VFB_connect test_vfb-connect publish-to-pypi PyPI version DOI

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VFB_connect is a Python lib that wraps data/knowledgeBase query endpoints and returns DataFrame tables.

Available on PyPi:

pip install vfb_connect

Some examples:

# VFB connect object wraps connections and queries to public VFB servers.

from vfb_connect import vfb

# Get TermInfo for Types/Classes, DataSets and anatomical individuals.

vfb.term('FBbt_00003686')

vfb.terms(['Ito02013'])

vfb.terms(['VFB_00010001'])

# Get all terms relevant to a brain region (all parts and all overlapping cells. You can query by label, symbol, synonym, id or xref.

vfb.get_terms_by_region('fan-shaped body')

TermInfo returns a pandas DataFrame by default but can also return a dict summary or full VFBTerms.

For more examples see our Quick Guide Jupyter Notebook

Cached query results

Several queries — similar morphology, the neurons and neuron types in a region, parts, subtypes, lineage clones and innervating tracts — are answered from VFBquery's pre-computed results at https://v3-cached.virtualflybrain.org, the same source the Virtual Fly Brain website reads. Results and column names are unchanged; the query is simply not re-derived. If the service is unavailable, slow or returns an incomplete result, the original Neo4j/Owlery query runs instead, so nothing depends on it being up.

Results larger than one response (25,000 rows) are paged, with a progress bar — a whole neuropil can be hundreds of thousands of rows. vfb._load_limit truncates them, and any truncation is reported rather than silent.

vfb.query_counts(id) returns how many results every query on a term would give, in one request and without running any of them:

vfb.query_counts('FBbt_00003748')
# {'NeuronsSynaptic': 464, 'PartsOf': 28, 'ImagesNeurons': 226524, ...}

A count of -1 there means VFBquery could not count that query — not that it is empty.

Environment variables:

  • VFB_USE_CACHED_QUERIES=false — always run queries directly.
  • VFB_CACHED_QUERY_URL — point at a different VFBquery deployment.
  • VFB_CACHED_QUERY_MAX_ROWS — row ceiling before a result is truncated (default 250,000).

Methods that use it also take use_cached=True|False to override per call.

Project links

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Owner

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Credits

Author: Robert Court

GitHub Statistics

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The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

GPL-3.0-or-later

Requires

Python >=3.8

Classifiers

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