Closed wbwakeman closed 2 years ago
There does appear to be an existing implementation of this class using just the from_lims and warehouse APIs
Metadata tables we need to be able to get are:
units.csv
channels.csv
probes.csv
sessions.csv
behavior_sessions.csv
These should all be such that they can be read in with pandas.read_csv()
, yielding a DataFrame.
For now: NWB files will only be looked up from sessions.csv
(because we aren't releasing behavior sessions yet). The column for file ID will be called file_id
.
This is a project-level class that is used by public AllenSDK users to get metadata about all sessions. This allows them to filter and retrieve specific files of interest to them.
Need to create a Visual Behavior Ecephys project class. This will analogous to the VBO cache class implemented in
https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/brain_observatory/behavior/behavior_project_cache/behavior_project_cache.py (modern - Sprint 2021)
Implement a project class that provides methods to:
We are only supporting a from_s3 API. There will be no from_lims API for this data release.
Tasks
Instructions to create bucket https://github.com/AllenInstitute/informatics_data_release_tools/tree/main/deploy
Instructions to upload data https://github.com/AllenInstitute/informatics_data_release_tools
Validation criteria:
from_s3_cache
method like the VBO cache class (VisualBehaviorOphysProjectCache
) to instantiate the class with a from_s3 API that points to the bucket being used for the release.get_ecephys_session
method to download NWB files from S3 and instantiate them intoBehaviorEcephysSession
objects.Note: they will not include local file paths or unique file ID column.