Zenodo tools

This repository provides tools for uploading, downloading and manipulating seatizen sessions on the zenodo platform

Summary

• Installation
• Usage upload
• Usage download
• Contributing
• License

Installation

To ensure a consistent environment for all users, this project uses a Conda environment defined in a zenodo_env.yml file. Follow these steps to set up your environment:

1. Install Conda: If you do not have Conda installed, download and install Miniconda or Anaconda.

2. Create the Conda Environment: Navigate to the root of the project directory and run the following command to create a new environment from the zenodo_env.yml file:

   conda env create -f zenodo_env.yml

3. Activate the Environment: Once the environment is created, activate it using:

   conda activate zenodo_env

4. Create config.json: To use this repository, you need a config.json file at the root of the project containing your own ACCESS_TOKEN:

   {
       "ACCESS_TOKEN": "ACCESS_TOKEN",
       "ZENODO_LINK": "https://zenodo.org/api/deposit/depositions"
   }

5. Other lib: Install mod-spatialite. Here for ubuntu 22.04

sudo apt-get install libsqlite3-mod-spatialite

6. Troubleshooting: If sqlite3.OperationalError: /home/bioeos/miniconda3/envs/zenodo_env/bin/../lib/libstdc++.so.6: version 'GLIBCXX_3.4.32' not found (required by /usr/lib/x86_64-linux-gnu/libproj.so.25)

Use:

sudo find / -name libstdc++.so.6 to find your local file.

strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX to check if the version 'GLIBCXX_3.4.32' is present.

Then:

ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /home/bioeos/miniconda3/envs/zenodo_env/lib/libstdc++.so
ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /home/bioeos/miniconda3/envs/zenodo_env/lib/libstdc++.so.6

Cheatsheet command to generate all from seatizen data

python zenodo-manager.py -efol -pfol /media/bioeos/E/2015_plancha_session/ -ulo -ffi -fr -ne # Force inserting frame in database with no export and regenerate database.
python zenodo-manager.py -efol -pfol /media/bioeos/E/poulain_syc -ulo -ffi -ne # Force inserting frame in database with no export.
python zenodo-manager.py -ecsv -pcsv ../../Bioeos/OUTPUT_DATA/zenodo_suivi/processed_data_without_2015.csv -ulo -la ../../Bioeos/annotations_some_image/Export_human/ -ne # Add frames and import annotations.
python zenodo-manager.py -eno -ulo -ssn 1 # Update database data (all class and label).
python zenodo-manager.py -eno -ulo # Export all files.

Qgis command to load data

-- Load prediction map of a class 
SELECT f.GPSPosition, mlc.name, mlp.score
FROM multilabel_prediction mlp
JOIN frame f ON f.id = mlp.frame_id
JOIN multilabel_class mlc on mlc.id = mlp.ml_class_id;

-- Load deposit linestring
SELECT d.session_name, d.platform_type, dl.footprint_linestring
FROM deposit_linestring dl
JOIN deposit d on d.doi = dl.deposit_doi
WHERE dl.footprint_linestring NOT NULL;

Contributing

Contributions are welcome! To contribute, please follow these steps:

1. Fork the repository.
2. Create a new branch for your feature or fix.
3. Commit your changes with clear, descriptive messages.
4. Push your branch and submit a pull request.

License

This framework is distributed under the CC0-1.0 license. See LICENSE for more information.