Data Input and Quality Control Module - Server Function

Server logic for data input module handling file uploads, parsing of pedigree and genotype data files, and quality control validation.

Usage

modInputServer(id)

Arguments

id

character vector of length 1. Module namespace identifier.

Value

A list with reactive components:

• cleanedStudbook - The QC-cleaned studbook data

• genotypeData - Genotype data (id, first, second) taken from the cleaned studbook when it carries genotypes. A separately uploaded genotype file that fails checkGenotypeFile is dropped without a message, leaving NULL

• qcSummary - Summary of QC results: a list with errors, warnings and records (counts of error rows, warning rows and cleaned records)

• minSireAge - The minimum sire age floor (numeric, or NULL to use the species+sex breeding-age table default). It is re-parsed from the live text box, so it can differ from the value the last "Read and Check Pedigree" used if the box was edited afterward

• minDamAge - The minimum dam age floor (numeric, or NULL to use the species+sex breeding-age table default); the same live-box caveat as minSireAge applies

• isReady - Logical indicating if data is ready for next step

• debugMode - Logical reflecting the Input tab's "Debug on" checkbox

• changedCols - Renamed/changed-column diagnostics from QC

• errorLst - The QC error list, used for dynamic tab management

• pedigreeFileName - The uploaded file's name, used for dynamic tab management

Note

(Developer note) This module is the reference implementation of the package's internal Shiny module contract – see docs/architecture/module-contract.md in the package source (a developer-only file; it does not ship with the installed package).

See also

modInputUI for the user interface.

modPedigreeServer for using the cleaned data.

Other Shiny modules: modBreedingGroupsServer(), modBreedingGroupsUI(), modCrossCenterIdentityServer(), modCrossCenterIdentityUI(), modDeidentifiedExportServer(), modDeidentifiedExportUI(), modGeneticDiversityServer(), modGeneticDiversityUI(), modGeneticValueServer(), modGeneticValueUI(), modGvAndBgDescServer(), modGvAndBgDescUI(), modInputUI(), modMarkerGeneticsServer(), modMarkerGeneticsUI(), modMatePairServer(), modMatePairUI(), modORIPReportingServer(), modORIPReportingUI(), modPedigreeServer(), modPedigreeUI(), modPotentialParentsServer(), modPotentialParentsUI(), modPyramidServer(), modPyramidUI(), modSnapshotTrendsServer(), modSnapshotTrendsUI(), modSummaryStatsServer(), modSummaryStatsUI()