[Fuge-devel] Antw: Re: Antw: Re: [Flowcyt-fuge] Antw: Re: FUGE, FlowCyt
Simon Schafferer
The 2 errors occured when I used the original FuGE-v1-profile.mdzip from
the Hibernate-STK, however when I used the FuGE-v1-profile.mdzip from
fugeFlow I got 5 errors.
One can find the error log in the attachement.
Kind regards,
Simon
>>> Allyson Lister <allyson...@googlemail.com> 22.08.09 21.55 Uhr
>>>
Hi all,
These errors:
[Data::net.sourceforge.fuge::common::protocol::Protocol::protocol]:One-to-one
associations must have one side of the association indicating
aggregation
(aggregation defines the parent/owning entity).
2009-08-22 21:11:40,825 ERROR [AndroMDA] 2)
[Data::net.sourceforge.fuge::common::protocol::ProtocolApplication::protocolApplication]:One-to-one
associations must have one side of the association indicating
aggregation
(aggregation defines the parent/owning entity).
are part of the FuGE schema and not the flowcyt schema. I won't have
time to
look at this until Monday, but I'm sort of surprised there are any such
problems with FuGE, as the hibernate stk on its on works OK for me. I'll
check the associations in the hibernate stk on monday, though. Could it
be
that the this version the schema has a different version / slightly
modified
version of FuGE?
thanks :)
Allyson
2009/8/22 Simon Schafferer <Simon.Sc...@umit.at>
> Hi all,
>
> I tested the hibernate-stk installation with the new fugeflow.mdzip
file
> from Josef and unfortunately I got 2 model validation errors.
> One can find the error log in the attachement.
>
> Kind regards,
> Simon
>
> Thanks Allyson,
> that would actually be really helpful.
>
> I believe/hope I have located all the 1-to-1 associations and turned
> them into shared aggregations. However, based on Simon's log file,
some
> of these seemed to be within FuGE rather than the FCM extension... not
> sure about that. Unfortunately, I have no easy way to test that it
> solves all hybernate-stk related issues (no appropriate DBMS and most
> likely not enough experience with setting up the FuGE Hibernate STK
> database to get it running smoothly). So it would be great if you
could
> check it; the mdzip file is attached.
>
> Thanks a lot,
> Josef
>
> Max, I checked our uml->xsd and it still basically works, except there
> seems to be a minor issue with the VSL template: at two spots, it
> generates the "xsd:datatype.String" rather than just "xsd:string". It
is
> for the catalogNumber and cloneNumber. I am having a feeling that we
> used to have this issue before, not sure how/if we solved it, so I
just
> fixed these two manually. I also checked that the new XSD corresponds
to
> the old one and yes, it does (as long as you put in shared
aggregations
> - open diamonds; if you would replace these with composite
aggregations
> - closed diamonds - then the XSD would change quite a bit). I
validated
> our XML examples against the new XSD and it is all fine. The new files
> have been committed to our SVN.
>
>
>
>
> Allyson Lister wrote:
> > Hi all,
> >
> > If you need any more help once you've made the changes to the mdzip
> file, just let me know if I can help at all with the hibernate stk
side
> of things :)
> >
> > 2009/8/20 Josef Spidlen <jspi...@bccrc.ca>
> >
> > Hi Simon,
> > Ok, I'll look into that and let you know.
> >
> > Cheers,
> > Josef
> >
> >
> > Simon Schafferer wrote:
> > > Hi,
> > > I appreciate your offer to help us fixing the mdzip file. In
> fact, it
> > > would be of great help to us.
> > >
> > > Thanks in advance for your effort.
> > >
> > > Kind regards,
> > > Simon
> > >
> > >
> > >>>> "Yu Qian" <Yu....@UTSouthwestern.edu> 20.08.09 20.18 Uhr
>>>
> > >>>>
> > > I am not sure whether we have located the reason why FuGEFlow
> doesn't
> > > work with hibernate-stk. Will fixing the 1:1 association
solve
> the
> > > problem?
> > >
> > > The MIFlowCyt model in that link is not
up-to-date. Also it
> doesn't
> > > sufficiently re-use> > > Max
> > >
> > > ---------------------------------------------
> > > Yu (Max) Qian, Ph.D.
> > > Department of Pathology
> > > University of Texas Southwestern Medical Center
> > > Phone: (214) 648-4191 (direct)
> > > Email: yu....@UTSouthwestern.edu
> > >
> > >
> > >>>> Josef Spidlen <jspi...@bccrc.ca> 8/20/2009 12:24 PM >>>
> > >>>>
> > > Hi Simon,
> > > sorry to hear that.
> > >
> > >
> > > Indeed, the better solution is to modify the "FugeFlow.mdzip"
> file so
> > > that it works with the Hibernate-STK. The problem is that we
> don't
> > > know
> > > how to do this and it would also be beyond the scope of our
> work.We
> > > could try to help modifying the FugeFlow.mdzip to work with
> > > Hibernate-STK; however, if you feel that this is going beyond
> the scope
> > > of your work (and I can eventually see that), the MIFlowCyt
> object model
> > > could be an easier start. The only thing is that it may be in
> kind of a
> > > "draft form"... I believe we only used it as an internal
> document to
> > > formalize MIFlowCyt to help us map it on the FuGE concepts
later
> on.
> > >
> > > The file seems to be from October 2007 while the normative
> MIFlowCyt
> > > document is from Februar
> y 2008. I assume the delay was due to
> > > formalities rel> > check the model and extend it if it
does not
> cover all the
> concepts you
> > > need. I assume Olga would know more about it but she may be on
a
> > > maternity leave right now?
> > >
> > > Good luck and please let us know if there is anything we could
> do to
> > > help. If you still feel like giving FugeFlow.mdzip a try,
please
> let me
> > > know and I can try to fix the 1:1 associations.
> > >
> > > Cheers,
> > > Josef
> > >
> > >
> > > Simon Schafferer wrote:
> > >
> > > Dear Fuge and FugeFlow developers,
> > > Thanks for your help. We tried all your suggestions,
> unfortunately
> > > nothing worked.
> > >
> > > Another possibility we figured out, is to use the Hibernate
> mapping
> > > file of the Hibernate-STK as object model.
> > > Therefore we would write the FugeFlow extension on our own,
> according
> > > to
> > > Olga’s FuGE-motivated approach to encode MIFlowCyt into UML
> > > (http://wiki.ficcs.org/ficcs/MIFlowCyt_ObjectModel).
> > >
> > > What do yout think about this approach, is this in your
opinion
> a
> > > proper
> > > solution?
> > >
> > > Indeed, the better solution is to modify the "FugeFlow.mdzip"
> file so
> > > that it works with the Hibernate-STK. The problem is that we
> don't
> > > know
> > > how to do this and it would also be beyond the scope of our
> work.
> > >
> > > Kind regards,
> > > Simon
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > "Jones, Andy" <Andrew...@liverpool.ac.uk> (
> > > mailto:Andrew...@liverpool.ac.uk ) 06.08.09 10.31 Uhr >>>
> > > Hi Simon,
> > > I didn’t have a chance to look through your log file yet but
> based
> > > on
> > > Josef’s answer I think I can respond. I recall when developing
> the
> > > FuGE
> > > hibernate STK there was a problem with 1:1 associations that
> were not
> > > composite or aggregate (closed or open diamonds), because the
> > > processing
> > > software did not know in which direction to build the
> association (for
> > > foreign keys for the SQL perhaps) - even though the arrow
should
> give
> > > this away. I think my solution was to add aggregations (open
> diamond)
> > > on
> > > the non-arrow end of the association, since these don’t affect
> the
> > > generation of anything else. I’m sure there will be
other
> > > work-arounds
> > > if you don’t wan> > > Sent: 05 August 2009 20:17
> > > To: Simon Schafferer
> > > Cc: fuge-...@lists.sourceforge.net; FlowCyt FuGE; Benjamin
> > > Weidenholzer
> > > Subject: Re: [Flowcyt-fuge] [Fuge-devel] FUGE, FlowCyt
> > >
> > > Hi Simon,
> > >
> > > Based
> > > on your log file, it seems that there is only one error
> beingassociation indicating aggregation (aggregation defines the
> > > parent/owning entity). In the model, not all
> > > 1-1 associations are
> > > aggregations since "aggregations" do not really express the
type
> of
> > > these relations (i.e, they are one "part of the other").
> > > This wasn't a problem for us in order to derive the XML
schema;
> > > however,
> > > I guess it should be technically possible to twist the model a
> bit,
> > > add
> > > change the associations to aggregations and try again.
> > >
> > > In theory, I think hyperjaxb should work; however, it may
> require some
> > > tweaking as well. Specifically, it is relatively
straightforward
> to to
> > > generate FuGEFlow java classes and the persistence
> configuration;
> > > however, using the default settings, you will probably
encounter
> a few
> > > foreign key circularity dependencies that you will have to
> fight.
> > >
> > > Not sure if the FuGE core developers have some better ideas?
> > >
> > > Cheers,
> > > Josef
> > >
> > >
> >
> > Simon Schafferer wrote:
> > >
> > > Hi,
> > >
> > > By now I imported the SNAPSHOT jars (hibernate-core,
> > > hibernate-common...) generated by maven in my Eclipse
workspace,
> > > because
> > > I am currently developing a web application for flow cytometry
> > > analyisis
> > > with wicket and hibernate as persistence layer.
> > >
> > >
> > >
> > > So I installed the fuge-hibernate-stk and everything worked
> fine. Then
> > > I
> > > tried to integrate FuGEFlow:
> > >
> > >
> > >
> > > 1. I downloaded FuGE-v1-profile.mdzip and FuGEFlow.mdzip
> > >
> fromhttp://flowcyt.svn.sourceforge.net/viewvc/flowcyt/FuGEFlow/model/
> > > 2. I exported FuGEFlow.mdzip as EMF UML2(v1.x) XMI in
MagicDraw
> 15.0
> > > into fuge-hibernate-mda/src/main/uml
> > >
> > > 3. I changed the path in the fuge-hibernate-mda/pom.xml to
> > > FuGEFlow.uml2
> > >
> > > 4. mvn clean and afterwards mvn install
> > >
> > >
> > >
> > > An error in the validation of the andromda model occured, you
> can find
> > > the log file in the attachment.
> > >
> > >
> > >
> > > Do you suggest any other solution?
> > >
> > >
> > >
> > > Is it possible for example, to generate Java Classes plus the
> > > hibernate
> > > configuration and mapping files from the FlowCyt XML schema
> files with
> > > hyperJaxB?
> > >
> > >
> > >
> > > Kind regards,
> > >
> > > Simon
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > >
> > > Josef Spidlen, Ph.D.
> > >
> > > Terry Fox Laboratory, BC
> > > http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx
> > >
> > >
> > >
> > >
>
>
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> > >
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> >
> > --
> > Allyson Lister
> > http://themindwobbles.wordpress.com
> >
> > CISBAN, http://www.cisban.ac.uk
> > Newcastle University
>
>
> --
> Josef Spidlen, Ph.D.
> Terry Fox Laboratory, BC Cancer Agency
> 675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada
>
> Tel: +1 (604) 675-8000 x 7755
> http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx
>
>
>
>
>
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Allyson Lister
http://themindwobbles.wordpress.com
CISBAN, http://www.cisban.ac.uk
Newcastle University
Allyson Lister
I've been much busier than I had expected this week, and last week I was on vacation, so my apologies. I don't have as much time to devote to this as I had thought, but here are my conclusions - they may help you out.
- If you want to have a version of the fuge hibernate STK that runs with the FlowCyt additions, then you reallyneed to use the version of the FuGE mdzip file that comes from the hibernate STK. There was a lot more done to that file to sort out issues with code generation than just a few aggregation issues. The full list of changes is here: http://fuge.sourceforge.net/stks/hibernate-stk/fuge-hibernate-books/fuge-hibernate/fugeom-modifications.html
- You said when using the hibernate-stk-specific FuGE mdzip file that you had the two errors I discussed in my earlier email. This is odd, as all errors in aggregation are been fixed in the hibernate stk (they must be fixed, because the project compiles - I just checked it again today). These errors are of the same type (aggregation) that Josef and others have described, and can therefore be fixed in the FuGE UML just the same way as the others have been fixed. Their presence in when FlowCyt is put into the mix (and lack of presence in the plain vanilla hibernate stk) is probably due to the fact that FlowCyt uses protocols and protocol applications. When they were making their own protocols and protocol applications, I'm guessing that somehow (I don't know how), the incorrect links described in the log message were copied from the original non-hibernate FuGE UML document.
Let me know how it goes.
Thanks,