Re: parsing XML

From: Kevin Viel <kviel@xxxxxxxxxxxxxxx>

I have obtain results of a query in XML format:

<?xml version="1.0"?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD eSummaryResult, 29
October 2004//EN"
"http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd";>
<eSummaryResult> <DocSum>
<Id>4609</Id>
<Item Name="Name" Type="String">MYC</Item>
<Item Name="Description" Type="String">v-myc myelocytomatosis
viral oncogene homolog (avian)</Item>
<Item Name="Orgname" Type="String">Homo sapiens</Item>
<Item Name="Status" Type="Integer">0</Item>
<Item Name="CurrentID" Type="Integer">0</Item>
<Item Name="Chromosome" Type="String">8</Item>
<Item Name="GeneticSource" Type="String">genomic</Item>
<Item Name="MapLocation" Type="String">8q24.12-q24.13</Item>
<Item Name="OtherAliases" Type="String">c-Myc</Item> <Item
Name="OtherDesignations" Type="String">avian myelocytomatosis viral oncogene homolog|myc proto-oncogene
protein|v-myc avian myelocytomatosis viral oncogene homolog</Item>
<Item Name="NomenclatureSymbol" Type="String">MYC</Item>
<Item Name="NomenclatureName" Type="String">v-myc myelocytomatosis viral oncogene homolog (avian)</Item>
<Item Name="NomenclatureStatus" Type="String">Official</Item>
<Item Name="TaxID" Type="Integer">9606</Item> <Item
Name="Mim" Type="List">
<Item Name="int" Type="Integer">190080</Item>
</Item>
</DocSum>


Jenda Krynicky kindly provided:

use XML::Rules;

my $parser = XML::Rules->new(
rules => [
Id => 'content',
Item => sub {$_[1]->{Name} => $_[1]->{_content}},
# from the <Item> tags we are interested in the content # and want to use the Name attribute as the key to access # that value. We ignore the Type attribute.
DocSum => sub {
# by now all the data from the <Item>s are in the %{$_[1]} hash

if ($_[1]->{Chromosome} != 8 or $_[1]->{NomenclatureName} !~ /\bviral\b/) {
# ignore everything outside the 8th chromosome that's not 'viral'
return;
}

# do something with the data
# or return the part of the data you want to keep using whatever
# you suits you best as the key
return $_[1]->{Name} => $_[1];
},
eSummaryResult => 'pass no content',
]
);

my $data = $parser->parse($the_xml_or_file);

print $data->{MYC}{NomenclatureName}, "\n";
__END__

I'd like to understand this better. It seems to be a reference (little arrow). Is that the same as using /@referenced_array, for instance?

It seems to be a hash with the key "rules" and a four-item array as its value. The third item of this array is a hash with a subroutine, or anonymous function declaration, as its value.

I am wrong, correct?

A) Correct, you were incorrect.
B) Incorrect, you were correct.
C) You're still buying beer.

To start with specific questions, could someone explain:

> Item => sub {$_[1]->{Name} => $_[1]->{_content}}

Thanks,

Kevin


--
Kevin Viel
Department of Genetics kviel@xxxxxxxxxxxxxxx
Southwest Foundation for Biomedical Research phone: (210)258-9884
P.O. Box 760549 fax: (210)258-9444
San Antonio, TX 78245-0549

Kevin Viel
PhD Candidate
Department of Epidemiology
Rollins School of Public Health
Emory University
Atlanta, GA 30322
.