I have not thought that hard about how to pass binary data, probably the
thing to do would be to enhance the Exec actor to optionally pass an
ObjectToken that would contain the binary data.
Offhand, I don't know of anything in the StringToken that should prevent
binary data from being used, but there could be issues. Some simple test
cases would help here.
One thing is that reading data from files can result in transformation
of the data. ptolemy/util/FileUtilities.java has a method that safely
reads a file and outputs it using ByteArrayOutputStream.
BTW - I'm used to Unix passing data as files that have newline
characters and using tools and scripts on textual data. A few
line-based tools tend to fail if the file does not have at least one
newline at the end of the file. Interestingly, the find command can
generate an output that has file names separated by null characters and
xargs can process that data with the -0 option. For example, these
commands find file names with spaces in them and then call xargs to run
a command.
find . -name "* *" -print0 | xargs -0 ls -l
(Of course, one could just do find . -name "* *" -ls, but the point is
to show how to pass filenames with spaces to xargs)
On 4/19/13 6:06 PM, Jianwu Wang wrote:
Hi David,
External execution assume the data for output port is string and
process it accordingly. So I don't think it can correctly send binary
data from its output port.
One way workaround is to redirect the binary output into a file and
the next 'External execution' actor will read data from the file. If
it fits your needs, I can send a demo workflow for it.
Best wishes
Sincerely yours
Jianwu Wang, Ph.D.
jia...@sdsc.edu
http://users.sdsc.edu/~jianwu/
Assistant Project Scientist
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.
On 4/18/13 11:02 AM, Brown, David M JR wrote:
To whom it may concern,
I've got a set of binary tools that use standard unix style pipes to
communicate and process data. So to write this up in Kepler I chose
to use the external execution component and run each command
separately connecting one components standard output to the other
components standard input. However, the communication isn't in text
its binary. I'm having issues where the first part of the process
doesn't recognize the header sent to the program as valid.
Are there any issues with sending binary data from external execution
components output port?
Thanks,
- David Brown
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Academic Program Manager & Software Engineer US Mail: 337 Cory Hall
CHESS/iCyPhy/Ptolemy/TerraSwarm Berkeley, CA 94720-1774
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