chore: update hgnc_complete_set download url

[tedil]

Summary by CodeRabbit

• New Features

  • Updated URLs for genomic data sources, including the HGNC complete set now hosted on Google Cloud Storage.
  • Added multiple new URLs related to the gnomAD project, including various VCF files for different chromosomes and versions.

• Bug Fixes

  • Removed outdated URLs pointing to OrphaData API endpoints and other genomic data sources.

• Chores

  • Marked some URLs with skip_upstream_check: true for reliability during tests.

[coderabbitai]

Walkthrough

The changes involve updates to the download_urls.yml file and the Snakemake workflow in rules/work/genes/hgnc.smk. The download_urls.yml file underwent modifications to URLs, including the removal of several endpoints and the addition of new genomic data sources. Notably, the URL for the HGNC complete set JSON file was changed from an FTP link to a Google Cloud Storage link. In the Snakemake workflow, the genes_hgnc_download rule was updated to reflect this new URL, while other rules remained unchanged.

Changes

File Path	Change Summary
download_urls.yml	Updated URLs, removed several endpoints, added new genomic data URLs, modified excerpt strategies.
rules/work/genes/hgnc.smk	Updated HGNC JSON download URL in genes_hgnc_download rule; no changes to other rules.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Snakemake
    participant HGNC

    User->>Snakemake: Request HGNC data
    Snakemake->>HGNC: Download JSON from new URL
    HGNC-->>Snakemake: Return JSON data
    Snakemake-->>User: Provide processed data

Loading

🐰 In fields so wide and bright,
URLs changed, a joyful sight!
From FTP to clouds we leap,
New data sources, promises to keep.
With every hop, our knowledge grows,
In genomic tales, the rabbit knows! 🌼

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 7557523 and 61706be.

📒 Files selected for processing (2)

• download_urls.yml (1 hunks)
• rules/work/genes/hgnc.smk (1 hunks)

🔇 Additional comments (2)

rules/work/genes/hgnc.smk (1)

17-17: Verify the URL path structure

The new URL contains a redundant "json/json/" path segment which may be a typo. Please verify if this is the correct path structure.

Run the following script to verify the URL accessibility and correct path:

✅ Verification successful

URL path structure is correct and accessible

The current URL with "json/json/" in the path is correct and accessible, returning a 200 status code with a valid JSON file (33MB). The alternative URL without the redundant "json" returns a 404 error. The file was last modified on December 6, 2024, indicating it's actively maintained.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check URL accessibility and compare with potential alternatives

# Test the current URL
echo "Testing current URL..."
curl -sI "https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json"

# Test without redundant json/
echo -e "\nTesting alternative URL..."
curl -sI "https://storage.googleapis.com/public-download-files/hgnc/json/hgnc_complete_set.json"

Length of output: 1314

download_urls.yml (1)

254-257: LGTM! Configuration is properly structured

The new URL entry is well-configured with appropriate flags:

• skip_upstream_check is set due to potential reliability issues
• Manual excerpt strategy is consistent with other similar entries

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[github-actions]

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