EMBL-EBI Web Services

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====== Perl ======

===== Web Services Tool-kits =====

There are many modules available for developing Web Services clients or servers available for Perl ((Perl - http://www.perl.com/)). These fall into two broad categories:
  - General purpose modules which implement Web Services technologies (i.e. REST or SOAP)
  - Service libraries which implement the client and/or server interface for a service type (e.g. OpenSearch ((OpenSearch - http://www.opensearch.org/))) or for a specific service.

A selection of modules commonly used to access Web Services are listed below.

==== General Purpose ====

Perl modules which implement Web Services technologies, for example:

^ Web Service Style ^ Perl Module ^
| REST              | [[http://gitorious.org/libwww-perl|LWP]] ([[http://search.cpan.org/perldoc?LWP|CPAN]]) |
|                   | REST::Client ([[http://search.cpan.org/perldoc?REST::Client|CPAN]]) |
|                   | WWW::Curl ([[http://search.cpan.org/perldoc?WWW::Curl|CPAN]]) |
|                   | WWW::Curl::Simple ([[http://search.cpan.org/perldoc?WWW::Curl::Simple|CPAN]]) |
| SOAP              | SOAP ([[http://search.cpan.org/perldoc?SOAP|CPAN]]) |
|                   | [[http://www.soaplite.com/|SOAP::Lite]] ([[http://search.cpan.org/perldoc?SOAP::Lite|CPAN]]) |
|                   | [[http://soap-wsdl.sourceforge.net/|SOAP::WSDL]] ([[http://search.cpan.org/perldoc?SOAP::WSDL|CPAN]]) |
|                   | [[http://perl.overmeer.net/xml-compile/|XML::Compile::SOAP]] ([[http://search.cpan.org/perldoc?XML::Compile::SOAP|CPAN]]) |

**Note**: When building a SOAP client the choice of Perl module is driven by compatibility with the Web Service(s) being used (e.g. RPC/encoded vs. Document/literal support), see [[..:03_soap#soap_styles|SOAP Styles]] and the [[#tutorials]].

==== Client Libraries ====

Purpose built libraries for a type of service or a specific service, for example:

^ Web Service Type ^ Perl Module ^
| [[http://www.atomenabled.org/|AtomPub]] | Atompub ([[http://search.cpan.org/perldoc?Atompub|CPAN]]) |
| [[http://www.biodas.org/|DAS]]          | Bio::Das ([[http://search.cpan.org/perldoc?Bio::Das|CPAN]]) |
|                                         | Bio::Das::Lite ([[http://search.cpan.org/perldoc?Bio::Das::Lite|CPAN]]) |
| [[http://www.drugbank.ca/|DrugBank]]    | WWW::Search::DrugBank ([[http://search.cpan.org/perldoc?WWW::Search::DrugBank|CPAN]]) |
| [[http://gmod.org/|GMOD]]               | Bio::GMOD ([[http://search.cpan.org/perldoc?Bio::GMOD|CPAN]]) |
| [[http://www.genenames.org/|HGNC]]      | WWW::Search::HGNC ([[http://search.cpan.org/perldoc?WWW::Search::HGNC|CPAN]]) |
| [[http://www.ebi.ac.uk/integr8/HelpAction.do?action=searchById&refId=59|Integr8]] | SOAP::Integr8 ([[http://search.cpan.org/perldoc?SOAP::Integr8|CPAN]]) |
| [[http://www.isiknowledge.com/|ISI Web of Knowledge]] | SOAP::ISIWoK ([[http://search.cpan.org/perldoc?SOAP::ISIWoK|CPAN]]) |
| [[http://www.ncbi.nlm.nih.gov/|NCBI]]   | Boulder::Genbank ([[http://search.cpan.org/perldoc?Boulder::Genbank|CPAN]]) |
|                                         | NCBIx::BigFetch ([[http://search.cpan.org/perldoc?NCBIx::BigFetch|CPAN]]) |
| [[http://www.opensearch.org/|OpenSearch]] | WWW::OpenSearch ([[http://search.cpan.org/perldoc?WWW::OpenSearch|CPAN]]) |
| [[http://www.pdb.org/|PDB]] | WWW::PDB ([[http://search.cpan.org/perldoc?WWW::PDB|CPAN]]) |
| [[http://www.pharmgkb.org/|PharmGKB]]   | WWW::Search::PharmGKB ([[http://search.cpan.org/perldoc?WWW::Search::PharmGKB|CPAN]]) |
| [[http://pubchem.ncbi.nlm.nih.gov/|PubChem]] | WWW::Search::PubChem ([[http://search.cpan.org/perldoc?WWW::Search::PubChem|CPAN]]) |
| [[http://www.pubmed.gov/|PubMed]]       | WWW::Search::NCBI::PubMed ([[http://search.cpan.org/perldoc?WWW::Search::NCBI::PubMed|CPAN]]) |
|                                         | WWW::Search::PubMed ([[http://search.cpan.org/perldoc?WWW::Search::PubMed|CPAN]]) |
|                                         | WWW::Search::PubMedLite ([[http://search.cpan.org/perldoc?WWW::Search::PubMedLite|CPAN]]) |

==== BioPerl ====

[[http://www.bioperl.org/|BioPerl]] ([[http://search.cpan.org/perldoc?BioPerl|CPAN]]) includes support for a number of bioinformatics Web Services, for example:

^ Web Service ^ BioPerl Module ^
| [[http://www.ebi.ac.uk/cgi-bin/dbfetch|dbfetch]]     | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Biblio.html|Bio::Biblio]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/BioFetch.html|Bio::DB::BioFetch]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/EMBL.html|Bio::DB::EMBL]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/RefSeq.html|Bio::DB::RefSeq]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/SwissProt.html|Bio::DB::SwissProt]] |
| [[http://eutils.ncbi.nlm.nih.gov/|NCBI E-Utilities]] | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Biblio.html|Bio::Biblio]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/EUtilities.html|Bio::DB::EUtilities]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/EntrezGene.html|Bio::DB::EntrezGene]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenBank.html|Bio::DB::GenBank]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/GenPept.html|Bio::DB::GenPept]] |
|                                                      | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Taxonomy.html|Bio::DB::Taxonomy]] |
| Open Biological Database Access (OBDA) ((Open Biological Database Access - http://obda.open-bio.org/)) | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Registry.html|Bio::DB::Registry]] ((BioPerl OBDA HOWTO - http://www.bioperl.org/wiki/HOWTO:OBDA)) |
| [[http://www.ebi.ac.uk/~senger/openbqs/|OpenBQS]]    | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Biblio.html|Bio::Biblio]] |
| [[http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html|QBlAST URL API]] | [[http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Tools/Run/RemoteBlast.html|Bio::Tools::Run::RemoteBlast]] |
| [[:soaplab:overview|Soaplab]]                        | Bio::Tools::Run::AnalysisFactory |

===== Tutorials =====

==== Prerequisites ====

Knowledge of the following is required for these tutorials:
  * [[http://www.perl.com/|Perl]]. In particular the following:
    * [[http://perldoc.perl.org/perlref.html|Perl references and nested data structures]]
    * [[http://perldoc.perl.org/perlobj.html|Perl objects]]
  * Extensible Markup Language (XML) ((Extensible Markup Language (XML) - http://www.w3.org/XML/))
    * [[http://www.w3schools.com/xml/|XML Tutorial]] from w3schools.com
  * XML Schema ((XML Schema - http://www.w3.org/XML/Schema))
    * [[http://www.w3schools.com/schema/|XML Schema Tutorial]] from w3schools.com

==== Web Services Tutorials Examples and Solutions ====

The examples and solutions for the exercises are available: [[http://www.ebi.ac.uk/Tools/webservices/downloads/perl_exercises.zip|perl_exercises.zip]]

The download is based on the [[http://www.epic-ide.org/|E.P.I.C.]] project used to develop the tutorials. The files are explicitly referenced in the tutorials and links provided to the on-line versions. [[http://www.epic-ide.org/|E.P.I.C.]] is not required to work though the exercises, a text editor and a working Perl installation are the only requirements.

To import the project into [[http://www.eclipse.org/|Eclipse]]:
  - Download and install [[http://www.eclipse.org/|Eclipse]]
  - If necessary install Perl, see http://www.perl.com/download.csp
  - Install the [[http://www.epic-ide.org/|E.P.I.C.]] plug-in for Eclipse
  - Configure [[http://www.epic-ide.org/|E.P.I.C.]] to use the installed Perl
  - Download the [[http://www.ebi.ac.uk/Tools/webservices/downloads/perl_exercises.zip|project]]
  - Unpack the project into a working directory
  - Import the project into Eclipse using "File" -> "Import..."
    - For "import source" select "General" -> "Existing Projects into Workspace"
    - Specify the working directory containing the project
    - Select the project

Initially the project will contain errors due to some code generated as part of the exercises not being present. Additionally there may be some errors due to some of the Perl modules required by the scripts not being installed.

==== Web Services Tutorials ====

Tutorials on using a selection of popular Perl modules to develop clients for Web Services:
  * REST
    * [[.:Perl:REST:LWP]]
    * [[.:Perl:REST:WWW-OpenSearch|WWW::OpenSearch]]
  * SOAP
    * [[.:Perl:SOAP:SOAP-Lite|SOAP::Lite]]
    * [[.:Perl:SOAP:XML-Compile-SOAP|XML::Compile::SOAP]]

\\
^ Up | [[..:06_Programming|Programming Web Services]] ^ Contents | [[..:00_Contents|Contents]] |
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