SOAP Simple Object Access Protocol SCGAP Introduction Central Gene - - PowerPoint PPT Presentation

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Jan 05, 2023 1.19k likes •1.41k views

SOAP Simple Object Access Protocol SCGAP Introduction Central Gene Expression Query at scgap.org Source data at 7 member organizations Varying architectures, data stores www.scgap.org Member Member Member Member Member ...

SLIDE 1

SOAP

Simple Object Access Protocol

SLIDE 2

SCGAP Introduction

Central Gene Expression Query at

scgap.org

Source data at 7 member organizations
Varying architectures, data stores

www.scgap.org

Member Site Member Site Member Site Member Site Member Site

...

SLIDE 3

SOAP Introduction

Protocol for the exchange of information in

heterogeneous environments

Lightweight: XML Based
Simple: No code modification needed
Ubiquitous: Over 41 Implementations
Not a new idea: CORBA, DCOM, XML-RPC

SLIDE 4

Bad News, Good News

SOAP

, and web services in general, are a huge, hot, topic.

But it is called the SIMPLE object access

protocol for a reason...

SLIDE 5

SOAP::Lite

Primary Perl Implementation
Public Beta, September 2000
Both Server and Client code
“Don’t be misled by the ‘Lite’ suffix-- this

refers to the effort it takes to use the module, not its capabilities”

SLIDE 6

SOAP::Lite Client

#!perl -w

use SOAP::Lite; my $server = SOAP::Lite

> uri('http://www.cbil.upenn.edu/Demo')
> proxy('http://www.cbil.upenn.edu/webservices/labdemo.cgi');

print $server->hi()->result;

<?xml version="1.0" encoding="UTF-8"?>

<SOAP-ENV:Envelope xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance”

xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/1999/XMLSchema" SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">

<SOAP-ENV:Body> <namesp1:hi xmlns:namesp1="http://www.cbil.upenn.edu/Demo"/> </SOAP-ENV:Body> </SOAP-ENV:Envelope>

SLIDE 7

SOAP::Lite Server

#!perl -w

use SOAP::Transport::HTTP; SOAP::Transport::HTTP::CGI

> dispatch_to('Demo')
> handle;

package Demo; sub hi { return "hello, world"; }

<?xml version="1.0" encoding="UTF-8"?>

<SOAP-ENV:Envelope ... > <SOAP-ENV:Body> <namesp1:hiResponse xmlns:namesp1="http://www.cbil.upenn.edu/Demo"> <s-gensym3 xsi:type="xsd:string"> Hello from CBIL </s-gensym3> </namesp1:hiResponse> </SOAP-ENV:Body> </SOAP-ENV:Envelope>

SLIDE 8

SCGAP Overview

Request:
GeneType

name genome_build_id genomiccoordinateType chromosome start_coord end_coord strand *

Response:
GeneType

gene_expression expressed * evidence population population_id population_link image ** link ** source

SLIDE 9

Getting Complicated

Perl Model:
GeneType -> Gene.pm
Response ->

GeneExpressionResponse.pm

Gene Expression ->

Expression.pm

GeneExpression.pm
Query Information
Results
Abstract Class

XML Model:

GeneType name genome_build_id genomiccoordinateType chromosome start_coord end_coord strand * GeneType gene_expression expressed * evidence population population_id population_link image ** link ** source

SLIDE 10

Resolving Complexity

Overrode Serialization
WSDL: Web Services Description Language
XML
Used to describe the services offered by a

web service, as well as the location of the service.

SLIDE 11

Keeping in Simple

All but two files are common to all groups
WSDL-- One line change
GeneExpression -- Implement search
Second look at the client and server...

SLIDE 12

More...

Error Handling
Dynamic Dispatch
Security (SSL, Tickets, Cookies, ACL, etc.)