R/MVdetails.R

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

MVdetails<-function(xml){
options(warn=-1)
suppressMessages(require(dplyr))
require(xml2)
require(rvest)
 
  cleansplit<-function(u){
  A<-strsplit(u,split=",") %>% unlist
  A[1]<-paste0("Well: ",A[1])
  strsplit(A,"[:] ") %>%
    lapply(.,function(u){
      h<-data.frame(X=u[2],stringsAsFactors=FALSE);
      names(h)<-u[1];h}) %>%
    bind_cols()
}
cleansplit_all<-function(u){
  lapply(u,cleansplit) %>%
    bind_rows()
}

getPlat<-function(u){
  c("W"="XFe96","B"="XFe24","C"="XFp")[u]
}

check<-function(b){   
xml2::xml_text( xml_nodes(b, xpath = "//InspectionDetailsItem[Name='Result']//Details"))!="OK"
}

findTable<-function(b){  
  xml_nodes(b, xpath = "//InspectionDetailsItem[Name='Results']//Details") %>%  
    xml2::xml_text()
}

getBarcode<-function(b){
  xml_nodes(b, xpath = "//InspectionDetailsItem[Name='Bar Code']//Details") %>%  
    xml2::xml_text()
}

gsubTable<-function(TBL){
   gsub("Optical Window","",TBL) %>%
    gsub('center-x:',',center-x:',.) %>%
    gsub('center-y:',',center-y:',.) %>%
    gsub('radius' , ',radius',.) %>%
    gsub('num ',',num_',.) %>%
    gsub('mean diameter:',',mean_diameter:',.) %>%
    gsub('inner diameter:',',inner_diameter:',.) %>%
    gsub('outer diameter:',',outer_diameter:',.) %>%
    gsub('total area:',',total_area:',.) %>%
    gsub('circularity:',',circularity:',.) %>%
    gsub('mean intensity:',',mean_intensity:',.) %>%
    gsub('min intensity:',',min_intensity:',.) %>%
    gsub('max intensity:',',max_intensity:',.) %>%
    gsub('intensity stdev:',',intensity_stdev:',.) %>%
    gsub('Drug Ports',"",.) %>%
    gsub("Port 1, diameter:",",Port_1_diameter:",.) %>%
    gsub("Port 2, diameter:",",Port_2_diameter:",.) %>%
    gsub("Port 3, diameter:",",Port_3_diameter:",.) %>%
    gsub("Port 4, diameter:",",Port_4_diameter:",.) %>%
    gsub('Spot 1:','',.) %>%
    read_html() %>% html_table() %>%
    .[[1]]
}

munge<-function(Y){
  lapply(Y,cleansplit_all) %>%
  bind_rows() %>%
  arrange(.,Well) %>%
  rename(.,center_x=`center-x`,center_y=`center-y`) %>%
  group_by(Well) %>%
  mutate_all(.,as.numeric) %>%
  ungroup() %>%
  mutate(.,
         Lot=paste0(substr(Barcode,1,1),substr(Barcode,7,11)),
         sn=substr(Barcode,2,6),
         platform=getPlat(substr(Lot,1,1)))
}


b<-read_xml(xml)
if(check(b)){return(c("FAILURE"))}

Barcode<-getBarcode(b)
  findTable(b) %>%
  gsubTable() %>%
  munge()

}