[Mged-mage-java] Audits for MAGE object

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Hi David,

To be a little more specific about Joe's reply. The MAGE-OM, from which =20=

both Bio::MAGE and MAGE-ML are derived, does not actually contain a =20
MAGE class. It is understood that the MAGE class is a container for all =20=

the packages and classes defined within the MAGE-OM UML model.

As such, the rules to produce this top-level MAGE class did not follow =20=

the normal inheritance driven production rules and is in fact ad-hock. =20=

Hence the only available methods/attributes are the "identifier" and =20
the various methods to get/set the packages.

But as far as the DTD is concerned, the production rules for the MAGE =20=

element call for the ENTITY %Identifiable_content, which in point of =20
fact is the bit of XML that you gave as an example.

Thus there is a disconnect between the DTD and the class production =20
rules. BTW, this is also a problem for MAGE-Java.

Thanks for pointing this out. Anyone interested in putting in some time =20=

to fix this?

For the time being, you can assign the user role "data_coder" from the =20=

MGED Ontology and it is understood that it is this person that created =20=

the MAGE doc.

http://mged.sourceforge.net/ontologies/MGEDontology.php#data_coder

Angel

On Wednesday, August 13, 2003, at 09:55 AM, White, Joseph A. wrote:

> Hi David,
>
> I think you have some of the objects out of order.  The main interface =
=20
> is:
>
> Extendable  <--  Describable  <--  Identifiable
>     |                 |
> NameValueType       Audit
>
> So if you want to add an Audit object, you need to use Desribable, but
> Describable is an abstract class, so you have to call its methods =20
> through
> MAGE objects that inherit from it, i.e. instantiate an Identifiable =20=

> object.
> Then you should be able to use 'setAuditTrail($audit_object)'.
>
> The MAGE object simply doesn't have the methods you want.
>
> If you have access to the project site on sourceforge, you may want to =
=20
> get
> the UML images for MAGEstk.  This may help.
>
> Joe White
> TIGR
>
>
> -----Original Message-----
> From: David J Craigon [mailto:dav...@ar...]
> Sent: Wednesday, August 13, 2003 6:34 AM
> To: mge...@li...
> Cc: Sean [NASC]
> Subject: Re: [Mged-mage-perl] Audits for MAGE object
>
>
> It's not the creating the people I have problem with. Perhaps I should
> be more verbose. I want to create this valid MAGE-ML using MAGEstk...
>
>
> <?xml version=3D"1.0" encoding=3D"UTF-8"?>
> <!DOCTYPE MAGE-ML SYSTEM "MAGE-ML.dtd">
> <MAGE-ML identifier=3D"formailinglist">
>
> <AuditTrail_assnlist>
> <Audit date=3D"2003-08-11" action=3D"creation">
> <Performer_assnref>
> <Person_ref identifier=3D"JRandom"/>
> </Performer_assnref>
> </Audit>
> </AuditTrail_assnlist>
>
>
>    <AuditAndSecurity_package>
>      <Contact_assnlist>
>        <Person email=3D"ra...@ra..." firstName=3D"J. Random"
> midInitials=3D"" lastName=3D"Hacker" identifier=3D"JRandom" name=3D"J. =
Random
> Hacker" phone=3D"+44 11 11 88">
>          <Roles_assnlist>
>            <OntologyEntry category=3D"Roles" =20
> value=3D"example"></OntologyEntry>
>          </Roles_assnlist>
>        </Person>
>      </Contact_assnlist>
>    </AuditAndSecurity_package>
> </MAGE-ML>
>
>
> As you can see, this MAGE-ML creates one person object. This person is
> registered as the creator of this piece of MAGE-ML in the AuditTrail.
>
>
> Now in the perldoc for Bio::MAGE, it says that...
>
> "
> CLASSES
>         The Bio::MAGE module contains the following Bio::MAGE classes:
>
>         =B7 Extendable
>         =B7 Identifiable
>         =B7 Describable
>         =B7 NameValueType
> "
>
> So I think that means that the MAGE object is supposed to inherit from
> Identifiable. That's what I expect. However, I can't call any of the
> Identifiable member functions from the MAGE object. So:
>
> my $foo=3DBio::MAGE->new();
>
> $foo->setAuditTrail(....);
>
> doesn't work. Also the MAGE object has none of the Identifiable slots.
>
> So that's my problem.
>
> 	Hope I've been clear.
> 		David, NASC
>
>
>
>
>
>
>
>
> White, Joseph A. wrote:
>> Hi David,
>>
>> I think these are part of the AuditAndSecurity_package.  We usually =20=

>> add
>> these to the Security object.  I suppose you could add them to any =20=

>> object,
>> but the AASP was meant to describe the MAGE document as a whole, so =
it
> makes
>> sense to me to add them in that package.
>>
>> Joe
>>
>>
>> -----Original Message-----
>> From: David J Craigon [mailto:dav...@ar...]
>> Sent: Monday, August 11, 2003 8:17 AM
>> To: mge...@li...
>> Subject: [Mged-mage-perl] Audits for MAGE object
>>
>>
>> Hi there,
>> 	I'm using MAGEstk perl. How do I create Audit objects for the =
MAGE
>> object itself? According to the docs it should inherit from =20
>> Describable
>> and should have an AuditTrail slot, but this doesn't seem to work. =
Any
>> help appreciated.
>>
>> David
>>
>>
>>
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