[kepler-dev] Modifying MoML files

[Hogan, D. (GE Energy)]

Thanks Derik.  That answers another question that I had: since Kepler is
versioned and BackwardCompatibility is global, how do I associate
transformations with only certain versions?  I don't have an Initialize
class in our modules so I'll look into adding one.

Re: LSID.  Your approach makes sense.  Do you have any recommendations
on how I can get meaningful differences between kar files?  After I run
it through the filter, there are many trivial differences.  If I apply a
specific format to MoML files by running it through XSLT, will it break
anything?  For instance, I'm not sure where it decides the order for I/O
on actors in the GUI.  Is it from the XML or the order they are
initialized in Java?

-----Original Message-----
From: Derik Barseghian [mailto:barseghian at nceas.ucsb.edu] 
Sent: Tuesday, April 10, 2012 8:08 PM
To: Hogan, D. (GE Energy)
Cc: kepler-dev at kepler-project.org
Subject: Re: [kepler-dev] Modifying MoML files

I wouldn't take the approach of writing a script to unzip, process MoML,
and zip your KARs. I don't have much experience with the filters, but
Kepler utilizes them; I'd look into how it does. I think a better
approach would be to make your changes to your actor(s), addFilters to
Kepler's list(s) as you deem fit in your module's Intialize class, and
distribute a new version of your module. Users get the updated module,
open their old KARs, and the filters will be applied to the MoML (if the
user simply opens the KAR and makes no changes, they will be prompted to
save when closing since these changes have been automatically applied).
I believe this way you'll avoid issues to do with proper
versioning/identification of objects. Kepler maintains LSIDs and derived
from LSID lists for components, workflows and KARs. E.g. when you modify
an actor, its LSID revision is incremented, the workflow's LSID is
incremented, and when you save this workflow, the KAR gets a new LSID,
and its manifest is updated appropriately.


Derik

On Apr 10, 2012, at 4:05 PM, Christopher Brooks wrote:

> You've found the ptolemy/moml/filter classes which is how we handle
> sorts of changes at Berkeley.
> 
> My comments are interspersed with your message below.
> 
> On 4/10/12 10:02 AM, Hogan, D. (GE Energy) wrote:
>> What's the best way to modify MoML inside of kar files?  Should I use
>> ptolemy.moml.MoMLParser, some other class in Kepler, standard tools
>> (XSLT/DOM) or something else?
> Unfortunately, MoML is not well structured xml.  This is because
> of the <configure> tag.  There is something in either the kepler email
> archives or the ptolemy-hackers archives about this.
> 
> I have a test at ptolemy/configs/test/validDemos.tcl
> that strips out the <configure> tags and runs a validating parser on
the results.
> However, the problem is that you need those configure tags for
plotters etc.
> So, using a validating parser will not be much help.
> 
> You could use other XSLT tools as long as the tool does not require
valid xml.
> 
>> 
>> I'm trying to do two types of operations with MoML.  After I update
>> source code for actors, I want to have a way to update all of the
>> affected kar files.  This could be adding, removing or renaming ports
>> and parameters or changing types and class names across all local kar
>> files.  All of these operations appear to be supported as filters in
the
>> MoML parser.
> Right, the ptolemy/moml/filter classes are the way to go here.
> Let me know if the filters need any changes like accessor or reset
methods.
> You would need to write a script that unjars (I think) the .kar files,
updates
> the moml file and recreates the kar file.
> 
>>   The second task is doing a diff on MoML files without GUI
>> or documentation related elements.  The automated layout in the GUI
is
>> great, but small changes in the workflow can result in big changes in
>> the layout.   If I give a kar to someone and they update it, I want
to
>> be able to see what changes they made besides GUI placement or
>> documentation.  This also appears to be supported by MoMLParser since
>> there are filters to remove parts of the file.
> Right, ptolemy/moml/filter/RemoveGraphicalClasses.java will remove
> the gui xml.  That class has a main() method so that it can be run
from
> the command line.
> 
> To see if there are any changes, you could get part way there by
> using RemoveGraphicalClasses, then, if necessary removing the
> <configure> tags and then using tool to do a diff
>> When I tried ptolemy.moml.MoMLParser with
>> org.kepler.moml.filter.BackwardCompatibility.initialize(), I get a
lot
>> of unnecessary changes.  It would cause problems if I checked in the
>> MoML files and ran 'svn blame'.  I noticed there is a file
>> ptolemy-kepler-2.3/src/adm/bin/updatemoml which calls
>> ptolemy-kepler-2.3/src/adm/bin/updateMoMLFile.tcl and runs diff to
see
>> if there were any differences.  I don't think that would work
properly
>> on a MoML from Kepler because there would be many changes.
> 
> I had forgotten about org.kepler.moml.filter.BackwardCompatibility,
which
> is found at
./core/src/org/kepler/moml/filter/BackwardCompatibility.java
> 
> I'm not sure I totally understand your question, but are you saying
that the
> MoML files included in the Kepler .kar files change when the
Kepler-specific
> BackwardCompatibility filter is run on them?
> 
> In Ptolemy II, we don't run the BackwardCompatibility filter on all
the files
> before a release.  In other words - the ptII tree includes files that
would be
> different if the BackwardCompatibility filter was run on them.  We
partly
> do this so that we can test the filters.  Another reason is so that we
don't
> have arbitrary changes in the change log.  Running the
BackwardCompatibility
> filter would make a number of changes which would make using 'svn
blame'
> less useful.
> 
> You could either run the BackwardCompatibility filters on all the moml
files in the kar
> files and provide an updated release to your users or you could try
running
> the BackwardCompatibility filter after the fact and comparing the
output.
> In other words, for any given model, you would need to run the filter
on the
> moml file from the Kepler distribution and on the updated version.
> 
> Kar files probably have a versioning system associated with them.
> Ptolemy II updates the VersionAttribute in each file with the version
of the PtolemyII
> that is used.
> There is also ptolemy/vergil/kernel/attributes/IDAttribute.java, which
is not used
> very much, but could be used to store version information.
> 
> In general, library management is a big issue.  Ptolemy II uses Actor
Oriented Classes,
> where a model is declared to be a class definition and there are
derived instances
> that are what is actually run.  There are rules about what can be
updated or deleted.
> 
> _Christopher
>> 
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> 
> -- 
> 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                                (Office: 545Q Cory)
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> 
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