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From Suresh Marru <>
Subject Re: Experiment Summary retrieval
Date Fri, 14 Mar 2014 20:13:52 GMT
Hi Borries,

I think it is worth considering to do a google hangout screen presentation instead of a VNC.
Hangouts have good support for multiple operating systems and you can look here if your system
is supported -


On Mar 14, 2014, at 3:16 PM, Miller, Mark <> wrote:

> Borries,
> I haven't used this vnc thing before.
> Do I just need the free client mentioned on this page?
> Mark
> -----Original Message-----
> From: Borries Demeler [] 
> Sent: Friday, March 14, 2014 11:48 AM
> To:
> Subject: Re: Experiment Summary retrieval
> Marlon,
> would it be possible to put me on the agenda for about 30 mins. during our next telecon?
> Everyone should have a vnc viewer client on their computer to follow along.
> Thanks, -borries
> On Fri, Mar 14, 2014 at 06:42:46PM +0000, Miller, Mark wrote:
>> I think that would be useful, personally. 
>> -----Original Message-----
>> From: Borries Demeler []
>> Sent: Friday, March 14, 2014 11:37 AM
>> To:
>> Subject: Re: Experiment Summary retrieval
>> Mark, Lahiru and others:
>> If you guys aren't averse to yet another online conference, I would be happy to give
an on-screen demo of our system. It is a bit difficult to explain per email how this rather
complicated system is organized, but it may be worthwhile to get some insights of one possible
solution to how this can be handled. I wouldn't say that the gateway is completely separated
from the task of processing output data, but the task is abstracted to a very basic and uncomplicated
level, and then the more complex issues are handled in a custom fashion by our software. This
way we can on the one hand have robust communications and on the other fine-grained and customized
data handling for the specific needs of the user. I would probably need about 20-30 mins of
your time. Perhaps during the next SciGap meeting?
>> It would be best if everyone had a vnc viewer on their desktop to follow along.
>> -Borries
>> On Fri, Mar 14, 2014 at 04:49:15PM +0000, Miller, Mark wrote:
>>> Very interesting Borries. So if I read that right, delivery of results for your
Gateway takes place by a completely separate system.
>>> I think the RESTful access we provide will be similar in some ways.  We will
be passing results directly to the user's application, which will be in effect like the UltraScan
package, I think. In that case, what the user extracts from the data will be up to their application.
Of course we will track the relevant usage parameters just as we do currently on our side.
>>> The access to intermediate results for ongoing jobs is also critically important
for us as well, and very much outside of the main Gateway software. But we don't currently
support access to status of a list of running jobs. Although the idea of being able to provide
users with a window into the status of all their tasks is certainly a nice feature, and we
would likely consume it and present it to users if it was easy to access.
>>> Mark
>>> -----Original Message-----
>>> From: Borries Demeler []
>>> Sent: Friday, March 14, 2014 9:12 AM
>>> To:
>>> Subject: Re: Experiment Summary retrieval
>>> I am not sure if this relates at all to the getAllExperiments() question, but
I thought it may help to see how we deal with retrieving expt. data from the gateway in UltraScan.
>>> In the case of UltraScan we have the HPC output very much separated from the
information of the results that are useful to the user. All data are getting tar.gzipped into
a single archive which is transported back out and automatically parsed into a relational
database that is part of the UltraScan software, and not a function of the gateway. The user
will then access the database with secondary software and create a type of meta-analysis and
visualization of the results that ultimately are then useful to the user. Having said this,
while data are being calculated on the HPC resource, the user can monitor the process of the
calculation by reviewing a queue viewer that shows all pending and active jobs and their actual
state. This state include a lot of information keeping the user apprised of the state. This
information is continually being sent via UDP from the HPC resource and monitored by a daemon
on our backend LIMS server, again, this is semi-independent from the gateway software. This
may be very specialized for our use case, but it is one example of how the problem can be
>>> -borries
>>> On Fri, Mar 14, 2014 at 11:37:02AM -0400, Saminda Wijeratne wrote:
>>>> Thanks for identifying the problem Sachith. To be precise 
>>>> potentially there are many subset variations of interested fields 
>>>> in the Experiment Data which different gateways will be interested 
>>>> in the same usecase or different usecase. We cannot scale by 
>>>> providing different functions for each of these scenarios.
>>>> On Fri, Mar 14, 2014 at 11:25 AM, Sachith Withana <>wrote:
>>>>> Hi all,
>>>>> Almost all gateways have a requirement of retrieving the 
>>>>> experiment summaries of all the experiments . The fields that 
>>>>> are required differ based on the gateway.
>>>>> For Example:
>>>>> CIPRES requires : Experiment name and status Some gateways 
>>>>> requires the Experiment name with the inputs only.
>>>>> But right now the getAllExperiments() method returns the list of 
>>>>> all the Experiments with all the experiment related attributes 
>>>>> filled ( the whole Experiment Model).
>>>>> It's costly to get the whole Experiment objects from the API 
>>>>> rather than getting the required few attributes.
>>>>> Any suggestions on how we could achieve this?
>>>>> One suggestion would be to have a getAllExperiments method with 
>>>>> the parameters as a list of required fields of the Experiments 
>>>>> and return only those fields.
>>>>> --
>>>>> Thanks,
>>>>> Sachith Withana

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