neuromorpho-api

Querying the neuromorpho.org database in Python with requests.


As of May 2024, the SSL key for neuromorpho.org has been updated, and the
workaround packaged here is no longer necessary!
The [requests](https://pypi.org/project/requests/) package can now be used
directly with the neuromorpho.org API.
This project will be archived, though the documentation will remain live and
updated to demonstrate programmatic access of neuromorpho data.

Quickstart

>>> import requests

>>> neuron_endpoint = "https://neuromorpho.org/api/neuron/"
>>> resp = requests.get(neuron_endpoint + "fields")
>>> resp.json()
{'Neuron Fields': ['neuron_id',
  'neuron_name',
  'archive',
  'age_scale',
  'gender',
  ...

See the tutorial for more detailed examples, including selecting neurons by attribute pattern matching and downloading SWC traces.

What is was this package?

The neuromorpho-api package provides a requests.Session instance with a custom SSLContext needed for interacting with neuromorpho.org.

Why can't I just use `requests` directly?

NOTE: should no longer be an issue as of 05-24

You may see something like the following:

>>> import requests
>>> requests.get("https://neuromorpho.org/api/neuron/id/1")
Traceback (most recent call last)
   ...
SSLError: HTTPSConnectionPool(host='neuromorpho.org', port=443): Max retries exceeded with url: /api/neuron/id/1 (Caused by SSLError(SSLError(1, '[SSL: DH_KEY_TOO_SMALL] dh key too small (_ssl.c:1006)')))

It appears the key provided by neuromorpho.org is incompatible with the default Python SSL cipher. This package works around this issue using Robin De Schepper's solution posted on Stack Overflow. At some point in the future, the neuromorpho certificate may (hopefully) be updated, at which point this package will be archived.

Future compatibility

The requestor provided by this package is intended as a temporary workaround for the current DH key issue with neuromorpho.org. If the neuromorpho.org certificate is updated, the requestor with the custom SSLContext will no longer be necessary, and users can switch to using requests directly. Therefore, the following import alias is recommended:

from neuromorpho-api import requestor as requests

With an updated certificate, the above can be changed to:

import requests

and all code that depends on requests.get should continue to work as expected.