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It looks like the taxomachine neo4j on the dev server has a maximum connection timeout of about 3 minutes. I am not sure how to increase this, but it definitely needs to be much longer if we want to get TNRS results for large trees.
An alternative would be to use a local instance of taxomachine to do the TNRS. This would require downloading the taxonomy. We could use/provide a snapshot of the taxonomy db so people would not have to build it. This is related to the issue of bringing taxonomy into OTU. See #14.