如何为 Perl 使用 SOAP API？

Question

我正在尝试调整以下 PHP code in Perl. It's a bioDBnet SOAP API. I tried following the example on the SOAP::WSDL 模块（在 SYNOPSIS 下），但它无法连接。我收到一条错误消息：

尝试 1

#!perl -w
use SOAP::WSDL;

my $client = SOAP::WSDL->new(
    wsdl => "http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet.wsdl",
);

错误信息：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.

尝试 2

接下来我尝试使用 SOAP::LITE 模块。我遵循了 HERE 中的示例代码（在 6.b.client 下）。

#!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;

上面的代码没有打印任何东西。我如何让 bioDBnet SOAP API 为 Perl 工作？

Answer 1

除 db2db 部分外，您的第二个脚本有效。我的猜测是发送到服务器的 SOAP XML 信封在使用 SOAP::LITE.

发送时状态不佳

我在第二行启用了调试：

#!/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;

.. 从你的尝试 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;

..我也尝试使用SOAP:Data重写它...但失败了。

# 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;

切换到 PHP 以查看工作请求。我已在 PHP 脚本上启用调试以打印请求 headers 并从 PHP 获取正在工作的 XML 请求，并将其作为来自 PERL 的 POST 内容重新使用。基本上，通过在 SoapClient 上添加跟踪参数，然后转储最后一个请求 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);

这将打印 headers 和 XML，预期输出为：

Gene Symbol     Gene ID Ensembl Gene ID
MYC     4609    ENSG00000136997
A1BG    1       ENSG00000121410

我将 "working" XML 请求数据包含在 $message 中并执行 POST 请求。

#!/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;
}

最后：在 header 输出旁边我们终于得到了一些数据：

<?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>

现在，您需要做的就是从 $response->as_string 中提取 ns1:db2dbResponse 中的 return 元素（可能使用 LibXML）。

换句话说：这会绕过 SOAP::Lite 并使用 LWP 和一个带有 XML 的简单 POST 请求，解析 XML 响应。您丢失了自动提取，必须手动处理 return 数据。

Answer 2

不要使用 SOAP::Lite 服务方法，大多数情况下它不起作用。手动构建 soap 结构。我尝试尽可能地遵循 php xml，尽管大多数前缀都不是必需的。

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";
}

这会从服务器生成所需的输出。

如何为 Perl 使用 SOAP API？

How to use a SOAP API for Perl?

php

perl

soap

wsdl

web-services