NAME
FAIR::Accessor - all this does is assign the HTTP call to the correct routine
VERSION
version 1.001
SYNOPSIS
The following code is a complete implementation of a 'Hello, World!' FAIR Accessor
C<##!/usr/local/bin/perl -w
package MyFirstAccessor; # this should be the same as your filename!
use FindBin; # where was script installed?
use lib "$FindBin::Bin"; # use that dir for libs, too
use strict;
use warnings;
use JSON;
use FAIR::Accessor::Distribution;
use FAIR::Accessor::Container;
use FAIR::Accessor::MetaRecord;
#-----------------------------------------------------------------
# Configuration and Daemon
#-----------------------------------------------------------------
use base 'FAIR::Accessor';
my $config = {
title => 'Example FAIR Accessor',
serviceTextualDescription => 'Bare-bones FAIR Accessor',
textualAccessibilityInfo => "The information from this server requries no authentication; HTTP GET is sufficient", # this could also be a $URI describing the accessibiltiy
mechanizedAccessibilityInfo => "", # this must be a URI to an RDF document
textualLicenseInfo => "CC0", # this could also be a URI to the license info
mechanizedLicenseInfo => "https://creativecommons.org/choose/zero/", # this must be a URI to an RDF document
ETAG_Base => "SomeIdentifierOfMyAccessor", # this is a unique identificaiton string for the service (required by the LDP specification)
localNamespaces => {
pfund => 'http://vocab.ox.ac.uk/projectfunding#term_',
up => 'http://uniprot.org/ontology/core#',
}, # add a few new namespaces to the list of known namespaces....
basePATH => 'cgi-bin/Accessors/MyFirstAccessor', # REQUIRED regexp to match the PATH part of the URL, before the ID number
};
my $service = UniProtAccessor->new(%$config);
# start daemon
$service->handle_requests;
#-----------------------------------------------------------------
# Accessor Implementation
#-----------------------------------------------------------------
#------------- Container Resource --------------
sub Container { REQUIRED SUBROUTINE NAME!!!!
my ($self, %ARGS) = @_;
my $Container = FAIR::Accessor::Container->new(NS => $self->Configuration->Namespaces);
my $BASE_URL = "http://" . $ENV{'SERVER_NAME'} . $ENV{'REQUEST_URI'};
my @recordIDs = (1,2,3,4,5,6,7);
my @recordURLs;
foreach my $ID (@recordIDs) {
push @recordURLs, "$BASE_URL/$ID"; # need to make a URL for each of the meta-records, based on the ID of the PHIBase record, push it onto a list
}
$Container->addRecords(\@recordURLs); # the listref of record ids
$self->fillContainerMetadata($Container);
return $Container;
}
# --------------------MetaRecord Resource ---------------
sub MetaRecord { REQUIRED SUBROUTINE NAME
my ($self, %ARGS) = @_;
my $ID = $ARGS{'ID'};
my $MetaRecord = FAIR::Accessor::MetaRecord->new(ID => $ID,
NS => $self->Configuration->Namespaces);
$self->fillMetaRecordMetadata($MetaRecord);
$MetaRecord->addDistribution(availableformats => ['text/html'],
downloadURL => "http://www.uniprot.org/uniprot/$ID.html");
$MetaRecord->addDistribution(availableformats => ['application/rdf+xml'],
downloadURL => "http://www.uniprot.org/uniprot/$ID.rdf");
my $encodedsubject = urlencode("http://identifiers.org/uniprot/$ID");
my $encodedpredicate = urlencode("http://purl.uniprot.org/core/organism");
my $TPF = "http://my.TPF.server.org/fragments?subject=$encodedsubject&predicate=$encodedpredicate";
$MetaRecord->addDistribution(
availableformats => ["application/x-turtle", "application/rdf+xml", "text/html"],
downloadURL => $TPF,
source => "http://identifiers.org/uniprot/$ID",
subjecttemplate => "http://identifiers.org/uniprot/{ID}",
subjecttype => "http://purl.uniprot.org/core/organism",
predicate => "http://purl.uniprot.org/core/organism",
objecttemplate => "http://identifiers.org/taxon/{TAX}",
objecttype => "http://edamontology.org/data_1179",
);
return $MetaRecord;
}
sub fillContainerMetadata {
my ($self, $Container) = @_;
$Container->addMetadata({
'dc:title' => "Generic FAIR Accessor example",
'dcat:description' => "For Example",
'dcat:identifier' => "http://linkeddata.systems/cgi-bin/Accessors/MyFirstAccessor", # NOTE the filename and path! set in the top-level %config hash!
'dcat:keyword' => ["Go", "FAIR"],
'dc:license' => 'https://creativecommons.org/choose/zero',
'rdf:type' => ['prov:Collection', 'dctypes:Dataset'],
});
}
sub fillMetaRecordMetadata {
my ($self, $MetaRecord) = @_;
my $ID = $MetaRecord->ID;
$MetaRecord->addMetadata({
'foaf:primaryTopic' => "http://my.database.org/records/$ID",
'dc:title' => "Record $ID",
'dcat:identifier' => "http://my.database.org/records/$ID",
'dcat:keyword' => ["Go", "FAIR"],
'dc:creator' => 'Me',
'dc:bibliographicCitation' => "Joe Bloggs (2016). How to write a FAIR Accessor, Online Journal 4:3.",
'void:inDataset' => 'http://linkeddata.systems/cgi-bin/Accessors/UniProtAccessor/',
'dc:license' => 'https://creativecommons.org/choose/zero',
});
}
sub urlencode {
my $s = shift;
$s =~ s/ /+/g;
$s =~ s/([^A-Za-z0-9\+-])/sprintf("%%%02X", ord($1))/seg;
return $s;
}>
DESCRIPTION
FAIR Accessors are inspired by the W3Cs Linked Data Platform "Containers".
FAIR Accessors follow a two-stage interaction, where the first stage retrieves metadata about the repository "Container"), and (optionally) a series of URLs representing 'MetaRecords' for every record in that repository (or whatever slice of the repository is being served). This is accomplished by the Container subroutine. These URLs will generally point back at this same Accessor script (e.g. with the record number appended to the URL: http://this.host/thisscript/12345).
The second stage involves retrieving metadata about individual recoreds. The metadata is up to you, but optimally it would include the available DCAT distributions and their file formats. The second stage can be accomplished by this same Accessor script, using the Distributions subroutine.
The two subroutine names - Container and MetaRecord - are not flexible, as they are called by-name, by the Accessor libraries.
You MUST create the Container subroutine, at a minimum, and it should return some metadata. It does not have to return a list of known records (in which case it simply acts as a metadata descriptor of the repository in general, nothing more... which is fine!... and there will be no second stage interaction. In this case, you do not need to provide a MetaRecord subroutine.)
NAME
FAIR::Accessor - Module for creating Linked Data Platform Accessors for the FAIR Data projectCommand-line testing
If you wish to test your Accessor server at the command line, you can run it with the following commandline arguments (in order):
Method (always GET, at the moment)
Domain
Request URI (i.e. the path to this script, including the script name)
PATH_INFO (anything that should appear in the PATH_INFO variable of the webserver)
perl myAccessorScript GET example.net /this/myAccessorScript /1234567AUTHOR
Mark Denis Wilkinson (markw [at] illuminae [dot] com)
COPYRIGHT AND LICENSE
This software is Copyright (c) 2016 by Mark Denis Wilkinson.
This is free software, licensed under:
The Apache License, Version 2.0, January 2004