check_files_manifest: Check that files are present in manifest

In dccvalidator: Metadata Validation for Data Coordinating Centers

Description

Given a manifest and vector of file names, checks that the file names appear in the manifest. This is useful to ensure that metadata files (not just data files) are included in the manifest for upload.

Usage

check_files_manifest(
  manifest,
  filenames,
  strict = FALSE,
  success_msg = "All required files are present in manifest",
  fail_msg = "Some files may be missing from manifest"
)

Arguments

manifest	The manifest as a data frame or tibble
filenames	File names to look for in the path column of the manifest
strict	If FALSE, return a "check_warn" object; if TRUE, return a "check_fail" object
success_msg	Message indicating the check succeeded.
fail_msg	Message indicating the check failed.

Value

A condition object indicating whether the files are present in the path column of the manifest

Examples

manifest <- data.frame(
  path = c("individual_metadata.csv", "biospecimen_metadata.csv"),
  parent = c("syn123", "syn123")
)
check_files_manifest(
  manifest,
  c(
    "individual_metadata.csv",
    "biospecimen_metadata.csv",
    "assay_metadata.csv"
  )
)

dccvalidator documentation built on July 2, 2020, 4:05 a.m.