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HTTP response code 502 for phylographter nexson export #38

Closed
josephwb opened this Issue · 10 comments

3 participants

Joseph W. Brown Jonathan A Rees Peter Midford
Joseph W. Brown
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).

Jonathan A Rees
Owner
Joseph W. Brown
Owner

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

Peter Midford
Owner
Joseph W. Brown
Owner

Yes.

Joseph W. Brown
Owner

Oops.Timeout is back.

Peter Midford
Owner
Peter Midford
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.

Jonathan A Rees
Owner
Joseph W. Brown josephwb referenced this issue in OpenTreeOfLife/treemachine
Closed

pull nexson trees from phylografter and add to graph #18

Peter Midford
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.

Joseph W. Brown
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.

Joseph W. Brown josephwb closed this
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