[Fuge-devel] Antw: Re: [Flowcyt-fuge] Antw: Re: FUGE, FlowCyt
Simon Schafferer
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 FuGE classes. I still think the better
solution is
> > to modify the FuGEFlow.mdzip if we know where to fix.
> >
> > 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 want to alter the UML,
> > Cheers
> > Andy
> >
> > From: Josef Spidlen [mailto:jspi...@bccrc.ca]
> > 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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> >
> >
> >
>
>
> --
> 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
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--
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
Allyson Lister
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