lib/SGN/Controller/AJAX/SpatialModel.pm

   1  use strict;
   2
   3 package SGN::Controller::AJAX::SpatialModel;
   4
   5 use Moose;
   6 use Data::Dumper;
   7 use File::Temp qw | tempfile |;
   8 use File::Slurp;
   9 use File::Spec qw | catfile|;
  10 use File::Basename qw | basename |;
  11 use File::Copy;
  12 use List::Util qw | any |;
  13 use CXGN::Dataset;
  14 use CXGN::Dataset::File;
  15 use CXGN::Tools::Run;
  16 use CXGN::Page::UserPrefs;
  17 use CXGN::Tools::List qw/distinct evens/;
  18 use CXGN::Blast::Parse;
  19 use CXGN::Blast::SeqQuery;
  20 use SGN::Model::Cvterm;
  21 use Cwd qw(cwd);
  22
  23 BEGIN { extends 'Catalyst::Controller::REST' }
  24
  25 __PACKAGE__->config(
  26     default   => 'application/json',
  27     stash_key => 'rest',
  28     map       => { 'application/json' => 'JSON' },
  29     );
  30
  31
  32 sub shared_phenotypes: Path('/ajax/spatial_model/shared_phenotypes') Args(0) {
  33     my $self = shift;
  34     my $c = shift;
  35     my $dataset_id = $c->req->param('dataset_id');
  36     my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  37     my $people_schema = $c->dbic_schema("CXGN::People::Schema", undef, $sp_person_id);
  38     my $schema = $c->dbic_schema("Bio::Chado::Schema", "sgn_chado", $sp_person_id);
  39     my $ds = CXGN::Dataset->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id);
  40     my $traits = $ds->retrieve_traits();
  41
  42     $c->tempfiles_subdir("spatial_model_files");
  43     my ($fh, $tempfile) = $c->tempfile(TEMPLATE=>"spatial_model_files/trait_XXXXX");
  44     my $temppath = $c->config->{basepath}."/".$tempfile;
  45     my $ds2 = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema, sp_dataset_id => $dataset_id, file_name => $temppath, quotes => 0);
  46     my $phenotype_data_ref = $ds2->retrieve_phenotypes();
  47
  48     print STDERR Dumper($traits);
  49     $c->stash->{rest} = {
  50         options => $traits,
  51         tempfile => $tempfile."_phenotype.txt",
  52 #        tempfile => $file_response,
  53     };
  54 }
  55
  56
  57
  58 sub extract_trait_data :Path('/ajax/spatial_model/getdata') Args(0) {
  59     my $self = shift;
  60     my $c = shift;
  61
  62     my $file = $c->req->param("file");
  63     my $trait = $c->req->param("trait");
  64
  65     $file = basename($file);
  66     my @data;
  67
  68     my $temppath = File::Spec->catfile($c->config->{basepath}, "static/documents/tempfiles/spatial_model_files", $file);
  69     print STDERR Dumper($temppath);
  70
  71     my $F;
  72     if (! open($F, "<", $temppath)) {
  73         $c->stash->{rest} = { error => "Can't find data." };
  74         return;
  75     }
  76
  77     $c->stash->{rest} = { data => \@data, trait => $trait};
  78 }
  79
  80 sub generate_results: Path('/ajax/spatial_model/generate_results') Args(1) {
  81     my $self = shift;
  82     my $c = shift;
  83     my $trial_id = shift;
  84
  85     print STDERR "TRIAL_ID: $trial_id\n";
  86
  87     $c->tempfiles_subdir("spatial_model_files");
  88     my $spatial_model_tmp_output = $c->config->{cluster_shared_tempdir}."/spatial_model_files";
  89     mkdir $spatial_model_tmp_output if ! -d $spatial_model_tmp_output;
  90     my ($tmp_fh, $tempfile) = tempfile(
  91       "spatial_model_download_XXXXX",
  92       DIR=> $spatial_model_tmp_output,
  93     );
  94     my $temppath = $c->config->{basepath}."/".$tempfile;
  95
  96     my $pheno_filepath = $temppath . "_phenotype.txt";
  97
  98     print STDERR "pheno_filepath: $pheno_filepath\n";
  99
 100     my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
 101     my $people_schema = $c->dbic_schema("CXGN::People::Schema", undef, $sp_person_id);
 102     my $schema = $c->dbic_schema("Bio::Chado::Schema", "sgn_chado", $sp_person_id);
 103
 104
 105
 106
 107     my $ds = CXGN::Dataset::File->new(people_schema => $people_schema, schema => $schema,  file_name => $temppath, quotes=>0);
 108     $ds -> trials([$trial_id]);
 109     print STDERR "DS: $ds\n";
 110     open(my $PF, "<", $pheno_filepath) || die "Can't open pheno file $pheno_filepath";
 111     open(my $CLEAN, ">", $pheno_filepath.".clean") || die "Can't open pheno_filepath clean for writing";
 112
 113     my $header = <$PF>;
 114     chomp($header);
 115
 116     my @fields = split /\t/, $header;
 117
 118     my @file_traits = @fields[ 39 .. @fields-1 ];
 119     my @other_headers = @fields[ 0 .. 38 ];
 120
 121
 122
 123     print STDERR "FIELDS: ".Dumper(\@file_traits);
 124
 125     foreach my $t (@file_traits) {
 126         $t = make_R_trait_name($t);
 127     }
 128
 129     my $si_traits = join(",", @file_traits);
 130
 131     print STDERR "FILE TRAITS: ".Dumper(\@file_traits);
 132
 133     my @new_header = (@other_headers, @file_traits);
 134     print $CLEAN join("\t", @new_header)."\n";
 135
 136     my $last_index = scalar(@new_header)-1;
 137
 138     #while(<$PF>) {
 139         #chomp;
 140         #my @f = split /\t/;
 141
 142
 143         my $cmd = CXGN::Tools::Run->new({
 144             backend => $c->config->{backend},
 145             submit_host=>$c->config->{cluster_host},
 146             temp_base => $c->config->{cluster_shared_tempdir} . "/spatial_model_files",
 147             queue => $c->config->{'web_cluster_queue'},
 148             do_cleanup => 0,
 149             # don't block and wait if the cluster looks full
 150             max_cluster_jobs => 1_000_000_000,
 151         });
 152
 153     $cmd->run_cluster(
 154         "Rscript ",
 155         $c->config->{basepath} . "/R/spatial_modeling.R",
 156         $pheno_filepath.".clean",
 157         "'".$si_traits."'",
 158
 159         );
 160
 161     while ($cmd->alive) {
 162         sleep(1);
 163     }
 164
 165 #    my $figure_path = $c->config->{basepath} . "/static/documents/tempfiles/stability_files/";
 166
 167     my @data;
 168
 169     open(my $F, "<", $pheno_filepath.".clean.out") || die "Can't open result file $pheno_filepath".".clean.out";
 170     my $header = <$F>;
 171     while (<$F>) {
 172         chomp;
 173         my @fields = split /\,/;
 174         foreach my $f (@fields) { $f =~ s/\"//g; }
 175         push @data, \@fields;
 176     }
 177
 178     print STDERR "FORMATTED DATA: ".Dumper(\@data);
 179
 180     my $basename = basename($pheno_filepath.".clean.out");
 181
 182     copy($pheno_filepath.".clean.out", $c->config->{basepath}."/static/documents/tempfiles/spatial_model_files/".$basename);
 183
 184     my $download_url = '/documents/tempfiles/spatial_model_files/'.$basename;
 185     my $download_link = "<a href=\"$download_url\">Download Results</a>";
 186
 187     $c->stash->{rest} = {
 188         data => \@data,
 189         download_link => $download_link,
 190     };
 191 }
 192
 193
 194 sub make_R_trait_name {
 195     my $trait = shift;
 196     $trait =~ s/\s/\_/g;
 197     $trait =~ s/\//\_/g;
 198     $trait =~ tr/ /./;
 199     $trait =~ tr/\//./;
 200     $trait =~ s/\:/\_/g;
 201     $trait =~ s/\|/\_/g;
 202     $trait =~ s/\-/\_/g;
 203
 204     return $trait;
 205 }
 206
 207 1;