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ICTV: Virus Metadata Conversion and Automation

This repository automates the conversion of virus metadata stored in VMR.xlsx into multiple machine-readable formats using GitHub Actions. When a new version of VMR.xlsx is committed, the repository automatically generates the following:

• TSV (Tab-Separated Values)
• JSON (JavaScript Object Notation)
• XML (Extensible Markup Language)

These files are output to a dedicated folder named converted_files/.

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📦 File Overview

📂 Source

• VMR.xlsx: Source Excel file containing virus metadata
  • The conversion targets the sheet named "VMR MSL40".

🧮 Script

• convert.py: Python script that performs the actual conversion of Excel data to .tsv, .json, and .xml.

📁 Output

• converted_files/: Directory containing converted files:
  • VMR MSL40.tsv
  • VMR MSL40.json
  • VMR MSL40.xml

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⚙️ GitHub Actions Automation

This repository includes a GitHub Actions workflow defined in:

.github/workflows/convert-vmr.yml

🔁 Trigger

The workflow runs automatically when VMR.xlsx is updated (pushed to the repository).

🔨 Workflow Process

1. Checks out the repository.
2. Sets up Python 3.9 and installs dependencies.
3. Converts VMR.xlsx sheet "VMR MSL40" into TSV, JSON, and XML.
4. Commits and pushes the converted files back to the repository.

✅ Permissions

Ensure GitHub Actions has write access to the repository under:

Settings → Actions → General → Workflow permissions → Enable "Read and write permissions"

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Steps

1. merge ICTV files, based on the ICTV ID by combineing the informationo f Exampler and Addisionals (uf exists) into one record. [0_merge_ictv_files.py]
2. convert GenBank Accession ID to Taxonomy ID using NCBI resources. [1_fetch_taxids.py]
3. find the species taxon ID using the TaxID, species name or virus name. [2_species_taxid.py]
4. insert the taxonomy information using the species taxid into the database. [3_ictv2db.py]