R/MVdetails.R

In JARS3N/sortMV: sortMV

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]
  }

  b<-read_xml(xml)
   check<-b %>%  
   rvest::xml_nodes(.,"Details") %>% 
   xml2::xml_text() %>% 
   grepl("Could not find",.) %>% any()
 if(check){return(c("FAILURE"))}
  Y<-  b %>%
    rvest::xml_nodes(.,"Details") %>%
    .[grepl("&lt;table",.)] %>%
    xml2::xml_text() %>%
    gsub("Optical Window","",.) %>%
    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]]
  #
  Barcode<-rvest::xml_nodes(b,"Details") %>%
    .[grepl("[A-Z]{1}[0-9]{5}[A-Z|0-9]{1}[0-9]{4}B",
            .)
      ] %>%
    xml_text()
  #
 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)))
}