[kepler-dev] Latest SPA Release (updated)
Vouk
vouk at ncsu.edu
Thu Mar 4 17:52:31 PST 2004
Christopher,
Best way to run the demo is to
a) start it from the desktop
b) based on instruction on the PN Director tabletop (blue lettering)
either enter accession numbers, or use
one of the demo files that should be in the Program Files/ SDM/SWE/Demo file
(should open in that directory automatically).
Thanks
Mladen
Ilkay Altintas wrote:
>The input clustalW is passed thorugh a file as it is accumulated
>from the execution of a loop. The error looks like that file is
>not in the distribution. The lineWriter doesn't create that file
>if the file doesn't exist. We should add that file to the new
>distribution. (Comment#7)
>
>For comment#9, we have a browser use interface actor that outputs
>html output.(The browserUI in the spa folder)It works similar to
>what you said. It needs to be improved in several issues (like
>specifying the default browser in the system, displaying a url
>without having to copy the content of it to a file, etc). It would
>ne nice to discuss these issues with you sometime and get your
>opinion on them.
>
>Thanks,
>Ilkay
>
>-----Original Message-----
>From: kepler-dev-admin at ecoinformatics.org
>[mailto:kepler-dev-admin at ecoinformatics.org]On Behalf Of Christopher
>Hylands Brooks
>Sent: Thursday, March 04, 2004 4:03 PM
>To: Ilkay Altintas
>Cc: sdmctr-integrate at llnl.gov; Zhengang Cheng; Vouk; buttler1 at llnl.gov;
>sdm-dev at sdsc.edu; sdm at renoir.csc.ncsu.edu; kepler-dev at ecoinformatics.org
>Subject: Re: [kepler-dev] Latest SPA Release (updated)
>
>
>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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