/usr/share/perl5/Bio/GMOD/Config2.pm is in libchado-perl 1.23-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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use strict;
=head1 NAME
Bio::GMOD::Config2 -- an extended GMOD utility package for reading config files
=head1 SYNOPSIS
$ export GMOD_ROOT=/usr/local/gmod
..
use Bio::GMOD::Config2;
my $conf2 = Bio::GMOD::Config2->new();
my $confdir = $conf2->confdir();
$confhash = $conf2->config();
$confhash = $conf2->readConfig($file); # can be XML, Perl-Struct or key=value
$confhash = $conf2->readConfDir($dir, '(gmod|\w+db)\.conf');
$dbname = $conf2->get('CHADO_DB_NAME');
$oldname = $conf2->put( CHADO_DB_NAME => 'mydb');
print $conf2->showConfig(); # XML::Simple output
=head1 NOTES
Check %ENV for GMOD variables (ROOT path, etc.)
and reads if needed conf/gmod.conf key value files into ENV
Assumes program is in project subfolder bin/ or like, and sibling conf/
folder exists with gmod.conf key=value settings to be loaded in %ENV at
run time.
merge/extend of Bio::GMOD::Config from Scott Cain and older dgg version
=head1 AUTHOR
Don Gilbert, Feb..Aug 2004.
=head1 METHODS
=cut
use Config; # system Config ... namespace problems w/ lib use
use FindBin qw( $Bin ); ## dang, this uses system Config.pm, name conflict here
use Cwd qw(abs_path);
use File::Spec::Functions qw/ catdir catfile /;
use File::Basename;
### use Bio::GMOD::Config;
use vars qw/@ISA $BASE @CONF_SUF $ROOT $INIT $Variables/;
our $DEBUG;
our $VERSION = "0.5";
BEGIN {
### @ISA = qw/ Bio::GMOD::Config /; ## DO WE NEED THIS base package at all?
#? $DEBUG = 0;
$ROOT= "GMOD_ROOT";
$INIT= "GMOD_INIT";
$BASE= undef;
@CONF_SUF= (".conf", ".cnf", ".xml", "" );
$Variables= \%ENV; #?
}
=head2 new
Title : new
Usage : my $config = Bio::GMOD::Config2->new('/path/to/gmod');
Function: create new Bio::GMOD::Config object
Returns : new Bio::GMOD::Config2
Args : optional path to gmod installation
Status : Public
Takes one optional argument that is the path to the root of the GMOD
installation. If that argument is not provided, Bio::GMOD::Config will
fall back to the environment variable GMOD_ROOT, which should be defined
for any GMOD installation.
=cut
sub new {
my $self = shift;
my $arg = shift;
my $root;
my %args=();
if (ref($arg) =~ /ARRAY/) { %args= @$arg; $root= $args{'gmod_root'}; }
elsif (ref($arg) =~ /HASH/) { %args= %$arg; $root= $args{'gmod_root'}; }
elsif ($arg) { $root = $arg; } #can override the environment variable
$DEBUG= $args{debug} if defined $args{debug};
unless($root){
if ($BASE) { $root= $BASE->{'gmod_root'}; }
else { $root = $ENV{'GMOD_ROOT'}; } #required
}
my @db= (); # dgg - drop this ?
my $confhash= {};
# need options for subdirs inside conf/ at least: bulkfiles/ gbrowse.conf/ ...
my @sp= ();
if ($args{searchpath}) {
foreach my $sp (@ { $args{searchpath} }) {
##print STDERR "Config2: searchpath $sp\n"; #DEBUG
if (-d $sp) { push(@sp, $sp); }
else {
$sp= catdir($root, $sp);
push(@sp, $sp) if (-d $sp);
}
}
}
my $searchpath= \@sp;
my $confdir = $args{confdir} || 'conf';
$confdir= catdir($root, $confdir) unless($confdir =~ m,^/,); #unixism
my $confpatt= $args{confpatt} || '(gmod|[\w_\-]+db)\.conf$'; # FIXME - need caller opts
my $read_includes= $args{read_includes} || 0;
my $showtags= $args{showtags} || [];
if (%args) {
delete $args{conf}; # can we delete @args{qw( conf confdir ..)}
delete $args{confdir};
delete $args{confpatt};
delete $args{read_includes};
delete $args{showtags};
delete $args{gmod_root};
delete $args{searchpath};
my @keys= keys %args;
@$confhash{@keys}= @args{@keys} if @keys;
}
return bless {db => \@db,
conf => $confhash,
confdir => $confdir,
confpatt => $confpatt,
showtags => $showtags,
read_includes => $read_includes,
searchpath => $searchpath,
gmod_root=> $root }, $self;
}
sub setargs {
my $self = shift;
my %args= @_;
# searchpath confdir need handlin....
foreach my $k (qw(confpatt read_includes showtags)) {
$self->{$k}= $args{$k} if defined $args{$k};
}
}
=head2 $confhash= config()
=head2 $rootpath= gmod_root()
=head2 $configdir= confdir()
=head2 get(key)
return value of key found in gmod.conf
$db= $conf->get('CHADO_DB_NAME');
%keyvals= $conf->get( qw(CHADO_DB_NAME CHADO_DB_USERNAME) );
SEE ALSO get_tag_value
=head2 put(key,val)
put/set GMOD::Config value, returns any old value
$conf->put('CHADO_DB_NAME',$dbname);
%oldvals= $conf->put(
CHADO_DB_NAME => $dbname,
CHADO_DB_USERNAME => 'me',
CHADO_DB_PASSWORD => 'guess',
);
=cut
sub config { return shift->{'conf'}; }
# same as Bio::GMOD::Config
sub gmod_root { return shift->{gmod_root}; }
sub confdir { return shift->{confdir}; }
sub get {
my $self = shift;
my $confhash = $self->{'conf'}; # \%GmodConfig;
my @keys= @_;
if (@keys>1 || wantarray) {
my %vals=();
@vals{@keys} = @{%$confhash}{@keys};
return %vals;
}
else {
return (defined $confhash->{$keys[0]} ? $confhash->{$keys[0]} : undef);
}
}
sub put {
my $self = shift;
my $confhash = $self->{'conf'}; # \%GmodConfig;
my %keyvals= @_;
my %oldvals=();
my @keys= keys %keyvals;
@oldvals{@keys} = @{%$confhash}{@keys};
@{%$confhash}{@keys} = @keyvals{@keys};
return %oldvals;
}
sub _cleanval {
local $_= shift;
s/^\s*//; s/\\?\s*$//; if (s/^(["'])//) { s/$1$//; }
if ($Variables) {
s/\$\{(\w+)\}/$Variables->{$1}/g; # convert $KEY to $ENV{$KEY} to value
}
return $_;
}
sub _find_file {
my($file, @search_path) = @_;
my($filename, $filedir) = File::Basename::fileparse($file);
if(!@search_path || $filename ne $file) {
return($file) if(-e $file);
}
else {
foreach my $path (@search_path) {
my $fullpath = catfile($path, $file);
return($fullpath) if(-e $fullpath);
}
}
return undef;
}
sub _find_file2 {
my($file, $suffix, $search_path) = @_;
my($filename, $filedir) = File::Basename::fileparse($file);
if(!$search_path || $filename ne $file) {
foreach my $sf (@$suffix) {
my $fullpath = $file . $sf;
##print STDERR "Config2::_find_file2 look at $fullpath\n" ;#if $DEBUG;
return($fullpath) if(-e $fullpath);
}
}
else {
foreach my $path (@$search_path) {
foreach my $sf (@$suffix) {
my $fullpath = catfile($path, $file) . $sf;
##print STDERR "Config2::_find_file2 look at $fullpath\n" ;#if $DEBUG;
return($fullpath) if(-e $fullpath);
}
}
}
return undef;
}
=head2 appendHash($tohash, $addhash, $replace)
add keys to hash without replacing existing .. preferred behavior ?
unless $replace is flagged
=cut
sub appendHash
{
my $self = shift;
my ($tohash, $addhash, $replace)= @_;
# -- need to be careful here, DONT replace existing key ?
my @keys= keys %$addhash;
if ($replace) {
@{$tohash}{@keys}= @{%$addhash}{@keys};
}
else {
foreach my $k (@keys) { $$tohash{$k}= $$addhash{$k} unless defined $$tohash{$k}; }
}
}
=head2 readKeyValue($confval, $confhash)
Read $confval string for key=value lines
Return hash-ref options
=cut
sub readKeyValue
{
my $self = shift;
my ($confval, $confhash, $replace)= @_;
$confhash = $self->{'conf'} unless(ref $confhash);
$confhash = {} unless(ref $confhash);
my ($k,$v,$noappend);
foreach (split(/\n/,$confval)) {
next if(/^\s*[\#\!]/ || /^\s*$/); # skip comments, etc.
if (/^([^\s=:]+)\s*[=:]\s*(.*)$/) { # must have value=(*.) to allow blanks
($k,$v)=($1,$2);
$noappend= (defined $confhash->{$k} && !$replace);
$confhash->{$k}= _cleanval($v) unless($noappend);
}
elsif ($k && s/^\s+//) {
$confhash->{$k} .= _cleanval($_) unless($noappend);
}
}
return $confhash;
}
our $readConfigOk;
sub readConfigOk { return $readConfigOk; }
=head2 readConfigFile($file, $opts)
read one file; see readConfig
=cut
sub readConfigFile
{
my $self = shift;
my($file, $opts, $included)= @_;
my $confhash = {};
unless ($file && -e $file) {
my($filename, $filedir);
$filedir= $self->{confdir}; # full path
push(@{$opts->{searchpath}},$filedir) if (-d $filedir);
$filedir= "conf/";
push(@{$opts->{searchpath}},$filedir) if (-d $filedir);
($filename, $filedir) = File::Basename::fileparse($0);
push(@{$opts->{searchpath}},$filedir) if (-d $filedir);
if ($file) {
($filename, $filedir) = File::Basename::fileparse($file);
push(@{$opts->{searchpath}},$filedir) if (-d $filedir);
}
}
unless( $file ) {
my ($ScriptDir, $Extension);
($file, $ScriptDir, $Extension) = File::Basename::fileparse($0, '\.[^\.]+');
}
if ($file && !-e $file) {
my @suf= @CONF_SUF; ##(".conf", ".cnf", ".xml", "" );
my $cnf= _find_file2( $file, \@suf, $opts->{searchpath} );
if ($cnf) { $file= $cnf; }
}
##print STDERR "Config2::readConfig look at $file\n" if $DEBUG;
$self->{filename}= $file unless($included);
if (!$file || ($file =~ /\.xml/ && -e $file)) {
require XML::Simple; ## will attemp to read $0.xml file if no file given
my $xs = new XML::Simple(%$opts); # (NoAttr => 1, KeepRoot => 1);#options
$confhash = $xs->XMLin( $file);
}
elsif (-f $file) {
## handle key-value file OR perl-struct
open(F,$file); my $confval= join("",<F>); close(F);
if ($confval =~ m/=>/s && $confval =~ m/[\{\}\(\)]/s) {
$confhash= eval $confval;
if ($@) { warn " error $@"; }
}
else {
#? check for \w+ [:=] lines first ?
$confhash= $self->readKeyValue($confval, $confhash);
}
}
if (scalar(%$confhash)) { $readConfigOk= 1; }
print STDERR "Config2: read: $file ok=$readConfigOk\n" if $DEBUG;
if (ref $self->{showtags} && !$self->{showntags}{$file}) {
$self->{showntags}{$file}=1;
my $show='';
foreach my $tag (@{$self->{showtags}}) {
my $showval='';
my $val= $$confhash{$tag};
if( ref($val) eq 'HASH') { # hash of hash :(
my @keys = sort keys %$val;
foreach my $k (@keys) {
my $vv= $$val{$k};
if(ref($vv) eq 'HASH') { $vv= $vv->{content}; }
$showval .= "\n $k = ". $vv;
}
##$showval .= join("\n", @{$val}{@keys});
} elsif( ref($val) eq 'ARRAY') {
$showval .= join("\n", @{$val});
} elsif($val) {
$showval .="$val";
}
$show.= "$tag = $showval; " if $showval;
}
print STDERR "Config: $show from $file\n" if $show;
}
return $confhash;
}
=head2 readConfig($file, $opts)
Read configurations in these formats
XML::Simple OR Perl-struct OR key=value config file
Parameters
$file = input file;
$opts = XML::Simple options hash-ref
Return hash-ref options
=cut
sub readConfig
{
my $self = shift;
my($file, $opts, $confhash)= @_;
$readConfigOk= 0;
if(ref $opts) {
$opts= { %$opts };
$opts->{Variables}= $Variables unless($opts->{Variables});
} else {
$opts= { Variables => $Variables };
}
$confhash = $self->{'conf'} unless(ref $confhash); # always exists ?
$confhash = {} unless(ref $confhash);
$DEBUG= delete $opts->{debug} if (defined $opts->{debug});
my $replacekeys= delete $opts->{replace} || 0;
##print STDERR "Config2::readConfig in=$file\n" if $DEBUG;
unless ($opts->{searchpath}) {
$opts->{searchpath}= [ @{$self->{'searchpath'}} ];
}
my $conf1 = $self->readConfigFile($file, $opts, 0);
$self->appendHash($confhash, $conf1, $replacekeys) if ($conf1);
## $self->{filename}= $file;
if ($self->{read_includes} && $$confhash{include}) {
## $self->{read_includes}= 0; ## MUST NOT RECURSE HERE...
##? but can we do nested includes ?? need to check each conf1
my %didinc=();
my $inc= $$confhash{include};
my @inc= (ref($inc) =~ /ARRAY/) ? @$inc : ($inc);
my $saveConfigOk= $readConfigOk;
foreach $inc (@inc) {
next if ($didinc{$inc}); $didinc{$inc}++;
$readConfigOk= 0;
$conf1= $self->readConfigFile($inc, $opts, 1);
## need some warning/die if not found
warn "Config2: MISSING include=$inc \n" unless $readConfigOk;
if ($conf1) {
my $inc1= delete $$conf1{include};
if($inc1) { push(@inc, (ref($inc1) =~ /ARRAY/) ? @$inc1 : ($inc1)); }
$self->appendHash($confhash, $conf1, $replacekeys);
}
$saveConfigOk=0 unless($readConfigOk);
}
$readConfigOk= $saveConfigOk;
}
return $confhash;
}
sub updateVariables
{
my $self = shift;
my( $confhash, $opts)= @_;
$DEBUG= delete $opts->{debug} if (defined $opts->{debug});
$confhash = $self->{'conf'} unless(ref $confhash); # always exists ?
$confhash = {} unless(ref $confhash);
my $env= (ref $opts and ref $opts->{Variables}) ? $opts->{Variables} : $Variables;
_update1Value( $confhash, $env);
return $confhash;
}
sub _update1Value
{
my($val,$env)= @_;
if( ref($val) eq 'HASH') {
foreach my $tag (sort keys %$val) {
$$val{$tag} = _update1Value( $$val{$tag}, $env);
}
} elsif( ref($val) eq 'ARRAY') {
foreach (@$val){ $_= _update1Value( $_, $env); }
} else {
while ( $val =~ m/\$\{(\w+)\}/g) {
my $var=$1;
my $enval= $env->{$var}; #only if defined, leave otherwise
if (defined $enval) {
if($enval =~ m/\$\{(\w+)\}/) { $enval= _update1Value( $enval, $env); }
print STDERR "UPVAL1: \$\{$var\} => $enval\n" if $DEBUG;
$val =~ s/\$\{$var\}/$enval/;
}
}
}
return $val;
}
=head2 showConfig($confhash, $opts)
$confhash = options hash-ref
$opts = XML::Simple options hash-ref (debug => 1 Data dumper out)
return XML::Simple of input
=cut
sub showConfig
{
my $self = shift;
my($confhash,$opts)= @_;
$confhash = $self->{'conf'} unless(ref $confhash); # always exists ?
$opts= ($opts) ? { %$opts } : {};
my $debug= delete $$opts{debug};
$debug= $DEBUG unless defined $debug;
my $xml ='';
if ($debug) {
require Data::Dumper;
my $dd = Data::Dumper->new([$confhash]);
$dd->Terse(1);
$xml.= "<!-- ========= config struct ===========\n";
$xml.= $dd->Dump();
$xml.= "======================================== -->\n";
}
require XML::Simple;
my $xs = new XML::Simple( %$opts); #NoAttr => 1, KeepRoot => 1
$xml .= $xs->XMLout( $confhash );
return $xml;
}
sub _updir
{
#? my $self = shift;
my ($atdir,$todirs)= @_;
my $dir= $atdir;
my $ok= 0;
my $cod;
foreach my $td (@$todirs) { $cod= catdir($dir, $td); $ok= (-d $cod); last if $ok; }
while (!$ok && length($dir)>2) {
$dir= "$dir/.."; ##NOT File::Basename::dirname($dir)."/..";
$dir=`cd "$dir" && pwd`; chomp($dir);
##warn " _updir $dir\n" if $DEBUG;
foreach my $td (@$todirs) { $cod= catdir($dir, $td); $ok= (-d $cod); last if $ok; }
}
return ($ok) ? $dir : $atdir;
}
=head2 $confhash= readConfDir( $dir, $confpatt, $confhash)
Process all config files of confpatt in dir folder.
note: this can load in things you may not want
(e.g. all the .xml.old files...)
=cut
our $readConfDirOk;
sub readConfDir {
my $self = shift;
my( $confdir, $confpatt, $confhash)= @_;
$confdir = $self->{'confdir'} unless($confdir);
$confpatt = $self->{'confpatt'} unless($confpatt);
$confhash = $self->{'conf'} unless(ref $confhash); # always exists ?
$confhash = {} unless(ref $confhash);
$readConfDirOk= 0;
if ( opendir( DIR, $confdir ) ) {
my @conf = grep ( /$confpatt/, readdir(DIR));
closedir(DIR);
foreach my $file (sort @conf) {
my $confpath= catfile($confdir,$file);
$confhash= $self->readConfig( $confpath, { debug => $DEBUG, Variables => $Variables }, $confhash);
$readConfDirOk ||= $readConfigOk;
}
}
warn " readConfDir $confdir ok=$readConfDirOk\n" if $DEBUG;
return $confhash;
}
sub init_conf
{
my $self= shift;
my $myroot = $self->{'gmod_root'};
my $confpatt = $self->{'confpatt'};
my $confhash = $self->readConfDir();
unless($readConfDirOk) {
warn " no $confpatt file at $myroot/conf; setenv $ROOT to locate."
}
else { # if ($SetEnv)
$self->appendHash( \%ENV, $confhash, 0);
# -- need to be careful here, DONT replace existing key ?
# my @keys= keys %$confhash;
# foreach my $k (@keys) { $ENV{$k}= $$confhash{$k} unless defined $ENV{$k}; }
# @ENV{@keys}= @{%$confhash}{@keys};
}
$ENV{$INIT}= 1;
my @inc=();
my $libdir= catdir($myroot,"lib");
push(@inc, $libdir) if (-d $libdir);
push(@inc, split /:/, $ENV{'PERL5LIB'}) if (defined $ENV{'PERL5LIB'});
foreach my $p (@inc) { unshift(@INC,$p) unless( grep /^$p$/i,@INC ); }
}
=head2 BEGIN
At eval time (use, require), this checks %ENV for GMOD_ROOT and
GMOD_INIT. If not found, it looks in folder above calling script
for conf/gmod.conf as KEY=value to be loaded into %ENV.
$ENV{GMOD_INIT}=1 prevents this loading.
=cut
BEGIN {
$DEBUG = $ENV{'DEBUG'} unless defined $DEBUG;
unless($ENV{$INIT}) {
my $myroot;
if (defined $ENV{$ROOT} && -d $ENV{$ROOT}) { $myroot= $ENV{$ROOT}; }
else { $myroot= abs_path("$Bin"); }
$myroot= _updir( $myroot, ["conf"] ); # in case we are not in bin/ folder
$BASE= __PACKAGE__->new($myroot);
#?? my $self= Bio::GMOD::Config2->new($myroot);
$BASE->init_conf();
}
}
1;
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