ConversionSupport.pm 52.9 KB
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=head1 LICENSE
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  Copyright (c) 1999-2011 The European Bioinformatics Institute and
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  Genome Research Limited.  All rights reserved.
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  This software is distributed under a modified Apache license.
  For license details, please see
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    http://www.ensembl.org/info/about/code_licence.html
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=head1 CONTACT
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  Please email comments or questions to the public Ensembl
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  developers list at <dev@ensembl.org>.
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  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.
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=cut
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=head1 NAME
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Bio::EnsEMBL::Utils::ConversionSupport - Utility module for Vega release and
schema conversion scripts
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=head1 SYNOPSIS
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  my $serverroot = '/path/to/ensembl';
  my $support = new Bio::EnsEMBL::Utils::ConversionSupport($serverroot);
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  # parse common options
  $support->parse_common_options;
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  # parse extra options for your script
  $support->parse_extra_options( 'string_opt=s', 'numeric_opt=n' );
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  # ask user if he wants to run script with these parameters
  $support->confirm_params;
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  # see individual method documentation for more stuff
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=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
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=cut

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

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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);
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use Cwd qw(abs_path);
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use DBI;
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use Data::Dumper;
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=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 {
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  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;
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}

=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 {
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  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',
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	       'nolog|nolog=s',
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	       'logpath=s',
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	       'log_base_path=s'
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	       '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);
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    }
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    $self->param('conffile', $conffile);
  } elsif ($conffile) {
    warning("Unable to open configuration file $conffile for reading: $!");
  }

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# override configured parameter with commandline options
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  map { $self->param($_, $h{$_}) } keys %h;
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  # if logpath & logfile are not se, set them here to /ensemblweb/vega_dev/shared/logs/conversion/DBNAME/SCRIPNAME_NN.log
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  if (defined($self->param('log_base_path')))  {
    if (not (defined($self->param('logpath')))){
      $self->param('logpath', "/ensemblweb/vega_dev/shared/logs/conversion/".$self->param('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");
    }
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  }

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  return(1);
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}

=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 {
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  my ($self, @params) = @_;
  Getopt::Long::Configure("no_pass_through");
  eval {
    # catch warnings to pass to $self->error
    local $SIG{__WARN__} = sub { die @_; };
    &GetOptions(\%{ $self->{'_param'} }, @params);
  };
  $self->error($@) if $@;
  return(1);
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}

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=head2 allowed_params

  Arg[1-N]    : (optional) List of allowed parameters to set
  Example     : my @allowed = $self->allowed_params(qw(param1 param2));
  Description : Getter/setter for allowed parameters. This is used by
                $self->confirm_params() to avoid cluttering of output with
                conffile entries not relevant for a given script. You can use
                $self->get_common_params() as a shortcut to set them.
  Return type : Array - list of allowed parameters
  Exceptions  : none
  Caller      : general

=cut

sub allowed_params {
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  my $self = shift;

  # setter
  if (@_) {
    @{ $self->{'_allowed_params'} } = @_;
  }

  # getter
  if (ref($self->{'_allowed_params'}) eq 'ARRAY') {
    return @{ $self->{'_allowed_params'} };
  } else {
    return ();
  }
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}

=head2 get_common_params

  Example     : my @allowed_params = $self->get_common_params, 'extra_param';
  Description : Returns a list of commonly used parameters in the conversion
                scripts. Shortcut for setting allowed parameters with
                $self->allowed_params().
  Return type : Array - list of common parameters
  Exceptions  : none
  Caller      : general

=cut

sub get_common_params {
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  return qw(
	    conffile
	    dbname
	    host
	    port
	    user
	    pass
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	    nolog
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	    logpath
	    logfile
	    logappend
	    verbose
	    interactive
	    dry_run
	  );
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}

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=head2 get_loutre_params
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  Arg         : (optional) return a list to parse or not
  Example     : $support->parse_extra_options($support->get_loutre_params('parse'))
  Description : Returns a list of commonly used loutre db parameters - parse option is
                simply used to distinguish between reporting and parsing parameters
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  Return type : Array - list of common parameters
  Exceptions  : none
  Caller      : general

=cut

sub get_loutre_params {
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  my ($self,$p) = @_;
  if ($p) {
    return qw(
	      loutrehost=s
	      loutreport=s
	      loutreuser=s
	      loutrepass=s
	      loutredbname=s
	    );
  }
  else {
    return qw(
	      loutrehost
	      loutreport
	      loutreuser
	      loutrepass
	      loutredbname
	    );
  }
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}

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=head2 remove_vega_params

  Example     : $support->remove_vega_params;
  Description : Removes Vega db conection parameters. Usefull to avoid clutter in log files when
                working exclusively with loutre
  Return type : none
  Exceptions  : none
  Caller      : general

=cut

sub remove_vega_params {
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  my $self = shift;
  foreach my $param (qw(dbname host port user pass)) {
    $self->{'_param'}{$param} = undef;
  }
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}
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=head2 confirm_params

  Example     : $support->confirm_params;
  Description : Prints a table of parameters that were collected from config
                file and commandline and asks user to confirm if he wants
                to proceed.
  Return type : true on success
  Exceptions  : none
  Caller      : general

=cut

sub confirm_params {
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  my $self = shift;

  # print parameter table
  print "Running script with these parameters:\n\n";
  print $self->list_all_params;

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  if ($self->param('host') eq 'ensdb-1-10') {
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    # ask user if he wants to proceed
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    exit unless $self->user_proceed("**************\n\n You're working on ensdb-1-10! Is that correct and you want to continue ?\n\n**************");
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  }
  else {
    # ask user if he wants to proceed
    exit unless $self->user_proceed("Continue?");
  }
  return(1);
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}

=head2 list_all_params

  Example     : print LOG $support->list_all_params;
  Description : prints a table of the parameters used in the script
  Return type : String - the table to print
  Exceptions  : none
  Caller      : general

=cut

sub list_all_params {
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  my $self = shift;
  my $txt = sprintf "    %-21s%-40s\n", qw(PARAMETER VALUE);
  $txt .= "    " . "-"x71 . "\n";
  $Text::Wrap::colums = 72;
  my @params = $self->allowed_params;
  foreach my $key (@params) {
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    my @vals = $self->param($key);
    if (@vals) {
      $txt .= Text::Wrap::wrap( sprintf('   %-21s', $key),
				' 'x24,
				join(", ", @vals)
			      ) . "\n";
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    }
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  }
  $txt .= "\n";
  return $txt;
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}

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=head2 create_commandline_options

  Arg[1]      : Hashref $settings - hashref describing what to do
                Allowed keys:
                    allowed_params => 0|1   # use all allowed parameters
                    exclude => []           # listref of parameters to exclude
                    replace => {param => newval} # replace value of param with
                                                 # newval
  Example     : $support->create_commandline_options({
                    allowed_params => 1,
                    exclude => ['verbose'],
                    replace => { 'dbname' => 'homo_sapiens_vega_33_35e' }
                });
  Description : Creates a commandline options string that can be passed to any
                other script using ConversionSupport.
  Return type : String - commandline options string
  Exceptions  : none
  Caller      : general

=cut

sub create_commandline_options {
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  my ($self, $settings) = @_;
  my %param_hash;

  # get all allowed parameters
  if ($settings->{'allowed_params'}) {
    # exclude params explicitly stated
    my %exclude = map { $_ => 1 } @{ $settings->{'exclude'} || [] };
    foreach my $param ($self->allowed_params) {
      unless ($exclude{$param}) {
	my ($first, @rest) = $self->param($param);
	next unless (defined($first));
	
	if (@rest) {
	  $first = join(",", $first, @rest);
	}
	$param_hash{$param} = $first;
      }
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    }
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  }
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  # replace values
  foreach my $key (keys %{ $settings->{'replace'} || {} }) {
    $param_hash{$key} = $settings->{'replace'}->{$key};
  }
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  # create the commandline options string
  my $options_string;
  foreach my $param (keys %param_hash) {
    $options_string .= sprintf("--%s %s ", $param, $param_hash{$param});
  }
  return $options_string;
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}

=head2 check_required_params

  Arg[1-N]    : List @params - parameters to check
  Example     : $self->check_required_params(qw(dbname host port));
  Description : Checks $self->param to make sure the requested parameters
                have been set. Dies if parameters are missing.
  Return type : true on success
  Exceptions  : none
  Caller      : general

=cut

sub check_required_params {
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  my ($self, @params) = @_;
  my @missing = ();
  foreach my $param (@params) {
    push @missing, $param unless $self->param($param);
  }
  if (@missing) {
    throw("Missing parameters: @missing.\nYou must specify them on the commandline or in your conffile.\n");
  }
  return(1);
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}

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=head2 user_proceed

  Arg[1]      : (optional) String $text - notification text to present to user
  Example     : # run a code snipped conditionally
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                if ($support->user_proceed("Run the next code snipped?")) {
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                    # run some code
                }
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                # exit if requested by user
                exit unless ($support->user_proceed("Want to continue?"));
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  Description : If running interactively, the user is asked if he wants to
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                perform a script action. If he doesn't, this section is skipped
                and the script proceeds with the code. When running
                non-interactively, the section is run by default.
  Return type : TRUE to proceed, FALSE to skip.
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  Exceptions  : none
  Caller      : general

=cut

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sub user_proceed {
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  my ($self, $text) = @_;

  if ($self->param('interactive')) {
    print "$text\n" if $text;
    print "[y/N] ";
    my $input = lc(<>);
    chomp $input;
    unless ($input eq 'y') {
      print "Skipping.\n";
      return(0);
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    }
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  }
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  return(1);
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}

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=head2 user_confirm

  Description : DEPRECATED - please use user_proceed() instead

=cut

sub user_confirm {
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  my $self = shift;
  exit unless $self->user_proceed("Continue?");
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}

=head2 read_user_input

  Arg[1]      : (optional) String $text - notification text to present to user
  Example     : my $ret = $support->read_user_input("Choose a number [1/2/3]");
                if ($ret == 1) {
                    # do something
                } elsif ($ret == 2) {
                    # do something else
                }
  Description : If running interactively, the user is asked for input.
  Return type : String - user's input
  Exceptions  : none
  Caller      : general

=cut

sub read_user_input {
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  my ($self, $text) = @_;
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  if ($self->param('interactive')) {
    print "$text\n" if $text;
    my $input = <>;
    chomp $input;
    return $input;
  }
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}

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=head2 comma_to_list

  Arg[1-N]    : list of parameter names to parse
  Example     : $support->comma_to_list('chromosomes');
  Description : Transparently converts comma-separated lists into arrays (to
                allow different styles of commandline options, see perldoc
                Getopt::Long for details). Parameters are converted in place
                (accessible through $self->param('name')).
  Return type : true on success
  Exceptions  : none
  Caller      : general

=cut

sub comma_to_list {
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  my $self = shift;
  foreach my $param (@_) {
    $self->param($param,
		 split (/,/, join (',', $self->param($param))));
  }
  return(1);
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}

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=head2 list_or_file
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  Arg[1]      : Name of parameter to parse
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  Example     : $support->list_or_file('gene_stable_id');
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  Description : Determines whether a parameter holds a list or it is a filename
                to read the list entries from.
  Return type : true on success
  Exceptions  : thrown if list file can't be opened
  Caller      : general

=cut

sub list_or_file {
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  my ($self, $param) = @_;
  my @vals = $self->param($param);
  return unless (@vals);

  my $firstval = $vals[0];
  if (scalar(@vals) == 1 && -e $firstval) {
    # we didn't get a list of values, but a file to read values from
    @vals = ();
    open(IN, $firstval) or throw("Cannot open $firstval for reading: $!");
    while(<IN>){
      chomp;
      push(@vals, $_);
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    }
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    close(IN);
    $self->param($param, @vals);
  }
  $self->comma_to_list($param);
  return(1);
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}

=head2 param

  Arg[1]      : Parameter name
  Arg[2-N]    : (optional) List of values to set
  Example     : my $dbname = $support->param('dbname');
                $support->param('port', 3306);
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                $support->param('chromosomes', 1, 6, 'X');
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  Description : Getter/setter for parameters. Accepts single-value params and
                list params.
  Return type : Scalar value for single-value parameters, array of values for
                list parameters
  Exceptions  : thrown if no parameter name is supplied
  Caller      : general

=cut

sub param {
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  my $self = shift;
  my $name = shift or throw("You must supply a parameter name");
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  # setter
  if (@_) {
    if (scalar(@_) == 1) {
      # single value
      $self->{'_param'}->{$name} = shift;
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    } else {
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      # list of values
      undef $self->{'_param'}->{$name};
      @{ $self->{'_param'}->{$name} } = @_;
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    }
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  }

  # getter
  if (ref($self->{'_param'}->{$name}) eq 'ARRAY') {
    # list parameter
    return @{ $self->{'_param'}->{$name} };
  } elsif (defined($self->{'_param'}->{$name})) {
    # single-value parameter
    return $self->{'_param'}->{$name};
  } else {
    return ();
  }
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}

=head2 error

  Arg[1]      : (optional) String - error message
  Example     : $support->error("An error occurred: $@");
                exit(0) if $support->error;
  Description : Getter/setter for error messages
  Return type : String - error message
  Exceptions  : none
  Caller      : general

=cut

sub error {
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  my $self = shift;
  $self->{'_error'} = shift if (@_);
  return $self->{'_error'};
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}

=head2 warnings

  Example     : print LOG "There were ".$support->warnings." warnings.\n";
  Description : Returns the number of warnings encountered while running the
                script (the warning counter is increased by $self->log_warning).
  Return type : Int - number of warnings
  Exceptions  : none
  Caller      : general

=cut

sub warnings {
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  my $self = shift;
  return $self->{'_warnings'};
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}

=head2 serverroot

  Arg[1]      : (optional) String - root directory of your ensembl sandbox
  Example     : my $serverroot = $support->serverroot;
  Description : Getter/setter for the root directory of your ensembl sandbox.
                This is set when ConversionSupport object is created, so
                usually only used as a getter.
  Return type : String - the server root directory
  Exceptions  : none
  Caller      : general

=cut

sub serverroot {
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  my $self = shift;
  $self->{'_serverroot'} = shift if (@_);
  return $self->{'_serverroot'};
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}

=head2 get_database

  Arg[1]      : String $database - the type of database to connect to
                (eg core, otter)
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  Arg[2]      : (optional) String $prefix - the prefix used for retrieving the
                connection settings from the configuration
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  Example     : my $db = $support->get_database('core');
  Description : Connects to the database specified.
  Return type : DBAdaptor of the appropriate type
  Exceptions  : thrown if asking for unknown database
  Caller      : general

=cut

sub get_database {
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  my $self = shift;
  my $database = shift or throw("You must provide a database");
  my $prefix = shift || '';
  $self->check_required_params(
    "${prefix}host",
    "${prefix}port",
    "${prefix}user",
    "${prefix}dbname",
  );
  my %adaptors = (
    core    => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
    ensembl => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
    evega   => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
    otter   => 'Bio::Otter::DBSQL::DBAdaptor',
    vega    => 'Bio::Otter::DBSQL::DBAdaptor',
    compara => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
    loutre  => 'Bio::Vega::DBSQL::DBAdaptor',
  );
  throw("Unknown database: $database") unless $adaptors{$database};

  $self->dynamic_use($adaptors{$database});
  my $dba = $adaptors{$database}->new(
    -host   => $self->param("${prefix}host"),
    -port   => $self->param("${prefix}port"),
    -user   => $self->param("${prefix}user"),
    -pass   => $self->param("${prefix}pass") || '',
    -dbname => $self->param("${prefix}dbname"),
    -group  => $database,
  );
  #can use this approach to get dna from another db
#  my $dna_db = $adaptors{$database}->new(
#    -host => 'otterlive',
#    -port => '3301',
#    -user => $self->param("${prefix}user"),
#    -pass => $self->param("${prefix}pass"),
#    -dbname => 'loutre_human',
#  );
#  $dba->dnadb($dna_db);

  # otherwise explicitely set the dnadb to itself - by default the Registry assumes
  # a group 'core' for this now
  $dba->dnadb($dba);

  $self->{'_dba'}->{$database} = $dba;
  $self->{'_dba'}->{'default'} = $dba unless $self->{'_dba'}->{'default'};
  return $self->{'_dba'}->{$database};
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}

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=head2 get_dbconnection

  Arg[1]      : (optional) String $prefix - the prefix used for retrieving the
                connection settings from the configuration
  Example     : my $dbh = $self->get_dbconnection;
  Description : Connects to the database server specified. You don't have to
                specify a database name (this is useful for running commands
                like $dbh->do('show databases')).
  Return type : DBI database handle
  Exceptions  : thrown if connection fails
  Caller      : general
  Status      : At Risk

=cut

sub get_dbconnection {
  my $self = shift;
  my $prefix = shift;
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  $self->check_required_params(
      "${prefix}host",
      "${prefix}port",
      "${prefix}user",
  );

  my $dsn = "DBI:" . ($self->param('driver')||'mysql') .
            ":host=" . $self->param("${prefix}host") .
            ";port=" . $self->param("${prefix}port");

  if ($self->param("${prefix}dbname")) {
    $dsn .= ";dbname=".$self->param("${prefix}dbname");
  }

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#  warn $dsn;

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  my $dbh;
  eval{
    $dbh = DBI->connect($dsn, $self->param("${prefix}user"),
      $self->param("${prefix}pass"), {'RaiseError' => 1, 'PrintError' => 0});
  };

  if (!$dbh || $@ || !$dbh->ping) {
    $self->log_error("Could not connect to db server as user ".
      $self->param("${prefix}user") .
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      " using [$dsn] as a locator:\n" . $DBI::errstr . $@);
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  }

  $self->{'_dbh'} = $dbh;
  return $self->{'_dbh'};

}

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=head2 dba
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  Arg[1]      : (optional) String $database - type of db apaptor to retrieve
  Example     : my $dba = $support->dba;
  Description : Getter for database adaptor. Returns default (i.e. created
                first) db adaptor if no argument is provided.
  Return type : Bio::EnsEMBL::DBSQL::DBAdaptor or Bio::Otter::DBSQL::DBAdaptor
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  Exceptions  : none
  Caller      : general

=cut

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sub dba {
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  my ($self, $database) = shift;
  return $self->{'_dba'}->{$database} || $self->{'_dba'}->{'default'};
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}

=head2 dynamic_use

  Arg [1]    : String $classname - The name of the class to require/import
  Example    : $self->dynamic_use('Bio::EnsEMBL::DBSQL::DBAdaptor');
  Description: Requires and imports the methods for the classname provided,
               checks the symbol table so that it doesnot re-require modules
               that have already been required.
  Returntype : true on success
  Exceptions : Warns to standard error if module fails to compile
  Caller     : internal

=cut

sub dynamic_use {
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  my ($self, $classname) = @_;
  my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ? ($1,$2) : ('::', $classname);

  no strict 'refs';
  # return if module has already been imported
  return 1 if $parent_namespace->{$module.'::'} && %{ $parent_namespace->{$module.'::'}||{} };

  eval "require $classname";
  throw("Failed to require $classname: $@") if ($@);
  $classname->import();

  return 1;
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}

=head2 get_chrlength

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  Arg[1]      : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $dba
  Arg[2]      : (optional) String $version - coord_system version
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  Arg[3]      : (optional) String $type - type of region eg chromsome (defaults to 'toplevel')
  Arg[4]      : (optional) Boolean - return non reference slies as well (required for haplotypes eq 6-COX)
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  Example     : my $chr_length = $support->get_chrlength($dba);
  Description : Get all chromosomes and their length from the database. Return
                chr_name/length for the chromosomes the user requested (or all
                chromosomes by default)
  Return type : Hashref - chromosome_name => length
  Exceptions  : thrown if not passing a Bio::EnsEMBL::DBSQL::DBAdaptor
  Caller      : general

=cut

sub get_chrlength {
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  my ($self, $dba, $version,$type,$include_non_reference) = @_;
  $dba ||= $self->dba;
  $type ||= 'toplevel';
  throw("get_chrlength should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n")
    unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));

  my $sa = $dba->get_SliceAdaptor;

  my @chromosomes = map { $_->seq_region_name } 
    @{ $sa->fetch_all($type, $version,$include_non_reference) };
  my %chr = map { $_ => $sa->fetch_by_region($type, $_, undef, undef, undef, $version)->length } @chromosomes;

  my @wanted = $self->param('chromosomes');
  if (@wanted) {
    # check if user supplied invalid chromosome names
    foreach my $chr (@wanted) {
      my $found = 0;
      foreach my $chr_from_db (keys %chr) {
	if ($chr_from_db eq $chr) {
	  $found = 1;
	  last;
	}
      }
      unless ($found) {
	warning("Didn't find chromosome $chr in database " .
		  $self->param('dbname'));
      }
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    }

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    # filter to requested chromosomes only
  HASH:
    foreach my $chr_from_db (keys %chr) {
      foreach my $chr (@wanted) {
	if ($chr_from_db eq $chr) {
	  next HASH;
	}
      }
      delete($chr{$chr_from_db});
    }
  }

  return \%chr;
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}

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=head2 get_ensembl_chr_mapping

  Arg[1]      : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $dba
  Arg[2]      : (optional) String $version - coord_system version
  Example     : my $ensembl_mapping = $support->get_ensembl_chr_mapping($dba);
  Description : Gets a mapping between Vega chromosome names and their
                equivalent Ensembl chromosomes.
  Return type : Hashref - Vega name => Ensembl name
  Exceptions  : thrown if not passing a Bio::EnsEMBL::DBSQL::DBAdaptor
  Caller      : general

=cut

sub get_ensembl_chr_mapping {
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  my ($self, $dba, $version) = @_;
  $dba ||= $self->dba;
  throw("get_ensembl_chr_mapping should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n") unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));

  my $sa = $dba->get_SliceAdaptor;
  my @chromosomes = map { $_->seq_region_name } 
    @{ $sa->fetch_all('chromosome', $version) };

  my %chrs;
  foreach my $chr (@chromosomes) {
    my $sr = $sa->fetch_by_region('chromosome', $chr, undef, undef, undef, $version);
    my ($ensembl_name_attr) = @{ $sr->get_all_Attributes('ensembl_name') };
    if ($ensembl_name_attr) {
      $chrs{$chr} = $ensembl_name_attr->value;
    } else {
      $chrs{$chr} = $chr;
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    }
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  }
  return \%chrs;
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}

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=head2 get_taxonomy_id

  Arg[1]      : Bio::EnsEMBL::DBSQL::DBAdaptor $dba
  Example     : my $sid = $support->get_taxonony_id($dba);
  Description : Retrieves the taxononmy ID from the meta table
  Return type : Int - the taxonomy ID
  Exceptions  : thrown if no taxonomy ID is found in the database
  Caller      : general

=cut

sub get_taxonomy_id {
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  my ($self, $dba) = @_;
  $dba ||= $self->dba;
  my $sql = 'SELECT meta_value FROM meta WHERE meta_key = "species.taxonomy_id"';
  my $sth = $dba->dbc->db_handle->prepare($sql);
  $sth->execute;
  my ($tid) = $sth->fetchrow_array;
  $sth->finish;
  $self->throw("Could not determine taxonomy_id from database.") unless $tid;
  return $tid;
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}

=head2 get_species_scientific_name

  Arg[1]      : Bio::EnsEMBL::DBSQL::DBAdaptor $dba
  Example     : my $species = $support->get_species_scientific_name($dba);
  Description : Retrieves the species scientific name (Genus species) from the
                meta table
  Return type : String - species scientific name
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  Exceptions  : thrown if species name can not be determined from db
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  Caller      : general

=cut

sub get_species_scientific_name {
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  my ($self, $dba) = @_;
  $dba ||= $self->dba;
  my $sql_tmp = "SELECT meta_value FROM meta WHERE meta_key = \'species.classification\' ORDER BY meta_id";
  my $sql = $dba->dbc->add_limit_clause($sql_tmp,2);
  my $sth = $dba->dbc->db_handle->prepare($sql);
  $sth->execute;
  my @sp;
  while (my @row = $sth->fetchrow_array) {
    push @sp, $row[0];
  }
  $sth->finish;
  my $species = join(" ", reverse @sp);
  $self->throw("Could not determine species scientific name from database.")
    unless $species;
  return $species;
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}

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=head2 species

  Arg[1]      : (optional) String $species - species name to set
  Example     : my $species = $support->species;
                my $url = "http://vega.sanger.ac.uk/$species/";
  Description : Getter/setter for species name (Genus_species). If not set, it's
                determined from database's meta table
  Return type : String - species name
  Exceptions  : none
  Caller      : general

=cut

sub species {
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  my $self = shift;
  $self->{'_species'} = shift if (@_);
  # get species name from database if not set
  unless ($self->{'_species'}) {
    $self->{'_species'} = join('_',
			       split(/ /, $self->get_species_scientific_name));
  }
  return $self->{'_species'};
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}

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=head2 sort_chromosomes

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  Arg[1]      : (optional) Hashref $chr_hashref - Hashref with chr_name as keys
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  Example     : my $chr = { '6-COX' => 1, '1' => 1, 'X' => 1 };
                my @sorted = $support->sort_chromosomes($chr);
  Description : Sorts chromosomes in an intuitive way (numerically, then
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                alphabetically). If no chromosome hashref is passed, it's
                retrieve by calling $self->get_chrlength()
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  Return type : List - sorted chromosome names
  Exceptions  : thrown if no hashref is provided
  Caller      : general

=cut

sub sort_chromosomes {
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  my ($self, $chr_hashref) = @_;
  $chr_hashref = $self->get_chrlength unless ($chr_hashref);
  throw("You have to pass a hashref of your chromosomes")
    unless ($chr_hashref and ref($chr_hashref) eq 'HASH');
  return (sort _by_chr_num keys %$chr_hashref);
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}

=head2 _by_chr_num

  Example     : my @sorted = sort _by_chr_num qw(X, 6-COX, 14, 7);
  Description : Subroutine to use in sort for sorting chromosomes. Sorts
                numerically, then alphabetically
  Return type : values to be used by sort
  Exceptions  : none
  Caller      : internal ($self->sort_chromosomes)

=cut

sub _by_chr_num {
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  my @awords = split /-/, $a;
  my @bwords = split /-/, $b;

  my $anum = $awords[0];
  my $bnum = $bwords[0];

  if ($anum !~ /^[0-9]*$/) {
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    if ($bnum !~ /^[0-9]*$/) {
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      return $anum cmp $bnum;
    } else {
      return 1;
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    }
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  }
  if ($bnum !~ /^[0-9]*$/) {
    return -1;
  }
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  if ($anum <=> $bnum) {
    return $anum <=> $bnum;
  } else {
    if ($#awords == 0) {
      return -1;
    } elsif ($#bwords == 0) {
      return 1;
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    } else {
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      return $awords[1] cmp $bwords[1];
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    }
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  }
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}

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=head2 split_chromosomes_by_size

  Arg[1]      : (optional) Int $cutoff - the cutoff in bp between small and
                large chromosomes
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  Arg[2]      : (optional) Boolean to include duplicate regions, ie PAR or not
                (default is no)
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  Arg[3]      : (optional) Coordsystem version to retrieve
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  Example     : my $chr_slices = $support->split_chromosomes_by_size;
                foreach my $block_size (keys %{ $chr_slices }) {
                    print "Chromosomes with blocksize $block_size: ";
                    print join(", ", map { $_->seq_region_name }
                                        @{ $chr_slices->{$block_size} });
                }
  Description : Determines block sizes for storing DensityFeatures on
                chromosomes, and return slices for each chromosome. The block
                size is determined so that you have 150 bins for the smallest
                chromosome over 5 Mb in length. For chromosomes smaller than 5
                Mb, an additional smaller block size is used to yield 150 bins
                for the overall smallest chromosome. This will result in
                reasonable resolution for small chromosomes and high
                performance for big ones.
  Return type : Hashref (key: block size; value: Arrayref of chromosome
                Bio::EnsEMBL::Slices)
  Exceptions  : none
  Caller      : density scripts

=cut

sub split_chromosomes_by_size {
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  my $self   = shift;
  my $cutoff = shift || 5000000;
  my $dup    = shift || 0;
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  my $cs_version = shift;
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  my $slice_adaptor = $self->dba->get_SliceAdaptor;
  my $top_slices;
  if ($self->param('chromosomes')) {
    foreach my $chr ($self->param('chromosomes')) {
      push @{ $top_slices }, $slice_adaptor->fetch_by_region('chromosome', $chr);
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    }
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  } else {
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    $top_slices = $slice_adaptor->fetch_all('chromosome',$cs_version,0,$dup);
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  }
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  my ($big_chr, $small_chr, $min_big_chr, $min_small_chr);
  foreach my $slice (@{ $top_slices }) {
    next if ($slice->length eq 10000); #hack for chrY pseudoslice
    if ($slice->length < $cutoff) {
      if (! $min_small_chr or ($min_small_chr > $slice->length)) {
	$min_small_chr = $slice->length;
      }
      # push small chromosomes onto $small_chr
      push @{ $small_chr }, $slice;
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    }
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    elsif (! $min_big_chr or ($min_big_chr > $slice->length) ){
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      $min_big_chr = $slice->length;
    }
    # push _all_ chromosomes onto $big_chr
    push @{ $big_chr }, $slice;
  }
  my $chr_slices;
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  $chr_slices->{int($min_big_chr/150)}   = $big_chr if $min_big_chr;
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  $chr_slices->{int($min_small_chr/150)} = $small_chr if $min_small_chr;
  return $chr_slices;
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}

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=head2 log

  Arg[1]      : String $txt - the text to log
  Arg[2]      : Int $indent - indentation level for log message
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  Example     : my $log = $support->log_filehandle;
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                $support->log('Log foo.\n', 1);
  Description : Logs a message to the filehandle initialised by calling
                $self->log_filehandle(). You can supply an indentation level
                to get nice hierarchical log messages.
  Return type : true on success
  Exceptions  : thrown when no filehandle can be obtained
  Caller      : general

=cut

sub log {
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  my ($self, $txt, $indent) = @_;
  $indent ||= 0;

  # strip off leading linebreaks so that indenting doesn't break
  $txt =~ s/^(\n*)//;

  $txt = $1."    "x$indent . $txt;
  my $fh = $self->{'_log_filehandle'};
  throw("Unable to obtain log filehandle") unless $fh;
  print $fh "$txt";
  return(1);
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}

=head2 log_warning

  Arg[1]      : String $txt - the warning text to log
  Arg[2]      : Int $indent - indentation level for log message
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  Arg[3]      : Bool - add a line break before warning if true
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  Example     : my $log = $support->log_filehandle;
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                $support->log_warning('Log foo.\n', 1);
  Description : Logs a message via $self->log and increases the warning counter.
  Return type : true on success
  Exceptions  : none
  Caller      : general

=cut

sub log_warning {
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  my ($self, $txt, $indent, $break) = @_;
  $txt = "WARNING: " . $txt;
  $txt = "\n$txt" if ($break);
  $self->log($txt, $indent);
  $self->{'_warnings'}++;
  return(1);
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}

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=head2 log_error

  Arg[1]      : String $txt - the error text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     : my $log = $support->log_filehandle;
                $support->log_error('Log foo.\n', 1);
  Description : Logs a message via $self->log and exits the script.
  Return type : none
  Exceptions  : none
  Caller      : general

=cut

sub log_error {
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  my ($self, $txt, $indent) = @_;
  $txt = "ERROR: ".$txt;
  $self->log($txt, $indent);
  $self->log("Exiting.\n");
  exit;
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}

=head2 log_verbose

  Arg[1]      : String $txt - the warning text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     : my $log = $support->log_filehandle;
                $support->log_verbose('Log this verbose message.\n', 1);
  Description : Logs a message via $self->log if --verbose option was used
  Return type : TRUE on success, FALSE if not verbose
  Exceptions  : none
  Caller      : general

=cut

sub log_verbose {
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  my ($self, $txt, $indent) = @_;
  return(0) unless $self->param('verbose');
  $self->log($txt, $indent);
  return(1);
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}

=head2 log_stamped

  Arg[1]      : String $txt - the warning text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     : my $log = $support->log_filehandle;
                $support->log_stamped('Log this stamped message.\n', 1);
  Description : Appends timestamp and memory usage to a message and logs it via
                $self->log
  Return type : TRUE on success
  Exceptions  : none
  Caller      : general

=cut

sub log_stamped {
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  my ($self, $txt, $indent) = @_;
  # append timestamp and memory usage to log text
  $txt =~ s/(\n*)$//;
  $txt .= " ".$self->date_and_mem.$1;
  $self->log($txt, $indent);
  return(1);
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}

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=head2 log_filehandle

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  Arg[1]      : (optional) String $mode - file access mode
  Example     : my $log = $support->log_filehandle;
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                # print to the filehandle
                print $log 'Lets start logging...\n';
                # log via the wrapper $self->log()
                $support->log('Another log message.\n');
  Description : Returns a filehandle for logging (STDERR by default, logfile if
                set from config or commandline). You can use the filehandle
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                directly to print to, or use the smart wrapper $self->log().
                Logging mode (truncate or append) can be set by passing the
                mode as an argument to log_filehandle(), or with the
                --logappend commandline option (default: truncate)
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  Return type : Filehandle - the filehandle to log to
  Exceptions  : thrown if logfile can't be opened
  Caller      : general

=cut

sub log_filehandle {
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  my ($self, $mode) = @_;
  $mode ||= '>';
  $mode = '>>' if ($self->param('logappend'));
  my $fh = \*STDERR;
  if (my $logfile = $self->param('logfile')) {
    if (my $logpath = $self->param('logpath')) {
      unless (-e $logpath) {
	system("mkdir $logpath") == 0 or
	  $self->log_error("Can't create log dir $logpath: $!\n");
      }
      $logfile = "$logpath/$logfile";
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    }
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    open($fh, "$mode", $logfile) or throw(
      "Unable to open $logfile for writing: $!");
  }
  $self->{'_log_filehandle'} = $fh;
  return $self->{'_log_filehandle'};
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}

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=head2 filehandle

  Arg[1]      : String $mode - file access mode
  Arg[2]      : String $file - input or output file
  Example     : my $fh = $support->filehandle('>>', '/path/to/file');
                # print to the filehandle
                print $fh 'Your text goes here...\n';
  Description : Returns a filehandle (*STDOUT for writing, *STDIN for reading
                by default) to print to or read from.
  Return type : Filehandle - the filehandle
  Exceptions  : thrown if file can't be opened
  Caller      : general

=cut

sub filehandle {
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  my ($self, $mode, $file) = @_;
  $mode ||= ">";
  my $fh;
  if ($file