MOBYXSLT - CommonSubs using XSLT
Because huge XML message parsing with XML::Dom take too much time. xsltproc is a binary very very efficient to parse huge files.
Globals variables are defined in this package:
my $TMP_DIR = '/tmp/'; #Where your temporary files will be written
my $XSLTPROC = '/usr/bin/xsltproc'; #Where your xsltproc binary is located
my $XSL_SHEET = './parseMobyMessage.xsl'; #Where your xsltproc style-sheet is located
sub MonWebservice {
my ($caller, $message) = (@_);
my $moby_response;
my $service_name = 'MonWebservice';
#Message Parsing
my ($service_notes,$ra_queries) = MOBYXSLT::getInputs($message); #Message Parsing
foreach my $query (@{$ra_queries})
{
my $query_id = MOBYXSLT::getInputID($query);#Retrieve Query ID
my @a_input_articles = MOBYXSLT::getArticles($query);#Retrieve articles
my ($fasta_sequences, $fasta_namespace, $fasta_id) = ('','','');
foreach my $input_article (@a_input_articles)
{
my ($article_name, $article) = @{$input_article};
if (MOBYXSLT::isSimpleArticle($article))
{
my $object_type = MOBYXSLT::getObjectType($article);
if (IsTheCorrectType($object_type))
{
$fasta_sequences = MOBYXSLT::getObjectContent($article);
$fasta_namespace = MOBYXSLT::getObjectNamespace($article);
$fasta_id = MOBYXSLT::getObjectId($article);
}
}
elsif (MOBYXSLT::isCollectionArticle($article))
{
}
elsif (MOBYXSLT::isSecondaryArticle($article))
{
my ($param_name,$param_value) = MOBYXSLT::getParameter($article);#Retrieve parameters
}
}
######
#What you want to do with your data
######
my $cmd ="...";
system("$cmd");
#########
#Send result
#########
$moby_response .= MOBYXSLT::simpleResponse("<$output_object_type1>$out_data</$output_object_type1>", $output_article_name1, $query_id);
}
return SOAP::Data->type(
'base64' => (MOBYXSLT::responseHeader(-authority => $auth_uri, -note => "Documentation about $service_name at $url_doc"))
. $moby_response
. MOBYXSLT::responseFooter());
}
my $TMP_DIR = '/tmp/'; #Where your temporary files will be written
my $XSLTPROC = '/usr/bin/xsltproc'; #Where your xsltproc binary is located
my $XSL_SHEET = './parseMobyMessage.xsl'; #Where your xsltproc style-sheet is located
Note: many functions have same names as those from MOBY::CommonSubs
Title : getInputs
Usage : my ($servicenotes, $ra_queries) = getInputs($moby_message)
Prerequisite :
Function : Parse Moby message and build Perl structures to access
for each query to their articles and objects.
Returns : $servicenotes: Notes returned by service provider
$ra_queries: ARRAYREF of all queries analysed in MOBY message
Args : $moby_message: MOBY XML message
Globals : $XSLTPROC: /path/to/xsltproc binary
$XSL_SHEET: XSL Sheet for MobyMessage Parsing
$TMP_DIR: /where
Title : getInputID Usage : my $query_id =getInputID($rh_query); Prerequisite : Function : Return query_id of a query from getInputs Returns : $query_id Args : $rh_query: query HASHREF structure from getInputs Globals : none
Title : getArticles
Usage : my @a_input_articles =getArticles($rh_query);
Prerequisite :
Function : For a query from getInputs, retrieve list of articles
represented by a ARRAYREF corresponding to REF(articleName, articlePerlStructure)
Returns : @a_input_articles: ARRAY of articles ARRAYREF
Args : $rh_query: query HASHREF structure from getInputs
Globals : none
Title : getCollectedSimples
Usage : my @a_simple_articles =getCollectedSimples($rh_collection_article);
Prerequisite :
Function : For a collection query from getArticles, retrieve list of
simple articles
Returns : @a_simple_articles: ARRAY of articles HASHREF
Args : $rh_collection_article: collection article HASHREF structure from getArticles
Globals : none
Title : getCrossReferences
Usage : my @a_crossreferences =getCrossReferences($rh_simple_article);
Prerequisite :
Function : Takes a simple article structure (from getArticles or getCollectedSimples)
and retrieve the list of crossreferences HASHREF
Returns : @a_crossreferences: ARRAY of crossreferences HASHREF
Args : $rh_simple_article: simple article HASHREF structure from getArticles or getCollectedSimples
Globals : none
Title : getProvisionInformation
Usage : my @a_pib =getProvisionInformation($rh_simple_article);
Prerequisite :
Function : Takes a simple article structure (from getArticles or getCollectedSimples)
and retrieve the list of Provision Information HASHREF
Returns : @a_pib: ARRAY of provisionInformation HASHREF
Args : $rh_simple_article: simple article HASHREF structure from getArticles or getCollectedSimples
Globals : none
Title : getObjectHasaElements
Usage : my @a_hasa_elements =getObjectHasaElements($rh_simple_article);
Prerequisite :
Function : Takes a simple article structure (from getArticles or getCollectedSimples)
and retrieve the list of "HASA" element HASHREF
Returns : @a_hasa_elements: ARRAY of "HASA" element HASHREF
Args : $rh_object: simple article HASHREF structure from getArticles or getCollectedSimples
Globals : none
Title : getObjectType Usage : my $object_type =getObjectType($rh_object); Prerequisite : Function : Returns object MOBY class/type Returns : $object_type: object MOBY class/type Args : $rh_object: simple article (object) HASHREF structure from getArticles,getCollectedSimples or getObjectHasaElements Globals : none
Title : getObjectName Usage : my $object_name =getObjectName($rh_object); Prerequisite : Function : Returns object moby:articleName Returns : $object_name: moby:articleName Args : $rh_object: simple article (object) HASHREF structure from getArticles,getCollectedSimples or getObjectHasaElements Globals : none
Title : getObjectNamespace Usage : my $object_namespace =getObjectNamespace($rh_object); Prerequisite : Function : Returns object moby:namespace Returns : $object_name: moby:namespace Args : $rh_object: simple article (object) HASHREF structure from getArticles,getCollectedSimples or getObjectHasaElements Globals : none
Title : getObjectContent
Usage : my $object_content =getObjectContent($rh_object);
Prerequisite :
Function : Returns object content (using HTML::Entities::decode)
Warning: this content could contain emptylines if
your objects contains Crossreferences or Hasa Elements ...
Returns : $object_content: object content (decoded using HTML::Entities::decode)
Args : $rh_object: simple article (object) HASHREF structure from getArticles,getCollectedSimples or getObjectHasaElements
Globals : none
Title : getObjectXML Usage : my $object_xml =getObjectXML($rh_object); Prerequisite : Function : Returns full object moby:xml string Returns : $object_xml: object moby:xml string Args : $rh_object: simple article (object) HASHREF structure from getArticles,getCollectedSimples or getObjectHasaElements Globals : none
Title : getObjectId Usage : my $object_id =getObjectId($rh_object); Prerequisite : Function : Returns object moby:id Returns : $object_id: moby:id Args : $rh_object: simple article (object) HASHREF structure from getArticles,getCollectedSimples or getObjectHasaElements Globals : none
Title : getParameter
Usage : my ($parameter_name,$parameter_value) =getParameter($rh_article);
Prerequisite :
Function : Returns parameter name an value for a Secondary aricle
Returns : $parameter_name
$parameter_value
Args : $rh_article: secondary article HASHREF structure from getArticles
Globals : none
Title : getNodeContentWithArticle
Usage : my $content = getNodeContentWithArticle($rh_query, $article_type, $article_name)
Prerequisite :
Function : inside a mobyData bloc (structured in $rh_query),
look for an article of a defined type (Simple, Collection or Parameter).
Foreach matching article, search for an object named $article_name.
If found, return its content.
Returns : $content: content of article requested
Args : $rh_query: query HASHREF structure from getInputs
$article_type: 'Simple/Collection/Parameter'
$article_name: attribute moby:articleName
Globals :
Title : isSimpleArticle Usage : isSimpleArticle($rh_article) Prerequisite : Function : Test if an article is a moby:Simple Returns : $response: BOOLEAN Args : $rh_article: article HASHREF structure from getArticles Globals : none
Title : isCollectionArticle Usage : isCollectionArticle($rh_article) Prerequisite : Function : Test if an article is a moby:Collection Returns : $response: BOOLEAN Args : $rh_article: article HASHREF structure from getArticles Globals : none
Title : isSecondaryArticle Usage : isSecondaryArticle($rh_article) Prerequisite : Function : Test if articleType is moby:Parameter (secondary article) Returns : $response: BOOLEAN Args : $rh_article: article HASHREF structure from getArticles Globals : none
Title : _AnalyseSimple
Usage : _AnalyseSimple($simple_bloc)
Prerequisite :
Function : Analyse a "Simple Bloc" from XSL transformation parsing
Build a $rh_simple_article structure with fields:
'object_name' => moby:articleName
'object_type' => moby:Class
'object_namespace' => moby:namespace
'object_id' => moby:id
'object_content' => text content of simple article
'object_xml' => full xml content of article
'object_hasa' => ARRAYREF of hasa elements
(each one is structured in a same
structured hash (recursivity)
'object_crossreference' => ARRAYREF of crossreferences objects
(each one is structured in a hash with fields
'type', 'id', 'namespace')
Returns : $rh_simple: article HASHREF Args : $simple_bloc: from parsing of a "simple" XSLT transformation Globals : none
name : simpleResponse
function : wraps a simple article in the appropriate (mobyData) structure
usage : $resp .= &simpleResponse($object, 'MyArticleName', $queryID);
args : (in order)
$object - (optional) a MOBY Object as raw XML
$article - (optional) an articeName for this article
$query - (optional, but strongly recommended) the queryID value for the
mobyData block to which you are responding
notes : as required by the API you must return a response for every input.
If one of the inputs was invalid, you return a valid (empty) MOBY
response by calling &simpleResponse(undef, undef, $queryID) with no arguments.
name : collectionResponse
function : wraps a set of articles in the appropriate mobyData structure
usage : return responseHeader . &collectionResponse(\@objects, 'MyArticleName', $queryID) . responseFooter;
args : (in order)
\@objects - (optional) a listref of MOBY Objects as raw XML
$article - (optional) an articeName for this article
$queryID - (optional, but strongly recommended) the mobyData ID
to which you are responding
notes : as required by the API you must return a response for every input.
If one of the inputs was invalid, you return a valid (empty) MOBY
response by calling &collectionResponse(undef, undef, $queryID).
name : complexResponse
function : wraps a set of articles in the one mobyData structure
usage : return responseHeader . &complexResponse(\@a_article_structures, $queryID) . responseFooter;
args : (in order)
\@a_article_structures - (optional) a listref of structured articles
%h_article = (
article_type => 'collection/simple',
article_content => 'MOBY XML formatted content',
article_name => 'articleName attribut')
$queryID - (optional, but strongly recommended) the mobyData ID
to which you are responding
=cut
sub complexResponse { my ($ra_data, $qID) = @_;
$ra_data ||= [];
$qID ||= '';
unless ((ref($ra_data) =~ /array/i) && $ra_data->[0])
{ # we're expecting an arrayref as input data,and it must not be empty
return "<moby:mobyData moby:queryID='$qID'/>";
}
my $moby_data_content = '';
foreach my $rh_data_block (@{$ra_data})
{
my $article_name = $rh_data_block->{article_name};
my $article_content = $rh_data_block->{article_content};
if ($rh_data_block->{article_type} =~ /collection/i)
{
my $collection_content = "<moby:Collection moby:articleName='$article_name'>\n";
if ((ref($article_content) =~ /array/i) && $article_content->[0])
{
foreach my $simple_element (@{$article_content})
{
$collection_content .= "\t<moby:Simple>\n\t$simple_element\n\t</moby:Simple>\n";
}
}
else
{
$collection_content .= "\t<moby:Simple/>\n";
}
$collection_content .= "</moby:Collection>\n";
$moby_data_content .= $collection_content;
}
else
{
my $simple_content = "<moby:Simple moby:articleName='$article_name'>\n\t$article_content\n</moby:Simple>";
$moby_data_content .= $simple_content;
}
}
return "<moby:mobyData moby:queryID='$qID'>\n\t$moby_data_content\n</moby:mobyData>\n";
}
function: print the XML string of a MOBY response header +/- serviceNotes +/- Exceptions
usage:
responseHeader('illuminae.com')
responseHeader(
-authority => 'illuminae.com',
-note => 'here is some data from the service provider'
-exception=>'an xml encoded exception string')
args: a string representing the service providers authority URI, OR a set of named arguments with the authority and the service provision notes which can include already xml encoded exceptions
caveat :
notes: returns everything required up to the response articles themselves. i.e. something like:
<?xml version='1.0' encoding='UTF-8'?>
<moby:MOBY xmlns:moby='http://www.biomoby.org/moby'>
<moby:Response moby:authority='http://www.illuminae.com'>
function: wraps a Biomoby Exception with all its parameters into the appropiate MobyData structure
usage:
encodeException(
-refElement => 'refers to the queryID of the offending input mobyData',
-refQueryID => 'refers to the articleName of the offending input Simple or Collection'
-severity=>'error'
-exceptionCode=>'An error code '
-exceptionMessage=>'a human readable description for the error code')
args:the different arguments required by the mobyException API severity can be either error, warning or information valid error codes are decribed on the biomoby website
notes: returns everything required to use for the responseHeader:
<moby:mobyException moby:refElement='input1' moby:refQueryID='1' moby:severity =''>
<moby:exceptionCode>600</moby:exceptionCode>
<moby:exceptionMessage>Unable to execute the service</moby:exceptionMessage>
</moby:mobyException>
name : responseFooter
function : print the XML string of a MOBY response footer
usage : return responseHeader('illuminae.com') . $DATA . responseFooter;
notes : returns everything required after the response articles themselves
i.e. something like:
</moby:Response>
</moby:MOBY>
Title : _IsCollection
Usage : _IsCollection($article_type)
Prerequisite :
Function : Compares a string to string 'collection'
Remove namespace 'moby:' from parameter string
Case insensitive
Returns : BOOLEAN
Args : $articletype: a string
Globals : none
Title : _IsSimple
Usage : _IsSimple($article_type)
Prerequisite :
Function : Compares a string to string 'simple'
Remove namespace 'moby:' from parameter string
Case insensitive
Returns : BOOLEAN
Args : $articletype: a string
Globals : none
Title : _IsSecondary
Usage : _IsSecondary($article_type)
Prerequisite :
Function : Compares a string to string 'parameter'
Remove namespace 'moby:' from parameter string
Case insensitive
Returns : BOOLEAN
Args : $articletype: a string
Globals : none
Title : _AnalyseServiceNotes
Usage : _AnalyseServiceNotes($simple_bloc)
Prerequisite :
Function : Analyse a "Simple Bloc" from XSL transformation parsing
Build a $rh_simple_article structure with fields:
'object_name' => moby:articleName
'object_type' => moby:Class
'object_namespace' => moby:namespace
'object_id' => moby:id
'object_content' => text content of simple article
'object_xml' => full xml content of article
'object_hasa' => ARRAYREF of hasa elements
(each one is structured in a same
structured hash (recursivity)
'object_crossreference' => ARRAYREF of crossreferences objects
(each one is structured in a hash with fields
'type', 'id', 'namespace')
Returns : $services_notes: article HASHREF
$ra_exceptions: article HASHREF
Args : $service_notes_bloc: from parsing of a "serviceNotes" XSLT transformation
Globals : none