[Biojava-l] Running apps with Java

[Patrick McConnell]

For maximum flexibility and ease of use, I think describing the parameters
in an external (editable) file would be preferrable.  I do not think it
would be too hard to come up with an XML schema for describing how programs
should be run.  Something like:

<program>
  <name>NCBI Blast</name>
  <parameterSet>
    <platform>default</platform>
    <flag>-</flag>
    <delimiter> </delimiter>
    <parameter>
      <name>p</name>
      <description>blast program</description>
      <allowableValues>
        <allowableValue>blastn</allowableValue>
        <allowableValue>blastp</allowableValue>
        <allowableValue>blastx</allowableValue>
      </allowableValues>
    </parameter>
    . . .
  </parameterSet>
</program>

You could define defaults that can be overridden per program, per platform,
and per parameter.  This way, users can easily add/change programs for
their platform, and you do not need to rebuild BioJava for these changes.

The code for invoking the program would be like:

      ExternalProgram prog = new ExternalProgram("NCBI Blast");
      prog.addParameter("p", "blastn");
      . . .

      String stdin = null;
      StringBuffer stdout = new StringBuffer();
      StringBuffer stderr = new StringBuffer();
      prog.exec(pathToBlastall, stdin, stdout, stderr);

You could also query a particular program for its parameters, allowable
values, defaults, etc.

Again, the file could be located and loaded from the BioJava jar, the
directory the BioJava jar is in, and the user's home directory.

I would love to see something like this in BioJava.  Please comment on the
advantages/drawbacks of such a system because I am now considering
implementing it for my own use!

-Patrick





"Schreiber, Mark" <mark.schreiber at agresearch.co.nz>@biojava.org on
08/12/2003 10:39:04 PM

Sent by:    biojava-l-bounces at biojava.org


To:    "Keith James" <kdj at sanger.ac.uk>, "Thomas Down"
       <thomas at derkholm.net>
cc:    biojava-l at biojava.org

Subject:    RE: [Biojava-l] Running apps with Java

I would tend to agree with Keith. Making hardcoded command lines can loose
platform independence pretty quickly. I would prefer to see users register
their own command lines, preferences etc with some kind of registry object.

- Mark


             -----Original Message-----
             From: Keith James [mailto:kdj at sanger.ac.uk]
             Sent: Tue 12/08/2003 10:46 p.m.
             To: Thomas Down
             Cc: biojava-l at biojava.org
             Subject: Re: [Biojava-l] Running apps with Java



             >>>>> "Thomas" == Thomas Down <thomas at derkholm.net> writes:

             [...]

                 Thomas> Yes, I quite agree.  Although I think I'd prefer
something
                 Thomas> more like:

                 Thomas>    params.addParameter(NCBIBlast.PROGRAM_NAME,
"blastn")

                 Thomas> Have you looked at the AnnotationType class?  We
could
                 Thomas> probably use those to do the parameter set
validation.

             IMO having program names hardcoded in the method names or even
as
             parameters greatly increases the amount to code required for a
typical
             system. A public exec method per program will result in a lots
of
             methods and requires rebuilding the jars to deploy a new
external
             program (same with static parameters specific to a program).

             Having a single, generic exec method with a means of
discovering local
             native programs is simpler and more maintainable. This can be
done
             simply with ResourceBundles (which also means that one can
             internationalize for free)

             e.g.

             NCBIBlast_en_GB.properties

             -p = String : Program name
             -d = String : Database, default = nr
             -i = String : Query file, default = stdin
             -e = Double : Expectation value (E), default = 10.0

             etc.

             NCBIBlast_fr.properties

             -p = String : Nom de programme

             etc.

             I think it is important to allow end users to configure their
biojava
             to run their native applications without writing any code.

                 Thomas> The other big win would be to do something at
least
                 Thomas> vaguely sane about finding executables.  Hardcoded
paths
                 Thomas> aren't a problem if you are running on your own
machines,
                 Thomas> but if people want to deploy BioJava-based
applications
                 Thomas> widely, they really need to be able find blast on
their
                 Thomas> own...

             You can do this simply by adding a key/value to the resouce
giving the
             full path. Alternatively this keyed value could be the name of
a JNDI
             resource etc. for situations which require it.

             I've been running a simple Java-based workflow & execing
system in
             anger for the past year (lots of different native programs)
and native
             program maintenance requiring rebuilding production of jar
files is
             not something I'd want to deal with.

             cheers,

             Keith

             --

             - Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65
-
             - The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
-
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             Biojava-l mailing list  -  Biojava-l at biojava.org
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