ConversionSupport.pm

=head1 LICENSE

  Copyright (c) 1999-2011 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <dev@ensembl.org>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut

=head1 NAME

Bio::EnsEMBL::Utils::ConversionSupport - Utility module for Vega release and
schema conversion scripts

=head1 SYNOPSIS

  my $serverroot = '/path/to/ensembl';
  my $support = new Bio::EnsEMBL::Utils::ConversionSupport($serverroot);

  # parse common options
  $support->parse_common_options;

  # parse extra options for your script
  $support->parse_extra_options( 'string_opt=s', 'numeric_opt=n' );

  # ask user if he wants to run script with these parameters
  $support->confirm_params;

  # see individual method documentation for more stuff

=head1 DESCRIPTION

This module is a collection of common methods and provides helper
functions for the Vega release and schema conversion scripts. Amongst
others, it reads options from a config file, parses commandline options
and does logging.

=head1 METHODS

=cut

package Bio::EnsEMBL::Utils::ConversionSupport;

use strict;
use warnings;
no warnings 'uninitialized';

use Getopt::Long;
use Text::Wrap;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use FindBin qw($Bin $Script);
use POSIX qw(strftime);
use Cwd qw(abs_path);
use DBI;
use Data::Dumper;

my $species_c = 1; #counter to be used for each database connection made

=head2 new

  Arg[1]      : String $serverroot - root directory of your ensembl sandbox
  Example     : my $support = new Bio::EnsEMBL::Utils::ConversionSupport(
                                        '/path/to/ensembl');
  Description : constructor
  Return type : Bio::EnsEMBL::Utils::ConversionSupport object
  Exceptions  : thrown if no serverroot is provided
  Caller      : general

=cut

sub new {
  my $class = shift;
  (my $serverroot = shift) or throw("You must supply a serverroot.");
  my $self = {
    '_serverroot'   => $serverroot,
    '_param'        => { interactive => 1 },
    '_warnings'     => 0,
  };
  bless ($self, $class);
  return $self;
}

=head2 parse_common_options

  Example     : $support->parse_common_options;
  Description : This method reads options from a configuration file and parses
                some commandline options that are common to all scripts (like
                db connection settings, help, dry-run). Commandline options
                will override config file settings. 

                All options will be accessible via $self->param('name').
  Return type : true on success 
  Exceptions  : thrown if configuration file can't be opened
  Caller      : general

=cut

sub parse_common_options {
  my $self = shift;

  # read commandline options
  my %h;
  Getopt::Long::Configure("pass_through");
  &GetOptions( \%h,
	       'dbname|db_name=s',
	       'host|dbhost|db_host=s',
	       'port|dbport|db_port=n',
	       'user|dbuser|db_user=s',
	       'pass|dbpass|db_pass=s',
	       'conffile|conf=s',
	       'logfile|log=s',
               'nolog|nolog=s',
	       'logpath=s',
               'log_base_path=s',
	       'logappend|log_append=s',
	       'verbose|v=s',
	       'interactive|i=s',
	       'dry_run|dry|n=s',
	       'help|h|?',
	     );

  # reads config file
  my $conffile = $h{'conffile'} || $self->serverroot . "/sanger-plugins/vega/conf/ini-files/Conversion.ini";
  $conffile = abs_path($conffile);
  if (-e $conffile) {
    open(CONF, $conffile) or throw( 
      "Unable to open configuration file $conffile for reading: $!");
    my $serverroot = $self->serverroot;
    while (<CONF>) {
      chomp;

      # remove comments
      s/^[#;].*//;
      s/\s+[;].*$//;

      # read options into internal parameter datastructure, removing whitespace
      next unless (/(\w\S*)\s*=\s*(\S*)\s*/);
      my $name = $1;
      my $val = $2;
      if ($val =~ /\$SERVERROOT/) {
	$val =~ s/\$SERVERROOT/$serverroot/g;
	$val = abs_path($val);
      }
      $self->param($name, $val);
    }
    $self->param('conffile', $conffile);
  }
  elsif ($conffile) {
    warning("Unable to open configuration file $conffile for reading: $!");
  }

# override configured parameter with commandline options
  map { $self->param($_, $h{$_}) } keys %h;

  # if logpath & logfile are not set, set them here to /ensemblweb/vega_dev/shared/logs/conversion/DBNAME/SCRIPNAME_NN.log

  if (defined($self->param('log_base_path')))  {
    my $dbname = $self->param('dbname');
    $dbname =~ s/^vega_//;
    if (not (defined($self->param('logpath')))){
      $self->param('logpath', $self->param('log_base_path')."/".$dbname."/" );
    }
    if (  (not defined $self->param('logfile') ) && (not defined $self->param('nolog') )  ){
      my $log = $Script;
      $log =~ s/.pl$//g;
      my $counter;
      for ($counter=1 ; (-e $self->param('logpath')."/".$log."_".sprintf("%03d", $counter).".log"); $counter++){
#        warn  $self->param('logpath')."/".$log."_".$counter.".log";
      }
      $self->param('logfile', $log."_".sprintf("%03d", $counter).".log");
    }
  }
  
  return(1);
}

=head2 parse_extra_options

  Arg[1-N]    : option descriptors that will be passed on to Getopt::Long
  Example     : $support->parse_extra_options('string_opt=s', 'numeric_opt=n');
  Description : Parse extra commandline options by passing them on to
                Getopt::Long and storing parameters in $self->param('name).
  Return type : true on success
  Exceptions  : none (caugth by $self->error)
  Caller      : general

=cut

sub parse_extra_options {