R/fct_metadataFromId.R

In chasemc/IDBacApp: MALDI-TOF MS Protien and Small Molecule Analysis

#' Extract a metadata column 
#'
#' @param strainID strain_id
#' @param metadataColumn metadata column name ('species')
#' @param pool pool connection
#'
#' @return data.frame with two columns 'strain_id' and  whatever metadataColumn is requested; rows filtered by ID
#' @export
#'
idbac_get_metadata <- function(strainID = NULL,
                               metadataColumn = NULL,
                               pool){
  
  .checkPool(pool = pool)
  
  if (is.null(strainID) && is.null(metadataColumn)) {
    
    pool::poolWithTransaction(pool, 
                              function(conn){
                                statement <- glue::glue(
                                  "SELECT *
                                FROM metadata"
                                )
                                query <- DBI::dbSendStatement(statement = statement,
                                                              con = conn)
                                selectedMeta <- DBI::dbFetch(query)
                                DBI::dbClearResult(query)
                                return(selectedMeta)
                                
                              })
  } else if (is.null(strainID)) {
    
    pool::poolWithTransaction(pool, 
                              function(conn){
                                glued <- c("strain_id", metadataColumn)
                                
                                query <- glue::glue_sql(
                                  "SELECT {`glued`*}
                                FROM metadata
                                WHERE `strain_id` = $ids",
                                  .con = conn)
                                
                                DBI::dbBind(query, list(ids = strainID))
                                selectedMeta <- DBI::dbFetch(query)
                                DBI::dbClearResult(query)
                                return(selectedMeta)
                                
                              })
    
  } else if (is.null(metadataColumn)) {
    
    pool::poolWithTransaction(pool, 
                              function(conn){
                                statement <- glue::glue(
                                  "SELECT *
                                FROM metadata
                                WHERE `strain_id` = $ids"
                                )
                                query <- DBI::dbSendStatement(statement = statement,
                                                              con = conn)
                                DBI::dbBind(query, list(ids = strainID))
                                selectedMeta <- DBI::dbFetch(query)
                                DBI::dbClearResult(query)
                                return(selectedMeta)
                                
                              })
    
  } else {
    
    pool::poolWithTransaction(pool, 
                              function(conn){
                                
                                glued <- c("strain_id", metadataColumn)
                                
                                statement  <- glue::glue_sql(
                                  "SELECT {`glued`*}
                                FROM metadata
                                WHERE `strain_id` = $ids",
                                  .con = conn)
                                
                                query <- DBI::dbSendStatement(statement = statement,
                                                              con = conn)
                                DBI::dbBind(query, list(ids = strainID))
                                selectedMeta <- DBI::dbFetch(query)
                                DBI::dbClearResult(query)
                                return(selectedMeta)
                              })
    
  }
}