[Fuge-devel] Antw: Re: [Flowcyt-fuge] FUGE, FlowCyt
Simon Schafferer
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> 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 being
repeated 30 times: One-to-one associations must have one side of the
association 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,
is there a possibility to extend the hibernate-STK with the
FuGEFlow.mdzip?
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 from
http://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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Simon Schafferer
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 February 2008. I assume the delay was due to
formalities related to the ISAC approval process but you may want to
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,
Based
on your log file, it seems that there is only one error beingassociation indicating aggregation (aggregation defines the
Cheers,
Josef
Simon Schafferer wrote:
Hi,
fromhttp://flowcyt.svn.sourceforge.net/viewvc/flowcyt/FuGEFlow/model/
Kind regards,
Simon
--
Josef Spidlen, Ph.D.
Fuge-devel mailing
listFuge-devel@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/fuge-devel
--
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
7755http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx
Josef Spidlen
Ok, I'll look into that and let you know.
Cheers,
Josef
Allyson Lister
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 :)
--
Allyson Lister
http://themindwobbles.wordpress.com
CISBAN, http://www.cisban.ac.uk
Newcastle University
Josef Spidlen
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 :)
>
>
>
--
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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_______________________________________________
Fuge-devel mailing list
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--
Allyson Lister
http://themindwobbles.wordpress.com
CISBAN, http://www.cisban.ac.uk
Newcastle University