| Name | np_codeocean JSON |
| Version |
0.2.1
JSON |
| download |
| home_page | None |
| Summary | Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean |
| upload_time | 2024-09-05 18:09:52 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# np_codeocean
Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean
Requires running as admin on Windows in order to create remote-to-remote symlinks
on the Isilon.
- `upload` CLI tool is provided, which uses the
[`np_session`](https://github.com/AllenInstitute/np_session) interface to find
and upload
raw data for one ecephys session:
```
pip install np_codeocean
upload <session-id>
```
where session-id is a valid input to `np_session.Session()`:
- a lims ID (`1333741475`)
- a workgroups foldername (`DRPilot_366122_20230101`)
- a path to a session folder ( `\\allen\programs\mindscope\workgroups\np-exp\1333741475_719667_20240227`)
- a folder of symlinks pointing to the raw data is created, with a new structure suitable for the KS2.5 sorting pipeline on Code Ocean
- the symlink folder, plus metadata, are entered into a csv file, which is
submitted to [`http://aind-data-transfer-service`](http://aind-data-transfer-service), which in turn runs the
[`aind-data-transfer`](https://github.com/AllenNeuralDynamics/aind-data-transfer)
tool on the HPC, which follows the symlinks to the original data,
median-subtracts/scales/compresses ephys data, then uploads with the AWS CLI tool
- all compression/zipping acts on copies in temporary folders: the original raw data is not altered in anyway
Raw data
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