Create and populate complex XML with Perl script

Question

I have following XML file template that I want to create and populate with Perl script. All the values of XML attributes are coming from SQL database by different queries. My XML contain few collection type of attributes.

I'm finding it difficult that which perl module should I use because there are a lot of alternatives available on CPAN. Also, I want to know how should I approach to this problem.

Any help is greatly appreciated.

`

<TumorDetails>
    <personUpi>String</personUpi>
    <ageAtDiagnosis>3.14159E0</ageAtDiagnosis>
    <biopsyPathologyReportSummary>String</biopsyPathologyReportSummary>
    <primarySiteCollection>
        <tissueSite>
            <description>String</description>
            <name>String</name>
        </tissueSite>
    </primarySiteCollection>
    <distantMetastasisSite>
        <description>String</description>
        <name>String</name>
    </distantMetastasisSite>
    <siteGroup>
        <description>String</description>
        <name>String</name>
    </siteGroup>
    <tmStaging>
        <clinicalDescriptor>String</clinicalDescriptor>
        <clinicalMStage>String</clinicalMStage>
        <siteGroupEdition5>
            <description>String</description>
            <name>String</name>
        </siteGroupEdition5>
        <siteGroupEdition6>
            <description>String</description>
            <name>String</name>
        </siteGroupEdition6>
    </tmStaging>
    <pediatricStaging>
        <doneBy>String</doneBy>
        <group>String</group>
    </pediatricStaging>
    <histologicTypeCollection>
        <histologicType>
            <description>String</description>
            <system>String</system>
            <value>String</value>
        </histologicType>
    </histologicTypeCollection>
    <histologicGradeCollection>
        <histologicGrade>
            <gradeOrDifferentiation>String</gradeOrDifferentiation>
        </histologicGrade>
    </histologicGradeCollection>
    <familyHistoryCollection>
        <familyHistory>
            <otherCancerDiagnosed>String</otherCancerDiagnosed>
            <sameCancerDiagnosed>String</sameCancerDiagnosed>
        </familyHistory>
    </familyHistoryCollection>
    <comorbidityOrComplicationCollection>
        <comorbidityOrComplication>
            <value>String</value>
        </comorbidityOrComplication>
    </comorbidityOrComplicationCollection>
    <tumorBiomarkerTest>
        <her2NeuDerived>String</her2NeuDerived>
        <her2NeuFish>String</her2NeuFish>
    </tumorBiomarkerTest>
    <patientHistoryCollection>
        <patientHistory>
            <cancerSite>String</cancerSite>
            <sequence>2147483647</sequence>
        </patientHistory>
    </patientHistoryCollection>
    <tumorHistory>
        <cancerStatus>String</cancerStatus>
        <cancerStatusFollowUpDate>1967-08-13</cancerStatusFollowUpDate>
        <cancerStatusFollowUpType>String</cancerStatusFollowUpType>
        <qualityOfSurvival>String</qualityOfSurvival>
    </tumorHistory>
    <placeOfDiagnosis>
        <initials>String</initials>
    </placeOfDiagnosis>
    <followUp>
        <dateFollowUpChanged>String</dateFollowUpChanged>
        <dateOfLastCancerStatus>1967-08-13</dateOfLastCancerStatus>
        <nextFollowUpHospital>
            <initials>String</initials>
        </nextFollowUpHospital>
        <lastFollowUpHospital>
            <initials>String</initials>
        </lastFollowUpHospital>
        <tumorFollowUpBiomarkerTest>
            <her2NeuDerived>String</her2NeuDerived>
            <her2NeuFish>String</her2NeuFish>
        </tumorFollowUpBiomarkerTest>
    </followUp>
</TumorDetails>

`

Have a look at XML::Simple.

mpe
– mpe

2012-11-27 14:34:47 +00:00
Commented Nov 27, 2012 at 14:34 — mpe
– mpe, Commented Nov 27, 2012 at 14:34

creaktive · Accepted Answer · 2012-11-28 00:50:34Z

First, the very, very important concept: there is no such thing as "XML template"! The whole point of using XML is being capable to read/write data according to some schema. If you have a (consistent) XML sample but no schema definition (XSD), use trang to figure it out:

java -jar trang.jar sample.xml sample.xsd

For provided sample, the generated XSD file looks like this:

<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified">
  <xs:element name="TumorDetails">
    <xs:complexType>
      <xs:sequence>
        <xs:element ref="personUpi"/>
        <xs:element ref="ageAtDiagnosis"/>
        <xs:element ref="biopsyPathologyReportSummary"/>
        <xs:element ref="primarySiteCollection"/>
        <xs:element ref="distantMetastasisSite"/>
        <xs:element ref="siteGroup"/>
        <xs:element ref="tmStaging"/>
        <xs:element ref="pediatricStaging"/>
        <xs:element ref="histologicTypeCollection"/>
        <xs:element ref="histologicGradeCollection"/>
        <xs:element ref="familyHistoryCollection"/>
        <xs:element ref="comorbidityOrComplicationCollection"/>
        <xs:element ref="tumorBiomarkerTest"/>
        <xs:element ref="patientHistoryCollection"/>
        <xs:element ref="tumorHistory"/>
        <xs:element ref="placeOfDiagnosis"/>
        <xs:element ref="followUp"/>
      </xs:sequence>
    </xs:complexType>
  </xs:element>
...
</xs:schema>

And now, the best part, called XML::Compile. It takes your XSD schema, compiles it and fits/validates native Perl structures, producing XML as an output:

#!/usr/bin/env perl
use strict;
use warnings;
use XML::Compile::Schema;

my $node = {
    personUpi                    => 'String',
    ageAtDiagnosis               => '3.14159E0',
    biopsyPathologyReportSummary => 'String',
    primarySiteCollection        => {
        tissueSite => {
            description => 'String',
            name        => 'String',
        },
    },
    ...
};

my $schema = XML::Compile::Schema->new('sample.xsd');
my $writer = $schema->compile(WRITER => 'TumorDetails');
my $doc = XML::LibXML::Document->new(q(1.0), q(UTF-8));

print $writer->($doc, $node)->toString;

I found this tutorial which provides a working example: blogs.perl.org/users/brian_e_lozier/2011/10/…

Borodin · Accepted Answer · 2012-11-27 16:32:48Z

A lot depends on what you are already familiar with. If you are comfortable navigating XML documents using the Document Object Model then XML::DOM, XML::LibXML or XML::Twig are nice, while XML::TreeBuilder is a similar module that has its own API, and you will discover whether it suits you only by trying it.

However, all these modules are intended promarily for navigating and accessing existing XML data, and they are only partially useful for creating new XML from scratch. Instead, the modules XML::Generator, XML::Writer and XML::API are designed specifically for this purpose, and all have similar interfaces. My preference, and my recommendation to you, is XML::API, which has the most flexible interface and should suit your purpose well.

Using XML::API, the code to generate a given XML document has a one-to-one correspondence with the resultant XML. Each statement corresponds to a single XML element or tag, and the tag and attrbute names and text values can be derived run time, for instance using information from a database.

This program recreates your sample XML. Note that the subsections could be coded separately and parcelled up into subroutines, passing the XML::API object to each of them. It is also possible to generate the XML in a non-linear fashion, as each method returns a reference to the element is creates, and there is a _goto method which takes such a reference and sets the location of subsequent additions. Indeed, the _close method, rather than writing any data, just executes a _goto to the parent of the current element.

use strict;
use warnings;

use XML::API;

my $xml = XML::API->new(doctype => 'xhtml');

$xml->_open('TumorDetails');

  $xml->_element('personUpi', 'String');
  $xml->_element('ageAtDiagnosis', '3.14159E0');
  $xml->_element('biopsyPathologyReportSummary', 'String');

  $xml->_open('primarySiteCollection');
    $xml->_open('tissueSite');
      $xml->_element('description', 'String');
      $xml->_element('name', 'String');
    $xml->_close('tissueSite');
  $xml->_close('primarySiteCollection');

  $xml->_open('distantMetastasisSite');
    $xml->_element('description', 'String');
    $xml->_element('name', 'String');
  $xml->_close('distantMetastasisSite');

  $xml->_open('siteGroup');
    $xml->_element('description', 'String');
    $xml->_element('name', 'String');
  $xml->_close('siteGroup');

  $xml->_open('tmStaging');
    $xml->_element('clinicalDescriptor', 'String');
    $xml->_element('clinicalMStage', 'String');
    $xml->_open('siteGroupEdition5');
      $xml->_element('description', 'String');
      $xml->_element('name', 'String');
    $xml->_close('siteGroupEdition5');
    $xml->_open('siteGroupEdition6');
      $xml->_element('description', 'String');
      $xml->_element('name', 'String');
    $xml->_close('siteGroupEdition6');
  $xml->_close('tmStaging');

  $xml->_open('pediatricStaging');
    $xml->_element('doneBy', 'String');
    $xml->_element('group', 'String');
  $xml->_close('pediatricStaging');

  $xml->_open('histologicTypeCollection');
    $xml->_open('histologicType');
      $xml->_element('description', 'String');
      $xml->_element('system', 'String');
      $xml->_element('value', 'String');
    $xml->_close('histologicType');
  $xml->_close('histologicTypeCollection');

  $xml->_open('histologicGradeCollection');
    $xml->_open('histologicGrade');
      $xml->_element('gradeOrDifferentiation', 'String');
    $xml->_close('histologicGrade');
  $xml->_close('histologicGradeCollection');

  $xml->_open('familyHistoryCollection');
    $xml->_open('familyHistory');
      $xml->_element('otherCancerDiagnosed', 'String');
      $xml->_element('sameCancerDiagnosed', 'String');
    $xml->_close('familyHistory');
  $xml->_close('familyHistoryCollection');

  $xml->_open('comorbidityOrComplicationCollection');
    $xml->_open('comorbidityOrComplication');
      $xml->_element('value', 'String');
    $xml->_close('comorbidityOrComplication');
  $xml->_close('comorbidityOrComplicationCollection');

  $xml->_open('tumorBiomarkerTest');
    $xml->_element('her2NeuDerived', 'String');
    $xml->_element('her2NeuFish', 'String');
  $xml->_close('tumorBiomarkerTest');

  $xml->_open('patientHistoryCollection');
    $xml->_open('patientHistory');
      $xml->_element('cancerSite', 'String');
      $xml->_element('sequence', '2147483647');
    $xml->_close('patientHistory');
  $xml->_close('patientHistoryCollection');

  $xml->_open('tumorHistory');
    $xml->_element('cancerStatus', 'String');
    $xml->_element('cancerStatusFollowUpDate', '1967-08-13');
    $xml->_element('cancerStatusFollowUpType', 'String');
    $xml->_element('qualityOfSurvival', 'String');
  $xml->_close('tumorHistory');

  $xml->_open('placeOfDiagnosis');
    $xml->_element('initials', 'String');
  $xml->_close('placeOfDiagnosis');

  $xml->_open('followUp');
    $xml->_element('dateFollowUpChanged', 'String');
    $xml->_element('dateOfLastCancerStatus', '1967-08-13');
    $xml->_open('nextFollowUpHospital');
      $xml->_element('initials', 'String');
    $xml->_close('nextFollowUpHospital');
    $xml->_open('lastFollowUpHospital');
      $xml->_element('initials', 'String');
    $xml->_close('lastFollowUpHospital');
    $xml->_open('tumorFollowUpBiomarkerTest');
      $xml->_element('her2NeuDerived', 'String');
      $xml->_element('her2NeuFish', 'String');
    $xml->_close('tumorFollowUpBiomarkerTest');
  $xml->_close('followUp');

$xml->_close('TumorDetails');

print $xml;

Borodin · Accepted Answer · 2012-11-27 16:33:50Z

1

If the data will always be identical then ddoxey's TemplateToolkit solution is a good one, however, if some of the tags are sometimes not present then you'll need to build up the XML from scratch each time.

I've recently done some work with XML and was very happy with XML::Writer.

edited Nov 27, 2012 at 16:33

Borodin

127k9 gold badges72 silver badges146 bronze badges

answered Nov 27, 2012 at 16:32

Bart B

6698 silver badges18 bronze badges

2 Comments

ddoxey Over a year ago

FYI, TT does include a rich interface for supporting conditionals and iteration if the situation calls for it.

thatisvivek Over a year ago

I solved my problem with the same module. Thanks for your replay.

szabgab · Accepted Answer · 2014-04-26 19:42:14Z

I am somewhat partial to the Template toolkit. See:

#!/usr/bin/perl -Tw

use strict;
use warnings;
use Template;

my $tmpl = get_template();
my $rec  = get_record();
my $xml;

my $template = Template->new();

$template->process( \$tmpl, $rec, \$xml )
    || die $template->error();

print "$xml";

# ...

sub get_record {

    return {
        personUpi                    => 'String',
        ageAtDiagnosis               => '3.14159E0',
        biopsyPathologyReportSummary => 'String',
        primarySiteCollection        => {
            tissueSite => {
                description => 'String',
                name        => 'String',
            },
        },
        distantMetastasisSite => {
            description => 'String',
            name        => 'String',
        },
        siteGroup => {
            description => 'String',
            name        => 'String',
        },
        tmStaging => {
            clinicalDescriptor => 'String',
            clinicalMStage     => 'String',
            siteGroupEdition5  => {
                description => 'String',
                name        => 'String',
            },
            siteGroupEdition6 => {
                description => 'String',
                name        => 'String',
            },
        },
        pediatricStaging => {
            doneBy => 'String',
            group  => 'String',
        },
        histologicTypeCollection => {
            histologicType => {
                description => 'String',
                system      => 'String',
                value       => 'String',
            },
        },
        histologicGradeCollection => {
            histologicGrade => { gradeOrDifferentiation => 'String', }, },
        familyHistoryCollection => {
            familyHistory => {
                otherCancerDiagnosed => 'String',
                sameCancerDiagnosed  => 'String',
            },
        },
        comorbidityOrComplicationCollection => {
            comorbidityOrComplicationCollection => { value => 'String', },
        },
        tumorBiomarkerTest => {
            her2NeuDerived => 'String',
            her2NeuFish    => 'String',
        },
        patientHistoryCollection => {
            patientHistory => {
                cancerSite => 'String',
                sequence   => '2147483647',
            },
        },
        tumorHistory => {
            cancerStatus             => 'String',
            cancerStatusFollowUpDate => '1967-08-13',
            cancerStatusFollowUpType => 'String',
            qualityOfSurvival        => 'String',
        },
        placeOfDiagnosis => { initials => 'String', },
        followUp         => {
            dateFollowUpChanged        => 'String',
            dateOfLastCancerStatus     => '1967-08-13',
            nextFollowUpHospital       => { initials => 'String', },
            lastFollowUpHospital       => { initials => 'String', },
            tumorFollowUpBiomarkerTest => {
                her2NeuDerived => 'String',
                her2NeuFish    => 'String',
            },
        },
    };
}

sub get_template {

    return <<'END_TEMPL';
<TumorDetails>
    <personUpi>[% personUpi %]</personUpi>
    <ageAtDiagnosis>[% ageAtDiagnosis %]</ageAtDiagnosis>
    <biopsyPathologyReportSummary>[% biopsyPathologyReportSummary %]</biopsyPathologyReportSummary>
    <primarySiteCollection>
        <tissueSite>
            <description>[% primarySiteCollection.tissueSite.description %]</description>
            <name>[% primarySiteCollection.tissueSite.name %]</name>
        </tissueSite>
    </primarySiteCollection>
    <distantMetastasisSite>
        <description>[% distantMetastasisSite.description %]</description>
        <name>[% distantMetastasisSite.name %]</name>
    </distantMetastasisSite>
    <siteGroup>
        <description>[% siteGroup.description %]</description>
        <name>[% siteGroup.name %]</name>
    </siteGroup>
    <tmStaging>
        <clinicalDescriptor>[% tmStaging.clinicalDescriptor %]</clinicalDescriptor>
        <clinicalMStage>[% tmStaging.clinicalMStage %]</clinicalMStage>
        <siteGroupEdition5>
            <description>[% tmStaging.siteGroupEdition5.description %]</description>
            <name>[% tmStaging.siteGroupEdition5.name %]</name>
        </siteGroupEdition5>
        <siteGroupEdition6>
            <description>[% tmStaging.siteGroupEdition6.description %]</description>
            <name>[% tmStaging.siteGroupEdition6.name %]</name>
        </siteGroupEdition6>
    </tmStaging>
    <pediatricStaging>
        <doneBy>[% pediatricStaging.doneBy %]</doneBy>
        <group>[% pediatricStaging.group %]</group>
    </pediatricStaging>
    <histologicTypeCollection>
        <histologicType>
            <description>[% histologicTypeCollection.histologicType.description %]</description>
            <system>[% histologicTypeCollection.histologicType.system %]</system>
            <value>[% histologicTypeCollection.histologicType.value %]</value>
        </histologicType>
    </histologicTypeCollection>
    <histologicGradeCollection>
        <histologicGrade>
            <gradeOrDifferentiation>[% histologicGradeCollection.histologicGrade.gradeOrDifferentiation %]</gradeOrDifferentiation>
        </histologicGrade>
    </histologicGradeCollection>
    <familyHistoryCollection>
        <familyHistory>
            <otherCancerDiagnosed>[% familyHistoryCollection.familyHistory.otherCancerDiagnosed %]</otherCancerDiagnosed>
            <sameCancerDiagnosed>[% familyHistoryCollection.familyHistory.sameCancerDiagnosed %]</sameCancerDiagnosed>
        </familyHistory>
    </familyHistoryCollection>
    <comorbidityOrComplicationCollection>
        <comorbidityOrComplication>
            <value>[% comorbidityOrComplicationCollection.comorbidityOrComplicationCollection.value %]</value>
        </comorbidityOrComplication>
    </comorbidityOrComplicationCollection>
    <tumorBiomarkerTest>
        <her2NeuDerived>[% tumorBiomarkerTest.her2NeuDerived %]</her2NeuDerived>
        <her2NeuFish>[% tumorBiomarkerTest.her2NeuFish %]</her2NeuFish>
    </tumorBiomarkerTest>
    <patientHistoryCollection>
        <patientHistory>
            <cancerSite>[% patientHistoryCollection.patientHistory.cancerSite %]</cancerSite>
            <sequence>[% patientHistoryCollection.patientHistory.sequence %]</sequence>
        </patientHistory>
    </patientHistoryCollection>
    <tumorHistory>
        <cancerStatus>[% tumorHistory.cancerStatus %]</cancerStatus>
        <cancerStatusFollowUpDate>[% tumorHistory.cancerStatusFollowUpDate %]</cancerStatusFollowUpDate>
        <cancerStatusFollowUpType>[% tumorHistory.cancerStatusFollowUpType %]</cancerStatusFollowUpType>
        <qualityOfSurvival>[% tumorHistory.qualityOfSurvival %]</qualityOfSurvival>
    </tumorHistory>
    <placeOfDiagnosis>
        <initials>[% placeOfDiagnosis.initials %]</initials>
    </placeOfDiagnosis>
    <followUp>
        <dateFollowUpChanged>[% followUp.dateFollowUpChanged %]</dateFollowUpChanged>
        <dateOfLastCancerStatus>[% followUp.dateOfLastCancerStatus %]</dateOfLastCancerStatus>
        <nextFollowUpHospital>
            <initials>[% followUp.nextFollowUpHospital.initials %]</initials>
        </nextFollowUpHospital>
        <lastFollowUpHospital>
            <initials>[% followUp.nextFollowUpHospital.initials %]</initials>
        </lastFollowUpHospital>
        <tumorFollowUpBiomarkerTest>
            <her2NeuDerived>[% followUp.tumorFollowUpBiomarkerTest.her2NeuDerived %]</her2NeuDerived>
            <her2NeuFish>[% followUp.tumorFollowUpBiomarkerTest.her2NeuFish %]</her2NeuFish>
        </tumorFollowUpBiomarkerTest>
    </followUp>
</TumorDetails>
END_TEMPL
}

__END__

It seems that this approach is unnecessarily long because every node name has to be written at least twice - once in the record and once or more in the template.
Indeed the template is just as verbose as the document it will produce. This approach does offer the complete separation of application logic from presentation. Depending on the needs of the organization, this implementation could allow for expressing the data in any number of other formats without refactoring the application, but rather just supplying a different template.

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