[MOBY-guts] biomoby commit
Pieter Neerincs
pieter at dev.open-bio.org
Wed Nov 21 16:29:19 UTC 2007
pieter
Wed Nov 21 11:29:18 EST 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv31692
Modified Files:
InformationBlocks.html MessageStructure.html
MobyCentralObjects.html XMLPayloads.html
Added Files:
Authorities.html
Log Message:
Added documentation on Authorities and their URIs.
moby-live/Docs/MOBY-S_API Authorities.html,NONE,1.1 InformationBlocks.html,1.8,1.9 MessageStructure.html,1.11,1.12 MobyCentralObjects.html,1.10,1.11 XMLPayloads.html,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.html 2007/02/22 16:22:24 1.8
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.html 2007/11/21 16:29:18 1.9
@@ -105,13 +105,13 @@
<li> id: This is the ID within that namespace (as in the base Object)
</li>
-<li> authURI: the Authority of a service provider who can execute an
+<li> authURI: the <a href='Authorities.html'>Authority</a> of a service provider who can execute an
appropriate service on the piece of data referred to by this
cross-reference such that the intent of the cross-reference will be
realized. </li>
<li> serviceName: the name of the MOBY Service provided by that
-Authority that does the appropriate transaction. </li>
+<a href='Authorities.html'>Authority</a> that does the appropriate transaction. </li>
<li> xrefType: a term indicating the semantic type of this cross-reference.</li>
@@ -129,7 +129,8 @@
<p>All components are required, with the exception of the human readable
description. The namespace and id attributes fulfil the same role as
-their counterparts in the Object style cross-reference. The authURI
+their counterparts in the Object style cross-reference.
+The <a href='Authorities.html'>authURI</a>
and serviceName components together act as a unique identifier to a
particular MOBY Service that the current service provider suggests you
execute using this cross-reference (namespace/id) in order to
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/11/21 23:04:27 1.11
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2007/11/21 16:29:18 1.12
@@ -84,8 +84,8 @@
</p>
<p>
-This is <em>regardless</em> of the URI for the service provider! This is
-useful because the same service might be available from several
+This is <em>regardless</em> of the <a href='Authorities.html'>URI for the service provider</a>!
+This is useful because the same service might be available from several
providers. If they all use the same URI, then a computer (or human)
can infer that they are equivalent, and swap one for the other, based
on availability, or other criteria.
@@ -107,7 +107,7 @@
<Category>moby</Category>
<serviceName>retrieveSequence</serviceName>
<serviceType>Retrieve</serviceType>
- <authURI>services.serviceprovider.org</authURI>
+ <authURI><a href='Authorities.html'>services.serviceprovider.org</a></authURI>
<URL>http://serviceprovider.org/getService.pl</URL>;
<contactEmail>markw at illuminae.com</contactEmail>
<authoritativeService>0</authoritativeService>
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.html,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.html 2007/02/22 16:22:24 1.10
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.html 2007/11/21 16:29:18 1.11
@@ -94,7 +94,7 @@
To query MOBY Central, you fill out the relevant elements of a Query
Ojbect. These include the input and/or output data Classes (by name
from the Class ontology), the Service-type (by name from the
-Service-type ontology), the authority (service provider URI), or any
+Service-type ontology), the <a href='Authorities.html'>authority (service provider URI)</a>, or any
number of keywords that must appear in the service description.
<ul>
@@ -167,7 +167,7 @@
</outputObjects>
<serviceType>ServiceTypeTerm</serviceType>
<Category>moby</Category>
- <authURI>desired.service.provider</authURI>
+ <authURI><a href='Authorities.html'>desired.service.provider</a></authURI>
<signatureURL>http://location.to/service/description</signatureURL>
<serviceName>MyServiceName</serviceName>;
<expandObjects>1|0</expandObjects>
@@ -194,7 +194,7 @@
<pre class=MOBYcode>
<Services>
- <Service authURI="authority.URI.here" serviceName="MyService"
+ <Service authURI="<a href='Authorities.html'>authority.URI.here</a>" serviceName="MyService"
lsid='urn:lsid:authority.uri:serviceinstance:id'>
<serviceType lsid='urn:lsid:authority.uri:servicetype:OntologyTerm'>
Ontology_Term
@@ -220,9 +220,9 @@
</Services>
</pre>
-The "Service" XML element, contains the attributes of authority URI
+The "Service" XML element, contains the attributes of <a href='Authorities.html'>authority URI</a>
(authURI), service name (serviceName), and the LSID representing the
-service instance; the combination of authURI and serviceName is
+service instance; the combination of <a href='Authorities.html'>authURI</a> and serviceName is
sufficient to unambiguously describe any MOBY service instance in a
MOBY Central registry. Thus these are used to retrieve the service
definition using the MOBY Central <em>retrieveService</em> procedure
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2007/06/07 15:30:01 1.20
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2007/11/21 16:29:18 1.21
@@ -242,7 +242,7 @@
currently only 'moby' services are fully supported -->
<serviceName>YourServiceNameHere</serviceName>
<serviceType>TypeOntologyTerm</serviceType>
- <authURI>your.URI.here</authURI>
+ <authURI><a href='Authorities.html'>your.URI.here</a></authURI>
<signatureURL> http://some.URL.org/path/to/RDF/file </signatureURL>
<URL>http://URL.to.your/Service.script</URL>;
<contactEmail>your_name at contact.address.com</contactEmail>
@@ -293,11 +293,11 @@
<ul>
<li>If that RDF document contains a new Signature RDF, that new service (if valid) will be registered</li>
<ul>
- <li>An new service is recognized by the presence of a novel authorityURI + serviceName (predicates dc:publisher and mygrid:hasServiceNameText) in a mygrid:serviceDescription block of the <a href="http://biomoby.open-bio.org/index.php/for-developers/moby_extensions/moby_metadata#SIs">Signature RDF</a> document</li>
+ <li>An new service is recognized by the presence of a novel <a href='Authorities.html'>authorityURI</a> + serviceName (predicates dc:publisher and mygrid:hasServiceNameText) in a mygrid:serviceDescription block of the <a href="http://biomoby.open-bio.org/index.php/for-developers/moby_extensions/moby_metadata#SIs">Signature RDF</a> document</li>
</ul>
<li>If the retrieved RDF document contains a modified Signature RDF, the currently-registered service will be updated in MOBY Central</li>
<ul>
- <li>An updated service is recognized by the presence of a known authorityURI + serviceName in a Signature RDF service description, where other parameters have been altered compared to what is in the MOBY Central registry</li>
+ <li>An updated service is recognized by the presence of a known <a href='Authorities.html'>authorityURI</a> + serviceName in a Signature RDF service description, where other parameters have been altered compared to what is in the MOBY Central registry</li>
<li><i>uncertain</i>: the Agent will refuse to modify the service if you do not also <b><i>modify your service's LSID</i></b>.</li>
</ul>
<li>If a Signature RDF is missing from the document, the service formerly described by that RDF will be deregistered from MOBY Central</li>
@@ -381,7 +381,7 @@
<h4>Input XML</h4>
<pre class=MOBYcode>
<retrieveService>
- <Service authURI="authority.URI.here" serviceName="MyService"/>
+ <Service authURI="<a href='Authorities.html'>your.URI.here</a>" serviceName="MyService"/>
</retrieveService>
</pre>
@@ -390,7 +390,7 @@
<ul>
<li> moby
<pre class=MOBYcode>
- <Service authURI="authority.URI.here" serviceName="MyService"
+ <Service authURI="<a href='Authorities.html'>your.URI.here</a>" serviceName="MyService"
lsid='urn:lsid:authority.uri:serviceinstance:id'>
<![CDATA[WSDL document here]]>
</Service>
@@ -420,7 +420,7 @@
<h4>Notes</h4>
<ul>
-<li> <var>AuthURI</var> and <var>serviceName</var> attributes are
+<li> <var><a href='Authorities.html'>authURI</a></var> and <var>serviceName</var> attributes are
sufficient to identify a unique service, and both are required in the
<Service/> element. </li>
@@ -450,7 +450,7 @@
<h4>Output XML</h4>
<pre class=MOBYcode>
<serviceProviders>
- <serviceProvider name="authority.URI.here"/>
+ <serviceProvider name="<a href='Authorities.html'>your.URI.here</a>"/>
...
</serviceProviders>
</pre>
@@ -483,7 +483,7 @@
<h4>Output XML</h4>
<pre class=MOBYcode>
<serviceNames>
- <serviceName name="serviceName" authURI='authority.info.here'
+ <serviceName name="serviceName" authURI="<a href='Authorities.html'>your.URI.here</a>"
lsid='urn:lsid:authority.uri:namespace:id'/>
...
</serviceNames>
@@ -492,9 +492,9 @@
<ul>
<li> Retrieves minimal information about all registered MOBY services </li>
<ul>
- <li>serviceName
- <li>authority
- <li>service instance LSID
+ <li>Name</li>
+ <li><a href='Authorities.html'>Authority</a></li>
+ <li>LSID</li>
</ul>
</ul>
@@ -509,7 +509,7 @@
<serviceType name="serviceName" lsid='urn:lsid:authority.uri:servicetype:id'>
<Description><![CDATA[free text description here]]></Description>
<contactEmail>email at address here</contactEmail>
- <authURI>authority.uri.here</authURI>
+ <authURI><a href='Authorities.html'>your.URI.here</a></authURI>
</serviceType>
...
</serviceTypes>
@@ -575,7 +575,7 @@
<objectType articleName="SomeName" lsid='urn:lsid:authority.uri:namespace:id'>ExistingObjectType</objectType>
</Relationship>
...
- <authURI>owner.URI.here</authURI>
+ <authURI><a href='Authorities.html'>your.URI.here</a></authURI>
<contactEmail>owner at their.address.com</contactEmail>
</retrieveObjectDefinition>
</pre>
@@ -596,7 +596,7 @@
<Namespace name="namespace" lsid='urn:lsid:authority.uri:namespace:id'>
<Description><![CDATA[free text description here]]></Description>
<contactEmail>email at address here</contactEmail>
- <authURI>authority.uri.here</authURI>
+ <authURI><a href='Authorities.html'>your.URI.here</a></authURI>
</Namespace>
...
</Namespaces>
@@ -743,7 +743,7 @@
...
</Relationship>
...
- <authURI>Your.URI.here</authURI>
+ <authURI><a href='Authorities.html'>your.URI.here</a></authURI>
<contactEmail>You at your.address.com</contactEmail>
</registerObjectClass>
</pre>
@@ -825,7 +825,7 @@
<registerServiceType>
<serviceType>NewServiceType</serviceType>
<contactEmail>your_name at contact.address.com</contactEmail>
- <authURI>Your.URI.here</authURI>
+ <authURI><a href='Authorities.html'>your.URI.here</a></authURI>
<Description>
<![CDATA[ human description of service type here]]>
</Description>
@@ -891,7 +891,7 @@
<registerNamespace>
<namespaceType>NewNamespaceHere</namespaceType>
<contactEmail>your_name at contact.address.com</contactEmail>
- <authURI>Your.URI.here</authURI>
+ <authURI><a href='Authorities.html'>your.URI.here</a></authURI>
<Description>
<![CDATA[human readable description]]>
</Description>
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