seaflow-realtime-dbs

This repository contains popcycle database files for realtime monitoring of SeaFlow instrument deployments.

Each database file contains filtering and classification parameters for a single SeaFlow instrument on a research cruise. It should contain populated tables for

metadata information with cruise and serial (the metadata table)
filtering parameters (the filter table)
classification parameters (the gating and poly tables)
a filtering plan (the filter_plan table)
a classification plan ( the gating_plan table)

All other tables should be empty.

Each database file should be placed in the dbs subdirectory and filenames should be formatted as <cruise>_<instrument serial>.db, matching the metadata table.

Direct commits into main are prohibited. All modifications must be made through pull requests.

To upload a new database file to this repository, first create and checkout a new branch in a locally cloned copy of the repository. It's a good idea to start from main and make sure it's up to date with origin before creating the new branch. In this example the local branch will be called KM2206-2022-06-13.

git checkout main
git pull
git checkout -b KM2206-2022-06-13

Make modifications to an existing or new database file, test that file with .github/workflows/validate-dbs.R, then commit and push those changes.

Rscript .github/workflows/validate-dbs.R dbs/KM2206_740.db dbs/KM2206_130.db
# ...
# No errors
git add dbs/KM2206_740.db dbs/KM2206_130.db
git commit -m 'Modify KM2206 740 and 130 filt params to account for change in FSC PMT'
git push -u origin KM2206-2022-06-13

Then, from either the github web interface or using the gh cli tool, create a pull request to main from this branch. This will trigger automated tests (.github/workflows/validate-dbs.R) to make sure the database is compliant with the scheme laid out above and that the database can be used to filter and classify the popcycle test data set.

The github actions for automated tests are defined in.github/workflows/. To confirm that all tests passed, examine the action workflow in the Actions tab of the github repository.

Once all tests have passed the branch will be automatically merged into main.

ctberthiaume / realtime-dbs

seaflow-realtime-dbs

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