error with flywire_partner_summary

[Ibrahim Taştekin]

Dear Greg,

I hope you are well. 

I am getting the following error when I run:

post_synaptic<-flywire_partner_summary(rootid= query_neurons,
+                                  partners = 'outputs',
+                                  remove_autapses =TRUE, threshold = 0, cleft.threshold = 50) # remove autapse and define a minimum synaptic threshold
  |+++++++++                                         | 17% ~03m 25s      Error in curl::curl_fetch_memory(url, handle = handle) :
  HTTP/2 stream 0 was not closed cleanly: PROTOCOL_ERROR (err 1)

If I retry couple of times it is possible to run it successfully, though.

Best

Ibo

[Greg Jefferis]

Thanks, Ibo. That must be quite a lot of ids for the "live" query (flywire_partner_summary) to take ~4m and the whole CAVE+itanna server infrastructure is not completely robust when you start sending a lot of queries. A few options

1. try adding the retry argument eg retry=3. This doesn't apply to all of the server endpoints but can help with some

2. try method="cave" (if you haven't already). This moves all of the query to CAVE rather than itanna in case those are the flaky servers

3. try the hidden fafbseg:::flywire_partners_cave() method with multiple ids at once (by default it only sends one neuron at a time because of possible row limits in the response, but this is very conservative).

or if you can with you application,

4. switch to a connectivity dump with flywire_partner_summary2. The latest dump is v756 which is pretty recent. If you've never downloaded a dump before then flywire_partner_summary2 should tell you what do. If you want a newer one then see slack message at https://flywire-forum.slack.com/archives/C01M4LP2Y2D/p1644529750249139) for download link.

and you can also run

fafbseg:::flywire_connectome_data_message()

to be told where to put the resultant file. All the best,

Greg.

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[Ibrahim Taştekin]

Thanks a lot Greg! method ='cave' solved the problem!