[kepler-dev] Latest SPA Release (updated)
Christopher Hylands Brooks
cxh at eecs.berkeley.edu
Thu Mar 4 16:02:34 PST 2004
No worries about the copyrights, I'm happy with what is there now,
modulo the spelling.
Thanks for the info about accession numbers.
I created c:\tmp\access.txt with
AA045112
AA039967
7. Now, the first time I run, I get:
ptolemy.kernel.util.IllegalActionException: Cannot open file or URL
in .PIW-full.FileReader.fileOrURL
Because:
C:\Program Files\SDM\SWE\Demo\clustalinput.txt (The system cannot find
the file specified)
in .PIW-full.FileReader
at ptolemy.actor.lib.io.FileReader.fire(FileReader.java:152)
at ptolemy.actor.process.ProcessThread.run(ProcessThread.java:190)
However, the C:\Program Files\SDM\SWE\Demo\clustalinput.txt
file gets create and the second and successive time I run I do not
see the error.
8. It might be worth resizing the Display actors and laying them out
so they don't obscure each other. If the layout is updated and
the model saved, then when the model is reopened, the layout should be
preserved.
9. It would be cool if we had an actor that would display html
output in the browser. This actor would accumulate data and
then in wrapup() dump it to a file and invoke the browser.
Perhaps you already have such an actor?
-Christopher
--------
Hi Christopher,
The credit on your congrats should go to Zhengang as he's the one who built
it.
Thanks for the comments. We have built this version just for SDM-SPA.
Zhengang and I are working on another version for the whole Kepler right
now.
The typos, copyrights and the shortcuts will be fixed in that version.
For running the sdm version:
Accession number is a unique id for a gene in worldwide genebanks.
The filereader reads the accession number to be searched in the Genbank fro
m
a file.
So please create a file let's say c:\access.txt and put
AA045112
AA039967
in the file (two accession numbers, one per line).
If you browse this file from file reader (file reader for accession numbers
)
afterwards, you will not get an error.
Hope this helps to run it.
Ilkay
-----Original Message-----
From: owner-sdmctr-integrate at lists.llnl.gov
[mailto:owner-sdmctr-integrate at lists.llnl.gov]On Behalf Of Christopher
Hylands Brooks
Sent: Thursday, March 04, 2004 2:04 PM
To: Zhengang Cheng
Cc: Vouk; buttler1 at llnl.gov; sdm-dev at sdsc.edu; sdm at renoir.csc.ncsu.edu;
kepler-dev at ecoinformatics.org; sdmctr-integrate at llnl.gov
Subject: Re: [kepler-dev] Latest SPA Release (updated)
I downloaded the SDMSWE1v0-Beta3.exe and the installation worked fine
for me, there was no hanging problem that I've experienced with
the Sun JDK InstallShield installer and others.
The installer looks good!
Below are some minor nits.
1. I downloaded http://sdm2.csc.ncsu.edu/SWE/SDMSWE1v0-Beta3.exe
at about 1:30pm
2. In the installer licence agreement misspells "Ptolemey", it should
me "Ptolemy".
BTW - many thanks for including the copyright.
You might want to include the complete set of restrictions in
the License agreement, or you might just include the copyright
inside Ptolemy II.
If you were going to update the license agreement, I would say
something like:
--start--
SDM Scientific Workflow Engineering uses Ptolemy II, which has
the following copyright:
Copyright (c) 1995-2003 The Regents of the University of California.
All rights reserved.
Permission is hereby granted, without written agreement and without
license or royalty fees, to use, copy, modify, and distribute this
software and its documentation for any purpose, provided that the above
copyright notice and the following two paragraphs appear in all copies
of this software.
IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
ENHANCEMENTS, OR MODIFICATIONS.
--end--
Again, many thanks for including mention of our copyright in the
license page.
Eventually, it would be nice to have an easy way to add copyrights
to the about:copyright page so that your copyright could appear.
3. The ReadMe.txt that comes up after the installer runs
also misspells "Ptolemey", which should be "Ptolemy"
There are other spelling errors as well ("squeences")
4. I prefer not to dump icons on the desktop without asking the user.
5. It would be nice if there was a menu choice created for the package
Probably there should be SDM menu with a SWE1v0-beta3 submenu:
SDM
SWE1v0-beta3
README.txt
SWE Demo
SWE Documents
BTW - I liked the info message that appeared during installation that
told me what was going to happen to my installation.
6. The demo comes up for me, but does not run, I get:
ptolemy.kernel.util.IllegalActionException: No file name has been
specified.
in .PIW-full.FileReader for AcessNumbers.fileOrURL
The annotation says:
Double click the File Reader to change specify your access numbers to
be investigated. The access number should occupy one line each. Each
access number will be investigated.
Exactly what do I need to do to run the demo?
I don't know what access numbers are?
I'm being slightly pendantic here, but lots of people try demos
and have no clue as to what the demo does.
Again, congrats on shipping a good looking beta!
-Christopher
Christopher Hylands Brooks cxh at eecs.berkeley.edu University of California
Programmer/Analyst Chess/Ptolemy/GSRC US Mail: 558 Cory Hall #1770
ph: 510.643.9841 fax:510.642.2739 Berkeley, CA 94720-1770
home: (F-Tu) 707.665.0131 (W-F) 510.655.5480 (office: 400A Cory)
--------
Dear All,
We have made the changes Dr. Vouk identified.
The new release is accessible now at
http://sdm2.csc.ncsu.edu/SWE/SDMSWE1v0-Beta3.exe for
Windows platform.
This release expects that the machine has Java and
Ptolemy 3.02 installed. The above installer only contain component
specific
for SPA project (mainly matt's workflow).
When testing, please keep in mind that we are working to solve the
Transfac
problem. Any suggestion is welcome.
Thanks,
Zhengang
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