pathogens-portal-scripts

This repository holds the scripts produced for the Swedish Pathogens Portal that are not directly associated with visualisations or the underlying code used to generate the Portal itself. Those scripts can instead be found in our visualisations repository and our main web repository.

Available data

This folder contains all of the scripts and associated files used to update the available data table on the Portal. Instructions on the use of the scripts and files, as well as how they could potentially be changed to be used for other purposes.

All publications

This folder contains all of the scripts used to update the covid publications database. Instructions on the use of the scripts can be found in the directory.

EBI Indexing

This folder contains all of the scripts used to update EBI index JSON file. This will be run as a dialy cronjob in dc-dynamic. The index file is parsed by EBI (on regular basis) and the info about dataset/dashboards are put up in the main EU pathogens portal.

Ongoing Projects

This directory contains scripts and data related to fetching and processing information about ongoing research projects funded by the Swedish Research Council (Vetenskapsrådet).

get_ongoing_projects.py

This script fetches project data from the SweCRIS API (https://swecris-api.vr.se/v1/projects). It performs the following steps:

1. Loads API Token: Reads the SWECRIS_API_TOKEN from environment variables. For local development, create a .env file in the project root and add the token like this:

   SWECRIS_API_TOKEN="your_actual_token"
   

2. Fetches Projects: Retrieves all project data from the API.
3. Filters Ongoing Projects: Filters the projects to include only those whose start and end dates encompass the current date.
4. Matches Topics: Identifies projects related to specific scientific topics (e.g., Antibiotic resistance, COVID-19, Influenza) based on keywords found in the project title or abstract.
5. Formats Output: Structures the relevant information for each matched project (funder, title, funding amount, principal investigator, dates, URL).
6. Saves Data: Saves the filtered and formatted project data into Ongoing_projects/ongoing_research_projects.json JSON file.