ens-lgil / pgs_template_validator

Standalone Python validator for the PGS Catalog Curation Template (Metadata)

PGS Catalog template validator

Standalone Python validator for the PGS Catalog Curation Template (Metadata)

For more information about the PGS Catalog submission and its template, go to this page: https://www.pgscatalog.org/submit/

Installation

pip install -r requirements.txt

Example of command

As command line

python pgs_metadata_validator.py -f <my_template_file>.xlsx

As REST API endpoint

To launch the REST API (Flask)

python main.py

and then send the request to validate the file, e.g. with curl:

curl -X POST -H "Content-Type: application/json" -d "{ \"filename\": \"<my_template_file>.xlsx\" }" http://127.0.0.1:5000/validate

Deploy it as a REST API service on Google Cloud (App Engine)

Only possible if you already have a Google Cloud account!

To deploy it:

• Rename app.yaml_template to app.yaml
• Update app.yaml by replacing the variable(s) between <> with the right value(s)
• Install the Cloud SDK if you don't have it
• Run gcloud app deploy in this repository