R/dotInstQCOL.R

In JARS3N/PipeFish: pKa,outlier,pO2model,etc

# created a new function because pH isn't necessary
InstQCOL<-function(u=file.choose()){
require(dplyr)
X <- list(LVL = readxl::read_excel(u, sheet = PipeFish::fndLVLs(u)), 
          AC = readxl::read_excel(u, sheet = "Assay Configuration"))
Meta<-setNames(unlist(X$AC[,2]),unlist(X$AC[,1]))
metainfo <- data.frame(sn = Meta["Cartridge Serial"],
                       Lot = paste0(Meta["Cartridge Type"],
                                    Meta["Cartridge Lot"]), 
                       Instrument = Meta["Instrument Serial"], 
                       fl = basename(u),
                       platform=.Plat(Meta["Instrument Serial"]),
                       stringsAsFactors = FALSE)
select(X$LVL, O2 = contains("O2 (mmHg)"), Well,
           WellTemp=`Well Temperature`) %>% 
  mutate(., O2dif = abs(O2 - 152)) %>% 
  mutate(OL= O2dif>10) %>% 
  group_by(Well) %>% 
  filter(., O2dif == max(O2dif)) %>% 
  slice(., 1) %>% ungroup(.) %>% 
  mutate(.,grade=sapply(O2dif,PipeFish::gradeOL)) %>% 
  merge(.,metainfo) 
}

pullOLDATA<-function(dir=choose.dir()){
require(dplyr)
list.files(dir,pattern="xls",full.names=T) %>%
lapply(.,PipeFish::InstQCOL)%>%
bind_rows()
}

  uploadInstQCOL<-function(){
    DATA<-PipeFish::pullOLDATA()
    require(RMySQL)
    db<-PipeFish::rmysqlCon()
    dbWriteTable(db, name="inst_qc_ol",value=DATA,
                 append=TRUE,overwrite = FALSE,row.names=FALSE)
    dbDisconnect(db)
  }