[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Thu Apr 15 14:38:22 UTC 2004
mwilkinson
Thu Apr 15 10:38:22 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv16304/Client
Modified Files:
CollectionArticle.html ServiceInstance.html SimpleArticle.html
Log Message:
updating all documentation that has gone out of sync with the code
moby-live/Perl/MOBY/Client CollectionArticle.html,1.1,1.2 ServiceInstance.html,1.7,1.8 SimpleArticle.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.html 2003/07/01 15:00:47 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.html 2004/04/15 14:38:22 1.2
@@ -1,8 +1,8 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<title>MOBY::Client::CollectionArticle - a small object describing a MOBY Collection input or output</title>
-<link rev="made" href="mailto:markw at illuminae.(none)" />
+<title>MOBY::Client::CollectionArticle - a small object describing the Collection articles from the findService Response message of MOBY Central</title>
+<link rev="made" href="mailto:markw at illuminae.com" />
</head>
<body style="background-color: white">
@@ -23,8 +23,11 @@
<li><a href="#articlename">articleName</a></li>
<li><a href="#simples">Simples</a></li>
<li><a href="#addsimple">addSimple</a></li>
+ <li><a href="#xml">XML</a></li>
+ <li><a href="#xml_dom">XML_DOM</a></li>
<li><a href="#issimple">isSimple</a></li>
<li><a href="#iscollection">isCollection</a></li>
+ <li><a href="#issecondary">isSecondary</a></li>
</ul>
</ul>
@@ -34,19 +37,52 @@
<p>
</p>
<h1><a name="name">NAME</a></h1>
-<p>MOBY::Client::CollectionArticle - a small object describing a MOBY Collection input or output</p>
+<p>MOBY::Client::CollectionArticle - a small object describing the Collection articles from the findService Response message of MOBY Central</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
+<p>experimental - please do not use in your code</p>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
+<p>This describes the Collection articles from either the findService Response of MOBY Central
+(i.e. the description of the service), or Collection articles
+as provided in a service invocation or response message
+(i.e. simple articles containing data)</p>
+<p>Basically it parses the following part of a findService response:</p>
+<pre>
+ <Collection articleName="foo">
+ <Simple>
+ <objectType>someNbject</objectType>
+ <Namespace>someNamespace</Namespace>
+ <Namespace>someNamespace2</Namespace>
+ </Simple>
+ <Simple>
+ <objectType>someNbject</objectType>
+ <Namespace>someNamespace</Namespace>
+ <Namespace>someNamespace2</Namespace>
+ </Simple>
+ </Collection></pre>
+<p>OR it parses the following part of a service invocation or response message:</p>
+<pre>
+ <Collection articleName="foo">
+ <Simple>
+ <SomeObject namespace='someNamespace' id='someID'>.....</SomeObject>
+ </Simple>
+ <Simple>
+ <SomeObject namespace='someNamespace' id='someID'>.....</SomeObject>
+ </Simple>
+ </Collection></pre>
+<p>The articleName is retrieved with ->articleName
+The contained Simples are retrieved as MOBY::Client::SimpleArticle objects
+using the ->Simples method call.</p>
<p>
</p>
<hr />
<h1><a name="authors">AUTHORS</a></h1>
+<p>Mark Wilkinson (markw at illuminae dot com)</p>
<p>
</p>
<hr />
@@ -59,8 +95,11 @@
Usage : my $IN = MOBY::Client::CollectionArticle->new(%args)
Function : create CollectionArticle object
Returns : MOBY::Client::SimpleArticle object
- Args : articleName => $articleName (optional)
- Simples => $objectType (required)</pre>
+ Args : either of the following two methods may be used to auto-generate the
+ object by passing the appropriate XML node as a string, or XML::DOM node object
+
+ XML => $XML
+ XML_DOM => $XML::DOM::NODE</pre>
<p>
</p>
<h2><a name="articlename">articleName</a></h2>
@@ -91,6 +130,24 @@
Arguments : a new MOBY::Client::SimpleArticle to add to collection</pre>
<p>
</p>
+<h2><a name="xml">XML</a></h2>
+<pre>
+ Title : XML
+ Usage : $SA = $SA->XML($XML)
+ Function : set/reset all parameters for this object from the XML
+ Returns : MOBY::Client::SimpleArticle
+ Arguments : (optional) XML fragment from and including <Simple>...</Simple></pre>
+<p>
+</p>
+<h2><a name="xml_dom">XML_DOM</a></h2>
+<pre>
+ Title : XML_DOM
+ Usage : $namespaces = $SA->XML_DOM($XML_DOM_NODE)
+ Function : set/reset all parameters for this object from the XML::DOM node for <Simple>
+ Returns : MOBY::Client::SimpleArticle
+ Arguments : (optional) an $XML::DOM node from the <Simple> article of a DOM</pre>
+<p>
+</p>
<h2><a name="issimple">isSimple</a></h2>
<pre>
Title : isSimple
@@ -100,7 +157,7 @@
get both Simple and Collection objects in your
Input and output lists, it is good to be able
to test what you have in-hand)
- Returns : 1 (true)</pre>
+ Returns : 0 (false)</pre>
<p>
</p>
<h2><a name="iscollection">isCollection</a></h2>
@@ -112,7 +169,16 @@
get both Simple and Collection objects in your
Input and output lists, it is good to be able
to test what you have in-hand)
- Returns : 0 for false</pre>
+ Returns : 1 (true)</pre>
+<p>
+</p>
+<h2><a name="issecondary">isSecondary</a></h2>
+<pre>
+ Title : isSecondary
+ Usage : $boolean = $IN->isSecondary()
+ Function : is this a SecondaryArticle type?
+ (yes, I know this is obvious)
+ Returns : 0 (true)</pre>
</body>
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/11/01 18:05:55 1.7
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2004/04/15 14:38:22 1.8
@@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>MOBY::Client::ServiceInstance - a small object describing a MOBY service</title>
-<link rev="made" href="mailto:markw at illuminae.(none)" />
+<link rev="made" href="mailto:markw at illuminae.com" />
</head>
<body style="background-color: white">
@@ -126,10 +126,10 @@
</p>
<h2><a name="input">input</a></h2>
<pre>
- Title : output
- Usage : $output = $Service->output($args)
+ Title : input
+ Usage : $input = $Service->input($args)
Args : (optional) listref of SimpleArticle and/or CollectionArticle objects
- Function : get/set output
+ Function : get/set input
Returns : listref of MOBY::Client::SimpleArticle
and/or MOBY::Client::CollectionArticle objects</pre>
<p>
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.html 2003/07/01 15:00:47 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.html 2004/04/15 14:38:22 1.2
@@ -1,8 +1,8 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
-<title>MOBY::Client::SimpleArticle - a small object describing a MOBY Simple input/output article</title>
-<link rev="made" href="mailto:markw at illuminae.(none)" />
+<title>MOBY::Client::SimpleArticle - a small object describing the Simple articles from the findService Response message of MOBY Central</title>
+<link rev="made" href="mailto:markw at illuminae.com" />
</head>
<body style="background-color: white">
@@ -23,9 +23,12 @@
<li><a href="#articlename">articleName</a></li>
<li><a href="#objecttype">objectType</a></li>
<li><a href="#namespaces">namespaces</a></li>
+ <li><a href="#xml">XML</a></li>
+ <li><a href="#xml_dom">XML_DOM</a></li>
<li><a href="#addnamespace">addNamespace</a></li>
<li><a href="#issimple">isSimple</a></li>
<li><a href="#iscollection">isCollection</a></li>
+ <li><a href="#issecondary">isSecondary</a></li>
</ul>
</ul>
@@ -35,19 +38,39 @@
<p>
</p>
<h1><a name="name">NAME</a></h1>
-<p>MOBY::Client::SimpleArticle - a small object describing a MOBY Simple input/output article</p>
+<p>MOBY::Client::SimpleArticle - a small object describing the Simple articles from the findService Response message of MOBY Central</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
+<p>experimental - please do not use in your code</p>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
+<p>This describes the Simple articles from either the findService Response of MOBY Central
+(i.e. the description of the service), or Simple articles
+as provided in a service invocation or response message
+(i.e. simple articles containing data)</p>
+<p>Basically it parses the following part of a findService response:</p>
+<p><Simple articleName='foo'>
+ <objectType>someNbject</objectType>
+ <Namespace>someNamespace</Namespace>
+ <Namespace>someNamespace2</Namespace>
+</Simple></p>
+<p>OR it parses the following part of a service invocation or response message:</p>
+<p><Simple articleName='foo'>
+ <SomeObject namespace='someNamespace' id='someID'>.....</SomeObject>
+</Simple></p>
+<p>The articleName is retrieved with ->articleName
+The <code>namespace(s)</code> are retrieved with ->namespaces
+The objectType is retrieved with ->objectType
+the id (if instantiated) is retrieved with ->id</p>
<p>
</p>
<hr />
<h1><a name="authors">AUTHORS</a></h1>
+<p>Mark Wilkinson (markw at illuminae dot com)</p>
<p>
</p>
<hr />
@@ -60,11 +83,11 @@
Usage : my $SA = MOBY::Client::SimpleArticle->new(%args)
Function : create SimpleArticle object
Returns : MOBY::Client::SimpleArticle object
- Args : articleName => $articleName (optional)
- objectType => $objectType (required)
- namespaces => \@namesapces (optional)
- XML_DOM => $XML_DOM node of the simple article (optional)
- XML => $XML XML string representing the simple article (optional)</pre>
+ Args : either of the following two methods may be used to auto-generate the
+ object by passing the appropriate XML node as a string, or XML::DOM node object
+
+ XML => $XML
+ XML_DOM => $XML::DOM::NODE</pre>
<p>
</p>
<h2><a name="articlename">articleName</a></h2>
@@ -94,6 +117,24 @@
Arguments : (optional) arrayref of namespace strings to set</pre>
<p>
</p>
+<h2><a name="xml">XML</a></h2>
+<pre>
+ Title : XML
+ Usage : $SA = $SA->XML($XML)
+ Function : set/reset all parameters for this object from the XML
+ Returns : MOBY::Client::SimpleArticle
+ Arguments : (optional) XML fragment from and including <Simple>...</Simple></pre>
+<p>
+</p>
+<h2><a name="xml_dom">XML_DOM</a></h2>
+<pre>
+ Title : XML_DOM
+ Usage : $namespaces = $SA->XML_DOM($XML_DOM_NODE)
+ Function : set/reset all parameters for this object from the XML::DOM node for <Simple>
+ Returns : MOBY::Client::SimpleArticle
+ Arguments : (optional) an $XML::DOM node from the <Simple> article of a DOM</pre>
+<p>
+</p>
<h2><a name="addnamespace">addNamespace</a></h2>
<pre>
Title : addNamespace
@@ -124,6 +165,15 @@
Input and output lists, it is good to be able
to test what you have in-hand)
Returns : 0 for false</pre>
+<p>
+</p>
+<h2><a name="issecondary">isSecondary</a></h2>
+<pre>
+ Title : isSecondary
+ Usage : $boolean = $IN->isSecondary()
+ Function : is this a SecondaryArticle type?
+ (yes, I know this is obvious)
+ Returns : 0 (true)</pre>
</body>
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