[SDM-SPA] Re: [kepler-dev] moving edu.ncsu to org.sdm.spa

Ilkay Altintas altintas at sdsc.edu
Tue Apr 6 15:59:56 PDT 2004


I would suggest we do the clean up (other than this
directory)slower and wait until everybody digests
Zhengang's changes first.(e.g. I'm waiting to check
in my kepler/lib clean up/changes due to this morning's
updates.) But we need to clean this directory.

I checked again and don't have any files to remove from
the src directory right now as I cleaned it recently.
Also, the rule in general is not to delete/move any files
from the kepler cvs unless they are yours or the owner
of the file asks you to do so. (Or maybe that's the way
I assume it. ;)

As I have told in a previous email, gui and cipres are
directories related to my "experimental at the time" work
and are associated with some test workflows. They are
under subdirectories so please don't remove them or include
them in the SPA release until I go back and make them useful.
I will remove the cipres directory after I get the command
line fully functioning.
WebServiceUsingWSIF.java was removed from NCSU CVS last
week for the same reason as well. CommandLine actor is
in the making and not ready for checking in to the SPA
repository as it is not finalized for release. I will
check in this file and any coming development myself to
the SPA cvs when it is ready. Hope this would make it
easier for you to see which file to include in SPA cvs.

I don't see the .bak and .orig files you have mentioned
in the repository.

ClustalW_SDSC.java is the original version of ClustalW site
wrapper that is published as a web service. I don't see any
use of it to be there right now. Must ask Zhengang if he
needs it.

The other files that were mentioned came from directory
that was merged today. The directory looks quite messy
right now but it is still new. Maybe Zhengang is still
working on it.

Zhengang: Could you please remove the old and unused files
when you can? The xml and read me and versions of the
WebService related actors seem old.


-----Original Message-----
From: sdm-dev-admin at sdsc.edu [mailto:sdm-dev-admin at sdsc.edu]On Behalf Of
Xiaowen Xin
Sent: Tuesday, April 06, 2004 1:39 PM
To: Zhengang Cheng
Cc: sdm-dev at sdsc.edu; kepler-dev at ecoinformatics.org
Subject: [SDM-SPA] Re: [kepler-dev] moving edu.ncsu to org.sdm.spa

Hi Zhengang,

Thanks for moving the files into org.sdm.spa.

I'm looking at everything in there now.

Since we're doing this reorganization, now is probably the best time to
clean it up as well, so we're perfectly happy with it.  It would also
make sync'ing between them a lot easier for me =)

There are a couple of questions I have about files in there, maybe you
can Ilkay can help me answer them.

1.  There are quite a few files that I didn't put into the NCSU CVS
repository.  Can you tell me whether they should go in there?

	- the cipres/ directory
	- the gui/ directory
	- bioservice.xml
	- bio.xml
	- CommandLine.java
	- DDBJ_DDBJ.xml
	- DDBJ_GetEntry.xml
	- DDBJ.xml
	- DDBJXML.dtd
	- DummyActor.java
	- spa.xml
	- WebServiceActor4.java
	- WebService.java.bak
	- WebServiceUsingWSIF.java
	- XSLTActor.java.orig

Ilkay, you've said that cipres/ and gui/ are test directories, do you
think it's ok to delete them from Kepler as well?

As far as I can tell, all the xml files listed (besides spa.xml) weren't
actually being used.  Is it left over from something before?  If that's
the case, is it ok with you guys if I delete them?

Ilkay, should I add CommandLine.java to the NCSU repository now?

Is the DummyActor.java being used?  If not, would it be ok to delete it?

README looks a bit out of date.  Is it still relevant?  Since I'm trying
to draft a developers' manual, could you tell me which parts I need to

WebServiceActor4.java, WebService.java.bak, XSLTActor.java.orig look
like temporary files, would it be ok with you if I deleted them?

Ilkay, should I add WebServiceUsingWSIF.java to NCSU's CVS repository?

2.  There exist ClustalW.java and ClustalW_SDSC.java.  It looks like PIW
currently uses a web service hosted at NCSU to do the clustal step, so I
don't think either of these files are being used.  I think the names are
confusing because they don't differentiate between the two of them other
than to say one comes from SDSC.  Since they're not being used, should
we just delete both?  If not, maybe we could remove one of them, so it
doesn't look redundant.

Please tell me what you think =)


On Tue, 2004-04-06 at 12:13, Zhengang Cheng wrote:
> I agree. Will move there shortly.
> Xiaowen where should I modify? In NCSU or Kepler.
> Either way, will you  sync that between ncsu and kepler.
> Sorry for the confusion.
> Zhengang
> ----- Original Message -----
> From: "Ilkay Altintas" <altintas at sdsc.edu>
> To: "Xiaowen Xin" <xin2 at llnl.gov>; "Zhengang Cheng" <zcheng at eos.ncsu.edu>
> Cc: <sdm-dev at sdsc.edu>; <kepler-dev at ecoinformatics.org>
> Sent: Tuesday, April 06, 2004 3:10 PM
> Subject: RE: [kepler-dev] moving edu.ncsu to org.sdm.spa
> > I aggree with Xiaowen. I think it is better if all the code
> > is under org.sdm.spa as it is now in the ncsu cvs. This will
> > make the synch between spa and Kepler cvs's easier.
> >
> > Ilkay
> >
> > -----Original Message-----
> > From: kepler-dev-admin at ecoinformatics.org
> > [mailto:kepler-dev-admin at ecoinformatics.org]On Behalf Of Xiaowen Xin
> > Sent: Tuesday, April 06, 2004 10:56 AM
> > To: Zhengang Cheng
> > Cc: sdm-dev at sdsc.edu; kepler-dev at ecoinformatics.org
> > Subject: Re: [kepler-dev] moving edu.ncsu to org.sdm.spa
> >
> >
> > Hi Zhengang,
> >
> > Can you tell me why you moved all the NCSU code into org.sdm.spa.lib?
> >
> > In the NCSU CVS repository for SPA, I've had all the code in org.sdm.spa
> > for a couple of weeks now, and although it hasn't seen much usage, I
> > think it works for everybody.
> >
> > I think we should make sure this particular directory hierarchy is the
> > same between the two repositories, or there will be many headaches
> > sync'ing between them.
> >
> > As far as I can tell, we don't need to have some actors in org.sdm.spa,
> > while other actors are in org.sdm.spa.lib.
> >
> > Since you probably know the code better than I, what do you think?
> >
> > Xiaowen
> >
> >
> >
> > On Tue, 2004-04-06 at 11:26, Zhengang Cheng wrote:
> > > I will move the package now in Kepler to
> > > org.sdm.spa.lib now. I know where files (XML) need to be updated.
> > >
> > > Zhengang
> > > ----- Original Message -----
> > > From: "Xiaowen Xin" <xin2 at llnl.gov>
> > > To: <altintas at sdsc.edu>
> > > Cc: <sdm-dev at sdsc.edu>; <kepler-dev at ecoinformatics.org>
> > > Sent: Tuesday, April 06, 2004 1:57 PM
> > > Subject: [kepler-dev] moving edu.ncsu to org.sdm.spa
> > >
> > >
> > > > Hi Ilkay,
> > > >
> > > > I'd like to begin moving the code in the edu.ncsu.sdm.ptolemy.lib
> > > > package in Kepler into the org.sdm.spa package.
> > > >
> > > > We've already agreed a few weeks ago, that merging the two packages
> > > > would be something desirable.
> > > >
> > > > I believe you're the only person who is currently actively working
> > > > code in there, right?  If you don't plan on checking anything into
> in
> > > > the next couple of days, then I will begin the merge today.  I will
> make
> > > > sure it compiles on my computer before I check it in though, to
> minimize
> > > > the impact it might have on you and the other Kepler developers =)
> > > >
> > > > Is this plan okay with you?
> > > >
> > > > I hope there are no objections from the rest of the Kepler
> > > >
> > > > Thanks,
> > > > Xiaowen
> > > >
> > > > _______________________________________________
> > > > kepler-dev mailing list
> > > > kepler-dev at ecoinformatics.org
> > > > http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
> > > >
> > >
> >
> > _______________________________________________
> > kepler-dev mailing list
> > kepler-dev at ecoinformatics.org
> > http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
> >
> >

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