Thanks for your interest, Spiros! I'll second Suresh's recommendation
for a hangout.
Marlon
On 2/11/15 10:56 AM, Suresh Marru wrote:
Hi Spiros,
Very glad to hear your interest and commitment to use Airavata. You have
already a head start by jumping into the weeds and figuring out. Especially in
terms of application registration, there is a web version, which will
illustrate the functionality more. Can we do a google hangout and discuss the
current state of Airavata, demo the web version, understand your usecase? Once
we understand the context better, we will be able to guide you better.
Suresh
On Feb 11, 2015, at 9:51 AM, Mihalakopoulos, Spiro
<[email protected]> wrote:
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 J) 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' <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' <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 <file://///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' <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
