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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| from typing import List | ||
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| import pandas as pd | ||
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| from allensdk.internal.api import PostgresQueryMixin | ||
| from allensdk.internal.api.queries.utils import build_in_list_selector_query | ||
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| def get_death_date_for_mouse_ids( | ||
| lims_connections: PostgresQueryMixin, | ||
| mouse_ids_list: List[int] | ||
| ) -> pd.DataFrame: | ||
| """ | ||
| Parameters | ||
| ---------- | ||
| lims_connections: | ||
| mouse_ids_list: list of mouse ids | ||
| Returns | ||
| ------- | ||
| Dataframe with columns: | ||
| - mouse id: int | ||
| - death on: datetime | ||
| """ | ||
| query = f""" | ||
| SELECT external_donor_name as mouse_id, death_on | ||
| FROM donors | ||
| {build_in_list_selector_query( | ||
| col='external_donor_name', | ||
| valid_list=mouse_ids_list | ||
| )} | ||
| """ | ||
| return lims_connections.select(query=query) |
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62
...k/brain_observatory/behavior/behavior_project_cache/behavior_neuropixels_project_cache.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| from allensdk.brain_observatory.behavior.behavior_project_cache.\ | ||
| project_apis.data_io import VisualBehaviorNeuropixelsProjectCloudApi | ||
| from allensdk.brain_observatory.behavior.behavior_project_cache.\ | ||
| project_cache_base import ProjectCacheBase | ||
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| class VisualBehaviorNeuropixelsProjectCache(ProjectCacheBase): | ||
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| PROJECT_NAME = "visual-behavior-neuropixels-2022" | ||
| BUCKET_NAME = "sfd-cloudcache-test-bucket" | ||
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| def __init__( | ||
| self, | ||
| fetch_api: VisualBehaviorNeuropixelsProjectCloudApi, | ||
| fetch_tries: int = 2, | ||
| ): | ||
| """ Entrypoint for accessing Visual Behavior Neuropixels data. | ||
| Supports access to metadata tables: | ||
| get_ecephys_session_table() | ||
| get_behavior_session_table() | ||
| get_probe_table() | ||
| get_channel_table() | ||
| get_unit_table | ||
| Provides methods for instantiating session objects | ||
| from the nwb files: | ||
| get_ecephys_session() to load BehaviorEcephysSession | ||
| get_behavior_sesion() to load BehaviorSession | ||
| Provides tools for downloading data: | ||
| Will download data from the s3 bucket if session nwb file is not | ||
| in the local cache, othwerwise will use file from the cache. | ||
| """ | ||
| super().__init__(fetch_api=fetch_api, fetch_tries=fetch_tries) | ||
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| @classmethod | ||
| def cloud_api_class(cls): | ||
| return VisualBehaviorNeuropixelsProjectCloudApi | ||
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| def get_ecephys_session_table(self): | ||
| return self.fetch_api.get_ecephys_session_table(), | ||
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| def get_behavior_session_table(self): | ||
| return self.fetch_api.get_behavior_session_table(), | ||
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| def get_probe_table(self): | ||
| self.fetch_api.get_probe_table(), | ||
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| def get_channel_table(self): | ||
| return self.fetch_api.get_channel_table(), | ||
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| def get_unit_table(self): | ||
| return self.fetch_api.get_unit_table(), | ||
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| def get_ecephys_session(self, ecephys_session_id: int): | ||
| return self.fetch_api.get_ecephys_session(ecephys_session_id) | ||
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| def get_behavior_session(self, behavior_session_id: int): | ||
| return self.fetch_api.get_behavior_session(behavior_session_id) |
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