[Shrine-users] Short-circuiting the adaptermappings requirement

[Trevvett, Philip]

Hi Michael,

Hoping you can provide a bit more detail to help me understand:

You have 2 shrine applications both pointing to the same i2b2 instance, right?
So does that mean shrine applications for 2 different networks, and if so are those networks using the same ontologies?
(multiple networks using the same i2b2 instance seems like a case where mapping files would be particularly necessary to maintain access at both networks, so just want to understand (even if ontologies are the same, different update schedules might cause problems without mappings)).

Thanks,
philip


-----Original Message-----
From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Michael Horvath
Sent: Tuesday, April 25, 2017 2:44 PM
To: Walend, David; shrine-users at open.med.harvard.edu
Subject: Re: [Shrine-users] Short-circuiting the adaptermappings requirement

Unfortunately, the available server that I must use has only 4g of memory, and supports an i2b2 server, two shrine applications, and a shrine client.  This isn't a lot of demand, but when you have very little every little bit counts.  The two shrine clients eat up the top two spots, claiming 30% and 22% of the available memory respectively, with the i2b2 server coming in around 14%.  

1) I'll look into jdk8, currently using 7.  Thanks for the tip.

2) External servers aren't in the cards for me, especially with anything that can touch PHI.

-----Original Message-----
From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Walend, David
Sent: Tuesday, April 25, 2017 2:27 PM
To: shrine-users at open.med.harvard.edu
Subject: Re: [Shrine-users] Short-circuiting the adaptermappings requirement

Michael,

What¹s the memory constraint on the server? What else is it running?

I have two quick-and-dirty suggestions before trying the work-around.

1) Try using JDK8. It makes better use of the heap, and may take enough pressure off SHRINE¹s use of memory to help.
2) If you have the freedom, consider renting a machine with enough memory from AWS EC2, or boosting the memory in the machine. If it is allowed then the expense is much less than the cost of your time.

If you¹d like to dig into the code, start at https://open.med.harvard.edu/stash/projects/SHRINE/repos/shrine/browse/adap
ter/adapter-service/src/main/scala/net/shrine/adapter/translators/Expressio
nTranslator.scala 

The code in the translators package has been extremely stable for some time, with no active worked planned. (I see in 2015 I cleaned up unused import statements while reading the code to get better error messages somewhere else.) Cloning either master (1.22.8) or develop (currently on 1.23.3.1), or even something older should be fine.


> git clone https://open.med.harvard.edu/stash/scm/shrine/shrine.git

We¹d be happy to take a pull request for this feature once it is in a state that can be shared.

David

David Walend
Tech Lead for SHRINE
HMS Catalyst

From:  <shrine-users-bounces at open.med.harvard.edu> on behalf of Michael Horvath <mhorvath at wakehealth.edu>
Date:  Monday, April 17, 2017 at 4:45 PM
To:  "shrine-users at open.med.harvard.edu"
<shrine-users at open.med.harvard.edu>
Subject:  Re: [Shrine-users] Short-circuiting the adaptermappings requirement


Bumping my own question from a year ago to see if anyone else has come across a solution for this.  I¹m running into tight memory constraints (server, not heap) with large adapter mappings files here, and am  going to see about implementing a workaround in the application server if no one else has any better options.
 
 
From: shrine-users-bounces at open.med.harvard.edu
[mailto:shrine-users-bounces at open.med.harvard.edu]
On Behalf Of Michael Horvath
Sent: Tuesday, February 23, 2016 12:14 PM
To: shrine-users at open.med.harvard.edu
Subject: [Shrine-users] Short-circuiting the adaptermappings requirement


 
Does anyone know if there is a way to eliminate the necessity of the adaptermappings file altogether?
 
For example, a network where every site is willing to ensure that there is a 1-1 mapping between each node in the ontologies doesn¹t necessarily need to have a mappings file at all.

 
I assume there isn¹t a switch I can set in shrine.conf, but if anyone else has tinkered with this issue and can point me in the right direction for a source modification I¹d be very grateful.
 
Michael Horvath    

Programmer / Analyst


Biomedical Research Services & Administration

Medical Center Boulevard  \  Winston-Salem, NC 27157 p 336.716.9755  \  f 336.716.5055
 

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