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#
# Bio::MAGE::XML::Writer.pm
# a module for exporting MAGE-ML
#
package Bio::MAGE::XML::Writer;
use strict;
use vars qw($VERSION $DEBUG);
use Carp;
use Bio::MAGE;
use XML::Xerces;
$VERSION = 2006_08_15.0;
=head1 NAME
Bio::MAGE::XML::Writer - a module for exporting MAGE-ML
=head1 SYNOPSIS
use Bio::MAGE::XMLUtils;
my $writer = Bio::MAGE::XML::Writer->new(@args);
$writer->write($mage);
#
# attributes to modify where the output is written
#
# set the output filehandle
my $fh = \*STDOUT;
$writer->fh($fh);
# whether to write data cubes externally (default == FALSE)
$writer->external_data($bool);
# which directory to write external data cubes (default == /tmp)
$writer->external_data_dir($path);
# whether the to interpret the C<cube> as data or a file
# path (default == FALSE)
$writer->cube_holds_path($bool);
#
# attributes to modify the output format
#
# which format is the external data file
$writer->data_format($dataformat);
# to change the level of indent for each new tag (defaul == 2)
$writer->indent_increment($num);
# to change the beginning indent level (defaul == 0)
$writer->indent_level($num);
# set to true to not format attributes (default == FALSE)
$writer->attrs_on_one_line($bool);
# how many extra spaces attributes should be indented past start
# tag end (default == 1)
$writer->attr_indent($num);
# whether to write all sub-tags on the same line (default == undef)
$writer->collapse_tag($bool);
#
# attributes to modify the the document
#
# to change the encoding (default == ISO-8859-1)
$writer->encoding($format);
# to set the public id (default == undef)
$writer->public_id($id);
# to change the system id (default == MAGE-ML.dtd)
$writer->system_id($id);
# check to see that objects set more than just identifier (default == TRUE)
$writer->empty_identifiable_check();
#
# attributes to handle identifiers
#
# whether to create identifiers if not specified (default == FALSE)
$writer->generate_new_identifiers();
# code reference to be invoked for creating new identifiers
$writer->generate_identifier();
=head1 DESCRIPTION
Methods for transforming information from a MAGE-OM objects into
MAGE-ML.
=cut
use base qw(Bio::MAGE::Base);
$DEBUG = 1;
sub initialize {
my ($self) = shift;
$self->tag_buffer([]);
$self->cube_holds_path(0)
unless defined $self->cube_holds_path();
$self->attrs_on_one_line(0)
unless defined $self->attrs_on_one_line();
$self->attr_indent(1)
unless defined $self->attr_indent();
$self->indent_increment(2)
unless defined $self->indent_increment();
$self->indent_level(0)
unless defined $self->indent_level();
$self->data_format('tab delimited')
unless defined $self->data_format();
$self->external_data(0)
unless defined $self->external_data();
$self->external_data_dir('/tmp')
unless defined $self->external_data_dir();
$self->empty_identifiable_check(1)
unless defined $self->empty_identifiable_check();
$self->encoding('ISO-8859-1')
unless defined $self->encoding();
$self->system_id('MAGE-ML.dtd')
unless defined $self->system_id();
$self->generate_identifier(sub {$self->identifier_generatation(shift)})
unless defined $self->generate_identifier();
$self->generate_new_identifiers(0)
unless defined $self->generate_new_identifiers();
}
sub incr_indent {
my $self = shift;
$self->indent_level($self->indent_level + $self->indent_increment);
}
sub decr_indent {
my $self = shift;
$self->indent_level($self->indent_level - $self->indent_increment);
}
=head1 METHODS
=item write($MAGE_object);
C<write()> prints the objects contained in $MAGE_object as MAGE-ML to
the file handle used by the writer.
=cut
sub write {
my ($self,$top_level_obj) = @_;
die __PACKAGE__."::write: must specify a file handle for output"
unless defined $self->fh();
# handle the basics
$self->write_xml_decl();
$self->write_doctype();
$top_level_obj->obj2xml($self);
}
sub write_xml_decl {
my $self = shift;
my $fh = $self->fh();
my $encoding = $self->encoding();
print $fh <<"MAGEML";
<?xml version="1.0" encoding="$encoding" standalone="no"?>
MAGEML
}
sub write_doctype {
my $self = shift;
my $public_id = $self->public_id();
my $PUBLIC;
if (defined $public_id) {
$PUBLIC = qq[PUBLIC "$public_id"];
} else {
$PUBLIC = '';
}
my $system_id = $self->system_id();
my $SYSTEM;
if (defined $public_id) {
$SYSTEM = qq["$system_id"];
} else {
$SYSTEM = qq[SYSTEM "$system_id"];
}
my $fh = $self->fh();
print $fh <<"MAGEML";
<!DOCTYPE MAGE-ML $PUBLIC $SYSTEM>
MAGEML
}
sub write_start_tag {
my ($self,$tag,$empty,%attrs) = @_;
my $indent = ' ' x $self->indent_level();
my $buffer;
my (@attrs);
foreach my $attribute_name (keys %attrs) {
my $attribute_val = $attrs{$attribute_name};
$attribute_val =~ s/\&/&/g;
$attribute_val =~ s/\&amp;/&/g;
$attribute_val =~ s/\"/"/g;
$attribute_val =~ s/\&quot;/"/g;
$attribute_val =~ s/\'/'/g;
$attribute_val =~ s/\&apos;/'/g;
$attribute_val =~ s/\>/>/g;
$attribute_val =~ s/\&gt;/>/g;
$attribute_val =~ s/\</</g;
$attribute_val =~ s/\&lt;/</g;
push(@attrs,qq[$attribute_name="$attribute_val"]);
}
my ($attrs,$attr_indent);
if ($self->attrs_on_one_line()) {
$attrs = join(' ',@attrs);
} else {
# we add one to compensate for the '<' in the start tag
$attr_indent = $self->attr_indent() + 1;
$attr_indent += length($tag);
$attr_indent = ' ' x $attr_indent . $indent;
$attrs = join("\n$attr_indent",@attrs);
}
if ($attrs) {
$buffer .= "$indent<$tag $attrs";
} else {
# don't print the space after the tag because Eric said so
$buffer .= "$indent<$tag";
}
if ($empty) {
$buffer .= '/>';
} else {
$buffer .= '>';
}
$buffer .= "\n" unless $self->collapse_tag();
$self->incr_indent()
unless $empty;
# we don't actually write out the tag yet. We buffer it on a stack
# until we actually know we should write it out
push(@{$self->tag_buffer},$buffer);
# if this was an empty tag, we immediately flush the buffer
$self->flush_tag_buffer()
if $empty;
}
sub flush_tag_buffer {
my $self = shift;
my $fh = $self->fh();
my $tag_buffer = $self->tag_buffer();
while (my $string = shift @{$tag_buffer}) {
print $fh $string;
}
}
sub write_end_tag {
my ($self,$tag) = @_;
$self->decr_indent();
# if there is still something on the tag buffer, we must not have
# had any data to write, so don't write the end tag
if (scalar @{$self->tag_buffer}) {
pop(@{$self->tag_buffer});
return;
}
my $indent = ' ' x $self->indent_level();
my $fh = $self->fh();
print $fh "$indent</$tag>\n";
}
# we purposefully avoid copying the text, since it may be BIG
sub write_text {
my $self = shift;
my $fh = $self->fh();
print $fh $_[0];
}
#
# Helper methods
#
sub identifier_generation {
my ($self,$obj) = @_;
my $known_identifiers = $self->identifiers();
return if exists $known_identifiers->{$obj->getIdentifier};
# stringify the object: Bio::MAGE::Identifiable=SCALAR(0x10379980)
my $identifier = $obj;
# strip of the leading class qualifiers: Identifiable=SCALAR(0x10379980)
$identifier =~ s/^Bio::MAGE:://;
# convert the '=' to a colon: Identifiable:SCALAR(0x10379980)
$identifier =~ tr/=/:/;
# remove the SCALAR: Identifiable:10379980
$identifier =~ s/SCALAR\(0x(.*)\)/$1/;
$obj->setIdentifier($identifier);
}
sub obj2xml_ref {
my ($self,$obj) = @_;
# create the <*_ref> tag
my $tag = $obj->class_name();
$tag =~ s/.+:://;
$tag .= '_ref';
# we create the empty tag with only the identifier
my $empty = 1;
$self->write_start_tag($tag,$empty,identifier=>$obj->getIdentifier());
}
sub flatten {
my ($self,$list) = @_;
my @list;
foreach my $item (@{$list}) {
if (ref($item) eq 'ARRAY') {
push(@list,$self->flatten($item));
} else {
push(@list,$item);
}
}
return join("\t",@list);
}
sub external_file_id {
my $self = shift;
my $num = $self->external_data();
$num++;
$self->external_data($num);
return "external-data-$num.txt";
}
sub write_bio_data_tuples() {
my ($self,$obj) = @_;
# has no attributes
# the tag name is the name of the class
my $tag = $obj->class_name();
$tag =~ s/.+:://;
$self->write_start_tag($tag,my $empty = 0);
# make the data structure
my %data;
my %des;
my %bas;
my %qts;
foreach my $datum (@{$obj->getBioAssayTupleData()}) {
my $de = $datum->getDesignElement();
my $ba = $datum->getBioAssay();
my $qt = $datum->getQuantitationType();
my $ba_id = $ba->getIdentifier();
my $qt_id = $qt->getIdentifier();
my $de_id = $de->getIdentifier();
# store the datum object
$data{$ba_id}->{$de_id}{$qt_id} = $datum;
# store the design element obj
$des{$de_id} = $de;
# store the quantitation type obj
$qts{$qt_id} = $qt;
# store the bioassay obj
$bas{$ba_id} = $ba;
}
# write the container tag
$tag = 'BioAssayTuples_assnlist';
my $EMPTY = 0;
my $NOT_EMPTY = 1;
$self->write_start_tag($tag,$EMPTY);
# write the XML
foreach my $ba (keys %data) {
# write the BioAssayTuple container tag
my $bat_tag = 'BioAssayTuple';
$self->write_start_tag($bat_tag,$EMPTY);
# write the container tag
my $tag = 'BioAssay_assnref';
$self->write_start_tag($tag,$EMPTY);
# write the BioAssay ref object
my $ba_obj = $bas{$ba};#bioassay
$self->obj2xml_ref($ba_obj);
# end the BioAssay_ref container tag
$self->write_end_tag($tag);
# write the container tag
$tag = 'DesignElementTuples_assnlist';
$self->write_start_tag($tag,$EMPTY);
foreach my $de (keys %{$data{$ba}}) {
# write the DesignElementTuple container tag
my $det_tag = 'DesignElementTuple';
$self->write_start_tag($det_tag,$EMPTY);
my $tag = 'DesignElement_assnref';
# write the container tag
$self->write_start_tag($tag,$EMPTY);
# write the DesignElement ref object
my $de_obj = $des{$de}; #design element
$self->obj2xml_ref($de_obj);
# end the DesignElement ref container tag
$self->write_end_tag($tag);
# write the container tag
$tag = 'QuantitationTypeTuples_assnlist';
$self->write_start_tag($tag,$EMPTY);
foreach my $qt (keys %{$data{$ba}->{$de}}) {
# write the QuantitationTypeTuple container tag
my $qtt_tag = 'QuantitationTypeTuple';
$self->write_start_tag($qtt_tag,$EMPTY);
my $tag = 'QuantitationType_assnref';
# write the container tag
$self->write_start_tag($tag,$EMPTY);
# write the QuantitationType ref object
my $ba_obj = $qts{$qt}; #quantitation type
$self->obj2xml_ref($ba_obj);
# end the Quantitation Type ref container tag
$self->write_end_tag($tag);
# write the datum container tag
my $datum_tag = 'Datum_assn';
$self->write_start_tag($datum_tag,$EMPTY);
# write the datum tag
$tag = 'Datum';
my $value = $data{$ba}->{$de}{$qt}->getValue();
die "no $value for BioAssay: ", $ba,
", DesignElement: ", $de,
", QuantitationType: ", $qt,
unless defined $value;
my %attrs = (value=>$value);
$self->write_start_tag($tag,$NOT_EMPTY,%attrs);
# end the Datum container tag
$self->write_end_tag($datum_tag);
# end the QuantitationTypeTuple container tag
$self->write_end_tag($qtt_tag);
}
# end the QuantitationTypeTuples_list container tag
$self->write_end_tag($tag);
# end the DesignElementTuple container tag
$self->write_end_tag($det_tag);
}
# end the DesignElementTuples_list container tag
$self->write_end_tag($tag);
# end the BioAssayTuple container tag
$self->write_end_tag($bat_tag);
}
# end the BioAssayTuples_list container tag
$self->write_end_tag($tag);
# end the BioDataTuples tag
$self->write_end_tag('BioDataTuples');
}
sub obj2xml {
my ($self,$obj) = @_;
if ($obj->isa("Bio::MAGE::BioAssayData::BioDataTuples")) {
return $self->write_bio_data_tuples($obj);
}
# all attributes are gathered into a hash
my %attributes;
my $data;
foreach my $attribute ($obj->get_attribute_names()) {
# $obj->get_attribute_names can return an array with empty ('')
# values.
next unless $attribute;
my $attribute_val;
{
no strict 'refs';
my $getter_method = 'get'.ucfirst($attribute);
$attribute_val = $obj->$getter_method();
if (defined $attribute_val) {
if ($attribute eq 'cube') {
if ($self->cube_holds_path()) {
# the cube holds the path to an already written file
# so we don't bother interpreting it
$data = $attribute_val;
} else {
$data = $self->flatten($attribute_val);
}
next;
}
$attribute_val =~ s/\&/&/g;
$attribute_val =~ s/\&amp;/&/g;
$attribute_val =~ s/\"/"/g;
$attribute_val =~ s/\&quot;/"/g;
$attribute_val =~ s/\'/'/g;
$attribute_val =~ s/\&apos;/'/g;
$attribute_val =~ s/\>/>/g;
$attribute_val =~ s/\&gt;/>/g;
$attribute_val =~ s/\</</g;
$attribute_val =~ s/\&lt;/</g;
$attributes{$attribute} = $attribute_val;
}
}
}
# the tag name is the name of the class
my $tag = $obj->class_name();
$tag =~ s/.+:://;
# we create the start tag, with the object attributes represented as
# element attributes. If the object has no associations we make it
# an empty element - this is to avoid XML validation errors
my $empty = not scalar $obj->associations();
my $xml_written = 0;
$self->write_start_tag($tag,$empty,%attributes);
# if we discover an object that only has it's identifier attribute set
# we don't flush the tag buffer
unless ($self->empty_identifiable_check() and
exists $attributes{identifier} and
scalar keys %attributes == 1) {
$self->flush_tag_buffer();
$xml_written = 1;
}
# associations are handled as sub-elements of the current element
# and we use the association meta-data to instruct how to represent
# each association
#
# We use the IxHash module because the associations are ordered
# in the same order the DTD expects to receive them, and IxHash
# preserves insertion order
tie my %assns_hash, 'Tie::IxHash', $obj->associations();
foreach my $association (keys %assns_hash) {
my $association_obj;
{
no strict 'refs';
my $getter_method = 'get'.ucfirst($association);
$association_obj = $obj->$getter_method();
}
if (defined $association_obj) {
# we've found an association object, so if we were delaying
# the writing of the code, we write it out now
unless ($xml_written) {
$self->flush_tag_buffer();
$xml_written = 1;
}
# if this is a bi-navigable association, and we there is an aggregate
# association from the other end, we do *not* write the object out
# we know it's bi-navigable if self->name is defined
# we know it's aggregate if other->is_ref is not true
if (defined $assns_hash{$association}->self->name()
and not $assns_hash{$association}->other->is_ref()
) {
next;
}
# we first create the container tag with the proper prefix
# to know if this is a ref element or not we look at the self
# side of the association
my $prefix;
my $is_ref = $assns_hash{$association}->self->is_ref();
if ($is_ref) {
$prefix = '_assnref';
} else {
$prefix = '_assn';
}
my @association_objects;
if ($assns_hash{$association}->other->is_list) {
$prefix .= 'list';
@association_objects = @{$association_obj};
} else {
@association_objects = ($association_obj);
}
my $container_tag = ucfirst("$association$prefix");
# container tags must not be empty
$self->write_start_tag("$container_tag",my $cont_empty=0);
# now we fill in the container with the object(s)
foreach $association_obj (@association_objects) {
if ($is_ref) {
$self->obj2xml_ref($association_obj)
} else {
$self->obj2xml($association_obj);
}
}
# now end the container tag
$self->write_end_tag("$container_tag");
}
}
if (defined $data) {
if ($self->external_data()) {
my %attributes;
if ($self->cube_holds_path()) {
$attributes{filenameURI} = $data;
} else {
$attributes{filenameURI} = $self->external_file_id();
}
$attributes{dataFormat} = $self->data_format();
my $tag = 'DataExternal_assn';
$self->write_start_tag($tag,my $empty=0);
# we need to make it external
{
my $tag = 'DataExternal';
$self->write_start_tag($tag,my $empty=1,%attributes);
# if we've been told the cube is already written, we don't
# bother re-writing it
unless ($self->cube_holds_path()) {
my $dir = $self->external_data_dir();
open(DATA, ">$dir/$attributes{filenameURI}")
or die "Couldn't open $dir/$attributes{filenameURI} for writing";
print DATA $data;
close(DATA);
}
}
$self->write_end_tag($tag);
} else {
# we make it internal
my $tag = 'DataInternal_assn';
$self->write_start_tag($tag,0);
{
my $tag = 'DataInternal';
$self->write_start_tag($tag,0);
$self->flush_tag_buffer;
my $fh = $self->fh();
print $fh "<![CDATA[$data]]>";
$self->write_end_tag($tag);
}
$self->write_end_tag($tag);
}
}
# now end the current element
$self->write_end_tag($tag)
unless $empty;
}
sub is_bio_mage_object {
my ($self,$obj) = @_;
return UNIVERSAL::isa($obj,'Bio::MAGE');
}
=head1 ATTRIBUTE METHODS
The following methods must all be invoked using an instance of Bio::MAGE::XML::Writer;
=over
=cut
=item indent_level($num)
This attribute controls the current level of indentation while writing
a document. It should not be manipulated by users, unless for some
reason you wanted to set the starting indent level to something other
than zero.
B<Default Value:> 0 (zero)
=cut
sub indent_level {
my $self = shift;
if (@_) {
$self->{__INDENT_LEVEL} = shift;
}
return $self->{__INDENT_LEVEL};
}
=item indent_increment($num)
This attribute controls the the number of spaces that added to the
indent for every new level of elements.
B<Default Value:> 2
=cut
sub indent_increment {
my $self = shift;
if (@_) {
$self->{__INDENT_INCREMENT} = shift;
}
return $self->{__INDENT_INCREMENT};
}
=item attrs_on_one_line($bool)
This attribute controls whether attribute values should be
pretty-printed. If true, attributes will not pretty-printed, but will
instead be written out all on one line.
B<Default Value:> false
=cut
sub attrs_on_one_line {
my $self = shift;
if (@_) {
$self->{__ATTRS_ON_ONE_LINE} = shift;
}
return $self->{__ATTRS_ON_ONE_LINE};
}
=item attr_indent($bool)
Controls how many spaces past the end start tag that attributes should
be indented. This example shows an C<attr_inden> of 1:
<Reporter identifier="Reporter:X Units Per Pixel"
name="X Units Per Pixel">
The following illustrates and C<attr_indent> of -2:
<Person firstName="John"
identifier="Person:John Smith"
name="John Smith"
lastName="Smith">
B<Default Value:> 1
=cut
sub attr_indent {
my $self = shift;
if (@_) {
$self->{__ATTR_INDENT} = shift;
}
return $self->{__ATTR_INDENT};
}
=item collapse_tag($bool)
This attribute is not very useful at the moment. In the future it may
be used to specify tags that should have their contents all on a
single line.
Currently it controls whether or not to write a newline after each
elements start tag, with no method to decide to write or not to write
based on the name of the tag.
B<Default Value:> false
=cut
sub collapse_tag {
my $self = shift;
if (@_) {
$self->{__COLLAPSE_TAG} = shift;
}
return $self->{__COLLAPSE_TAG};
}
=item encoding($string)
This is the value that value be written out as the encoding attribute
for the XML Declaration of the output MAGE-ML document:
<?xml version="1.0" encoding="ISO-8859-1" standalone="no"?>
B<Default Value:> ISO-8859-1
=cut
sub encoding {
my $self = shift;
if (@_) {
$self->{__ENCODING} = shift;
}
return $self->{__ENCODING};
}
=item public)_id($string)
If defined, this value will be written out as the value of the PUBLIC
attribute of the DOCTYPE tag in the output MAGE-ML document.
B<Default Value:> undef
=cut
sub public_id {
my $self = shift;
if (@_) {
$self->{__PUBLIC_ID} = shift;
}
return $self->{__PUBLIC_ID};
}
=item system_id($string)
If defined, this value will be written out as the value of the SYSTEM
attribute of the DOCTYPE tag in the output MAGE-ML document:
<!DOCTYPE MAGE-ML SYSTEM "MAGE-ML.dtd">
B<Default Value:> MAGE-ML.dtd
=cut
sub system_id {
my $self = shift;
if (@_) {
$self->{__SYSTEM_ID} = shift;
}
return $self->{__SYSTEM_ID};
}
=item generate_identifier($code_ref)
This attribute stores a code reference that will be invoked to create
a new identifier for any object that does not already have one
defined. This will happen only if the C<generate_new_identifiers>
attribute is set to true.
B<Default Value:> \&identifier_generation
=cut
sub generate_identifier {
my $self = shift;
if (@_) {
$self->{__GENERATE_IDENTIFIER} = shift;
}
return $self->{__GENERATE_IDENTIFIER};
}
=item generate_new_identifier($bool)
If this attribute is set to true, the code reference store in the
C<generate_identifier> attribute will be invoked to create a new
identifier for any object that does not already have one defined.
B<Default Value:> false
=cut
sub generate_new_identifiers {
my $self = shift;
if (@_) {
$self->{__GENERATE_NEW_IDENTIFIERS} = shift;
}
return $self->{__GENERATE_NEW_IDENTIFIERS};
}
=item fh($file_handle)
This is the file handle to which the MAGE-ML document will be written.
B<Default Value:> undef
=cut
sub fh {
my $self = shift;
if (@_) {
$self->{__FH} = shift;
}
return $self->{__FH};
}
sub tag_buffer {
my $self = shift;
if (@_) {
$self->{__TAG_BUFFER} = shift;
}
return $self->{__TAG_BUFFER};
}
=item external_data($bool)
If defined, this will cause all BioAssayData objects to write
themselves out using the DataExternal format.
B<Default Value:> false
=cut
sub external_data {
my $self = shift;
if (@_) {
$self->{__EXTERNAL_DATA} = shift;
}
return $self->{__EXTERNAL_DATA};
}
=item data_format($format)
$format is either 'tab delimited' or 'space delimited'
B<Default Value:> 'tab delimited'
=cut
sub data_format {
my $self = shift;
if (@_) {
$self->{__DATA_FORMAT} = shift;
}
return $self->{__DATA_FORMAT};
}
=item external_data_dir($path)
The C<fh> attribute only controls where the main MAGE-ML document is
written. If the C<external_data> attribute is set, the writer will
also create a separate external data file for each data cube.
The C<external_data_dir> controls what director those files are
written to.
B<Default Value:> /tmp
=cut
sub external_data_dir {
my $self = shift;
if (@_) {
$self->{__EXTERNAL_DATA_DIR} = shift;
}
return $self->{__EXTERNAL_DATA_DIR};
}
=item cube_holds_path($path)
Sometimes, you already have your data written to an external file, and
you simply want to reuse the file without any extra overhead. The
C<cube_holds_path> attribute controls indicates that you are storing
the path to the external file in the C<cube> attribute of the
C<BioDataCube> objects.
B<Default Value:> false
=cut
sub cube_holds_path {
my $self = shift;
if (@_) {
$self->{__CUBE_HOLDS_PATH} = shift;
}
return $self->{__CUBE_HOLDS_PATH};
}
=item empty_identifiable_check($bool)
If true, all objects that define an C<identifier> attribute and no
other attributes will only be included as <*_ref> elements.
B<NOTE:> Currently no checking of association values is made, only
attributes. So if you want to ensure that an Identifiable object is
written, make sure that you set the C<name> attribute as well as the
C<identifier> attribute.
B<Default Value:> true
=cut
sub empty_identifiable_check {
my $self = shift;
if (@_) {
$self->{__EMPTY_IDENTIFIABLE_CHECK} = shift;
}
return $self->{__EMPTY_IDENTIFIABLE_CHECK};
}
1;
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