[kepler-users] Workflow XML validator using JDOM

Matt Jones jones at nceas.ucsb.edu
Tue Jan 12 12:35:14 PST 2010 

Hi Christopher,

Actually, #PCDATA stands for *parsed* character data, and is explicitly the
type of element content that is parsed text (for additional markup and
entity substitutions, for example).  If you want configure to be plain text
and to not be parsed for markup, then it should be typed as CDATA content,
which is still character data, but is not parsed.  I think this has not been
an issue because in general you don't validate the MoML instance documents
against the DTD, but I suspect you will find a lot of validity errors if you
did.

Matt

2010/1/12 Christopher Brooks <cxh at eecs.berkeley.edu>

> 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
>
> _______________________________________________
> Kepler-users mailing list
> Kepler-users at kepler-project.org
> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>
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