lib/SMMID/Controller/REST/SMID.pm

   1 package SMMID::Controller::REST::SMID;
   2
   3 use Moose;
   4 use utf8;
   5 use Unicode::Normalize;
   6 use Chemistry::Mol;
   7 use Chemistry::File::SMILES;
   8 use JSON::XS;
   9 #use lib '~/SMMID/local-lib/lib/perl5/Chemistry/MolecularMass';
  10 #use Chemistry::MolecularMass;
  11
  12 BEGIN { extends 'Catalyst::Controller::REST' };
  13
  14 use Data::Dumper;
  15
  16 __PACKAGE__->config(
  17     default   => 'application/json',
  18     stash_key => 'rest',
  19     map       => { 'application/json' => 'JSON' },
  20    );
  21
  22
  23 =head1 NAME
  24
  25 SMMID::Controller::REST::SMID - REST-based controller to manage SMIDs
  26
  27 =head1 DESCRIPTION
  28
  29 Catalyst Controller.
  30
  31 =head1 METHODS
  32
  33 =cut
  34
  35 sub rest : Chained('/') PathPart('rest') CaptureArgs(0) {
  36     print STDERR "found rest...\n";
  37 }
  38
  39 sub browse :Chained('rest') PathPart('browse') Args(0) {
  40     my ($self, $c) = @_;
  41
  42     print STDERR "found rest/browse...\n";
  43
  44     my $rs = $c->model("SMIDDB")->resultset("SMIDDB::Result::Compound")->search( {}, { order_by => { -asc => 'smid_id' } } );
  45
  46     my @data;
  47     while (my $r = $rs->next()) {
  48
  49       my $cur_char = "<p style=\"color:green\"><b>\x{2713}</b></p>";
  50       if(!defined($r->curation_status()) || $r->curation_status() eq "unverified"){$cur_char = "<p style=\"color:red\">Unverified</p>";}
  51       elsif($r->curation_status() eq "review"){$cur_char = "<p style=\"color:blue\">Marked for Review</p>";}
  52
  53         push @data, ["<a href=\"/smid/".$r->compound_id()."\">".$r->smid_id()."</a>", $r->formula(), $r->molecular_weight(), $cur_char ];
  54     }
  55
  56     $c->stash->{rest} = { data => \@data };
  57 }
  58
  59 ###Deprecated
  60 sub molecular_weight {
  61   #...
  62   #The default variable will be used as the chemical Formula
  63   $_ = shift(@_);
  64
  65   my %elements = (
  66   "H" => 1.00794,
  67   "D" => 2.014101,
  68   "T" => 3.016049,
  69   "He" => 4.002602,
  70   "Li" => 6.941,
  71   "Be" => 9.012182,
  72   "B" => 10.811,
  73   "C" => 12.0107,
  74   "N" => 14.00674,
  75   "O" => 15.9994,
  76   "F" => 18.9984032,
  77   "Ne" => 20.1797,
  78   "Na" => 22.989770,
  79   "Mg" => 24.3050,
  80   "Al" => 26.981538,
  81   "Si" => 28.0855,
  82   "P" => 30.973761,
  83   "S" => 32.066,
  84   "Cl" => 35.4527,
  85   "Ar" => 39.948,
  86   "K" => 39.0983,
  87   "Ca" => 40.078,
  88   "Sc" => 44.955910,
  89   "Ti" => 47.867,
  90   "V" => 50.9415,
  91   "Cr" => 51.9961,
  92   "Mn" => 54.938049,
  93   "Fe" => 55.845,
  94   "Co" => 58.933200,
  95   "Ni" => 58.6934,
  96   "Cu" => 63.546,
  97   "Zn" => 65.39,
  98   "Ga" => 69.723,
  99   "Ge" => 72.61,
 100   "As" => 74.92160,
 101   "Se" => 78.96,
 102   "Br" => 79.904,
 103   "Kr" => 83.80,
 104   "Rb" => 85.4678,
 105   "Sr" => 87.62,
 106   "Y" => 88.90585,
 107   "Zr" => 91.224,
 108   "Nb" => 92.90638,
 109   "Mo" => 95.94,
 110   "Tc" => 98,
 111   "Ru" => 101.07,
 112   "Rh" => 102.90550,
 113   "Pd" => 106.42,
 114   "Ag" => 107.8682,
 115   "Cd" => 112.411,
 116   "In" => 114.818,
 117   "Sn" => 118.710,
 118   "Sb" => 121.760,
 119   "Te" => 127.60,
 120   "I" => 126.90447,
 121   "Xe" => 131.29,
 122   "Cs" => 132.90545,
 123   "Ba" => 137.327,
 124   "La" => 138.9055,
 125   "Ce" => 140.116,
 126   "Pr" => 140.90765,
 127   "Nd" => 144.24,
 128   "Pm" => 145,
 129   "Sm" => 150.36,
 130   "Eu" => 151.964,
 131   "Gd" => 157.25,
 132   "Tb" => 158.92534,
 133   "Dy" => 162.50,
 134   "Ho" => 164.93032,
 135   "Er" => 167.26,
 136   "Tm" => 168.93421,
 137   "Yb" => 173.04,
 138   "Lu" => 174.967,
 139   "Hf" => 178.49,
 140   "Ta" => 180.9479,
 141   "W" => 183.84,
 142   "Re" => 186.207,
 143   "Os" => 190.23,
 144   "Ir" => 192.217,
 145   "Pt" => 195.078,
 146   "Au" => 196.96655,
 147   "Hg" => 200.59,
 148   "Tl" => 204.3833,
 149   "Pb" => 207.2,
 150   "Bi" => 208.98038,
 151   "Po" => 209,
 152   "At" => 210,
 153   "Rn" => 222,
 154   "Fr" => 223,
 155   "Ra" => 226,
 156   "Ac" => 227,
 157   "Th" => 232.038,
 158   "Pa" => 231.03588,
 159   "U" => 238.0289,
 160   "Np" => 237,
 161   "Pu" => 244,
 162   "Am" => 243,
 163   "Cm" => 247,
 164   "Bk" => 247,
 165   "Cf" => 251,
 166   "Es" => 252,
 167   "Fm" => 257,
 168   "Md" => 258,
 169   "No" => 259,
 170   "Lr" => 262,
 171   "Rf" => 261,
 172   "Db" => 262,
 173   "Sg" => 266,
 174   "Bh" => 264,
 175   "Hs" => 269,
 176   "Mt" => 268,
 177   "Uun" => 271,
 178   "Uuu" => 272
 179 );
 180   my $weight = 0;
 181
 182   my @pairs = /([CHONPS][0-9]*)/g;
 183   foreach my $pair (@pairs){
 184     if (length($pair)==1){
 185       $weight += $elements{substr($pair, 0, 1)};
 186     }else{
 187       $weight += $elements{substr($pair, 0, 1)}*substr($pair, 1);
 188     }
 189   }
 190   return $weight;
 191 }
 192
 193 #Inserting a subroutine for the curator interface. At first, it will be a clone of the browse tab.
 194 sub curator : Chained('rest') PathPart('curator') Args(0) {
 195   my ($self, $c) = @_;
 196
 197   print STDERR "found rest/curator...\n";
 198
 199   my $rs = $c->model("SMIDDB")->resultset("SMIDDB::Result::Compound")->search({}, { order_by => { -asc => 'smid_id'}});
 200   my @data;
 201   while (my $r = $rs->next()) {
 202
 203     my $button = "<button id=\"unverify_".$r->compound_id()."\" onclick=\"mark_smid_for_review(".$r->compound_id().")\" type=\"button\" class=\"btn btn-primary\">Mark for Review</button>";
 204     my $cur_status = "<p style=\"color:green\"><b>\x{2713}</b></p>";
 205     my $disabled = "";
 206     my $advice = "Approve and Curate";
 207     my @missing;
 208
 209     my $hplcexperiments = $c->model("SMIDDB")->resultset("SMIDDB::Result::Experiment")->search({compound_id => $r->compound_id(), experiment_type => "hplc_ms"});
 210     my $msmsexperiments = $c->model("SMIDDB")->resultset("SMIDDB::Result::Experiment")->search({compound_id => $r->compound_id(), experiment_type => "ms_spectrum"});
 211
 212     if (!$r->organisms()){push(@missing, "organisms");}
 213     if (!$r->formula()){push(@missing, "Molecular Formula");}
 214     if (!$r->smid_id()){push(@missing, "SMID ID");}
 215     # ...requirement for HPLC-MS and MS/MS data
 216     if (!$hplcexperiments->next()){push(@missing, "HPLC-MS Data");}
 217     if (!$msmsexperiments->next()){push(@missing, "MS/MS Data");}
 218
 219     my $missinglist = "(Missing: ";
 220     $missinglist .= join(", ", @missing);
 221     $missinglist .= ")";
 222     if ($missinglist eq "(Missing: )"){$missinglist = "";} else {$advice = "Curation not Reccommended"; $disabled = "disabled";}
 223
 224     if(!defined($r->curation_status()) || $r->curation_status() eq "unverified"){
 225       $cur_status = "<p style=\"color:red\">Unverified $missinglist </p>";
 226       $button = "<button id=\"curate_".$r->compound_id()."\" onclick=\"curate_smid(".$r->compound_id().")\" type=\"button\" class=\"btn btn-primary\" $disabled>$advice</button>";
 227     }
 228     elsif($r->curation_status() eq "review"){
 229       $cur_status = "<p style=\"color:blue\">Marked for Review $missinglist </p> ";
 230       $button = "<button id=\"curate_".$r->compound_id()."\" onclick=\"curate_smid(".$r->compound_id().")\" type=\"button\" class=\"btn btn-primary\" $disabled>$advice</button>";
 231     }
 232
 233 push @data, [ $r->compound_id(), "<a href=\"/smid/".$r->compound_id()."/edit\">".$r->smid_id()."</a>", $r->formula(), $r->smiles(), $button, $cur_status];
 234   }
 235
 236   $c->stash->{rest} = { data => \@data };
 237
 238 }
 239
 240 #If I am correct, this subroutine formats the data, while the above subroutine collects the data
 241 sub curator_format :Chained('rest') PathPart('curator') Args(1) {
 242     my $self = shift;
 243     my $c = shift;
 244     my $format = shift;
 245
 246     $self->curator($c);
 247
 248     if ($format eq "html") {
 249
 250       print STDERR "found the curator html...\n";
 251
 252              my $html = "<table border=\"1\" width=\"100%\" cellpadding=\"10\" >\n
 253               <thead><th>SMID ID</th><th>Formula</th><th>SMILES</th><th><a width=\"50\"></a>Status</th></thead>\n";
 254
 255              foreach my $smid (@{$c->stash->{rest}->{data}}) {
 256                 $html .= "<tr><td><a href=\"/smid/$smid->[0]\">$smid->[1]</a></td><td>$smid->[2]</td><td>$smid->[3]</td><td><button id=\"curate_smid".$smid->compound_id()."\" disabled=\"false\" class=\"btn btn-primary\">Approve and Curate</button></td></tr>\n";
 257                }
 258              $html .= "</table>\n";
 259
 260              $c->stash->{rest} = { html => $html };
 261     }
 262
 263     if ($format eq "datatable") {
 264             #...
 265       print STDERR "found the curator data...\n";
 266
 267       my @data = $c->stash->{rest}->{data};
 268     }
 269 }
 270
 271 sub browse_format :Chained('rest') PathPart('browse') Args(1) {
 272     my $self = shift;
 273     my $c = shift;
 274     my $format = shift;
 275
 276     $self->browse($c);
 277
 278     if ($format eq "html") {
 279         my $html = "<table border=\"1\" width=\"100%\" cellpadding=\"10\" >\n
 280         <thead><th>SMID ID</th><th>Formula</th><th>SMILES</th></thead>\n";
 281
 282         foreach my $smid (@{$c->stash->{rest}->{data}}) {
 283             $html .= "<tr><td><a href=\"/smid/$smid->[0]\">$smid->[1]</a></td><td>$smid->[2]</td><td>$smid->[3]</td></tr>\n";
 284         }
 285         $html .= "</table>\n";
 286
 287         $c->stash->{rest} = { html => $html };
 288     }
 289
 290     if ($format eq "datatable") {
 291         #...
 292
 293   print STDERR "found the browse data...\n";
 294
 295   my @data = $c->stash->{rest}->{data};
 296     }
 297
 298
 299 }
 300
 301 sub clean {
 302     my $self = shift;
 303     my $str = shift;
 304
 305     # remove script tags
 306     $str =~ s/\<script\>//gi;
 307     $str =~ s/\<\/script\>//gi;
 308
 309     return $str;
 310 }
 311
 312
 313 sub store :Chained('rest') PathPart('smid/store') Args(0) {
 314     my $self  = shift;
 315     my $c = shift;
 316
 317     if (! $c->user()) {
 318         $c->stash->{rest} = { error => "Login required for updating SMIDs." };
 319         return;
 320     }
 321
 322     my $user_id = $c->user()->get_object()->dbuser_id();
 323
 324     my $smid_id = $self->clean($c->req->param("smid_id"));
 325     my $iupac_name = $self->clean($c->req->param("iupac_name"));
 326
 327     print STDERR "IUPAC name = $iupac_name\n";
 328     my $smiles_string = $self->clean($c->req->param("smiles_string"));
 329
 330     print STDERR "SMILES = $smiles_string\n";
 331
 332     my $formula = $self->clean($c->req->param("formula"));
 333     my $organisms = $self->clean($c->req->param("organisms"));
 334     my $description = $self->clean($c->req->param("description"));
 335     my $synonyms = $self->clean($c->req->param("synonyms"));
 336     my $curation_status = $self->clean($c->req->param("curation_status"));
 337     my $doi = $self->clean($c->req->param("doi"));
 338
 339     #my $mm = new Chemistry::MolecularMass;
 340     my $molecular_weight = molecular_weight($formula);
 341
 342     my $errors = "";
 343     if (!$smid_id) { $errors .= "Need smid id. "; }
 344     if (!$iupac_name) { $errors .= "Need a IUPAC name. "; }
 345     if (!$smiles_string) { $errors .= "Need smiles_string. "; }
 346     if (!$formula) { $errors .= "Need formula. "; }
 347
 348     if ($errors) {
 349         $c->stash->{rest} = { error => $errors };
 350         return;
 351     }
 352
 353     my $row = {
 354         smid_id => $smid_id,
 355         formula => $formula,
 356         smiles => $smiles_string,
 357         organisms => $organisms,
 358         doi => $doi,
 359         iupac_name => $iupac_name,
 360         curation_status => $curation_status,
 361         dbuser_id => $user_id,
 362         description => $description,
 363         synonyms => $synonyms,
 364         create_date => 'now()',
 365         molecular_weight => $molecular_weight,
 366         last_modified_date => 'now()',
 367     };
 368
 369     my $compound_id;
 370     eval {
 371         my $new = $c->model("SMIDDB")->resultset("SMIDDB::Result::Compound")->new($row);
 372         $new->insert();
 373         $compound_id = $new->compound_id();
 374     };
 375
 376     if ($@) {
 377         $c->stash->{rest} = { error => "Sorry, an error occurred storing the smid ($@)" };
 378         return;
 379     }
 380
 381     $c->stash->{rest} = {
 382         compound_id => $compound_id,
 383         message => "Successfully stored the smid $smid_id"
 384     };
 385
 386 }
 387
 388 sub smid :Chained('rest') PathPart('smid') CaptureArgs(1) {
 389     my $self = shift;
 390     my $c = shift;
 391
 392     my $compound_id = shift;
 393
 394     $c->stash->{compound_id} = $compound_id;
 395 }
 396
 397 sub delete_smid :Chained('smid') PathPart('delete') Args(0) {
 398     my $self = shift;
 399     my $c = shift;
 400
 401
 402
 403
 404 }
 405
 406
 407 #This is where the backend function will go to curate a smid. Use buttons modeled on smid_detail.js for help
 408 #Note that this function will both curate a smid and mark it as unverified depending on the parameters sent!
 409 sub curate_smid :Chained('smid') PathPart('curate_smid') Args(0){
 410
 411     my $self = shift;
 412     my $c = shift;
 413
 414     my $curation_status = $self->clean($c->req->param("curation_status"));
 415     my $compound_id = $c->stash->{compound_id};
 416     my $curator_id = $c->user()->get_object()->dbuser_id();
 417     my $row = $c->model("SMIDDB")->resultset("SMIDDB::Result::Compound")->find( { compound_id => $compound_id} );
 418
 419       if (!$row){
 420         $c->stash->{rest} = { error => "The SMID with id $compound_id does not exist." };
 421         return;
 422       }
 423
 424       my $smid_id = $row->smid_id();
 425
 426        my $data = {
 427          smid_id => $smid_id,
 428
 429          curation_status => $curation_status,
 430
 431          last_modified_date => 'now()',
 432
 433      last_curated_time => 'now()',
 434
 435      curator_id => $curator_id
 436        };
 437
 438       eval{
 439         $row->update($data);
 440       };
 441
 442       $c->stash->{rest} ={
 443         message => "Successfully updated the curation status of smid $smid_id"
 444       };
 445
 446     print STDERR "Smid ".$smid_id." curation status updated to $curation_status\n";
 447     return;
 448 }
 449
 450
 451 #Note that this one does not update curator id, last edited time, or last curated time. It is being marked for
 452 #review, so it is inappropriate to say that the smid has been edited or curated.
 453 sub mark_for_review : Chained('smid') PathPart('mark_for_review') Args(0) {
 454
 455   my $self = shift;
 456   my $c = shift;
 457
 458   my $curation_status = $self->clean($c->req->param("curation_status"));
 459   my $compound_id = $c->stash->{compound_id};
 460   my $row = $c->model("SMIDDB")->resultset("SMIDDB::Result::Compound")->find( { compound_id => $compound_id} );
 461
 462     if (!$row){
 463       $c->stash->{rest} = { error => "The SMID with id $compound_id does not exist." };
 464       return;
 465     }
 466
 467     my $smid_id = $row->smid_id();
 468
 469      my $data = {
 470    smid_id => $smid_id,
 471    curation_status => $curation_status,
 472      };
 473
 474     eval{
 475       $row->update($data);
 476     };
 477
 478     $c->stash->{rest} ={
 479   message => "Successfully updated the curation status of smid $smid_id"
 480     };
 481
 482   print STDERR "Smid ".$smid_id." curation status updated to $curation_status NOTE TO RYAN\n";
 483   return;
 484 }
 485
 486 sub update :Chained('smid') PathPart('update') Args(0) {
 487     my $self = shift;
 488     my $c = shift;
 489
 490     if (! $c->user()) {
 491         $c->stash->{rest} = { error => "Login required for updating SMIDs." };
 492         return;
 493     }
 494
 495     my $compound_id = $c->stash->{compound_id};
 496     my $smid_row = $c->model("SMIDDB")->resultset("SMIDDB::Result::Compound")->find( { compound_id => $compound_id } );
 497
 498     if (! $smid_row) {
 499         $c->stash->{rest} = { error => "The SMID with id $compound_id does not exist." };
 500         return;
 501     }
 502
 503     my $user_id = $c->user()->get_object()->dbuser_id();
 504     my $smid_owner_id = $smid_row->dbuser_id();
 505
 506
 507     if ( ($user_id != $smid_owner_id) && ($c->user->get_object()->user_type() ne "curator") )  {
 508         $c->stash->{rest} = { error => "The SMID with id $compound_id is (owned by $smid_owner_id) not owned by you ($user_id) and you cannot modify it." };
 509         return;
 510     }
 511
 512     my $smid_id = $self->clean($c->req->param("smid_id"));
 513     my $smiles_string = $self->clean($c->req->param("smiles_string"));
 514     my $formula = $self->clean($c->req->param("formula"));
 515     my $organisms = $self->clean($c->req->param("organisms"));
 516     my $iupac_name = $self->clean($c->req->param("iupac_name"));
 517     my $curation_status = $self->clean($c->req->param("curation_status"));
 518     my $synonyms = $self->clean($c->req->param("synonyms"));
 519     my $description = $self->clean($c->req->param("description"));
 520     my $doi = $self->clean($c->req->param("doi"));
 521     #my $mm <- new Chemistry::MolecularMass;
 522     my $molecular_weight = molecular_weight($formula);
 523
 524     my $errors = "";
 525     if (!$compound_id) {  $errors .= "Need compound id. "; }
 526     if (!$iupac_name) { $errors .= "Need IUPAC name. "; }
 527     if (!$smid_id) { $errors .= "Need smid id. "; }
 528     #if (!$smiles_string) { $errors .= "Need smiles_string. "; }
 529     if (!$formula) { $errors .= "Need formula. "; }
 530
 531     if (my $smiles_error = $self->check_smiles($smiles_string)) {
 532         $errors .= $smiles_error;
 533     }
 534
 535     if ($errors) {
 536         $c->stash->{rest} = { error => $errors };
 537         return;
 538     }
 539
 540     my $data = {
 541         smid_id => $smid_id,
 542         formula => $formula,
 543         smiles => $smiles_string,
 544         organisms => $organisms,
 545         doi => $doi,
 546         iupac_name => $iupac_name,
 547         curation_status => $curation_status,
 548         description => $description,
 549         synonyms => $synonyms,
 550         molecular_weight => $molecular_weight,
 551         last_modified_date => 'now()',
 552     };
 553
 554     eval {
 555         $smid_row->update($data);
 556     };
 557
 558     if ($@) {
 559         $c->stash->{rest} = { error => "Sorry, an error occurred storing the smid ($@)" };
 560         return;
 561     }
 562
 563     $c->stash->{rest} ={
 564         compound_id => $compound_id,
 565         message => "Successfully stored the smid $smid_id"
 566     };
 567
 568 }
 569
 570 sub check_smiles {
 571     my $self = shift;
 572     my $smiles = shift;
 573
 574     eval {
 575         Chemistry::Mol->parse($smiles, format => 'smiles');
 576     };
 577
 578     my $error;
 579     if ($@) {
 580         $error = $@;
 581     }
 582
 583     return $error;
 584 }
 585
 586
 587
 588 sub detail :Chained('smid') PathPart('details') Args(0) {
 589     my $self = shift;
 590     my $c = shift;
 591
 592     my $s = $c->model("SMIDDB")->resultset("SMIDDB::Result::Compound")->find( { compound_id => $c->stash->{compound_id} });
 593
 594     if (! $s) {
 595         $c->stash->{rest} = { error => "Can't find smid with id ".$c->stash->{compound_id}."\n" };
 596         return;
 597     }
 598
 599     my $data;
 600     $data->{smid_id} = $s->smid_id();
 601     $data->{compound_id} = $s->compound_id();
 602     $data->{formula}= $s->formula();
 603     $data->{organisms} = $s->organisms();
 604     $data->{doi} = $s->doi();
 605     $data->{iupac_name} = $s->iupac_name();
 606     $data->{smiles_string} = $s->smiles();
 607     $data->{curation_status} = $s->curation_status();
 608     $data->{last_modified_date} = $s->last_modified_date();
 609     $data->{create_date} = $s->create_date();
 610     $data->{curator_id} = $s->curator_id();
 611     $data->{last_curated_time} = $s->last_curated_time();
 612     $data->{description} = $s->description();
 613     $data->{synonyms} = $s->synonyms();
 614     $data->{molecular_weight} = $s->molecular_weight();
 615
 616     $c->stash->{rest} = { data => $data };
 617
 618     print STDERR "Found smid details...\n";
 619 }
 620
 621
 622 sub smid_dbxref :Chained('smid') PathPart('dbxrefs') Args(0) {
 623     my $self = shift;
 624     my $c = shift;
 625
 626     my $rs;
 627     if ($c->stash->{compound_id}) {
 628         $rs = $c->model("SMIDDB")->resultset("SMIDDB::Result::Dbxref")->search(  { 'compound_dbxrefs.compound_id' => $c->stash->{compound_id} }, { join => 'compound_dbxrefs' , { join => 'db'  }});
 629     }
 630     else {
 631         $c->stash->{rest} = { data => [] };
 632         return;
 633     }
 634
 635     my $data = [];
 636
 637     while (my $dbxref = $rs->next()) {
 638         print STDERR "Retrieved: ". $dbxref->dbxref_id()."...\n";
 639
 640         my $db_name = "";
 641         my $display_url = "";
 642
 643         if ($dbxref->db()) {
 644             $db_name = $dbxref->db->name();
 645             my $url = $dbxref->db->url();
 646             my $urlprefix = $dbxref->db->urlprefix();
 647             $display_url = join("",  $urlprefix, $url, $dbxref->accession());
 648         }
 649
 650         my $delete_link = "X";
 651
 652         if ($c->user()) {
 653             $delete_link = "<a href=\"javascript:delete_dbxref(".$dbxref->dbxref_id().")\" ><font color=\"red\">X</font></a>";
 654         }
 655         push @$data, [ $db_name, $dbxref->accession(), $display_url , $delete_link ];
 656     }
 657     $c->stash->{rest} = { data => $data };
 658 }
 659
 660 sub results : Chained('smid') PathPart('results') Args(0) {
 661     my $self = shift;
 662     my $c = shift;
 663
 664     my $experiment_type = $c->req->param("experiment_type");
 665
 666     my $rs = $c->model("SMIDDB")->resultset("SMIDDB::Result::Experiment")->search( { compound_id => $c->stash->{compound_id}, experiment_type => $experiment_type } );
 667
 668     print STDERR "Retrieved ".$rs->count()." rows...\n";
 669     my @data;
 670
 671     my $delete_link = "X";
 672     while (my $row = $rs->next()) {
 673         my $experiment_id = $row->experiment_id();
 674         if ($c->user()) {
 675             $delete_link = "<a href=\"javascript:delete_experiment($experiment_id)\"><font color=\"red\">X</font></a>";
 676         }
 677
 678         if ($experiment_type eq "hplc_ms") {
 679             my $json = $row->data();
 680             my $hash = JSON::XS->new()->decode($json);
 681             push @data, [ $hash->{hplc_ms_author}, $hash->{hplc_ms_method_type}, $hash->{hplc_ms_retention_time}, $hash->{hplc_ms_ionization_mode}, $hash->{hplc_ms_adducts_detected}, $hash->{hplc_ms_scan_number}, $hash->{hplc_ms_link}, $delete_link ];
 682         }
 683         if ($experiment_type eq "ms_spectrum") {
 684             my $json = $row->data();
 685             my $hash = JSON::XS->new()->decode($json);
 686             push @data, [ $hash->{ms_spectrum_author}, $hash->{ms_spectrum_ionization_mode}, $hash->{ms_spectrum_collision_energy}, $hash->{ms_spectrum_adduct_fragmented}, "<a href=\"/experiment/".$row->experiment_id()."\">Details</a>", $hash->{ms_spectrum_link},  $delete_link ];
 687         }
 688     }
 689
 690     $c->stash->{rest} = { data => \@data };
 691 }
 692
 693
 694 sub compound_images :Chained('smid') PathPart('images') Args(1) {
 695     my $self = shift;
 696     my $c = shift;
 697     my $size = shift;
 698
 699     my $rs = $c->model("SMIDDB")->resultset("SMIDDB::Result::CompoundImage")->search( { compound_id => $c->stash->{compound_id} });
 700
 701     my @source_tags;
 702     while (my $row = $rs->next()) {
 703         my $image = SMMID::Image->new( { schema => $c->model("SMIDDB"), image_id => $row->image_id() });
 704
 705         my $delete_link = "";
 706         if ($c->user()) {
 707             $delete_link = "<a href=\"javascript:delete_image(".$row->image_id().", ".$c->stash->{compound_id}.")\">X</a>";
 708         }
 709
 710
 711         my $file = "medium";
 712         if ($size =~ m/thumbnail|small|medium|large/) { $file = $size.".png"; }
 713         my $image_full_url =  "/".$c->config->{image_url}."/".$image->image_subpath()."/".$file;
 714         push @source_tags, "<img src=\"$image_full_url\" />$delete_link";
 715     }
 716     print STDERR "returning images for compound ".$c->stash->{compound_id} ." with size $size.\n";
 717     $c->stash->{rest} = { html => \@source_tags };
 718 }
 719
 720 =head1 AUTHOR
 721
 722 Lukas Mueller,,,
 723
 724 =head1 LICENSE
 725
 726 This library is free software, you can redistribute it and/or modify
 727 it under the same terms as Perl itself.
 728
 729 =cut
 730
 731 1;