[kepler-users] Workflow XML validator using JDOM

Christopher Brooks cxh at eecs.berkeley.edu
Tue Jan 12 12:22:02 PST 2010 

Hi Josep,
I'm not an XML expert, but my understanding is that things
inside a <configure> tag is #PCDATA, which should not be interpreted against the DTD?
http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd
has:
<!ELEMENT configure (#PCDATA)>

For information about the configure tag, see page 220 of Volume 1 of the Ptolemy II Design Doc at
http://www.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-28.html:
--start
A second, much more flexible mechanism is provided for parameterizing entities.  A configure
element can be used to specify a relative or absolute URL pointing to a file that configures the entity,
or it can be used to include the configuration information in line. That information need not be MoML
information. It need not even be XML, and can even be binary encoded data (although binary data cannot
be in line; it must be in an external file). For example,
<entity name="sink" class="ptolemy.actor.lib.SequencePlotter">
<configure source="url"/>
</entity>
Here, url can give the name of a file containing data, or a URL for a remote file. (For the Sequence-
Plotter actor, that external data will have PlotML syntax; PlotML is another XML schema for configuring
plotters.) Configure information can also be given in the body of the MoML file as follows:

<entity name="sink" class="ptolemy.actor.lib.SequencePlotter">
<configure>
configure information
</configure>
</entity>
With the above syntax, the configure information must be textual data. It can contain XML markup
with only one restriction: if the tag “</configure>” appears in the textual data, then it must be preceeded
by a matching “<configure>”. That is, any configure elements in the markup must have balanced
start and end tags.

You can give both a source attribute and in-line configuration information, as in the following:

<entity name="sink" class="ptolemy.actor.lib.SequencePlotter">
<configure source="url">
configure information
</configure>
</entity>
In this case, the file data will be passed to the application first, followed by the in-line configuration
data.
In Ptolemy II, the configure element is supported by any class that implements the Configurable
interface. That interface defines a configure() method that accepts an input stream. Both external file
data and in-line data are provided to the class as a character stream by calling this method.
There is a subtle limitation with using markup within the configure element. If any of the elements
within the configure element match MoML elements, then the MoML DTD will be applied to assign
default values, if any, to their attributes. Thus, this mechanism works best if the markup within the
configure element is not using an XML schema that happens to have element names that match those
in MoML. Alternatively, if it does use MoML element names, then those elements are used with their
MoML meaning. This limitation can be fixed using XML namespaces, something we will eventually
implement.
--end--

My guess is that JDOM needs to be adjusted so that it does not
try to interpret the #PCDATA?  A quick google search did not bring
up anything.

You could also try running JDOM on a model that has a Ptolemy PlotML xml in a configure tag.
For example,
http://ptolemy.eecs.berkeley.edu/ptolemyII/ptIIlatest/ptII/ptolemy/domains/sdf/demo/Butterfly/Butterfly.xml
has

     <entity name="XY Plotter" class="ptolemy.actor.lib.gui.XYPlotter">
         <property name="fillOnWrapup" class="ptolemy.data.expr.Parameter" value="true">
         </property>
         <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={258, 206, 500, 344}, maximized=false}">
         </property>
         <property name="_plotSize" class="ptolemy.actor.gui.SizeAttribute" value="[500, 300]">
         </property>
         <property name="startingDataset" class="ptolemy.data.expr.Parameter" value="0">
         </property>
         <property name="_location" class="ptolemy.kernel.util.Location" value="[488.5, 265.5]">
         </property>
         <configure>
<?plotml <!DOCTYPE plot PUBLIC "-//UC Berkeley//DTD PlotML 1//EN"
"http://ptolemy.eecs.berkeley.edu/xml/dtd/PlotML_1.dtd">
<plot>
<title></title>
<xRange min="-2.4845557281711192" max="3.9293144658408363"/>
<yRange min="-3.6505369457601655" max="3.6505369457601127"/>
<noGrid/>
</plot>?>
         </configure>
     </entity>

It could be that it would be better if the dtd was declared in <svg>...</svg> example,
but I'm no expert in this area.  It could be that by definition, a validating parser
tries to validate #PCDATA.

_Christopher




On 1/12/10 11:25 AM, Chad Berkley wrote:
> Hi Josep,
>
> I'll let Christopher Brooks explain why it's not in the DTD (the ptolemy
> project controls the MoML DTD). I can tell you that the <svg> element is
> used to set SVG icons in ptolemy. This attribute is not used (to my
> knowledge) in kepler since we have our own icon set.
>
> chad
>
>
> Josep Morer Muñoz wrote:
>> Hi all,
>>
>> I have build a XML validator using JDOM. I am trying to validate
>> Kepler workflows using DTD file
>> (http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd) but in most of
>> cases the validator fails when the workflow has parameters, for
>> example 02-LoktaVolterraPrey.xml in getting-started directory. The
>> validator fails because finds an unknown tag in XML file named *svg*.
>>
>> For example:
>>
>> <entity name="02-LotkaVolterraPredatorPrey"
>> class="ptolemy.actor.TypedCompositeActor">
>> <property name="_createdBy"
>> class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
>> </property>
>> <property name="r" class="ptolemy.data.expr.Parameter" value="2">
>> <property name="_hideName"
>> class="ptolemy.kernel.util.SingletonAttribute">
>> </property>
>> <property name="_icon" class="ptolemy.vergil.icon.ValueIcon">
>> </property>
>> <property name="_smallIconDescription"
>> class="ptolemy.kernel.util.SingletonConfigurableAttribute">
>> <configure>
>> <svg>
>> <text x="20" style="font-size:14; font-family:SansSerif; fill:blue"
>> y="20">-P-</text>
>> </svg>
>> </configure>
>> </property>
>> <property name="_editorFactory"
>> class="ptolemy.vergil.toolbox.VisibleParameterEditorFactory">
>> </property>
>> <property name="_location" class="ptolemy.kernel.util.Location"
>> value="410.0, 50.0">
>> </property>
>> </property>
>> <property name="a" class="ptolemy.data.expr.Parameter" value="0.1">
>> <property name="_icon" class="ptolemy.vergil.icon.ValueIcon">
>> </property>
>> <property name="_smallIconDescription"
>> class="ptolemy.kernel.util.SingletonConfigurableAttribute">
>> <configure>
>> <svg>
>> <text x="20" style="font-size:14; font-family:SansSerif; fill:blue"
>> y="20">-P-</text>
>> </svg>
>> ...
>>
>> This element (red highlighted) is not defined in DTD file. Can it be
>> avoided? What does this tag mean?
>>
>> Thanks for your help.
>> --
>> Josep
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Kepler-users mailing list
>> Kepler-users at kepler-project.org
>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users

-- 
Christopher Brooks, PMP                       University of California
CHESS Executive Director                      US Mail: 337 Cory Hall
Programmer/Analyst CHESS/Ptolemy/Trust        Berkeley, CA 94720-1774
ph: 510.643.9841 fax:510.642.2718	      (Office: 545Q Cory)
home: (F-Tu) 707.665.0131 cell: 707.332.0670

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