db/0002_remove_tigrtc_tables.pl

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 [ this script name ].pl
   7
   8 =head1 SYNOPSIS
   9
  10   this_script.pl [options]
  11
  12   Options:
  13
  14     -D <dbname> (mandatory)
  15       dbname to load into
  16
  17     -H <dbhost> (mandatory)
  18       dbhost to load into
  19
  20     -p <script_executor_user> (mandatory)
  21       username to run the script
  22
  23     -F force to run this script and don't stop it by
  24        missing previous db_patches
  25
  26   Note: If the first time that you run this script, obviously
  27         you have no previous dbversion row in the md_dbversion
  28         table, so you need to force the execution of this script
  29         using -F
  30
  31 =head1 DESCRIPTION
  32
  33 remove the tigrtc tracking tables
  34
  35 =head1 COPYRIGHT & LICENSE
  36
  37 Copyright 2010 Boyce Thompson Institute for Plant Research
  38
  39 This program is free software; you can redistribute it and/or modify
  40 it under the same terms as Perl itself.
  41
  42 =cut
  43
  44
  45 use strict;
  46 use warnings;
  47
  48 use Bio::Chado::Schema;
  49 use Pod::Usage;
  50 use Getopt::Std;
  51 use CXGN::DB::InsertDBH;
  52 use CXGN::Metadata::Dbversion;   ### Module to interact with the metadata.md_dbversion table
  53
  54
  55 ## Declaration of the parameters used to run the script
  56
  57 our ($opt_H, $opt_D, $opt_p, $opt_F, $opt_h);
  58 getopts("H:D:p:Fh");
  59
  60 ## If is used -h <help> or none parameters is detailed print pod
  61
  62 if (!$opt_H && !$opt_D && !$opt_p && !$opt_F && !$opt_h) {
  63     print STDOUT "No optionas passed. Printing help\n\n";
  64     pod2usage(1);
  65 }
  66 elsif ($opt_h) {
  67     pod2usage(1);
  68 }
  69
  70
  71 ## Declaration of the name of the script and the description
  72
  73 my $patch_name = '0001_load_tomato_gen_pubs.pl';
  74 my $patch_descr = 'This script stores pubprop for the tomato genome publications. It assumes these are ALREADY STORED in the database. The best way to load first the publications is by using the web interface ';
  75
  76 print STDOUT "\n+--------------------------------------------------------------------------------------------------+\n";
  77 print STDOUT "Executing the patch:\n   $patch_name.\n\nDescription:\n  $patch_descr.\n\nExecuted by:\n  $opt_p.";
  78 print STDOUT "\n+--------------------------------------------------------------------------------------------------+\n\n";
  79
  80 ## And the requeriments if you want not use all
  81 ##
  82 my @previous_requested_patches = (   ## ADD HERE
  83    );
  84
  85 ## Specify the mandatory parameters
  86
  87 if (!$opt_H || !$opt_D) {
  88     print STDOUT "\nMANDATORY PARAMETER ERROR: -D <db_name> or/and -H <db_host> parameters has not been specified for $patch_name.\n";
  89 }
  90
  91 if (!$opt_p) {
  92     print STDOUT "\nMANDATORY PARAMETER ERROR: -p <script_executor_user> parameter has not been specified for $patch_name.\n";
  93 }
  94
  95 ## Create the $schema object for the db_version object
  96 ## This should be replace for CXGN::DB::DBICFactory as soon as it can use CXGN::DB::InsertDBH
  97
  98 my $db =  CXGN::DB::InsertDBH->new(
  99                                      {
 100                                          dbname => $opt_D,
 101                                          dbhost => $opt_H
 102                                      }
 103                                    );
 104 my $dbh = $db->get_actual_dbh();
 105
 106 print STDOUT "\nCreating the Metadata Schema object.\n";
 107
 108 my $metadata_schema = CXGN::Metadata::Schema->connect(
 109                                                        sub { $dbh },
 110                                                       { on_connect_do => ['SET search_path TO metadata;'] },
 111                                                       );
 112
 113 print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
 114
 115 ### Now it will check if you have runned this patch or the previous patches
 116
 117 my $dbversion = CXGN::Metadata::Dbversion->new($metadata_schema)
 118                                          ->complete_checking( {
 119                                                                  patch_name  => $patch_name,
 120                                                                  patch_descr => $patch_descr,
 121                                                                  prepatch_req => \@previous_requested_patches,
 122                                                                  force => $opt_F
 123                                                               }
 124                                                              );
 125
 126
 127 ### CREATE AN METADATA OBJECT and a new metadata_id in the database for this data
 128
 129 my $metadata = CXGN::Metadata::Metadbdata->new($metadata_schema, $opt_p);
 130
 131 ### Get a new metadata_id (if you are using store function you only need to supply $metadbdata object)
 132
 133 my $metadata_id = $metadata->store()
 134                            ->get_metadata_id();
 135
 136 ### Now you can insert the data using different options:
 137 ##
 138 ##  1- By sql queryes using $dbh->do(<<EOSQL); and detailing in the tag the queries
 139 ##
 140 ##  2- Using objects with the store function
 141 ##
 142 ##  3- Using DBIx::Class first level objects
 143 ##
 144
 145 ## In this case we will use the SQL tag
 146
 147 print STDERR "\nExecuting the SQL commands.\n";
 148
 149 $db->do("drop table $_") for qw(
 150   sgn.tigrtc_index
 151   sgn.tigrtc_tracking
 152   sgn.tigrtc_membership
 153 );
 154
 155 ## Now it will add this new patch information to the md_version table.  It did the dbversion object before and
 156 ## set the patch_name and the patch_description, so it only need to store it.
 157
 158 $dbversion->store($metadata);
 159
 160 print STDOUT "DONE!\n";
 161
 162 $dbh->commit;
 163
 164 __END__
 165