lib/SGN/Controller/AJAX/ODK.pm

   1
   2 =head1 NAME
   3
   4 SGN::Controller::AJAX::ODK - a REST controller class to provide the
   5 backend for ODK services
   6
   7 =head1 DESCRIPTION
   8
   9 =head1 AUTHOR
  10
  11 =cut
  12
  13 package SGN::Controller::AJAX::ODK;
  14
  15 use Moose;
  16 use List::MoreUtils qw /any /;
  17 use Data::Dumper;
  18 use Try::Tiny;
  19 use CXGN::Phenome::Schema;
  20 use Bio::Chado::Schema;
  21 use DateTime;
  22 use SGN::Model::Cvterm;
  23 use LWP::UserAgent;
  24 use JSON;
  25 use CXGN::ODK::Crosses;
  26 use Carp;
  27 use File::Spec::Functions qw / catfile catdir/;
  28 use File::Path qw(make_path);
  29
  30 BEGIN { extends 'Catalyst::Controller::REST' }
  31
  32 __PACKAGE__->config(
  33     default   => 'application/json',
  34     stash_key => 'rest',
  35     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  36    );
  37
  38
  39 sub get_phenotyping_data : Path('/ajax/odk/get_phenotyping_data') : ActionClass('REST') { }
  40
  41 sub get_phenotyping_data_GET {
  42     my ( $self, $c ) = @_;
  43     my $odk_phenotyping_data_service_name = $c->config->{odk_phenotyping_data_service_name};
  44     my $odk_phenotyping_data_service_username = $c->config->{odk_phenotyping_data_service_username};
  45     my $odk_phenotyping_data_service_password = $c->config->{odk_phenotyping_data_service_password};
  46     if ($odk_phenotyping_data_service_name eq 'SMAP'){
  47         my $ua = LWP::UserAgent->new;
  48         my $server_endpoint = "https://".$odk_phenotyping_data_service_username.":".$odk_phenotyping_data_service_password."\@bio.smap.com.au/api/v1/data";
  49         print STDERR $server_endpoint."\n";
  50
  51         my $resp = $ua->get($server_endpoint);
  52         if ($resp->is_success) {
  53             my $message = $resp->decoded_content;
  54             my $message_hash = decode_json $message;
  55             print STDERR Dumper $message_hash;
  56         } else {
  57             print STDERR Dumper $resp;
  58         }
  59
  60     } else {
  61         $c->stash->{rest} = { error => 'Error: We only support SMAP as an ODK phenotyping service for now.' };
  62         $c->detach();
  63     }
  64     $c->stash->{rest} = { success => 1 };
  65 }
  66
  67 sub get_crossing_available_forms : Path('/ajax/odk/get_crossing_available_forms') : ActionClass('REST') { }
  68
  69 sub get_crossing_available_forms_GET {
  70     my ( $self, $c ) = @_;
  71     my $odk_crossing_data_service_name = $c->config->{odk_crossing_data_service_name};
  72     my $message_hash;
  73     if ($odk_crossing_data_service_name eq 'ONA'){
  74         my $ua = LWP::UserAgent->new;
  75         $ua->credentials( 'api.ona.io:443', 'DJANGO', $c->config->{odk_crossing_data_service_username}, $c->config->{odk_crossing_data_service_password} );
  76         my $login_resp = $ua->get("https://api.ona.io/api/v1/user.json");
  77         my $server_endpoint = "https://api.ona.io/api/v1/data";
  78         my $resp = $ua->get($server_endpoint);
  79
  80         if ($resp->is_success) {
  81             my $message = $resp->decoded_content;
  82             $message_hash = decode_json $message;
  83         }
  84     } else {
  85         $c->stash->{rest} = { error => 'Error: We only support ONA as an ODK crossing service for now.' };
  86         $c->detach();
  87     }
  88     $c->stash->{rest} = { success => 1, forms=>$message_hash };
  89 }
  90
  91 sub get_crossing_data : Path('/ajax/odk/get_crossing_data') : ActionClass('REST') { }
  92
  93 sub get_crossing_data_GET {
  94     my ( $self, $c ) = @_;
  95     my $cross_wishlist_id = $c->req->param('cross_wishlist_md_file_id');
  96     my $cross_wishlist_file_name = $c->req->param('cross_wishlist_file_name');
  97     my $form_id = $c->req->param('form_id');
  98     my $session_id = $c->req->param("sgn_session_id");
  99     my $user_id;
 100     my $user_name;
 101     my $user_role;
 102     if ($session_id){
 103         my $dbh = $c->dbc->dbh;
 104         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 105         if (!$user_info[0]){
 106             $c->stash->{rest} = {error=>'You must be logged in to request ODK crossing data import!'};
 107             $c->detach();
 108         }
 109         $user_id = $user_info[0];
 110         $user_role = $user_info[1];
 111         my $p = CXGN::People::Person->new($dbh, $user_id);
 112         $user_name = $p->get_username;
 113     } else{
 114         if (!$c->user){
 115             $c->stash->{rest} = {error=>'You must be logged in to request ODK crossing data import!'};
 116             $c->detach();
 117         }
 118         $user_id = $c->user()->get_object()->get_sp_person_id();
 119         $user_name = $c->user()->get_object()->get_username();
 120         $user_role = $c->user->get_object->get_user_type();
 121     }
 122     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 123     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 124     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 125     my $tempfiles_dir = $c->tempfiles_subdir('ODK_ONA_cross_info');
 126     my ($temp_file, $uri1) = $c->tempfile( TEMPLATE => 'ODK_ONA_cross_info/ODK_ONA_cross_info_downloadXXXXX');
 127     my $temp_file_path = $temp_file->filename;
 128
 129     my $progress_tree_dir = catdir($c->site_cluster_shared_dir, "ODK_ONA_cross_info");
 130
 131     my $odk_crosses = CXGN::ODK::Crosses->new({
 132         bcs_schema=>$bcs_schema,
 133         metadata_schema=>$metadata_schema,
 134         phenome_schema=>$phenome_schema,
 135         sp_person_id=>$user_id,
 136         sp_person_username=>$user_name,
 137         sp_person_role=>$user_role,
 138         archive_path=>$c->config->{archive_path},
 139         temp_file_dir=>$c->config->{basepath}.$tempfiles_dir,
 140         temp_file_path=>$temp_file_path,
 141         cross_wishlist_md_file_id=>$cross_wishlist_id,
 142         cross_wishlist_file_name=>$cross_wishlist_file_name,
 143         allowed_cross_properties=>$c->config->{cross_properties},
 144         odk_crossing_data_service_url=>$c->config->{odk_crossing_data_service_url},
 145         odk_crossing_data_service_username=>$c->config->{odk_crossing_data_service_username},
 146         odk_crossing_data_service_password=>$c->config->{odk_crossing_data_service_password},
 147         odk_crossing_data_service_form_id=>$form_id,
 148         odk_cross_progress_tree_file_dir=>$progress_tree_dir
 149     });
 150
 151     my $odk_crossing_data_service_name = $c->config->{odk_crossing_data_service_name};
 152     if ($odk_crossing_data_service_name eq 'ONA'){
 153         my $result = $odk_crosses->save_ona_cross_info($c);
 154         if ($result->{error}){
 155             $c->stash->{rest} = { error => $result->{error} };
 156             $c->detach();
 157         } elsif ($result->{success}){
 158             $c->stash->{rest} = { success => 1 };
 159             $c->detach();
 160         }
 161     } else {
 162         $c->stash->{rest} = { error => 'Error: We only support ONA as an ODK crossing service for now.' };
 163         $c->detach();
 164     }
 165 }
 166
 167 sub schedule_get_crossing_data : Path('/ajax/odk/schedule_get_crossing_data') : ActionClass('REST') { }
 168
 169 sub schedule_get_crossing_data_GET {
 170     my ( $self, $c ) = @_;
 171     if ($c->config->{production_server}){
 172         $c->stash->{rest} = { error=>'Please use contact form. Currently this cannot be set through the website.' };
 173         $c->detach();
 174     }
 175     my $form_id = $c->req->param('form_id');
 176     my $cross_wishlist_id = $c->req->param('cross_wishlist_md_file_id');
 177     my $cross_wishlist_file_name = $c->req->param('cross_wishlist_file_name');
 178     my $timing_select = $c->req->param('timing');
 179     my $session_id = $c->req->param("sgn_session_id");
 180     my $user_id;
 181     my $user_name;
 182     my $user_role;
 183     if ($session_id){
 184         my $dbh = $c->dbc->dbh;
 185         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 186         if (!$user_info[0]){
 187             $c->stash->{rest} = {error=>'You must be logged in to schedule ODK crossing data import!'};
 188             $c->detach();
 189         }
 190         $user_id = $user_info[0];
 191         $user_role = $user_info[1];
 192         my $p = CXGN::People::Person->new($dbh, $user_id);
 193         $user_name = $p->get_username;
 194     } else{
 195         if (!$c->user){
 196             $c->stash->{rest} = {error=>'You must be logged in to schedule ODK crossing data import!'};
 197             $c->detach();
 198         }
 199         $user_id = $c->user()->get_object()->get_sp_person_id();
 200         $user_name = $c->user()->get_object()->get_username();
 201         $user_role = $c->user->get_object->get_user_type();
 202     }
 203     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 204     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 205     my $tempfiles_dir = $c->tempfiles_subdir('ODK_ONA_cross_info');
 206     my ($temp_file, $uri1) = $c->tempfile( TEMPLATE => 'ODK_ONA_cross_info/ODK_ONA_cross_info_downloadXXXXX');
 207     my $temp_file_path = $temp_file->filename;
 208
 209     my $progress_tree_dir = catdir($c->site_cluster_shared_dir, "ODK_ONA_cross_info");
 210
 211     my $cross_properties = $c->config->{cross_properties};
 212     my $rootpath = $c->config->{rootpath};
 213     my $basepath = $c->config->{basepath};
 214     my $archive_path = $c->config->{archive_path};
 215     my $ODK_url = $c->config->{odk_crossing_data_service_url};
 216     my $ODk_username = $c->config->{odk_crossing_data_service_username};
 217     my $ODK_password = $c->config->{odk_crossing_data_service_password};
 218     my $database_name = $c->config->{dbname};
 219     my $database_user = $c->config->{dbuser};
 220     my $database_pass = $c->config->{dbpass};
 221     my $database_host = $c->config->{dbhost};
 222     my $www_user = $c->config->{www_user};
 223     my $crontab_log = $c->config->{crontab_log_filepath};
 224     my $include_path = 'export PERL5LIB="$PERL5LIB:'.$basepath.'/lib:'.$rootpath.'/cxgn-corelibs/lib:'.$rootpath.'/Phenome/lib:'.$rootpath.'/local-lib/lib/perl5"';
 225     my $perl_command = "$include_path; perl $basepath/bin/ODK/ODK_ONA_get_crosses.pl -u $user_id -i $user_name -r $user_role -a $archive_path -d $basepath.$tempfiles_dir -t $temp_file_path -n $ODk_username -m $ODK_password -o $form_id -w $cross_wishlist_id -x $cross_wishlist_file_name -f $progress_tree_dir -l $ODK_url -c $cross_properties -D $database_name -U $database_user -p $database_pass -H $database_host >> $crontab_log 2>&1";
 226     my $timing = '';
 227     if ($timing_select eq 'everyminute'){
 228         $timing = "0-59/1 * * * * ";
 229     } elsif ($timing_select eq 'everyday'){
 230         $timing = "1 0 * * * ";
 231     } elsif ($timing_select eq 'everyhour'){
 232         $timing = "0 * * * * ";
 233     } elsif ($timing_select eq 'twicedaily'){
 234         $timing = "0 0,12 * * * ";
 235     }
 236     my $crontab_line = $timing.$perl_command."\n";
 237     #print STDERR $crontab_line;
 238     my $crontab_file = $c->config->{crontab_file};
 239     open (my $F, ">", $crontab_file) || die "Could not open $crontab_file: $!\n";
 240         if ($timing){
 241             print $F $crontab_line;
 242         }
 243     close $F;
 244
 245     my $enable_new_crontab = "crontab -u $www_user $crontab_file";
 246     system($enable_new_crontab);
 247
 248     $c->stash->{rest} = { success => 1 };
 249     $c->detach();
 250 }
 251
 252
 253 sub get_crossing_data_cronjobs : Path('/ajax/odk/get_crossing_data_cronjobs') : ActionClass('REST') { }
 254
 255 sub get_crossing_data_cronjobs_GET {
 256     my ( $self, $c ) = @_;
 257     my $session_id = $c->req->param("sgn_session_id");
 258     my $user_id;
 259     my $user_name;
 260     my $user_role;
 261     if ($session_id){
 262         my $dbh = $c->dbc->dbh;
 263         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 264         if (!$user_info[0]){
 265             $c->stash->{rest} = {error=>'You must be logged in to see scheduled ODK crossing data import!'};
 266             $c->detach();
 267         }
 268         $user_id = $user_info[0];
 269         $user_role = $user_info[1];
 270         my $p = CXGN::People::Person->new($dbh, $user_id);
 271         $user_name = $p->get_username;
 272     } else{
 273         if (!$c->user){
 274             $c->stash->{rest} = {error=>'You must be logged in to see scheduled ODK crossing data import!'};
 275             $c->detach();
 276         }
 277         $user_id = $c->user()->get_object()->get_sp_person_id();
 278         $user_name = $c->user()->get_object()->get_username();
 279         $user_role = $c->user->get_object->get_user_type();
 280     }
 281
 282     my @entries;
 283     my $crontab_file = $c->config->{crontab_file};
 284     open(my $fh, '<:encoding(UTF-8)', $crontab_file)
 285         or die "Could not open file '$crontab_file' $!";
 286
 287     while (my $row = <$fh>) {
 288         chomp $row;
 289         my @c = split 'export', $row;
 290         push @entries, $c[0];
 291     }
 292     close $fh;
 293
 294     $c->stash->{rest} = { success => 1, entries=>\@entries };
 295     $c->detach();
 296 }
 297
 298 sub get_crossing_available_wishlists : Path('/ajax/odk/get_crossing_available_wishlists') : ActionClass('REST') { }
 299
 300 sub get_crossing_available_wishlists_GET {
 301     my ( $self, $c ) = @_;
 302     my $session_id = $c->req->param("sgn_session_id");
 303     my $user_id;
 304     my $user_name;
 305     my $user_role;
 306     if ($session_id){
 307         my $dbh = $c->dbc->dbh;
 308         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 309         if (!$user_info[0]){
 310             $c->stash->{rest} = {error=>'You must be logged in to see ODK cross wishlists!'};
 311             $c->detach();
 312         }
 313         $user_id = $user_info[0];
 314         $user_role = $user_info[1];
 315         my $p = CXGN::People::Person->new($dbh, $user_id);
 316         $user_name = $p->get_username;
 317     } else{
 318         if (!$c->user){
 319             $c->stash->{rest} = {error=>'You must be logged in to see ODK cross wishlists!'};
 320             $c->detach();
 321         }
 322         $user_id = $c->user()->get_object()->get_sp_person_id();
 323         $user_name = $c->user()->get_object()->get_username();
 324         $user_role = $c->user->get_object->get_user_type();
 325     }
 326     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 327     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 328
 329     my $wishlist_md_files = $metadata_schema->resultset("MdFiles")->search({filetype=> { '-like' => 'cross_wishlist_%',  }});
 330     my @wishlists;
 331     while (my $r=$wishlist_md_files->next){
 332         if (index($r->filetype, 'cross_wishlist_germplasm_info_') == -1) {
 333             push @wishlists, [$r->file_id, $r->filetype];
 334         }
 335     }
 336     #print STDERR Dumper \@wishlists;
 337
 338     $c->stash->{rest} = { success => 1, wishlists => \@wishlists };
 339     $c->detach();
 340 }
 341
 342 sub get_odk_cross_progress_cached : Path('/ajax/odk/get_odk_cross_progress_cached') : ActionClass('REST') { }
 343
 344 sub get_odk_cross_progress_cached_GET {
 345     my ( $self, $c ) = @_;
 346     my $wishlist_file_id = $c->req->param("cross_wishlist_file_id");
 347     my $session_id = $c->req->param("sgn_session_id");
 348     my $user_id;
 349     my $user_name;
 350     my $user_role;
 351     if ($session_id){
 352         my $dbh = $c->dbc->dbh;
 353         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 354         if (!$user_info[0]){
 355             $c->stash->{rest} = {error=>'You must be logged in to see ODK crossing data progress!'};
 356             $c->detach();
 357         }
 358         $user_id = $user_info[0];
 359         $user_role = $user_info[1];
 360         my $p = CXGN::People::Person->new($dbh, $user_id);
 361         $user_name = $p->get_username;
 362     } else{
 363         if (!$c->user){
 364             $c->stash->{rest} = {error=>'You must be logged in to see ODK crossing data progress!'};
 365             $c->detach();
 366         }
 367         $user_id = $c->user()->get_object()->get_sp_person_id();
 368         $user_name = $c->user()->get_object()->get_username();
 369         $user_role = $c->user->get_object->get_user_type();
 370     }
 371     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 372     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 373
 374     my $dir = catdir($c->site_cluster_shared_dir, "ODK_ONA_cross_info");
 375     eval { make_path($dir) };
 376     if ($@) {
 377         print "Couldn't create $dir: $@";
 378     }
 379     my $filename = $dir."/entire_odk_cross_progress_html_".$wishlist_file_id.".txt";
 380     print STDERR "Opening $filename \n";
 381     my $contents;
 382     open(my $fh, '<', $filename) or die "cannot open file $filename";
 383     {
 384         local $/;
 385         $contents = decode_json <$fh>;
 386     }
 387     close($fh);
 388     my $json = $contents->{top_level_json};
 389
 390     my $top_level_id = $c->req->param('id');
 391     print STDERR "ODK Cross Tree Progress Node: ".$top_level_id."\n";
 392     if ($top_level_id eq '#'){
 393         $top_level_id = undef;
 394     }
 395     if ($top_level_id){
 396         my $top_level_contents = $contents->{top_level_contents};
 397         $json = $top_level_contents->{$top_level_id};
 398     }
 399
 400     #print STDERR Dumper $json;
 401     $c->stash->{rest} = $json;
 402 }
 403
 404 sub get_odk_cross_summary_cached : Path('/ajax/odk/get_odk_cross_summary_cached') : ActionClass('REST') { }
 405
 406 sub get_odk_cross_summary_cached_GET {
 407     my ( $self, $c ) = @_;
 408     my $wishlist_file_id = $c->req->param("cross_wishlist_file_id");
 409     my $session_id = $c->req->param("sgn_session_id");
 410     my $user_id;
 411     my $user_name;
 412     my $user_role;
 413     if ($session_id){
 414         my $dbh = $c->dbc->dbh;
 415         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 416         if (!$user_info[0]){
 417             $c->stash->{rest} = {error=>'You must be logged in to see ODK crossing data progress!'};
 418             $c->detach();
 419         }
 420         $user_id = $user_info[0];
 421         $user_role = $user_info[1];
 422         my $p = CXGN::People::Person->new($dbh, $user_id);
 423         $user_name = $p->get_username;
 424     } else{
 425         if (!$c->user){
 426             $c->stash->{rest} = {error=>'You must be logged in to see ODK crossing data progress!'};
 427             $c->detach();
 428         }
 429         $user_id = $c->user()->get_object()->get_sp_person_id();
 430         $user_name = $c->user()->get_object()->get_username();
 431         $user_role = $c->user->get_object->get_user_type();
 432     }
 433     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 434     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 435
 436     my $dir = catdir($c->site_cluster_shared_dir, "ODK_ONA_cross_info");
 437     eval { make_path($dir) };
 438     if ($@) {
 439         print "Couldn't create $dir: $@";
 440     }
 441     my $filename = $dir."/entire_odk_cross_progress_html_".$wishlist_file_id.".txt";
 442     print STDERR "Opening $filename \n";
 443     my $contents;
 444     open(my $fh, '<', $filename) or die "cannot open file $filename";
 445     {
 446         local $/;
 447         $contents = decode_json <$fh>;
 448     }
 449     close($fh);
 450     my $summary = $contents->{summary_info};
 451     my $plant_status_summary = $contents->{summary_plant_status_info};
 452
 453     #print STDERR Dumper $summary;
 454     $c->stash->{rest} = { summary => $summary, plant_status_summary => $plant_status_summary };
 455 }
 456
 457 1;