[InterMine Dev] Fwd: web app restarts

Joe Carlson jwcarlson at lbl.gov
Fri May 8 18:01:02 BST 2015

Hi Josh,

Thanks for the quick response.

What I’d like to get is the chromosome sequence between two specified position. In earlier code, this was provided by the  URI 

/service/regions/sequence?query={“regions”:[“chromosome\tstart\tend”],”organism”:”short name”}

(we needed to tweak this a bit for our purposes, but this was the old endpoint in your code.) And it returned chromosome sequence in a fasta format.

In 1.4, I noticed that you changed this so that it returned the sequence of features - specified in the URI as an extra parameter such as genes, exons, introns, … - contained within these coordinates. This is the same as /service/regions/fasta. This isn’t quite what we want. I had tried to specify ‘chromosome’ as the feature type but that was rejected. I could not find another suitable endpoint.

There is a routine GenomicRegionFastaService. I don’t know if this is currently enabled in any service call, or how whether is would give me what I want.

The old code works for us but the caching is causing us heap out of memory errors. We’ve just recently determined that this was a cause of our restarts and are about to turn off caching. But if you know another way to get this information, let me know.



On May 8, 2015, at 7:57 AM, Josh Heimbach <josh at intermine.org> wrote:

> Hi Joe,
> While adding web service documentation in intermine 1.3.1, the endpoint /service/regions/sequence was retired for the reason that it was duplicating information found elsewhere. Much of the codebase has been refactored and improved since 1.3, so perhaps using a different servlet might solve the memory issue.
> Could you send me an example request that you would make to /service/regions/sequence along with its parameters? I'll look for a suitable alternative web service that returns the same information.
> Thanks,
> Josh
>> -------- Forwarded Message --------
>> Subject: [InterMine Dev] web app restarts
>> Date: Thu, 07 May 2015 17:28:06 -0700
>> From: Joe Carlson <jwcarlson at lbl.gov>
>> To: dev at intermine.org <dev at intermine.org>, David M. Goodstein <dmgoodstein at lbl.gov>
>> Hi Julie and gang
>> We have just deployed our latest phytozome build based on intermine 1.4.
>> This is our first public release using Hikari.
>> Our hopes were that going to hikari would solve some of the problem
>> we've been seeing about tomcat restarts. We've traded emails about this
>> in the past where we see that we have to restart every couple of hours
>> when under load. (We run a 'are you alive' cron job every 3 minuts and
>> force a restart if we don't get a response.)
>> At the time I think we had attributed it to the postgres connection and
>> we looking forward to the hikari pooling. It behaved well in internal
>> use, but now that we're public we continue to see the restarts.
>> I'm trying to do a little forensics to see what might be causing them.
>> I'm seeing "OutOfMemoryError: Java heap space", typically after a call
>> to retrieving the genomic sequence of a region
>> (service/regions/sequence). I had noticed that you had removed this
>> service in 1.4. I restored it since we're making use of it to deliver
>> sequence to our main web portal. Did you remove this because you had
>> seen it as being problematic?
>> At this point, I'm not absolutely sure this is the source of the
>> restarts but I'm very suspicious of
>> org.intermine.bio.web.export.GenomicRegionSequenceExporter. There is a
>> static map of entire chromosomes that is being stored. The substring is
>> retrieved by calling substring on elements of this map. This may work
>> for smaller mines but we have enough sequence in our database that I
>> suspect this is part of our problem.
>> Was this web service removed deliberately? Is there something to replace
>> it? As I recall, the other sequence retrieval services I found only
>> retrieved the sequence for specific features and not chromosome slices.
>> Thanks,
>> Joe Carlson
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