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HTTP response code 502 for phylographter nexson export #38

Closed
josephwb opened this Issue · 10 comments

3 participants

@josephwb
Owner

Calling up the list of updated studies from treemachine returns:

{"from": "2013-03-23T08:51:49", "studies": [12, 13, 14, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 33, 34, 37, 38, 40, 50, 51, 56, 59, 60, 63, 64, 66, 67, 71, 72, 73, 75, 76, 78, 82, 83, 84, 85, 86, 88, 90, 91, 93, 94, 95, 96, 97, 99, 102, etc...], "to": "2013-03-24T08:51:49"}

Many of these have null ottolids, but they are being skipped as a temporary workaround. Anyway, it proceeds well until hitting study 60:

java.io.IOException: Server returned HTTP response code: 502 for URL: http://www.reelab.net/phylografter/study/export_NexSON.json/60

Peter suggests this may be a timeout issue (the study has 22 trees, each with 640 taxa).

@jar398
Owner
@josephwb
Owner

No longer times out, but hangs (+20 minutes at least).

@pmidford
Owner
@josephwb
Owner

Yes.

@josephwb
Owner

Oops.Timeout is back.

@pmidford
Owner
@pmidford
Owner

I had a quick look at this:
As an aside, the "from" value doesn't seem consistent with the list of studies. Jonathan

If there is a problem, it isn't in the filtering - there are a lot of studies that have last_modified timestamps at 2013-03-23 11:44:50 and I did a spot check and couldn't find a discrepancy. I don't have an answer to why those (and only those) were all (apparently) modified at the same time.

@jar398
Owner
@josephwb josephwb referenced this issue in OpenTreeOfLife/treemachine
Closed

pull nexson trees from phylografter and add to graph #18

@pmidford
Owner

Fixes from yesterday seem to resolve the issue with study 60, but I found a larger study (227) that returns a 502 error, so the issue remains.

Study 438 is larger and also a problem.

@josephwb
Owner

Tested upgrade on treemachine end. Big studies coming through without hanging or timing out. Good job Peter! Closing this now.

On treemachine end, currently have to up the memory (e.g. -Xmx2g) or suffer:

java.lang.OutOfMemoryError: Java heap space

I'll look into this.

@josephwb josephwb closed this
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