R/server_generate_agrofims.R
In omarbenites/fbmlist: The Germoplam Manager for HiDAP
#' Server Side for generation of Material List in HIDAP-AGROFIMS
#'
#' @param input shinyserver input
#' @param output shinyserver output
#' @param session shinyserver session
#' @param values reactive values
#' @author Omar Benites
#' @export
server_generate_agrofims <- function(input,output,session, values){
#Reactive data after connecting to database or local lists
gmtl_data <- eventReactive(input$fbmlist_connect, {
dbf_file <- input$fbmlist_sel_list
n <- length(input$fbmlist_sel_list)
if(n==1){
path <- fbglobal::get_base_dir()
path <- file.path(path, dbf_file)
germlist_db <- readRDS(path)
}
if(n > 1){
combine <- list()
for(i in 1:n){
path <- fbglobal::get_base_dir()
path <- file.path(path, dbf_file)
combine[[i]] <- readRDS(file = dbf_file[i])
#path <- paste(path,dbf_file,sep = "\\")
combine[[i]] <- readRDS(file = dbf_file[i])
#combine[[i]] <- readRDS(file = dbf_file[i])
}
join_books <- data.table::rbindlist(combine,fill = TRUE)
join_books <- as.data.frame(join_books)
germlist_db <- join_books
}
n_row <- nrow(germlist_db)
germlist_db <- mutate(germlist_db, IDX = 1:n_row)
germlist_db
})
#reactive value for displaying box and panels
output$show_mtable <- reactive({
return(!is.null(gmtl_data()))
})
#reactive value for save button
output$show_save <- reactive({
return(length(input$fbmlist_select[1]))
})
#set options for show_mtable
outputOptions(output, 'show_mtable', suspendWhenHidden=FALSE)
#selectInput button for selection of local lists or databases
output$sel_list_on_btn <- renderUI({
#mtl_files()
#db_files_choices <- mtl_files()
#db_files_choices <- db_files_choices$short_name
#db_files_choices <- list("dspotatotrials_dpassport.dbf", "dssweettrials_dpassport.dbf" ,"potato_pedigree.dbf" ,"sweetpotato_pedigree.dbf")
crop <- input$fbmlist_sel_crop
type_db <- input$fbmlist_sel_type
mtl_db_sel <- mtl_files()$short_name
if(crop == "") {
db_files_choices <- ""
sel_multiple <- FALSE
}
if(crop == "potato") {
if(type_db=="Institutional"){
#db_files_choices <- list("dspotatotrials_dpassport.dbf", "potato_pedigree.dbf")
db_files_choices <- list("dspotatotrials_dpassport.rds", "potato_pedigree.rds")
sel_multiple <- FALSE
}
if(type_db=="Local"){
db_files_choices <- mtl_db_sel[str_detect(mtl_db_sel , "PT")]
sel_multiple <- TRUE
}
}
if(crop == "sweetpotato") {
if(type_db=="Institutional") {
db_files_choices <- list("dssweettrials_dpassport.rds", "sweetpotato_pedigree.rds")
sel_multiple <- FALSE
}
if(type_db=="Local"){
db_files_choices <- mtl_db_sel[str_detect(mtl_db_sel , "SP")]
sel_multiple <- TRUE
}
}
db_files_choices <- db_files_choices
shiny::selectizeInput(inputId ="fbmlist_sel_list", label = "Select list",
multiple = sel_multiple, width="100%", choices = db_files_choices,
options = list(
placeholder = 'Please select an option below',
onInitialize = I('function() { this.setValue(""); }')
)
)
})
#TextInput space to write list's name
output$create_on_name <- renderUI({
req(input$fbmlist_select)
textInput("fbmlist_create_on_name", label = h3("New list name"), value = "", placeholder = "Write a list name")
})
#save button to store information
output$savelist_on_btn <- renderUI({
req(input$fbmlist_select)
#shiny::actionButton("fbmlist_save", label = "Save List", icon = icon("save"))
shinysky::actionButton2("fbmlist_save", label = "Save list", icon = "save", icon.library = "bootstrap")
})
#Clones founded using textArea
output$fbmlist_foundclones_gen <- renderText({
mtl_table <- gmtl_data()
# mtl_headers <- c("Accession_Number", "Female_AcceNumb", "Female_codename", "Male_AcceNumb",
# "Male_codename", "Population", "Cycle", "Date_Created", "IDX")
#
mtl_table <- mtl_table[,1:6]
temp_mtl_table <- mtl_table
if(input$fbmlist_txtarea!="" || !str_detect(input$fbmlist_txtarea, "[[:space:]]") ){
#trimming search filter
search_filter <- str_split(input$fbmlist_txtarea,"\\n")[[1]]
search_filter <- stringr::str_trim(search_filter,side = "both")
search_filter <- as.character(search_filter)
#extracting columns Accesion Number and Accesion Name
material_db_accnum <- as.character(temp_mtl_table$Accession_Number)
material_db_accname <- as.character(temp_mtl_table$Accession_Name) #in case of generate (clone list), it has Accesion Name
material_acc_union <- union(material_db_accnum, material_db_accname)
out_dbacc_search <- setdiff(search_filter, material_acc_union) #find the element which are NOT in the inserction
out_dbacc_search <- out_dbacc_search[!is.na(out_dbacc_search)]
out_dbacc_search <- out_dbacc_search[out_dbacc_search!=""]
n_search <- length(out_dbacc_search)
print(n_search)
# Show messages according to accesion founder in accesion number or accesion name
if(n_search>0){ #for accession number, flag =1
out <- paste(out_dbacc_search, collapse = ", ")
out <- paste("N= ", n_search, " accesion(s) were not found: ", out, sep="")
} else {
out <- paste("", sep = "")
}
out
}
})
# Selection on generataed material list button ----------------------------------------------------
output$fbmlist_table <- DT::renderDataTable({
shiny::req(input$fbmlist_sel_list)
shiny::req(input$fbmlist_connect)
#shiny::req(input$fbmlist_selectgenlist)
shiny::withProgress(message = "Visualizing Table...",value= 0, #withProgress
{
row_click <- NULL
mtl_table <- gmtl_data()
#col_headers <- c("Accession_Number", "Female_AcceNumb","Female_codename", "Male_AcceNumb" ,"Male_codename", "Population" ,"IDX")
mtl_table <- mtl_table[,1:6]
n_row <- nrow(mtl_table)
mtl_table <- mutate(mtl_table, IDX = 1:n_row)
if(input$fbmlist_txtarea!=""){
#Deprecated IDX
#mtl_table <- mutate(mtl_table, IDX = 1:n())
#End deprecated IDX
search_filter <- str_split(input$fbmlist_txtarea,"\\n")[[1]]
search_filter <- stringr::str_trim(search_filter, side = "both")
mtl_table_f <- filter(mtl_table, Accession_Number %in% search_filter)
if(nrow(mtl_table_f)==0 && is.element("Accession_Name",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Accession_Name %in% search_filter)
}
# SEARCH ACCESSION BY DIFFERENTE PEDRIGREE ATRIBUTES (Temporary disable)
# if(nrow(mtl_table_f)==0 && is.element("Accession_Code",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Accession_Code %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Female_AcceNumb",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Female_AcceNumb %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Female_codename",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Female_codename %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Male_AcceNumb",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Male_AcceNumb %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Male_codename",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Male_codename %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Population",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Population %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Cycle",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Cycle %in% search_filter)
#
# }
#
# END SEARCH ACCESSION BY DIFFERENTE PEDRIGREE ATRIBUTES (Temporary disable)
if(nrow(mtl_table_f)>0){
row_click <- as.numeric(mtl_table_f$IDX)
Search <- rownames(mtl_table_f) %>% as.numeric(.)
}
DT::datatable( mtl_table_f, rownames = FALSE,
#selection = list( mode= "multiple", selected = rownames(mtl_table)),
options = list(scrollX = TRUE, scroller = TRUE),
selection = list( mode = "multiple", selected = Search),
filter = 'bottom'#,
# extensions = 'Buttons', options = list(
# dom = 'Bfrtip',
# buttons =
# list(list(
# extend = 'collection',
# buttons = c('csv', 'excel'),
# text = 'Download'
# ))
#
# )
)
} else {
DT::datatable(mtl_table, rownames = FALSE,
#selection = list( mode= "multiple", selected = rownames(mtl_table)),
options = list(scrollX = TRUE, scroller = TRUE),
selection = list( mode = "multiple"),
filter = 'bottom'#,
# extensions = 'Buttons', options = list(
# dom = 'Bfrtip',
# buttons =
# list(list(
# extend = 'collection',
# buttons = c('csv', 'excel'),
# text = 'Download'
# ))
#
# )
)
}
}) #end of Progress
})
#the index of selection material
gmtl_row_index <- eventReactive(input$fbmlist_select,{
row_click <- NULL
mtl_table <- gmtl_data()
mtl_table <- mtl_table[,1:6]
n_row <- nrow(mtl_table)
mtl_table <- mutate(mtl_table, IDX = 1:n_row)
print(input$fbmlist_txtarea)
if(input$fbmlist_txtarea!=""){
#Deprecated IDX
#mtl_table <- mutate(mtl_table, IDX = 1:n())
#End deprecated IDX
search_filter <- str_split(input$fbmlist_txtarea,"\\n")[[1]]
search_filter <- stringr::str_trim(search_filter,side = "both")
mtl_table_f <- filter(mtl_table, Accession_Number %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
# print(row_click)
#print(row_click)
if(nrow(mtl_table_f)==0 && is.element("Accession_Name",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Accession_Name %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
}
if(nrow(mtl_table_f)==0 && is.element("Accession_Code",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Accession_Code %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
}
if(nrow(mtl_table_f)==0 && is.element("Female_AcceNumb",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Female_AcceNumb %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
}
if(nrow(mtl_table_f)==0 && is.element("Female_codename",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Female_codename %in% search_filter)
}
if(nrow(mtl_table_f)==0 && is.element("Male_AcceNumb",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Male_AcceNumb %in% search_filter)
}
if(nrow(mtl_table_f)==0 && is.element("Male_codename",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Male_codename %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
}
if(nrow(mtl_table_f)==0 && is.element("Population",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Population %in% search_filter)
}
if(nrow(mtl_table_f)==0 && is.element("Cycle",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Cycle %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
# print(row_click)
}
if(nrow(mtl_table_f)>0){
row_click <- as.numeric(mtl_table_f$IDX)
} else {
row_click <- NULL
}
}
else {
row_select <- input$fbmlist_table_rows_selected #comand to get selected values
#row_filter <- input$fbmlist_table_new_rows_all #comand to get filtered values
#row_mtlist_selection <- dplyr::intersect(row_select,row_filter)
row_mtlist_selection <- sort(row_select)
row_click <- row_mtlist_selection
}
#print(row_select)
print(row_click)
row_click
})
#table of selected clones after pressing "Select marked"
output$fbmlist_choosen_table <- DT::renderDataTable({
#print(input$foo)
index <- gmtl_row_index()
mtl_table <- gmtl_data()
mtl_table_temp <- mtl_table #temporal table for visualizing
chosen_gmtl_table <- mtl_table_temp[index, ]
chosen_gmtl_table
}, options = list(searching = FALSE, scrollX = TRUE, scroller = TRUE) )
# Observers of fbmlist ----------------------------------------------------
shiny::observeEvent( input$fbmlist_save, {
index <- gmtl_row_index()
mtl_table <- gmtl_data()
chosen_gmtl_table <- mtl_table[index, ]
fbmlist_name_dbf <- str_trim(string = input$fbmlist_create_on_name, side = "both")
fbmlist_name_dbf <- gsub("\\s+", "_", fbmlist_name_dbf)
fbmlist_name_dbf_temp <- fbmlist_name_dbf #This variable is for control when user do not type empty names
#Adding the crop notation
crop <- input$fbmlist_sel_crop
if(crop=="potato") { fbmlist_name_dbf <- paste("PT","clon", fbmlist_name_dbf,sep = "_") }
if(crop=="sweetpotato") { fbmlist_name_dbf <- paste("SP","clon", fbmlist_name_dbf,sep = "_") }
#End of crop notation
#All the files names
db_files <- file_path_sans_ext(mtl_files()$short_name)
if(fbmlist_name_dbf %in% db_files) {
shinysky::showshinyalert(session, "alert_fbmlist_on", paste("WARNING: This list already exists"),
styleclass = "warning")
}
else if(fbmlist_name_dbf_temp==""){ #use of the temporary variable to control empty names given by users. in line 261
shinysky::showshinyalert(session, "alert_fbmlist_on", paste("WARNING: Please Type a Material List Name"),
styleclass = "warning")
}
else {
gen_headers <- c("Numeration","Is_control", "Scale_audpc", "Family_AcceNumb",
"Cycle" , "Seed_source", "Simultanious_trials", "Previous_trials")
if(all(is.element(gen_headers,names(chosen_gmtl_table)))){
gen_list_tbl <- chosen_gmtl_table
} else {
chosen_gmtl_table_list <- as.list(chosen_gmtl_table)
extra_parameters <- list(
Numeration = 1:nrow(chosen_gmtl_table),
Is_control = NA,
Scale_audpc = NA,
Family_AcceNumb = NA,
Cycle = NA,
Seed_source = NA,
Simultaneous_trials = NA,
list_name= fbmlist_name_dbf,
Previous_trials = NA,
Date_Created = format(Sys.Date(), "%d %m %Y")
)
gen_list_tbl <- c(chosen_gmtl_table_list, extra_parameters)
gen_list_tbl <- as.data.frame(gen_list_tbl, stringsAsFactors = FALSE)
}
#foreign::write.dbf(dataframe = chosen_gmtl_table, file = fbmlist_name_dbf, factor2char = FALSE)
gen_list_tbl <- gen_list_tbl
header_order <- c("Numeration", "Accession_Number", "Accession_Name", "Accession_Code", "Is_control", "Scale_audpc", "Family_AcceNumb", "Female_AcceNumb",
"Female_codename", "Male_AcceNumb", "Male_codename",
"Population", "Cycle" ,"Seed_source", "Simultaneous_trials", "Previous_trials", "list_name", "Previous_trials", "Date_Created")
header_found <- dplyr::intersect(header_order , colnames(gen_list_tbl))
gen_list_tbl <- gen_list_tbl[, header_found]
if(input$gen_type_trial=="Standard"){ #normal columns by default
gen_list_tbl <- gen_list_tbl
} else { #PVS #remove columns Is_Control, "Scale_Audpc"
gen_list_tbl <- dplyr::select(gen_list_tbl, -Is_control, -Scale_audpc)
gen_list_tbl <- as.data.frame(gen_list_tbl)
}
gen_list_tbl <- gen_list_tbl
crop <- input$fbmlist_sel_crop
fbmlist_name_dbf <- paste(fbmlist_name_dbf,".rds",sep = "")
## using fbglobal
path <- fbglobal::get_base_dir()
path <- file.path(path, fbmlist_name_dbf)
saveRDS(gen_list_tbl, file = path)
mtl_files()
shinyjs::reset("fbmlist_sel_list")
shinyjs::reset("form-gen")
shinyjs::reset("fbmlist_sel_type")
#to do
#Refresh a the textArea
shinysky::showshinyalert(session, "alert_fbmlist_on", paste("Material List successfully created!"),
styleclass = "success")
#for(i in 1:75000){print(i)}
#shinyjs::js$refresh()
}
})
}
omarbenites/fbmlist documentation built on May 24, 2019, 12:55 p.m.
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#' Server Side for generation of Material List in HIDAP-AGROFIMS
#'
#' @param input shinyserver input
#' @param output shinyserver output
#' @param session shinyserver session
#' @param values reactive values
#' @author Omar Benites
#' @export
server_generate_agrofims <- function(input,output,session, values){
#Reactive data after connecting to database or local lists
gmtl_data <- eventReactive(input$fbmlist_connect, {
dbf_file <- input$fbmlist_sel_list
n <- length(input$fbmlist_sel_list)
if(n==1){
path <- fbglobal::get_base_dir()
path <- file.path(path, dbf_file)
germlist_db <- readRDS(path)
}
if(n > 1){
combine <- list()
for(i in 1:n){
path <- fbglobal::get_base_dir()
path <- file.path(path, dbf_file)
combine[[i]] <- readRDS(file = dbf_file[i])
#path <- paste(path,dbf_file,sep = "\\")
combine[[i]] <- readRDS(file = dbf_file[i])
#combine[[i]] <- readRDS(file = dbf_file[i])
}
join_books <- data.table::rbindlist(combine,fill = TRUE)
join_books <- as.data.frame(join_books)
germlist_db <- join_books
}
n_row <- nrow(germlist_db)
germlist_db <- mutate(germlist_db, IDX = 1:n_row)
germlist_db
})
#reactive value for displaying box and panels
output$show_mtable <- reactive({
return(!is.null(gmtl_data()))
})
#reactive value for save button
output$show_save <- reactive({
return(length(input$fbmlist_select[1]))
})
#set options for show_mtable
outputOptions(output, 'show_mtable', suspendWhenHidden=FALSE)
#selectInput button for selection of local lists or databases
output$sel_list_on_btn <- renderUI({
#mtl_files()
#db_files_choices <- mtl_files()
#db_files_choices <- db_files_choices$short_name
#db_files_choices <- list("dspotatotrials_dpassport.dbf", "dssweettrials_dpassport.dbf" ,"potato_pedigree.dbf" ,"sweetpotato_pedigree.dbf")
crop <- input$fbmlist_sel_crop
type_db <- input$fbmlist_sel_type
mtl_db_sel <- mtl_files()$short_name
if(crop == "") {
db_files_choices <- ""
sel_multiple <- FALSE
}
if(crop == "potato") {
if(type_db=="Institutional"){
#db_files_choices <- list("dspotatotrials_dpassport.dbf", "potato_pedigree.dbf")
db_files_choices <- list("dspotatotrials_dpassport.rds", "potato_pedigree.rds")
sel_multiple <- FALSE
}
if(type_db=="Local"){
db_files_choices <- mtl_db_sel[str_detect(mtl_db_sel , "PT")]
sel_multiple <- TRUE
}
}
if(crop == "sweetpotato") {
if(type_db=="Institutional") {
db_files_choices <- list("dssweettrials_dpassport.rds", "sweetpotato_pedigree.rds")
sel_multiple <- FALSE
}
if(type_db=="Local"){
db_files_choices <- mtl_db_sel[str_detect(mtl_db_sel , "SP")]
sel_multiple <- TRUE
}
}
db_files_choices <- db_files_choices
shiny::selectizeInput(inputId ="fbmlist_sel_list", label = "Select list",
multiple = sel_multiple, width="100%", choices = db_files_choices,
options = list(
placeholder = 'Please select an option below',
onInitialize = I('function() { this.setValue(""); }')
)
)
})
#TextInput space to write list's name
output$create_on_name <- renderUI({
req(input$fbmlist_select)
textInput("fbmlist_create_on_name", label = h3("New list name"), value = "", placeholder = "Write a list name")
})
#save button to store information
output$savelist_on_btn <- renderUI({
req(input$fbmlist_select)
#shiny::actionButton("fbmlist_save", label = "Save List", icon = icon("save"))
shinysky::actionButton2("fbmlist_save", label = "Save list", icon = "save", icon.library = "bootstrap")
})
#Clones founded using textArea
output$fbmlist_foundclones_gen <- renderText({
mtl_table <- gmtl_data()
# mtl_headers <- c("Accession_Number", "Female_AcceNumb", "Female_codename", "Male_AcceNumb",
# "Male_codename", "Population", "Cycle", "Date_Created", "IDX")
#
mtl_table <- mtl_table[,1:6]
temp_mtl_table <- mtl_table
if(input$fbmlist_txtarea!="" || !str_detect(input$fbmlist_txtarea, "[[:space:]]") ){
#trimming search filter
search_filter <- str_split(input$fbmlist_txtarea,"\\n")[[1]]
search_filter <- stringr::str_trim(search_filter,side = "both")
search_filter <- as.character(search_filter)
#extracting columns Accesion Number and Accesion Name
material_db_accnum <- as.character(temp_mtl_table$Accession_Number)
material_db_accname <- as.character(temp_mtl_table$Accession_Name) #in case of generate (clone list), it has Accesion Name
material_acc_union <- union(material_db_accnum, material_db_accname)
out_dbacc_search <- setdiff(search_filter, material_acc_union) #find the element which are NOT in the inserction
out_dbacc_search <- out_dbacc_search[!is.na(out_dbacc_search)]
out_dbacc_search <- out_dbacc_search[out_dbacc_search!=""]
n_search <- length(out_dbacc_search)
print(n_search)
# Show messages according to accesion founder in accesion number or accesion name
if(n_search>0){ #for accession number, flag =1
out <- paste(out_dbacc_search, collapse = ", ")
out <- paste("N= ", n_search, " accesion(s) were not found: ", out, sep="")
} else {
out <- paste("", sep = "")
}
out
}
})
# Selection on generataed material list button ----------------------------------------------------
output$fbmlist_table <- DT::renderDataTable({
shiny::req(input$fbmlist_sel_list)
shiny::req(input$fbmlist_connect)
#shiny::req(input$fbmlist_selectgenlist)
shiny::withProgress(message = "Visualizing Table...",value= 0, #withProgress
{
row_click <- NULL
mtl_table <- gmtl_data()
#col_headers <- c("Accession_Number", "Female_AcceNumb","Female_codename", "Male_AcceNumb" ,"Male_codename", "Population" ,"IDX")
mtl_table <- mtl_table[,1:6]
n_row <- nrow(mtl_table)
mtl_table <- mutate(mtl_table, IDX = 1:n_row)
if(input$fbmlist_txtarea!=""){
#Deprecated IDX
#mtl_table <- mutate(mtl_table, IDX = 1:n())
#End deprecated IDX
search_filter <- str_split(input$fbmlist_txtarea,"\\n")[[1]]
search_filter <- stringr::str_trim(search_filter, side = "both")
mtl_table_f <- filter(mtl_table, Accession_Number %in% search_filter)
if(nrow(mtl_table_f)==0 && is.element("Accession_Name",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Accession_Name %in% search_filter)
}
# SEARCH ACCESSION BY DIFFERENTE PEDRIGREE ATRIBUTES (Temporary disable)
# if(nrow(mtl_table_f)==0 && is.element("Accession_Code",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Accession_Code %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Female_AcceNumb",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Female_AcceNumb %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Female_codename",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Female_codename %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Male_AcceNumb",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Male_AcceNumb %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Male_codename",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Male_codename %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Population",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Population %in% search_filter)
#
# }
#
# if(nrow(mtl_table_f)==0 && is.element("Cycle",names(mtl_table_f))) {
#
# mtl_table_f <- dplyr::filter(mtl_table, Cycle %in% search_filter)
#
# }
#
# END SEARCH ACCESSION BY DIFFERENTE PEDRIGREE ATRIBUTES (Temporary disable)
if(nrow(mtl_table_f)>0){
row_click <- as.numeric(mtl_table_f$IDX)
Search <- rownames(mtl_table_f) %>% as.numeric(.)
}
DT::datatable( mtl_table_f, rownames = FALSE,
#selection = list( mode= "multiple", selected = rownames(mtl_table)),
options = list(scrollX = TRUE, scroller = TRUE),
selection = list( mode = "multiple", selected = Search),
filter = 'bottom'#,
# extensions = 'Buttons', options = list(
# dom = 'Bfrtip',
# buttons =
# list(list(
# extend = 'collection',
# buttons = c('csv', 'excel'),
# text = 'Download'
# ))
#
# )
)
} else {
DT::datatable(mtl_table, rownames = FALSE,
#selection = list( mode= "multiple", selected = rownames(mtl_table)),
options = list(scrollX = TRUE, scroller = TRUE),
selection = list( mode = "multiple"),
filter = 'bottom'#,
# extensions = 'Buttons', options = list(
# dom = 'Bfrtip',
# buttons =
# list(list(
# extend = 'collection',
# buttons = c('csv', 'excel'),
# text = 'Download'
# ))
#
# )
)
}
}) #end of Progress
})
#the index of selection material
gmtl_row_index <- eventReactive(input$fbmlist_select,{
row_click <- NULL
mtl_table <- gmtl_data()
mtl_table <- mtl_table[,1:6]
n_row <- nrow(mtl_table)
mtl_table <- mutate(mtl_table, IDX = 1:n_row)
print(input$fbmlist_txtarea)
if(input$fbmlist_txtarea!=""){
#Deprecated IDX
#mtl_table <- mutate(mtl_table, IDX = 1:n())
#End deprecated IDX
search_filter <- str_split(input$fbmlist_txtarea,"\\n")[[1]]
search_filter <- stringr::str_trim(search_filter,side = "both")
mtl_table_f <- filter(mtl_table, Accession_Number %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
# print(row_click)
#print(row_click)
if(nrow(mtl_table_f)==0 && is.element("Accession_Name",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Accession_Name %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
}
if(nrow(mtl_table_f)==0 && is.element("Accession_Code",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Accession_Code %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
}
if(nrow(mtl_table_f)==0 && is.element("Female_AcceNumb",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Female_AcceNumb %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
}
if(nrow(mtl_table_f)==0 && is.element("Female_codename",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Female_codename %in% search_filter)
}
if(nrow(mtl_table_f)==0 && is.element("Male_AcceNumb",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Male_AcceNumb %in% search_filter)
}
if(nrow(mtl_table_f)==0 && is.element("Male_codename",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Male_codename %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
}
if(nrow(mtl_table_f)==0 && is.element("Population",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Population %in% search_filter)
}
if(nrow(mtl_table_f)==0 && is.element("Cycle",names(mtl_table_f))) {
mtl_table_f <- dplyr::filter(mtl_table, Cycle %in% search_filter)
#row_click <- as.numeric(rownames(mtl_table_f))
# row_click <- dplyr::select(mtl_table_f, IDX)[[1]]
# print(row_click)
}
if(nrow(mtl_table_f)>0){
row_click <- as.numeric(mtl_table_f$IDX)
} else {
row_click <- NULL
}
}
else {
row_select <- input$fbmlist_table_rows_selected #comand to get selected values
#row_filter <- input$fbmlist_table_new_rows_all #comand to get filtered values
#row_mtlist_selection <- dplyr::intersect(row_select,row_filter)
row_mtlist_selection <- sort(row_select)
row_click <- row_mtlist_selection
}
#print(row_select)
print(row_click)
row_click
})
#table of selected clones after pressing "Select marked"
output$fbmlist_choosen_table <- DT::renderDataTable({
#print(input$foo)
index <- gmtl_row_index()
mtl_table <- gmtl_data()
mtl_table_temp <- mtl_table #temporal table for visualizing
chosen_gmtl_table <- mtl_table_temp[index, ]
chosen_gmtl_table
}, options = list(searching = FALSE, scrollX = TRUE, scroller = TRUE) )
# Observers of fbmlist ----------------------------------------------------
shiny::observeEvent( input$fbmlist_save, {
index <- gmtl_row_index()
mtl_table <- gmtl_data()
chosen_gmtl_table <- mtl_table[index, ]
fbmlist_name_dbf <- str_trim(string = input$fbmlist_create_on_name, side = "both")
fbmlist_name_dbf <- gsub("\\s+", "_", fbmlist_name_dbf)
fbmlist_name_dbf_temp <- fbmlist_name_dbf #This variable is for control when user do not type empty names
#Adding the crop notation
crop <- input$fbmlist_sel_crop
if(crop=="potato") { fbmlist_name_dbf <- paste("PT","clon", fbmlist_name_dbf,sep = "_") }
if(crop=="sweetpotato") { fbmlist_name_dbf <- paste("SP","clon", fbmlist_name_dbf,sep = "_") }
#End of crop notation
#All the files names
db_files <- file_path_sans_ext(mtl_files()$short_name)
if(fbmlist_name_dbf %in% db_files) {
shinysky::showshinyalert(session, "alert_fbmlist_on", paste("WARNING: This list already exists"),
styleclass = "warning")
}
else if(fbmlist_name_dbf_temp==""){ #use of the temporary variable to control empty names given by users. in line 261
shinysky::showshinyalert(session, "alert_fbmlist_on", paste("WARNING: Please Type a Material List Name"),
styleclass = "warning")
}
else {
gen_headers <- c("Numeration","Is_control", "Scale_audpc", "Family_AcceNumb",
"Cycle" , "Seed_source", "Simultanious_trials", "Previous_trials")
if(all(is.element(gen_headers,names(chosen_gmtl_table)))){
gen_list_tbl <- chosen_gmtl_table
} else {
chosen_gmtl_table_list <- as.list(chosen_gmtl_table)
extra_parameters <- list(
Numeration = 1:nrow(chosen_gmtl_table),
Is_control = NA,
Scale_audpc = NA,
Family_AcceNumb = NA,
Cycle = NA,
Seed_source = NA,
Simultaneous_trials = NA,
list_name= fbmlist_name_dbf,
Previous_trials = NA,
Date_Created = format(Sys.Date(), "%d %m %Y")
)
gen_list_tbl <- c(chosen_gmtl_table_list, extra_parameters)
gen_list_tbl <- as.data.frame(gen_list_tbl, stringsAsFactors = FALSE)
}
#foreign::write.dbf(dataframe = chosen_gmtl_table, file = fbmlist_name_dbf, factor2char = FALSE)
gen_list_tbl <- gen_list_tbl
header_order <- c("Numeration", "Accession_Number", "Accession_Name", "Accession_Code", "Is_control", "Scale_audpc", "Family_AcceNumb", "Female_AcceNumb",
"Female_codename", "Male_AcceNumb", "Male_codename",
"Population", "Cycle" ,"Seed_source", "Simultaneous_trials", "Previous_trials", "list_name", "Previous_trials", "Date_Created")
header_found <- dplyr::intersect(header_order , colnames(gen_list_tbl))
gen_list_tbl <- gen_list_tbl[, header_found]
if(input$gen_type_trial=="Standard"){ #normal columns by default
gen_list_tbl <- gen_list_tbl
} else { #PVS #remove columns Is_Control, "Scale_Audpc"
gen_list_tbl <- dplyr::select(gen_list_tbl, -Is_control, -Scale_audpc)
gen_list_tbl <- as.data.frame(gen_list_tbl)
}
gen_list_tbl <- gen_list_tbl
crop <- input$fbmlist_sel_crop
fbmlist_name_dbf <- paste(fbmlist_name_dbf,".rds",sep = "")
## using fbglobal
path <- fbglobal::get_base_dir()
path <- file.path(path, fbmlist_name_dbf)
saveRDS(gen_list_tbl, file = path)
mtl_files()
shinyjs::reset("fbmlist_sel_list")
shinyjs::reset("form-gen")
shinyjs::reset("fbmlist_sel_type")
#to do
#Refresh a the textArea
shinysky::showshinyalert(session, "alert_fbmlist_on", paste("Material List successfully created!"),
styleclass = "success")
#for(i in 1:75000){print(i)}
#shinyjs::js$refresh()
}
})
}
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