MicrobiomeProfiler/.github/workflows/validate_external_data.yml at devel · YuLab-SMU/MicrobiomeProfiler · GitHub

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name: Validate External Data

on:
  pull_request:
    paths:
      - "R/**"
      - "data-raw/**"
      - "inst/extdata/**"
      - ".github/workflows/update_external_data.yml"
      - ".github/workflows/validate_external_data.yml"
  workflow_dispatch:

jobs:
  validate-external-data:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "release"
          use-public-rspm: true

      - name: Setup dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgload, any::jsonlite, any::digest, any::gson, any::testthat, bioc::bugsigdbr

      - name: Validate Disbiome builder with fixtures
        run: >
          Rscript -e 'pkgload::load_all(".");
          testthat::test_dir(
            "tests/testthat",
            filter = "build_disbiome",
            reporter = "summary"
          )'

      - name: Validate eggNOG builder and runtime with fixtures
        run: >
          Rscript -e 'pkgload::load_all(".");
          testthat::test_dir(
            "tests/testthat",
            filter = "build_eggnog|enrichEggNOG_external",
            reporter = "summary"
          )'

      - name: Build BugSigDB artifact
        run: >
          Rscript -e 'source("data-raw/build_bugsigdb.R");
          build_bugsigdb_artifact(
            output_dir = "build/external-data/bugsigdb/current",
            base_url = "https://yulab-smu.github.io/MicrobiomeProfiler/datasets/bugsigdb/current"
          )'

      - name: Validate manifests and artifacts
        run: >
          Rscript -e 'manifests <- list.files("build/external-data",
          pattern = "manifest.json$", recursive = TRUE, full.names = TRUE);
          stopifnot(length(manifests) >= 1);
          for (path in manifests) {
            manifest <- jsonlite::fromJSON(path, simplifyVector = FALSE);
            stopifnot(!is.null(manifest$dataset), !is.null(manifest$version),
              length(manifest$artifact_files) >= 1);
            artifact <- manifest$artifact_files[[1]];
            artifact_path <- file.path(dirname(path), artifact$name);
            stopifnot(file.exists(artifact_path));
            stopifnot(identical(
              digest::digest(file = artifact_path, algo = "sha256", serialize = FALSE),
              artifact$sha256
            ));
            object <- readRDS(artifact_path);
            if (identical(artifact$object_type, "gson")) {
              stopifnot(inherits(object, "GSON"));
            } else if (identical(artifact$object_type, "term2gene_bundle")) {
              stopifnot(all(c("dataset", "version", "term2gene", "term2name", "metadata") %in% names(object)));
            } else {
              stop("Unsupported object_type: ", artifact$object_type);
            }
          }'