Hi all,
This email is to say hi and to let you know that we at Umass Med School have
decided to use Airavata as a framework for building a Gateway to our cluster. I
am employed as an HPC Scientific Programmer and will be leading (and probably
doing it mostly myself :)) this project. If you want more details regarding our
plans, please let me know, since I don't want to bore you with the details in
this first email.
I also have a technical question. I've added simple applications, along the
lines of Add, Echo, Multiply ... etc. without a problem. I've also added an
application that takes an input file as an InputDataObjectType of type
DataType.URI. However, I must be doing something wrong when trying to generate
output files i.e., OutputDataObjectType of type DataType.URI.
RegisterSampleApplicationsUtils.createAppOutput("output_file", "",
DataType.URI);
It seems to work fine with strings still, since if in my script I put something
like this:
echo
"output_file='file://localhost:///opt/lampp/htdocs/PHP-Reference-Gateway/experimentData/spiros340e527dece195a74ac7455fbcc6f6fa/spiros_c.eps'"
Then it picks up the string.
My question is: how do I declare in the script that I want an actual file, not
a string?
I've tried:
output_file='file://localhost:///opt/lampp/htdocs/PHP-Reference-Gateway/experimentData/spiros340e527dece195a74ac7455fbcc6f6fa/spiros_c.eps'
output_file="file://localhost:///opt/lampp/htdocs/PHP-Reference-Gateway/experimentData/spiros340e527dece195a74ac7455fbcc6f6fa/spiros_c.eps"
and with the keywords "set", "declare", and "export" in front of "output_file"
but have had no success.
I think I'm missing something in the whole concept of output files, but as a
first step to better understand output files within Airavata, I would like to
know how to hardcode sth. like that in the script and see it appear as a... URI
type? For example, as a string it shows up like this:
array(1) { [0]=> object(Airavata\Model\Workspace\Experiment\DataObjectType)#15
(4) { ["key"]=> string(11) "output_file" ["value"]=> string(127)
"'file://localhost:///opt/lampp/htdocs/PHP-Reference-Gateway/experimentData/spiros340e527dece195a74ac7455fbcc6f6fa/spiros_c.eps'"
["type"]=> int(0) ["metaData"]=> NULL } }
But the array is empty when I try one of the above lines in the script
(output_file= ...).
Thanks in advance,
Spiros
