How to use a SOAP API for Perl? - php

Question

I'm trying to adapt the following PHP code in Perl. It's a bioDBnet SOAP API. I tried following the example on the SOAP::WSDL module (under SYNOPSIS) but it doesn't connect. I get an error message:
ATTEMPT 1
#!perl -w
use SOAP::WSDL;
my $client = SOAP::WSDL->new(
wsdl => "http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet.wsdl",
);
Error message: cannot import document for namespace >http://schemas.xmlsoap.org/soap/encoding/< without location at /Library/Perl/5.16/SOAP/WSDL/Expat/WSDLParser.pm line 90.
ATTEMPT 2
Next I tried using the SOAP::LITE module. I followed the sample code from HERE (under 6.b. client).
#!perl -w
use SOAP::Lite;
my $client = SOAP::Lite ->
service('http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet.wsdl');
my %db2dbParams;
$db2dbParams{'input'} = "Gene Symbol";
$db2dbParams{'outputs'} = "Gene ID, Ensembl Gene ID";
$db2dbParams{'inputValues'} = "MYC,A1BG";
$db2dbParams{'taxonId'} = "9606";
$db2dbRes = $client->db2db(%db2dbParams);
print $db2dbRes;
The code above doesn't print anything. How do I get the bioDBnet SOAP API to work for Perl?

Answer 1

Don't use a SOAP::Lite service method, mostly it doesn't work.
Build the soap structure manually. I tried to follow the php xml as much as possible, though most of prefixes is not necessary.
use strict;
use warnings;
use Data::Dumper;
use SOAP::Lite;
#use SOAP::Lite +trace=>'all';
$uri = 'urn:bioDBnet';
$proxy = 'http://biodbnet.abcc.ncifcrf.gov/webServices/biodbnetSoapServer.php';
$tns = 'urn:bioDBnet';
$soap = SOAP::Lite->new(uri => $uri,proxy => $proxy);
$soap->envprefix('SOAP-ENV');
$soap->encprefix('SOAP-ENC');
$soap->ns($tns,'tns1');
$soap->on_action(sub{$tns.'#db2db'});
#request = (SOAP::Data->name(db2dbParams => \SOAP::Data->value(
SOAP::Data->name(input => 'Gene Symbol'),
SOAP::Data->name(outputs => 'Gene ID, Ensembl Gene ID'),
SOAP::Data->name(inputValues => 'MYC,A1BG'),
SOAP::Data->name(taxonId => 9606),
))->type('ns1:db2dbParams'),
);
$db2db = $soap->db2db(#request);
if ($match = $db2db->match('/Envelope/Body/db2dbResponse')) {
print "match ok: $match\n";
$result = $db2db->result;
print Dumper($result);
} else {
print "match nok: $match\n";
}
This produces the required output from the server.

Answer 2

Your second scripts works, except the db2db part.
My guess is that the SOAP XML envelope send to the server is not in a good shape, when sending with SOAP::LITE.
I've enabled debugging on the second line:
#!/usr/bin/perl -w
use SOAP::Lite +trace =>'debug';
#use SOAP::Lite;
my $client = SOAP::Lite->service('http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet.wsdl');
$inputs = $client->getInputs();
print $inputs;
$input = "Gene Symbol";
$outputs = $client->getOutputsForInput($input);
print $outputs;
$dirOutputs = $client->getDirectOutputsForInput($input);
print $dirOutputs;
.. From your Attempt 2:
# doesn't work, the created XML envelope is not in a good shape
my %db2dbParams;
$db2dbParams{'input'} = "Gene Symbol";
$db2dbParams{'outputs'} = "Gene ID, Ensembl Gene ID";
$db2dbParams{'inputValues'} = "MYC,A1BG";
$db2dbParams{'taxonId'} = "9606";
$db2dbRes = $client->db2db(%db2dbParams);
print $db2dbRes;
.. I also tried to rewrite this using SOAP:Data...but failed.
# doesn't work, the created XML envelope is not in a good shape
$db2dbRes = $client->db2db(
SOAP::Data->name("db2dbParams")->type("ns1:db2dbParams")->prefix("ns1:db2db")->uri("urn:bioDBnet") =>
SOAP::Data->type("string")->name("input" => "Gene Symbol"),
SOAP::Data->type("string")->name("inputValues" => "MYC,MTOR"),
SOAP::Data->type("string")->name("outputs" => "Gene ID, Affy ID"),
SOAP::Data->type("string")->name("taxonId" => "9606")
);
print $db2dbRes;
Switched over to PHP to see a working request.
I've enabled debugging on the PHP script to print the request headers
and fetch the working XML request done from PHP and reuse it as POST content from PERL. Basically, by adding the trace parameter on the SoapClient and then dumping the last reqeust headers.
<?php
$wsdl = "http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet.wsdl";
$client = new SoapClient($wsdl, ['trace' => 1]);
$inputs = $client->getInputs();
print $inputs;
$input = "Gene Symbol";
$outputs = $client->getOutputsForInput($input);
print $outputs;
$dirOutputs = $client->getDirectOutputsForInput($input);
print $dirOutputs;
$db2dbParams['input'] = "Gene Symbol";
$db2dbParams['outputs'] = "Gene ID, Ensembl Gene ID";
$db2dbParams['inputValues'] = "MYC,A1BG";
$db2dbParams['taxonId'] = "9606";
$db2dbRes = $client->db2db($db2dbParams);
print $db2dbRes;
echo "====== REQUEST HEADERS =====" . PHP_EOL;
var_dump($client->__getLastRequestHeaders());
echo "========= REQUEST ==========" . PHP_EOL;
var_dump($client->__getLastRequest());
echo "========= RESPONSE =========" . PHP_EOL;
var_dump($db2dbRes);
This prints headers together with XML and the expected output is:
Gene Symbol Gene ID Ensembl Gene ID
MYC 4609 ENSG00000136997
A1BG 1 ENSG00000121410
I'm included the "working" XML request data into $message and do a POST request.
#!/usr/bin/perl -w
use strict;
use LWP::UserAgent;
use HTTP::Request;
my $message = '<?xml version="1.0" encoding="UTF-8" ?>
<SOAP-ENV:Envelope xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
xmlns:ns1="urn:bioDBnet" xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
<SOAP-ENV:Body>
<ns1:db2db>
<db2dbParams xsi:type="ns1:db2dbParams">
<input xsi:type="xsd:string">Gene Symbol</input>
<taxonId xsi:type="xsd:string">9606</taxonId>
<inputValues xsi:type="xsd:string">MYC,A1BG</inputValues>
<outputs xsi:type="xsd:string">Gene ID, Ensembl Gene ID</outputs>
</db2dbParams>
</ns1:db2db>
</SOAP-ENV:Body>
</SOAP-ENV:Envelope>';
my $userAgent = LWP::UserAgent->new();
my $request = HTTP::Request->new(POST => 'http://biodbnet.abcc.ncifcrf.gov/webServices/biodbnetSoapServer.php'); # ?debug=1
$request->content($message);
$request->content_type("text/xml; charset=utf-8");
my $response = $userAgent->request($request);
if($response->code == 200) {
print $response->as_string;
}
else {
print $response->error_as_HTML;
}
Finally: next to header output we finally got some data:
<?xml version="1.0" encoding="UTF-8" ?>
<SOAP-ENV:Envelope xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
xmlns:ns1="http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
<SOAP-ENV:Body>
<ns1:db2dbResponse>
<return xsi:type="xsd:string">Gene Symbol Gene ID Ensembl Gene ID
MYC 4609 ENSG00000136997 A1BG 1 ENSG00000121410
</return>
</ns1:db2dbResponse>
</SOAP-ENV:Body>
</SOAP-ENV:Envelope>
Now, all you need to do is to extract the return element inside the ns1:db2dbResponse from $response->as_string (probably using LibXML).
In other words: this bypasses SOAP::Lite and uses LWP and a simply POST request with XML, the parsing the XML response. You lose the automatical extraction and have to handle return data manually.