ValidateOutput Class for Contributors Table Validation

ValidateOutput Class for Contributors Table Validation

ValidateOutput Class for Contributors Table Validation

Details

The ValidateOutput class runs both column-based validation (ensuring required columns exist) and data-based validation (checking correctness of values) for a contributors table.

It integrates two validation classes:

• ColumnValidator: Ensures required columns are present.

• Validator: Runs content-based validation checks on contributor data.

This validation process is configured via a YAML file. The inst/config/ package di contains predefined YAML configuration files for each of the six output types.

Column Validation

The ColumnValidator ensures that required columns exist before running data-based checks. If a required column is missing, validation stops immediately with an error.

Example YAML Configuration (inst/config/title_validation.yaml):

column_config:
  rules:
    minimal:
      operator: "AND"
      columns:
        - Firstname
        - Middle name
        - Surname
        - Order in publication
      severity: "error"

    affiliation:
      operator: "OR"
      columns:
        - Primary affiliation
        - Secondary affiliation
      regex: "^Affiliation [0-9]+$"
      severity: "error"

    title:
      operator: "AND"
      columns:
        - Corresponding author?
        - Email address
      severity: "warning"

General Data Validation

The Validator runs content-based validation checks after column validation passes.

Example Validation Configuration (inst/config/title_validation.yaml):

validation_config:
  validations:
    - name: check_missing_order
    - name: check_duplicate_order
    - name: check_missing_surname
    - name: check_missing_firstname
    - name: check_duplicate_initials
    - name: check_missing_corresponding
      dependencies:
        - '"Corresponding author?" 
    - name: check_missing_email
      dependencies:
        - '"Corresponding author?" 
        - 'self$results[["check_missing_corresponding"]]$type == "success"'
        - '"Email address" 
    - name: check_duplicate_names
    - name: check_affiliation
    - name: check_affiliation_consistency

Dependencies:

• Some validation checks only run if other conditions are met.

• Example: check_missing_email only runs if:

  1. "Corresponding author?" exists.

  2. check_missing_corresponding has passed.

  3. "Email address" is in the dataset.

Integration

The class runs in the following order:

1. Column validation (via ColumnValidator).

2. If columns are valid → Run content validation (via Validator).

3. If column validation fails → Stop and return column validation errors.

Usage

# Load a validation configuration file
config_path <- "inst/config/title_validation.yaml"

# Create a ValidateOutput instance
validate_output <- ValidateOutput$new(config_path = config_path)

# Run validation on the contributors table
results <- validate_output$run_validations(contributors_table)
print(results)

See also

ColumnValidator, Validator

Public fields

validator

Instance of the Validator class for data validation.

column_validator

Instance of the ColumnValidator class for column validation.

config

Stores the combined YAML validation configuration.

Methods

Public methods

• ValidateOutput$new()

• ValidateOutput$run_validations()

• ValidateOutput$clone()

---

Method new()

Initializes the ValidateOutput class.

Usage

ValidateOutput$new(config_path)

Arguments

config_path

Path to the YAML configuration file.

---

Method run_validations()

Runs both column and data validation on a contributors table.

Usage

ValidateOutput$run_validations(contributors_table)

Arguments

contributors_table

A dataframe containing contributor data.

Returns

A list of validation results, each containing:

• type: "error", "warning", or "success".

• message: A descriptive validation message.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ValidateOutput$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.