Ok, speak tomorrow! From: Suresh Marru [mailto:[email protected]] Sent: Wednesday, February 11, 2015 4:40 PM To: [email protected] Subject: Re: New Use Case and output file question
Hi Spiros, Lets use this hangout - https://plus.google.com/events/cufp6v5dqd9ofgejbq67mg2dj4c?authkey=CLftz_rGotu4Dg Talk to you tomorrow, Suresh On Feb 11, 2015, at 1:49 PM, Mihalakopoulos, Spiro <[email protected]<mailto:[email protected]>> wrote: 10 am tomorrow morning sounds great! My email is: [email protected]<mailto:[email protected]> From: Suresh Marru [mailto:[email protected]] Sent: Wednesday, February 11, 2015 11:58 AM To: [email protected]<mailto:[email protected]> Subject: Re: New Use Case and output file question How about Thursday morning eastern time? Please throw a specific time, if you do not have a preference, how about say 10 am eastern, thursday 02/12? Suresh On Feb 11, 2015, at 11:37 AM, Mihalakopoulos, Spiro <[email protected]<mailto:[email protected]>> wrote: Thanks a lot for your quick responses Suresh, Marlon and Raminder! Yes, a hangout will be great. When would it suit you best? From: Raminder Singh [mailto:[email protected]] Sent: Wednesday, February 11, 2015 11:32 AM To: [email protected]<mailto:[email protected]> Subject: Re: New Use Case and output file question Thanks Spirio for your interest. You are in right direction and only problem i am able to see is setting the type of data(["type"]=> int(0)) while creating experiment. Following is a sample code from a PHP example. If you set the type to URI on experiment creation then airavata should treat it as a file. /* Experiment input and output data. */ $input = new DataObjectType(); $input->key = "input"; $input->value = $input_data; $input->type = DataType::URI; As Marlon and Suresh said, a handout can help us understand your use case better and point you to right examples. Thanks Raminder On Feb 11, 2015, at 9:51 AM, Mihalakopoulos, Spiro <[email protected]<mailto:[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 ☺) 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:///\\localhost\opt\lampp\htdocs\PHP-Reference-Gateway\experimentData\spiros340e527dece195a74ac7455fbcc6f6fa\spiros_c.eps%E2%80%9D> 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
