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Validate All Studies in a metawoRld Project

validate_world.Rd

Iterates through all study subdirectories within the project's data/ directory and runs validate_study() on each one to check conformity against the project schema and internal consistency.

Usage

validate_world(path = ".", check_linkages = TRUE)

Arguments

path

Character string. The path to the root directory of the metawoRld project. Defaults to the current working directory (.).

check_linkages

Logical. Passed down to validate_study() for each study. Should the consistency checks between data.csv and metadata.yml be performed? Defaults to TRUE.

Value

A list containing:

overall_status

Character string: "PASS" if all studies validated successfully, "FAIL" otherwise.

validated_studies

Integer: The number of study directories checked.

passed_studies

Integer: The number of studies that passed validation.

failed_studies_count

Integer: The number of studies that failed validation.

failed_studies_details

A list (named by study_id) containing the error messages for studies that failed validation. Empty if all passed.

Prints informative messages about the validation progress and summary.

Examples

if (FALSE) { # \dontrun{
# --- Setup: Create a project, add one valid study and one template ---
proj_path <- file.path(tempdir(), "validate_world_test")
create_metawoRld(
  path = proj_path,
  project_name = "Validate World Test",
  project_description = "Testing validate_world()"
)

# Add a valid study
meta1 <- list(
  study_id = "S1", title = "Valid Study", authors = list("A"), year = 2021,
  journal = "J1", study_design="Cohort", country="X", sample_type="Serum",
  outcome_groups = list(g1=list(name="Case", def="..."), g2=list(name="Ctrl", def="...")),
  measurement_methods = list(m1=list(unit="pg/mL", analysis_type="E"))
)
data1 <- data.frame(measurement_id="m1a", method_ref_id="m1", cytokine_name="CK1",
                    group_label="g1", gestational_age_timing="T1", n=10,
                    statistic_type="mean_sd", value1=5, value2=1)
add_study_data(proj_path, "S1", meta1, data1)

# Add a template study (which will likely fail validation initially)
add_study_template(proj_path, "TemplateStudy")

# Add an empty folder (should be skipped by validation logic within validate_study)
fs::dir_create(file.path(proj_path, "data", "EmptyFolder"))
# Add a folder with only metadata.yml (should fail in validate_study)
fs::dir_create(file.path(proj_path, "data", "MetadataOnly"))
file.copy(file.path(proj_path, "data", "S1", "metadata.yml"),
          file.path(proj_path, "data", "MetadataOnly", "metadata.yml"))

# --- Run validation ---
validation_results <- validate_world(path = proj_path)

# Print the results
print(validation_results)

# --- Clean up ---
unlink(proj_path, recursive = TRUE)
} # }