bin/ODK/ODK_ONA_get_crosses.pl

   1 #!/usr/bin/perl
   2
   3 =head1
   4 ODK/ODK_ONA_get_crosses.pl
   5
   6 =head1 SYNOPSIS
   7 ODK_ONA_get_crosses.pl
   8
   9 =head1 COMMAND-LINE OPTIONS
  10 ARGUMENTS
  11
  12 =head1 DESCRIPTION
  13
  14 =head1 AUTHOR
  15  Nicolas Morales (nm529@cornell.edu)
  16 =cut
  17
  18 use strict;
  19
  20 use Getopt::Std;
  21 use Data::Dumper;
  22 use Carp qw /croak/ ;
  23 use Pod::Usage;
  24 use CXGN::ODK::Crosses;
  25 use JSON;
  26 use Bio::Chado::Schema;
  27 use CXGN::Metadata::Schema;
  28 use CXGN::Phenome::Schema;
  29
  30 our ($opt_u, $opt_i, $opt_r, $opt_a, $opt_d, $opt_n, $opt_m, $opt_o, $opt_f, $opt_l, $opt_c, $opt_q, $opt_y, $opt_D, $opt_U, $opt_p, $opt_H);
  31
  32 getopts('u:i:r:a:d:n:m:o:w:f:l:c:q:y:D:U:p:H:');
  33
  34 if (!$opt_u || !$opt_i || !$opt_r || !$opt_a || !$opt_d || !$opt_n || !$opt_m || !$opt_o || !$opt_f || !$opt_l || !$opt_c || !$opt_q || !$opt_y || !$opt_D || !$opt_U || !$opt_p || !$opt_H) {
  35     die "Must provide options -u (sp_person_id) -i (sp_person_username )-r (sp_role) -a (archive_path) -d (temp_files_dir) -n (ODK username) -m (ODK password) -o (ODK form_id) -f (odk cross progress tree file dir) -l (ODK URL) -c (allowed cross properties) -q (temp cross wishlist file path for dl from ONA) -y (temp germplasm info file path for dl from ONA) -D (database name) -U (db user) -p (dbpass) -H (dbhost) \n";
  36 }
  37
  38 my $bcs_schema = Bio::Chado::Schema->connect(
  39     "dbi:Pg:database=$opt_D;host=$opt_H", # DSN Line
  40     $opt_U,                    # Username
  41     $opt_p           # Password
  42 );
  43 my $metadata_schema = CXGN::Metadata::Schema->connect(
  44     "dbi:Pg:database=$opt_D;host=$opt_H", # DSN Line
  45     $opt_U,                    # Username
  46     $opt_p           # Password
  47 );
  48 my $phenome_schema = CXGN::Phenome::Schema->connect(
  49     "dbi:Pg:database=$opt_D;host=$opt_H", # DSN Line
  50     $opt_U,                    # Username
  51     $opt_p           # Password
  52 );
  53
  54 my $odk_crosses = CXGN::ODK::Crosses->new({
  55     bcs_schema=>$bcs_schema,
  56     metadata_schema=>$metadata_schema,
  57     phenome_schema=>$phenome_schema,
  58     sp_person_id=>$opt_u,
  59     sp_person_username=>$opt_i,
  60     sp_person_role=>$opt_r,
  61     archive_path=>$opt_a,
  62     temp_file_dir=>$opt_d,
  63     allowed_cross_properties=>$opt_c,
  64     cross_wishlist_temp_file_path=>$opt_q,
  65     germplasm_info_temp_file_path=>$opt_y,
  66     odk_crossing_data_service_url=>$opt_l,
  67     odk_crossing_data_service_username=>$opt_n,
  68     odk_crossing_data_service_password=>$opt_m,
  69     odk_crossing_data_service_form_id=>$opt_o,
  70     odk_cross_progress_tree_file_dir=>$opt_f
  71 });
  72 my $result = $odk_crosses->save_ona_cross_info();
  73