resolving #46

DESCRIPTION

@@ -88,6 +88,7 @@ Collate:
     'generic_pkg_data_derive.R'
     'impl_data.R'
     'data_archive_md5.R'
+    'data_bioc_reverse_dependencies.R'
     'data_coverage.R'
     'data_desc.R'
     'data_documentation_examples.R'

R/data_bioc_reverse_dependencies.R

@@ -0,0 +1,107 @@
+#' @include impl_data.R
+
+# BioConductor reverse dependencies metrics implementation
+# Reuses the viable_revdep_packages() and get_reverse_deps() helpers defined
+# in data_reverse_dependencies.R (both are called at runtime, so no load-time
+# ordering dependency exists between the two files).
+
+#' Known BioConductor repository URLs
+#'
+#' Returns the standard BioConductor repository URLs used to build the package
+#' universe for reverse dependency analysis. Unlike \acronym{CRAN}, the
+#' BioConductor package universe is spread across several repositories
+#' (software, annotation, experiment data and workflows), so all are queried.
+#'
+#' The `"release"` alias always resolves to the current BioConductor release, so
+#' the metric does not need to track the BioConductor version explicitly. A
+#' different release (or an internal mirror) can be supplied through the
+#' `val.meter.bioc_repos` option.
+#'
+#' @param version BioConductor release to target. Defaults to `"release"`.
+#' @return Character vector of repository URLs.
+#' @noRd
+get_bioc_repos <- function(version = "release") {
+  repos <- getOption("val.meter.bioc_repos")
+  if (!is.null(repos)) {
+    return(repos)
+  }
+
+  file.path(
+    "https://bioconductor.org/packages",
+    version,
+    c("bioc", "data/annotation", "data/experiment", "workflows")
+  )
+}
+
+impl_data(
+  "bioc_reverse_dependencies",
+  class = class_character,
+  metric = FALSE,
+  tags = c("adoption", "transient"),
+  permissions = c("network"),
+  title = "BioConductor Reverse Dependencies",
+  description = paste(
+    "The names of packages on \\acronym{BioConductor} that directly depend on",
+    "this package through \\code{Depends}, \\code{Imports}, or",
+    "\\code{LinkingTo} fields."
+  )
+)
+
+impl_data(
+  "bioc_reverse_dependencies",
+  for_resource = cran_repo_resource,
+  function(pkg, resource, field, ...) {
+    # the BioConductor package universe is independent of the package's own
+    # resource, so it is queried from the known BioConductor repositories
+    # rather than from resource@repo.
+    bioc_matrix <- viable_revdep_packages(repos = get_bioc_repos())
+
+    get_reverse_deps(
+      pkg$name,
+      bioc_matrix,
+      dependencies = c("Depends", "Imports", "LinkingTo")
+    )
+  }
+)
+
+impl_data(
+  "bioc_reverse_dependencies",
+  for_resource = mock_resource,
+  function(pkg, resource, field, ...) {
+    # Simulate reverse dependencies with a random sample of package names
+    sample(
+      paste0("mockbiocpkg", seq_len(10)),
+      size = min(rpois(1, 2), 10),
+      replace = FALSE
+    )
+  }
+)
+
+
+impl_data(
+  "bioc_reverse_dependencies_count",
+  class = class_integer,
+  metric = TRUE,
+  tags = c("adoption", "transient"),
+  permissions = c(),
+  title = "BioConductor Reverse Dependencies Count",
+
+  description = paste(
+    "The number of packages on \\acronym{BioConductor} that directly depend",
+    "on this package through \\code{Depends}, \\code{Imports}, or",
+    "\\code{LinkingTo} fields. This metric reflects adoption within the",
+    "BioConductor ecosystem and indicates how many packages would be affected",
+    "by breaking changes. Higher counts suggest wider usage and community",
+    "trust, but also greater responsibility for maintaining backward",
+    "compatibility."
+  )
+)
+
+impl_data(
+  "bioc_reverse_dependencies_count",
+  for_resource = new_union(cran_repo_resource, mock_resource),
+  function(pkg, resource, field, ...) {
+    # Just count the length of rev dep vector
+    length(pkg$bioc_reverse_dependencies)
+  }
+)

tests/testthat/test-data_bioc_reverse_dependencies.R

@@ -0,0 +1,138 @@
+# Helper to create a mock BioConductor package matrix for testing
+create_mock_bioc_matrix <- function() {
+  matrix(
+    c(
+      # Package, Version, Priority, Depends, Imports, LinkingTo, Suggests
+      "biocA", "1.0.0", NA, "R (>= 3.5.0), targetpkg", NA, NA, NA,
+      "biocB", "2.0.0", NA, "R (>= 4.0.0)", "targetpkg, utils", NA, NA,
+      "biocC", "1.5.0", NA, NA, NA, NA, "targetpkg, testthat",
+      "biocD", "3.0.0", NA, NA, "targetpkg", NA, NA,
+      "biocE", "1.2.0", NA, NA, "otherpkg", NA, NA
+    ),
+    nrow = 5,
+    ncol = 7,
+    byrow = TRUE,
+    dimnames = list(
+      c("1", "2", "3", "4", "5"),
+      c(
+        "Package", "Version", "Priority", "Depends",
+        "Imports", "LinkingTo", "Suggests"
+      )
+    )
+  )
+}
+
+describe("get_bioc_repos", {
+  it("returns the standard BioConductor repository URLs", {
+    repos <- get_bioc_repos()
+
+    expect_type(repos, "character")
+    expect_true(length(repos) >= 1)
+    expect_true(all(grepl("^https://bioconductor.org/packages/", repos)))
+    expect_true(any(grepl("/bioc$", repos)))
+  })
+
+  it("targets a specific release when asked", {
+    expect_true(all(grepl("/3.18/", get_bioc_repos(version = "3.18"))))
+  })
+
+  it("honours the val.meter.bioc_repos option override", {
+    withr::with_options(
+      list(val.meter.bioc_repos = "file:///tmp/fake-bioc"),
+      expect_equal(get_bioc_repos(), "file:///tmp/fake-bioc")
+    )
+  })
+})
+
+describe("bioc_reverse_dependencies metric behavior with mocked data", {
+  it("returns dependent package names when the BioC universe is mocked", {
+    mock_matrix <- create_mock_bioc_matrix()
+
+    with_mocked_bindings(
+      viable_revdep_packages = function(repos) mock_matrix,
+      .package = "val.meter",
+      {
+        p <- pkg(
+          cran_repo_resource(
+            package = "targetpkg",
+            repo = "https://cloud.r-project.org/"
+          ),
+          permissions = permissions("network")
+        )
+
+        deps <- p$bioc_reverse_dependencies
+
+        expect_type(deps, "character")
+        # strong deps only (Depends/Imports/LinkingTo), not Suggests
+        expect_true(all(c("biocA", "biocB", "biocD") %in% deps))
+        expect_false("biocC" %in% deps)
+      }
+    )
+  })
+
+  it("returns an empty character vector when no reverse deps exist", {
+    mock_matrix <- create_mock_bioc_matrix()
+
+    with_mocked_bindings(
+      viable_revdep_packages = function(repos) mock_matrix,
+      .package = "val.meter",
+      {
+        p <- pkg(
+          cran_repo_resource(
+            package = "lonelypkg",
+            repo = "https://cloud.r-project.org/"
+          ),
+          permissions = permissions("network")
+        )
+
+        deps <- p$bioc_reverse_dependencies
+
+        expect_type(deps, "character")
+        expect_length(deps, 0)
+      }
+    )
+  })
+
+  it("generates realistic mock data for a mock resource (offline)", {
+    p <- pkg(
+      mock_resource(package = "fakepkg", version = "1.2.3"),
+      permissions("network")
+    )
+
+    deps <- p$bioc_reverse_dependencies
+
+    expect_type(deps, "character")
+    expect_true(length(deps) >= 0 && length(deps) <= 10)
+  })
+})
+
+describe("bioc_reverse_dependencies_count metric behavior", {
+  it("returns integer count matching dependency vector length", {
+    mock_matrix <- create_mock_bioc_matrix()
+
+    with_mocked_bindings(
+      viable_revdep_packages = function(repos) mock_matrix,
+      .package = "val.meter",
+      {
+        p <- pkg(
+          cran_repo_resource(
+            package = "targetpkg",
+            repo = "https://cloud.r-project.org/"
+          ),
+          permissions = permissions("network")
+        )
+
+        count <- p$bioc_reverse_dependencies_count
+        deps <- p$bioc_reverse_dependencies
+
+        expect_type(count, "integer")
+        expect_length(count, 1)
+        expect_equal(count, length(deps))
+      }
+    )
+  })
+
+  it("is registered as a metric", {
+    expect_true("bioc_reverse_dependencies_count" %in% names(metrics()))
+  })
+})