESMSDGHDNNTAYGFNDVFDDPTMTRSRTVYTNRIWVFNSGFFYLRPTLPSIELLDRVTDTLSKSGGWDQAVFNQHLFYPSHPGYTGLYASKRVMDVYEFMNSRVLFKTVRKDEEMKKLKPVIIHMNYHSDKLERMQAAVEFYVNGKQDALDRFRDGS*
  18 >AT1G17600.1 AI22=61.818 Gravy22=-0.2273 nR=2 nS=5 nT=0 nDRQPEN=6 Nitrogen=29 Oxygen=34
  19 MVSSSAPRVSKYDVFLSFRGEDTRKTIVSHLYAALDSRGIVTFKDDQRLEIGDHISDELHRALGSSSFAVVVLSENYATSRWCLLELQLIMELMKEGRLEVFPIFYGVDPSVVRHQLGSFSLVKYQGLEMVDKVLRWREALNLIANLSGVVSSHCVDEAIMVGEIARDISRRVTLMHKIDSGNIVGMKAHMEGLNHLLDQESNEVLLVGIWGMGGIGKTSIVKCLYDQLSPKFPAHCFIENIKSVSKDNGHDLKHLQKELLSSILCDDIRLWSVEAGCQEIKKRLGNQKVFLVLDGVDKVAQVHALAKEKNWFGPGSRIIITTRDMGLLNTCGVEVVYEVKCLDDKDALQMFKQIAFEGGLPPCEGFDQLSIRASKLAHGLPSAIQAYALFLRGRTASPEEWEEALGALESSLDENIMEILKISYEGLPKPHQNVFLHVVCLFNGDTLQRITSLLHGPIPQSSLWIRVLAEKSLIKISTNGSVIMHKLVEQMGREIIRDDMSLARKFLRDPMEIRVALAFRDGGEQTECMCLHTCDMTCVLSMEASVVGRMHNLKFLKVYKHVDYRESNLQLIPDQPFLPRSLRLFHWDAFPLRALPSGSDPCFLVELNLRHSDLETLWSGTPSNGVKTENPCEKHNSNYFHVLLYLAQMLKSLKRLDVTGSKHLKQLPDLSSITSLEELLLEQCTRLEGIPECIGKRSTLKKLKLSYRGGRRSALRFFLRKSTRQQHIGLEFPDAKVKMDALINISIGGDITFEFRSKFRGYAEYVSFNSEQQIPIISAMSLQQAPWVISECNRFNSLRIMRFSHKENGESFSFDVFPDFPDLKELKLVNLNIRKIPSGICHLDLLEKLDLSGNDFENLPEAMSSLSRLKTLWLQNCFKLQELPKLTQVQTLTLTNCRNLRSLAKLSNTSQDEGRYCLLELCLENCKSVESLSDQLSHFTKLTCLDLSNHDFETLPSSIRDLTSLVTLCLNNCKKLKSVEKLPLSLQFLDAHGCDSLEAGSAEHFEDIPNKEVNTWLLIRLYYD*
  20 >AT1G51380.1 AI22=84.091 Gravy22=-0.5318 nR=0 nS=0 nT=3 nDRQPEN=7 Nitrogen=26 Oxygen=36
  21 MEGTLDEENLVFETTKGIKPIKSFDDMGMNDKVLRGVYDYGYKKPSEIQQRALVPILKGRDVIAQAQSGTGKTSMIAISVCQIVNISSRKVQVLVLSPSRELASQTEKTIQAIGAHTNIQAHACIGGKSIGEDIKKLERGVHAVSGTPGRVYDMIKRGSLQTKAVKLLVLDESDEMLSKGLKDQIYDVYRALPHDIQVCLISATLPQEILEMTEKFMTDPVRILVKPDELTLEGIKQYYVDVDKEEWKFDTLCDLYGRLTINQAIIFCNTRQKVDWLTEKMRSSNFIVSSMHGDKRQKERDDIMNQFRSFKSRVLIASDVWARGIDVQTVSHVINYDIPNNPELYIHRIGRAGRFGREGVAINFVKSSDMKDLKDIERHYGTKIREMPADLV*
  22 >AT1G77370.1 AI22=159.091 Gravy22=1.3318 nR=2 nS=1 nT=0 nDRQPEN=6 Nitrogen=29 Oxygen=28
  23 MVDQSPRRVVVAALLLFVVLCDLSNSAGAANSVSAFVQNAILSNKIVIFSKSYCPYCLRSKRIFSQLKEEPFVVELDQREDGDQIQYELLEFVGRRTVPQVFVNGKHIGGSDDLGAALESGQLQKLLAAS*
  24 >AT1G44090.1 AI22=66.364 Gravy22=-0.0773 nR=2 nS=1 nT=2 nDRQPEN=6 Nitrogen=31 Oxygen=28
  25 MCIYASRQTVCPYLTPFKVKRPKSREMNSSDVNFSLLQSQPNVPAEFFWPEKDVAPSEGDLDLPIIDLSGFLNGNEAETQLAAKAVKKACMAHGTFLVVNHGFKSGLAEKALEISSLFFGLSKDEKLRAYRIPGNISGYTAGHSQRFSSNLPWNETLTLAFKKGPPHVVEDFLTSRLGNHRQEIGQVFQEFCDAMNGLVMDLMELLGISMGLKDRTYYRRFFEDGSGIFRCNYYPPCKQPEKALGVGPHNDPTAITVLLQDDVVGLEVFAAGSWQTVRPRPGALVVNVGDTFMALSNGNYRSCYHRAVVNKEKVRRSLVFFSCPREDKIIVPPPELVEGEEASRKYPDFTWAQLQKFTQSGYRVDNTTLHNFSSWLVSNSDKKST*
  26
  27 my @test_requests = (
  28     # simulate a pasted sequence with
  29     ( POST '/secretom/secretary/run', [ sequence => $test_data ] ),
  30
  31     # simulate an uploaded file
  32     ( POST '/secretom/secretary/run',
  33       Content_Type => 'form-data',
  34       Content => [
  35           sequence_file => [
  36               undef,
  37               'test.fasta',
  38               Content_Type => 'application/octet-stream',
  39               Content => $test_data,
  40              ],
  41          ],
  42      ),
  43
  44     # simulate a pasted sequence with sort box checked
  45     ( POST '/secretom/secretary/run', [ sequence => $test_data, sort => 'Sort by score' ] ),
  46
  47     # simulate both an uploaded file and a paste, both boxes checked
  48     ( POST '/secretom/secretary/run',
  49       Content_Type => 'form-data',
  50       Content => [
  51           sequence      => $test_data,
  52           sequence_file => [
  53               undef,
  54               'test.fasta',
  55               Content_Type => 'application/octet-stream',
  56               Content => $test_data,
  57              ],
  58            sort => 1,
  59          ],
  60      ),
  61
  62    );
  63
  64
  65 foreach my $test_req ( @test_requests ) {
  66     my $response = request $test_req;
  67
  68     like( $response->content, qr/(2|4) secreted sequences predicted out of (6|12)/,
  69           'got correct secreted sequence count' );
  70
  71     like( $response->content, qr/$_/, "ID $_ appears in output" )
  72         for qw( AT1G73440.1  AT1G75120.1  AT1G17600.1  AT1G51380.1  AT1G77370.1 AT1G44090.1 );
  73
  74     like( $response->content, qr/$_\s+YES/, "$_ shows as secreted" )
  75         for qw( AT1G77370.1  AT1G75120.1 );
  76
  77     like( $response->content, qr/$_\s+NO/, "$_ shows as NOT secreted" )
  78         for qw( AT1G73440.1 AT1G17600.1  AT1G51380.1 AT1G44090.1 );
  79 }
  80
  81 done_testing;