User story

As a user, I want to run a script that parses bonsai generated files, etc., into a session.json file that is valid under aind-data-schema so I can automatically generate and attach session.json files to my session.

Acceptance criteria

• Maps to the latest version of aind-data-schema
• Given a user has some generated files from bonsai and other acquisition hardware, when they run a command from bash with some arguments for an input directory and an output directory, then a session.json file will be generated.
• 100% test and docstring coverage

Sprint Ready Checklist

• 1. Acceptance criteria defined
• 2. Team understands acceptance criteria
• 3. Team has defined solution / steps to satisfy acceptance criteria
• 4. Acceptance criteria is verifiable / testable
• 5. External / 3rd Party dependencies identified
• 6. Ticket is prioritized and sized

Notes

• likely we should update whatever scripts Kenta runs on his rig to import and run the new mapper.

Talk to Camilo

User story

As a dev-ops engineer, I want to semantic versioning automated, so developers don't have to manually track the version.

Acceptance criteria

• Given a pull request is merged into main, then the version will automatically bumped.

Sprint Ready Checklist

• 1. Acceptance criteria defined
• 2. Team understands acceptance criteria
• 3. Team has defined solution / steps to satisfy acceptance criteria
• 4. Acceptance criteria is verifiable / testable
• 5. External / 3rd Party dependencies identified
• 6. Ticket is prioritized and sized

Notes

Add any helpful notes here.

Kayvon wrote some scripts for extracting metadata from tiffs generated by Bergamo rigs. Integrate them here.

Acceptance Criteria:

• a bergamo.py module exists
• python -m aind_metadata_mapper.bergamo input_path output_json works

Notes:

• files attached to this issue
  bergamo_session.zip

Sasha prototyped some code to automatically create a Session from OpenEphys log files. Let's integrate it here so that it can be run automatically.

reference code is here: https://codeocean.allenneuraldynamics.org/capsule/1630654/tree

Relevant data needs to be pulled from LIMS and sorted out into two folders for the transfer service. Two modalities (multiplane ophys and behavior data) need to be specified in the csv file for the aind-data-transfer to upload.

Is your feature request related to a problem? Please describe.
Right now the manual data entry model is too strict. The data model needs to be changed as experiments change.

Describe the solution you'd like
Refactor the bergamo mapper into two parts: 1) a module that extracts tiff header metadata into a custom data model, and 2) an example script the incorporates that information into a Session generation script.

User story

As a user, I want to save procedures metadata, so I can include it with my data acquisition sets.

Acceptance criteria

• Given a script is run with a subject id and output dir (default to current working dir), then a procedures json file will be saved.

Sprint Ready Checklist

• 1. Acceptance criteria defined
• 2. Team understands acceptance criteria
• 3. Team has defined solution / steps to satisfy acceptance criteria
• 4. Acceptance criteria is verifiable / testable
• 5. External / 3rd Party dependencies identified
• 6. Ticket is prioritized and sized

Notes

Add any helpful notes here.

User story

As a user, I want to save subject and procedures metadata, so I can include it with my data acquisition sets.

Acceptance criteria

• Given a script is run with a subject id and output dir (default to current working dir), then a subject file will be saved.

Sprint Ready Checklist

• 1. Acceptance criteria defined
• 2. Team understands acceptance criteria
• 3. Team has defined solution / steps to satisfy acceptance criteria
• 4. Acceptance criteria is verifiable / testable
• 5. External / 3rd Party dependencies identified
• 6. Ticket is prioritized and sized

Notes

Add any helpful notes here.

Acceptance criteria:

• existing conversion methods move to this repo
• update Kenta's existing repo to import and utilize this repo
• put the utility methods in fip.py.
• there is one module for extracting metadata from files.
• there is an example script showing how into create a Session from those files.

User story

As a user, I want the repo published to PyPI, so I can pip install it easily.

Acceptance criteria

• Given a pull request is merged into main, then the repository is automatically packaged and published to PyPI.

Sprint Ready Checklist

• 1. Acceptance criteria defined
• 2. Team understands acceptance criteria
• 3. Team has defined solution / steps to satisfy acceptance criteria
• 4. Acceptance criteria is verifiable / testable
• 5. External / 3rd Party dependencies identified
• 6. Ticket is prioritized and sized

Notes

Add any helpful notes here.