Lycophron is a CLI tool to support batch uploads of records to Zenodo.

The tool supports the upload through CSV files that describe each record to be uploaded.

1. Installation

   Install from PyPi:

   pip install --user lycophron 

   Alternatively, use pipx:

   pipx install lycophron 

   Or install directly from Github:

   pip install --user git+https://github.com/plazi/[email protected] 

2. Initalize a local project named "monkeys"

   lycophron init monkeys

   List the project contents:

   cd monkeys/  
   
   tree
   #|____lycophron.cfg
   #|____lycophron.db
   #|____files
   #| |____Adam_Hubert_1976.pdf
   #|____dev_logs.log

   You will be prompted to input the authentication token. You can leave it empty as this can be done afterward by directly editing the configuration file.

3. Configure the project (add or edit TOKEN and ZENODO_URL)

   cat lycophron.cfg
   # TOKEN = 'CHANGE_ME'
   # ZENODO_URL = 'https://zenodo.org/api'

4. Create a CSV file from a template

   Generate a template with all the fields:

   lycophron gen-template --filename output.csv --all

   Add custom fields (e.g. dwc and oc) to the template:

   lycophron gen-template --filename output.csv --custom "dwc,ac"

5. Fill in the metadata and load the file

   lycophron load --inputfile output.csv

6. Publish to Zenodo

   lycophron publish

• Installation
• Commands
• Configuration
• Metadata
• How to create a CSV
• Development
• Known issues

Requirements

• Python v3.9+

It is recommended to use a virtual environment to install and run the application.

To create a virtual environment named lycophron, run the following command in your terminal:

python3 -m venv lycophron
source lycophron/bin/activate

To install the CLI tool just run:

# For using the tool
python -m pip install -r requirements.txt

# For local development
python -m pip install requirements-dev.txt

init

This command initializes the project, creates necessary configuration files, and sets up a local database.

init [name] : initialize the app with the given name init --token : initialize the app with a token

⚠️ Adjust configurations in the generated files to meet specific upload requirements.

validate

This command validates the current project. I.e. it checks whether the application is properly configured, the directory structure is correct and the metadata is valid and ready to be loaded locally.

validate --filename : validate the project and the given file.

gen-template

This command generates a CSV file from the default template, containing all the required headers. The template can either be generated with all the fields or by explicitely adding custom fields on top of the required ones.

gen-template --filename : creates the output file in the given path and name. gen-template --all : creates a template using all fields (required and custom fields). gen-template --custom "x,y,z" : creates a template using the required fields plus the given custom fields.

load

This command loads records from a local file into the local Database, ensuring they are ready to upload to Zenodo.

load --inputfile: load records from a given file to a local DB

publish

Publishes the previously loaded records to Zenodo.

This command specifically targets records that are currently unpublished. Importantly, this operation is designed to be executed multiple times, allowing for a phased or incremental approach to publishing records as needed.

publish: publish records to Zenodo

• Generate the template by running lycophron gen-template and fill in the metadata.
• File names must match the files under the directory /files/

⚠️ When working with fields defined as a list in the CSV file, it is essential to separate each item with a new line ("\n"). This ensures proper formatting and accurate representation of the list structure in the CSV file, thus allowing lycophron to parse the values correctly.

Example:

• DOIs are generated on demand, existing or external DOIs are not accepted. issue
• Metadata is compliant with legacy Zenodo, not RDM
• Output is not clear for the user. E.g. user does not know what to run next, how to fix issues with the data, etc.
• init does not create the needed file structure, still requires manual intervention (e.g. creation of ./files/)
• Linking between rows is not supported. E.g. row 1 references a record from row 2

To manage Python dependencies, lycophron uses pip-tools.

You should not need to do this. More often, you will want to just bump all dependencies to their latest versions. See upgrading dependencies

Two major files are used by pip-tools:

• requirements.in, used for production
• requirements-dev.in, used for development

The files are generated from scratch like so:

# Generate requirements.txt
pip-compile requirements.in

# Generate requirements-dev.txt
pip-compile requirements-dev.in

To add a new dependency, add it in the dependencies section of the pyproject.toml file. Add testing/development dependencies under [project.optional-dependencies] section's tests extra.

# Update the requirements.txt file
pip-compile requirements.in --upgrade-package <new-package>

# Update the requirements.dev.txt file
pip-compile requirements-dev.in --upgrade-package <new-package>

To upgrade all dependencies in development, run the following command in your terminal:

pip-compile requirements-dev.in --upgrade

and for production:

pip-compile --upgrade
pip-compile requirements.in --upgrade