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Validate a molpath_db for referential integrity and completeness

Source: R/database.R
mp_validate_db.Rd

Checks that all foreign key relationships in the database are satisfied (e.g., every sample references an existing patient) and reports on data completeness across tables.

Usage

mp_validate_db(db)

Arguments

db

A molpath_db object to validate.

Value

Invisibly, a list with three elements:

valid

Logical. TRUE if no referential integrity issues were found.

issues

Character vector of issue descriptions (empty if valid).

completeness

Named numeric vector with percentages of patients having data in each table (e.g., pct_with_variants, pct_with_survival).

Details

The following referential integrity checks are performed:

  • All patient_id values in the samples table exist in patients.

  • All sample_id values in the variants table exist in samples.

  • All sample_id values in the reports table exist in samples.

  • All patient_id values in the clinical table exist in patients.

  • All patient_id values in the survival table exist in patients.

When called interactively, results are printed using cli formatting.

Examples

# \donttest{
db <- mp_example_db(n_patients = 10, seed = 1)
validation <- mp_validate_db(db)
#> 
#> ── Validating molpath database ──
#> 
#> ✔ No referential integrity issues found.
#> 
#> ── Data completeness 
#>   • Patients with samples: 100%
#>   • Patients with variants: 100%
#>   • Patients with reports: 100%
#>   • Patients with clinical: 100%
#>   • Patients with survival: 100%
validation$valid
#> [1] TRUE
# }