[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Wed Oct 22 10:29:09 EDT 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv7066/Perl/MOBY

Modified Files:
	Central.html 
Log Message:
updating documentation for the website

moby-live/Perl/MOBY Central.html,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html	2003/07/18 21:44:55	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html	2003/10/22 14:29:09	1.7
@@ -42,7 +42,7 @@
 		<li><a href="#retrievenamespaces">retrieveNamespaces</a></li>
 		<li><a href="#retrieveobject">retrieveObject</a></li>
 		<li><a href="#relationships">Relationships</a></li>
-		<li><a href="#dump">DUMP</a></li>
+		<li><a href="#dump_mysql">DUMP_MySQL</a></li>
 	</ul>
 
 	<li><a href="#internal_object_methods">Internal Object Methods</a></li>
@@ -92,13 +92,11 @@
          die ref $res ? $res-&gt;faultstring : $soap-&gt;transport-&gt;status, &quot;\n&quot;;
       };</pre>
 <pre>
- my $reg = $Central-&gt;registerService(&quot;
- );
- print &quot;success &quot;, $reg-&gt;success;
- print &quot;\nmessage &quot;, $reg-&gt;message;
- print &quot;\nregistration_id &quot;, $reg-&gt;registration_id;
- print &quot;\n\n&quot;;</pre>
-<p>----------------------------------------</p>
+ my $NAMES_XML = MOBY::Central-&gt;retrieveObjectNames;
+ print $NAMES_XML;
+ # ... do something with the XML
+ 
+----------------------------------------</pre>
 <p>
 </p>
 <hr />
@@ -633,8 +631,24 @@
  Returns   :    see input XML for registerObjectClass
  Input XML :
          &lt;retrieveObjectDefinition&gt;
-                         &lt;objectType&gt;ExistingObjectClassname&lt;/objectType&gt;
+                         &lt;obqjectType&gt;ExistingObjectClassname&lt;/objectType&gt;
                  &lt;/retrieveObjectDefinition&gt;</pre>
+<pre>
+ Ouptut XML :
+        &lt;retrieveObjectDefinition&gt;
+            &lt;objectType&gt;NewObjectType&lt;/objectType&gt;
+            &lt;Description&gt;&lt;![CDATA[
+                    human readable description
+                    of data type]]&gt;
+            &lt;/Description&gt;
+            &lt;Relationship relationshipType=&quot;RelationshipOntologyTerm&quot;&gt;
+               &lt;objectType articleName=&quot;SomeName&quot;&gt;ExistingObjectType&lt;/objectType&gt;
+            &lt;/Relationship&gt;
+            ...
+            ...
+            &lt;authURI&gt;owner.URI.here&lt;/authURI&gt;
+            &lt;contactEmail&gt;owner at their.address.com&lt;/contactEmail&gt;
+        &lt;/retrieveObjectDefinition&gt;</pre>
 <p>
 </p>
 <h2><a name="retrievenamespaces">retrieveNamespaces</a></h2>
@@ -692,6 +706,7 @@
  input XML :
         &lt;Relationships&gt;
            &lt;objectType&gt;$term&lt;/objectType&gt;
+           &lt;expandRelationship&gt;1|0&lt;/expandRelationship&gt;
            &lt;relationshipType&gt;$relationship_term&lt;/relationshipType&gt;
            ... more relationship types
            ...
@@ -699,6 +714,7 @@
  OR
         &lt;Relationships&gt;
            &lt;serviceType&gt;$term&lt;/serviceType&gt;
+           &lt;expandRelationship&gt;1|0&lt;/expandRelationship&gt;
            &lt;relationshipType&gt;$relationship_term&lt;/relationshipType&gt;
            ... more relationship types
            ...
@@ -728,10 +744,10 @@
   &lt;/Relationships&gt;</pre>
 <p>
 </p>
-<h2><a name="dump">DUMP</a></h2>
+<h2><a name="dump_mysql">DUMP_MySQL</a></h2>
 <pre>
- Title     :    DUMP
- Usage     :    ($central,$object,$service,$namespace,$relat) = $MOBY-&gt;DUMP()
+ Title     :    DUMP_MySQL
+ Usage     :    $SQL = $MOBY-&gt;DUMP_MySQL; ($central,$object,$service,$namespace,$relat) = @{$SQL};
  Function  :    return a mysql dump of each of the current MOBY Central databases
  Returns   :    an array of SQL strings that can be used to recreate the database locally
  Args      :    none</pre>
@@ -756,9 +772,7 @@
  Usage     :    @valid = $MOBY-&gt;_getValidServices($dbh, $sth_hash, $query)
  Function  :    execute the query in $query to return a non-redundant list of matching services
  Returns   :    list of response strings in wsdl
- Args      :    none
-
-</pre>
+ Args      :    none</pre>
 <p>
 </p>
 <h2><a name="_traverseservicedag">_traverseServiceDAG</a></h2>
@@ -768,9 +782,7 @@
  Function  :    starting from $serviceType, find all child services non-redundantly
                 by traversing the DAG.
  Returns   :    list of Service.id database entries.
- Args      :    none
-
-</pre>
+ Args      :    none</pre>
 <p>
 </p>
 <h2><a name="_traverseobjectdag">_traverseObjectDAG</a></h2>