TypeError when trying to fetch connectors

[bdpedigo]

Hi @schlegelp - currently having some trouble with trying to pull some connectivity data from the FANC dataset (which I believe is public and I should not need any credentials for?).

I created a fresh environment and re-installed latest pymaid.

Code I'm trying to run

import pymaid

print("pymaid version:")
print(pymaid.__version__)
print()

pymaid.CatmaidInstance(
    server="https://fanc.catmaid.virtualflybrain.org/", api_token=None
)

skids = pymaid.get_skids_by_annotation("Paper: Phelps, Hildebrand, Graham et al. 2020")
print("# fetched neurons:")
print(len(skids))
print()

connectors = pymaid.get_connectors(skids)

Output

pymaid version:
2.0.6

INFO  : Global CATMAID instance set. Caching is ON. (pymaid)
# fetched neurons:
1198

Traceback (most recent call last):
  File "/Users/bpedigo/JHU_code/maggot_models/maggot_models/notebooks/try_pull_vnc.py", line 17, in <module>
    connectors = pymaid.get_connectors(skids)
  File "/Users/bpedigo/miniconda3/envs/test-pymaid/lib/python3.9/site-packages/pymaid/cache.py", line 316, in wrapper
    res = function(*args, **kwargs)
  File "/Users/bpedigo/miniconda3/envs/test-pymaid/lib/python3.9/site-packages/pymaid/fetch.py", line 1247, in get_connectors
    user_list = get_user_list(remote_instance=remote_instance)
  File "/Users/bpedigo/miniconda3/envs/test-pymaid/lib/python3.9/site-packages/pymaid/cache.py", line 316, in wrapper
    res = function(*args, **kwargs)
  File "/Users/bpedigo/miniconda3/envs/test-pymaid/lib/python3.9/site-packages/pymaid/fetch.py", line 3724, in get_user_list
    df = pd.DataFrame([[e[c] for c in columns] for e in user_list],
  File "/Users/bpedigo/miniconda3/envs/test-pymaid/lib/python3.9/site-packages/pymaid/fetch.py", line 3724, in <listcomp>
    df = pd.DataFrame([[e[c] for c in columns] for e in user_list],
  File "/Users/bpedigo/miniconda3/envs/test-pymaid/lib/python3.9/site-packages/pymaid/fetch.py", line 3724, in <listcomp>
    df = pd.DataFrame([[e[c] for c in columns] for e in user_list],
TypeError: string indices must be integers

Any ideas right away as to what could be causing this, or am I using pymaid incorrectly? If nothing jumps out to you I'm happy to look into it further. Looks like something related to pymaid user so I'm guessing I am just not logged in properly or something?

[bdpedigo]

Update - this does work:

neurons = pymaid.find_neurons(
    annotations="Paper: Phelps, Hildebrand, Graham et al. 2020"
)
pymaid.adjacency_matrix(neurons)

so maybe specific to the get_connectors function? Individual connectors aren't that important for me right now so I think this will work, but still curious about how to use that properly

[schlegelp]

Hi Ben! Your minimal example works for me. Best guess is that this is an issue with missing user data (that data is scrubbed for release on public CATMAID instances). I fixed a few bugs there a while ago (see e.g. b7661e4) but haven't pushed a new release since.

With that said: I just released pymaid 2.1.0 which includes this fix. Let me know if that does it for you.

Two side notes:

1. This new release now supports (and requires) navis >= 1.0.0 which came with a couple renamed functions
2. With this release the default max_threads for CatmaidInstance went down from 100 to 10 to avoid connection warnings with the sometimes slower public CATMAID servers. If you server/internet connection supports that, you can of course go back up again.

[bdpedigo]

Awesome, with that release this looks to be working now. Thanks for the help!