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biobouncer (R package) biobouncer logo

This directory holds the R package for biobouncer. See the repository root README.md for what biobouncer does and PLAN.md for the architecture.

Offline pattern and cache modes, live remote mode, and existence mode (snapshot first, then remote) work across 46 sources.

Usage

library(biobouncer)

# List what can be checked.
sources()
source_info()

# pattern mode: is the string well-formed?
check_id(c("MONDO:0005148", "mondo:5148", "GO:0006915"), source_db = "mondo")

# cache mode: does the id exist in a pinned snapshot?
check_id("MONDO:0005148", source_db = "mondo", how = "cache", version = "sample")

# Snapshot management.
biobouncer_snapshots()
biobouncer_cache_dir()
biobouncer_pull("go") # download a full snapshot into the cache directory

# Just the verdict.
is_valid_id("P04637", source_db = "uniprot")

check_id() returns a tibble with one row per input and the columns input, valid, normalized, suggestion, source_db, version, species, how, and error (the reason a remote check was left indeterminate, else NA).

Validation frameworks

Adapters wrap the core classifier so it plugs into common validation frameworks. They never reimplement any checks.

# checkmate style: check, assert, or test.
check_valid_id(c("MONDO:0005148", "mondo:5148"), "mondo")
assert_valid_id("MONDO:0005148", "mondo")
test_valid_id("MONDO:0005148", "mondo")

# shinyvalidate rule.
iv <- shinyvalidate::InputValidator$new()
iv$add_rule("term", sv_biobouncer("mondo"))

# Data-frame validation. id_predicate() returns an elementwise predicate.
is_mondo <- id_predicate("mondo")

# assertr:
df |> assertr::assert(is_mondo, term)

# validate:
rules <- validate::validator(good_terms = is_mondo(term))
validate::confront(df, rules)

Development

From the repository root:

# generate NAMESPACE and man pages
roxygen2::roxygenise("pkg-r")

# run the tests
testthat::test_dir("pkg-r/tests/testthat")

Shared source definitions and the conformance corpus live in shared/ at the repository root and are vendored into inst/extdata/ by python tools/sync_shared.py. Do not edit the vendored copies by hand.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.