[kepler-dev] Re: [SDM-SPA] RFC new directory structure
Edward A Lee
eal at eecs.berkeley.edu
Thu Mar 18 10:47:36 PST 2004
There is an example of a customized "configuration" in
$PTII/ptolemy/configs/hyvisual.
If you run:
vergil -hyvisual
you get this configuration... You are actually running the regular
Ptolemy II, but the libraries, blank model templates, help files,
and splash screen are all customized.
I could take a stab at a kepler configuration, but I've been pretty
swamped, so I'm not sure how quickly I would get to it... If someone
else wants to try it, I suggest starting as follows:
cd $PTII/configs
cp -r hyvisual kepler
cd kepler
replace "HyVisual" with "Kepler" everywhere and start editing files...
You could then start the new configuration with:
vergil -kepler
It would also be easy to create an executable file in $PTII/bin so you could
just say:
kepler
Edward
At 08:24 AM 3/18/2004 -0900, Matt Jones wrote:
>Efrat,
>
>Which configuration file are you referring to? I think Chad is probably
>the best person to answer this question, or maybe Ilkay. And as
>Christopher has pointed out, Ptolemy/Kepler has a built-in way of allowing
>different customized views (that we are not now making use of) that would
>allow us to stop overwriting Ptolemy files. Maybe we should think some
>more about how we are layering our Kepler changes on top of the Ptolemy tree.
>
>Matt
>
>Efrat Jaeger wrote:
>>Hi all,
>>While making all these changes, I'd like to suggest another "rule", to avoid
>>overwriting Ptolemy files (if possible?). Now that we are wiser and have a
>>better understanding of the system, the exp directory can possibly be
>>disposed by extending the Ptolemy type classes instead of overwriting them.
>>Matt, Can the configuration file extend the Ptolemy one? Otherwise once
>>Kepler is loaded, Ptolemy can no longer be loaded.
>>Efrat
>>----- Original Message -----
>>From: "Matt Jones" <jones at nceas.ucsb.edu>
>>To: "Xiaowen Xin" <xin2 at llnl.gov>
>>Cc: <kepler-dev at ecoinformatics.org>; <sdm-dev at sdsc.edu>
>>Sent: Wednesday, March 17, 2004 4:15 PM
>>Subject: [kepler-dev] Re: [SDM-SPA] RFC new directory structure
>>
>>
>>>Xiaowen,
>>>
>>>Your suggestions overall sound good to me. A few comments below.
>>>Please don't make these changes until we've all agreed that they are
>>>good, which shouldn't take too long.
>>>
>>>Xiaowen Xin wrote:
>>>
>>>>Hi,
>>>>
>>>>David, Ilkay, Zhengang, Dan and I have discussed on the phone and over
>>>>email the last couple of days about the directory hierarchy
>>>>reorganization and have come to a rough consensus. This will be a long
>>>>email, so please bear with me =)
>>>>
>>>>The problem basically is that there is currently no clear organization
>>>>of the files in the CVS repository. Workflows are scattered around the
>>>>lib/ directory for example, and it's not clear, looking at the
>>>>repository, which files relate to SPA and which to one of the other
>>>>projects.
>>>>
>>>>Here's a pictorial view of how we would like to reorganize the
>>>>repository. I will be talking mostly about SPA, but the concepts should
>>>>carry over to the other Kepler projects as well.
>>>>
>>>>- copyright.txt
>>>>- README
>>>>- build.xml
>>>>- bin
>>>> - runVergil.bat
>>>> - runVergil.sh
>>>>- build (directory used for compiling the sources)
>>>>- docs
>>>>- lib
>>>> - jar (directory for all the jars)
>>>> - dll (directory for all the dlls)
>>>>- src
>>>> - org
>>>> - ecoinformatics
>>>> - geon
>>>> - sdm
>>>> - spa (directory for all the spa-related actors)
>>>>- util
>>>>- test
>>>>- workflows
>>>> - spa (directory for spa workflows)
>>>> - seek
>>>> - geon
>>>>
>>>>
>>>>So all the SPA related actors will be in the org.sdm.spa package.
>>>>Currently there are some SPA actors in edu.ncsu.sdm, but this doesn't
>>>>make much conceptual sense. There's no reason to divide up SPA source
>>>>files according to the organization that developed it, since all of SPA
>>>>will be working closely together to create _one_ set of interrelated
>>>>actors. Zhengang will work on moving the actors from edu.ncsu.sdm to
>>>>org.sdm.spa. It's better to divide up the source files by project
>>>>rather than by organization because the boundary between organizations
>>>>is artificial and only serves to confuse things.
>>>
>>>Good. If we must divide things up by project, then its best to have one
>>>tree per project. A functional classification of the actors would be
>>>better (because it would reduce inter-project redundancy and make things
>>>far easier to find). Have you considered a package hierarchy like this
>>>(this is rough, it would need much more careful thought, but I wanted to
>>>throw it out there):
>>>- src/org/ecoinformatics/kepler/
>>> - statistics
>>> - univariate
>>> - multivariate
>>> - clustering
>>> - nonparametric
>>> - models
>>> - simulation
>>> - ecological
>>> - geological
>>> - molecular
>>> - analytical
>>> - ecological
>>> - geological
>>> - molecular
>>> - utilities
>>> - dataaccess <== alternatively, this might be
>>> - genomics organized by protocol,
>>> - museumcollections like jdbc, gridftp, etc.
>>> - ecological
>>> - ...
>>>
>>>On top of this, in SEEK we've been contemplating ways of classifying the
>>>actors and data sources in an ontology so that scientists can easily
>>>locate the actors of interest to them in the tree. We have developed
>>>some ideas about dynamically organizing the tree of actors in the UI
>>>according to functional lines based on a preferred ontological view that
>>>a given scientist might have. Thus, an ecologist might want to view the
>>>models arranged in a different order than a molecular biologist, and
>>>this would be expressed in the interface as a different view on the
>>>ontology.
>>>
>>>Finally, people should be sure to review the changes we are proposing in
>>>SEEK to Kepler's UI regarding data access. The details are in
>>>kepler/docs/dev (both UML diagrams and screenshots of proposed changes).
>>>
>>>
>>>>Currently, there's a util/ directory in src/. This isn't really
>>>>consistent with our naming convention so far (i.e. putting source files
>>>>in packages that reflect which project made them). The argument for
>>>>having a util/ directory has been that we'd like to put useful classes
>>>>in there that can be shared between the projects. However, this
>>>>argument doesn't make much sense because theoretically, all of our
>>>>actors could be shared between the projects. So we'd like to move the
>>>>files in util/ to org/sdm/spa/util. If another project requires the
>>>>functionality of those two classes, then it would have to include the
>>>>org.sdm.spa.util package instead of simply the util package.
>>>>
>>>>After making these changes, all the SPA source files will be in
>>>>org/sdm/spa, thus making it much easier to distinguish SPA and its
>>>>contribution to Kepler.
>>>>
>>>>Currently, all the workflows are in lib/ and there are some that are not
>>>>in CVS at all. We would like create a top-level workflows/ directory to
>>>>store all of the workflows. spa, seek, and geon would be subdirectories
>>>>under there. Thus all SPA workflows will be put in workflows/spa/.
>>>>Similarly, GEON and SEEK should probably do the same with their
>>>>workflows.
>>>
>>>I think a top level workflows directory is a great idea. Again, I think
>>>a functional classification is best, but the organizational one you
>>>propose would be an improvement. Does it really matter which
>>>organization developed which workflow, and that the package structure
>>>reflect that? I think not, but I come from a functional rather than
>>>political perspective on this.
>>>
>>>
>>>>With this directory structure, it would be easy to tell which workflows
>>>>are designed for which project, but we must also remember to check all
>>>>of our workflows into CVS, and update them when/if they break. Having
>>>>PIW-full.xml, PIW-full_new_matt.xml, PIW-int-ex0.xml, and
>>>>PIW-full_new.xml, as we do right now is just plain confusing!
>>>>
>>>>Currently the lib/ directory is a mess. It appears to be the garbage
>>>>bin, where everything is dumped if the author can't find a better
>>>>container for it. So we propose a series of steps to clean this up.
>>>>
>>>>1. There are two dll's in lib/. There should probably be a subdirectory
>>>>called dll/ under lib/ that contains these dll's. The person who put
>>>>these there should probably move them ...
>>>
>>>I think this is chad's work. He'll be back soon and will address this.
>>>
>>>
>>>>2. demos.htm and ptolemy-index.html should probably be moved out of lib/
>>>>and into a more appropriate folder, probably into src/.
>>>
>>>I guess I conceive of lib as the location of resources (such as required
>>>libraries, html, xsl files, etc that are needed for an app to run),
>>>while src is for java code, etc. I'm not convinced this is a good
>>>proposal yet.
>>>
>>>
>>>>3. Ilkay will dispose of lib/forBerkeley/ and lib/forSB/ folders or move
>>>>them into the top-level test/ folder since they contain testing material
>>>>and so don't belong in lib/. Whoever's responsible for
>>>>lib/ecoPipelines/ should probably do the same because that's testing
>>>>material also as I understand it.
>>>
>>>agreed. The "test" folder should contain 1) directory structures that
>>>lead to JUnit source files, and 2) the resources such as testing data
>>>that is needed to run those or other tests.
>>>
>>>
>>>>4. Is everyone ok with our deleting makefile and makefile.lib from
>>>>lib/? These are also not library files, and we're not using makefiles
>>>>any more.
>>>
>>>Yes.
>>>
>>>
>>>>5. We should move runVergil.bat and runVergil.sh into a top-level bin/
>>>>directory.
>>>
>>>Fine.
>>>
>>>
>>>>6. Does anyone know what lib/sample.dat and lib/scew-0.3.1.tar.gz are?
>>>>Can we delete them?
>>>
>>>Ask Chad. He will know.
>>>
>>>
>>>>7. We will delete the lib/soap directory because it's empty, and there's
>>>>already a lib/jar/soap that contains jar files.
>>>
>>>You can't actually delete directories in CVS. Its a shortcoming of the
>>>software. When you checkout or update, be sure to set the "prune"
>>>option and it will remove any empty directories (e.g., cvs
>>update -d -P -A).
>>
>>>>8. We need to do something about lib/testdata/ because it's not a
>>>>library file. I personally think it should be moved into the global
>>>>test/ directory.
>>>
>>>Agreed.
>>>
>>>
>>>>9. We will move lib/workflow/ into the top-level workflows/ directory.
>>>
>>>OK. See comments above.
>>>
>>>
>>>>The existence of src/exp/ seems a bit questionable. It seems to stand
>>>>for "experimental". Maybe it's time to either make it stable and
>>>>incorporate it into an existing project, or delete it ...
>>>
>>>Sure. exp is a questionable practice. But at times it is ueful as a
>>>scratch area to get stuff into CVS for sharing that is not (or should
>>>not) be in the build process. If it is put into "src", it'll be built
>>>automatically by ant unless the build.xml is modified to specifically
>>>exclude it.
>>>
>>>
>>>>Please comment! If nobody objects to the proposed restructuring here, I
>>>>can do nothing but assume everybody loves it =) We'd like to get this
>>>>finalized as soon as possible, which would make it easier to create a
>>>>distribution. Matt will be back next week from travel I believe, and it
>>>>would be wonderful to have some kind of rudimentary installer for him.
>>>
>>>These are huge (but good) changes. Finalizing it quickly is good, but
>>>be sure to give everyone time to react, considering that some key
>>>developers (e.g., Chad) are traveling. I think at least 1 week for
>>>comments after the final revisions to the scheme is appropriate. I
>>>think a formal proposal and vote is warranted for a change of this
>>>magnitude.
>>>
>>>Matt
>>>
>>>
>>>>Xiaowen
>>>
>>>--
>>>-------------------------------------------------------------------
>>>Matt Jones jones at nceas.ucsb.edu
>>>http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496
>>>National Center for Ecological Analysis and Synthesis (NCEAS)
>>>University of California Santa Barbara
>>>Interested in ecological informatics? http://www.ecoinformatics.org
>>>-------------------------------------------------------------------
>>>_______________________________________________
>>>kepler-dev mailing list
>>>kepler-dev at ecoinformatics.org
>>>http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
>>
>>_______________________________________________
>>kepler-dev mailing list
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>
>--
>-------------------------------------------------------------------
>Matt Jones jones at nceas.ucsb.edu
>http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496
>National Center for Ecological Analysis and Synthesis (NCEAS)
>University of California Santa Barbara
>Interested in ecological informatics? http://www.ecoinformatics.org
>-------------------------------------------------------------------
>_______________________________________________
>kepler-dev mailing list
>kepler-dev at ecoinformatics.org
>http://www.ecoinformatics.org/mailman/listinfo/kepler-dev
------------
Edward A. Lee, Professor
518 Cory Hall, UC Berkeley, Berkeley, CA 94720
phone: 510-642-0455, fax: 510-642-2739
eal at eecs.Berkeley.EDU, http://ptolemy.eecs.berkeley.edu/~eal
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