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CIP-RIU
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Oct 10, 2019
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| Original file line number | Diff line number | Diff line change |
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@@ -62,20 +62,82 @@ fbcheck_server_sbase <- function(input, output, session, values) { | |
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| }) | ||
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| # Load dataset --------------------------------------------- | ||
| #Begin Load dataset --------------------------------------------- | ||
| # fb_sbase <- function(){ | ||
| # ####### Import CSV data ####### | ||
| # #file_fbapp <- input$file_fbapp_sbase | ||
| # if (is.null(input$file_fbapp_sbase)) { | ||
| # #shinyjs::disable("saveData") # Codigo R.ARIAS SAVE | ||
| # return(NULL) | ||
| # } else { | ||
| # dt <- readr::read_csv(input$file_fbapp_sbase$datapath) # Codigo R.ARIAS SAVE | ||
| # #shinyjs::enable("saveData") | ||
| # } | ||
| # | ||
| # } | ||
| #End load dataset --------------------------------------------- | ||
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| #NEW CODE | ||
| fb_sbase <- function(){ | ||
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| try({ | ||
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| ####### Import CSV data ####### | ||
| #file_fbapp <- input$file_fbapp_sbase | ||
| if (is.null(input$file_fbapp_sbase)) { | ||
| if (is.null(input$file_fbapp_sbase)) { | ||
| #shinyjs::disable("saveData") # Codigo R.ARIAS SAVE | ||
| return(NULL) | ||
| } else { | ||
| dt <- readr::read_csv(input$file_fbapp_sbase$datapath) # Codigo R.ARIAS SAVE | ||
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| if(length(input$file_fbapp_sbase)==1){ | ||
| fb <- readr::read_csv(input$file_fbapp_sbase$datapath) # Codigo R.ARIAS SAVE | ||
| } else { | ||
| print(input$file_fbapp_sbase) | ||
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| files_list <- input$file_fbapp_sbase | ||
| files_list <- files_list$datapath | ||
| print(files_list) | ||
| n <- length(files_list) | ||
| combine <- vector("list", length=n) | ||
| for(i in seq.int(files_list)){ | ||
| combine[[i]] <- readr::read_csv(files_list[i],na = "") | ||
| } | ||
| fb <- data.table::rbindlist(combine,fill = TRUE) | ||
| fb <- as.data.frame(fb,stringsAsFactors=FALSE) | ||
| } | ||
| #shinyjs::enable("saveData") | ||
| } | ||
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| fb | ||
| }) | ||
| } | ||
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| output$fbcheck_message_sbase <- shinydashboard::renderInfoBox({ | ||
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| if(class(fb_sbase())=="error" ){ | ||
| infoBox(title="Error", | ||
| subtitle = paste("There exist inconsistencies in your excel files"), icon = icon("refresh"), | ||
| color = "red",fill = TRUE, width = NULL) | ||
| } else if(class(fb_sbase())=="NULL"){ | ||
| infoBox(title="Import file", | ||
| subtitle = paste("Import your field book file"), icon= icon("upload", lib = "glyphicon"), | ||
| color = "blue",fill = TRUE, width = NULL) | ||
| } else if(length(fb_sbase()$accession_name[!is.na(fb_sbase()$accession_name)])!=nrow(fb_sbase())) { | ||
| infoBox(title="Error", | ||
| subtitle = paste("There are missing accession names. Check your file"), icon = icon("refresh"), | ||
| color = "red",fill = TRUE, width = NULL) | ||
| } else { | ||
| infoBox(title="Imported file", | ||
| subtitle = paste("File successfully uploaded"), icon= icon("ok", lib = "glyphicon"), | ||
| color = "green",fill = TRUE, width = NULL) | ||
| } | ||
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| }) | ||
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| #END NEW CODE | ||
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| #hot_btable represents fieldbook data ---------------------- | ||
| output$hot_btable_fbapp_sbase <- renderRHandsontable({ | ||
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@@ -229,27 +291,29 @@ fbcheck_server_sbase <- function(input, output, session, values) { | |
| else { | ||
| incProgress(2/6, detail = paste("Checking data...")) | ||
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| print(head(fb,n = 4)) | ||
| print(user) | ||
| print(password) | ||
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| res2<- fbcheck::check_credentials(dbname= "sweetpotatobase", user=user, password=password, | ||
| urltoken= "sgn:[email protected]/brapi/v1/token") | ||
| #urltoken= "https://sweetpotatobase.org/brapi/v1/token") | ||
| #urltoken= "sgn:[email protected]/brapi/v1/token") | ||
| urltoken= "https://sweetpotatobase.org/brapi/v1/token") | ||
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| if(res2$status=="error"){ | ||
| shinysky::showshinyalert(session, "alert_fbappsbase_upload", paste(res2$msg), styleclass = "danger") | ||
| incProgress(6/6, detail = paste("Errors detected")) | ||
| } else { | ||
| out <- fbcheck::upload_studies(dbname= "sweetpotatobase", | ||
| urltoken = "sgn:[email protected]/brapi/v1/token", | ||
| urlput= "sgn:[email protected]/brapi/v1/observations", | ||
| #urltoken = "https://sweetpotatobase.org/brapi/v1/token", | ||
| #urlput= "https://sweetpotatobase.org/brapi/v1/observations", | ||
| #urltoken = "sgn:[email protected]/brapi/v1/token", | ||
| #urlput= "sgn:[email protected]/brapi/v1/observations", | ||
| urltoken = "https://sweetpotatobase.org/brapi/v1/token", | ||
| urlput= "https://sweetpotatobase.org/brapi/v1/observations", | ||
| user= user, password=password, dfr=fb) | ||
| print("4") | ||
| if(out$metadata$status[[6]]$code=="200"){ | ||
| shinysky::showshinyalert(session, "alert_fbappsbase_upload", paste(res$msg), styleclass = "success") | ||
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| #shinysky::showshinyalert(session, "alert_fbappsbase_upload", paste(res$msg), styleclass = "success") | ||
| #New code | ||
| shinysky::showshinyalert(session = session, id = "alert_fbappsbase_upload", paste(res$msg), styleclass = res$styleclass) | ||
| #End new code | ||
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| print("5") | ||
| incProgress(5/6, detail = paste("Finishing upload to SweetPotatoBase...")) | ||
| incProgress(6/6, detail = paste("Refreshing page...")) | ||
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@@ -278,6 +342,10 @@ fbcheck_server_sbase <- function(input, output, session, values) { | |
| }, | ||
| content = function(con) { | ||
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| #fb22 <<- fb_sbase() | ||
| #saveRDS(fb, file = "/tests/testthat/excel/combine_fb_1.rds") | ||
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| shiny::withProgress(message = 'Downloading file', value = 0, { | ||
| incProgress(1/6, detail = paste("Reading table data...")) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,16 @@ | ||
| # Form checker ------------------------------------------------------------ | ||
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| #' Get headers from Solgenomic Databases | ||
| #' | ||
| get_solgenomic_headers <- function(){ | ||
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| factors <- c("plot_name", "abbr_user", "plot_id", "block_number", "plot_number", "rep_number" , "row_number", "col_number", | ||
| "accession_name", "is_a_control", "synosyms", "trial_name", "location_name", "year", "pedigree", | ||
| "tier", "seedlot_name", "seed_transaction_operator", "num_seed_per_plot", "range_number", "plot_geo_json", | ||
| "timestamp", "person" ,"location", "number") | ||
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| } | ||
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@@ -431,10 +444,10 @@ fbapp2json <- function(dfr, token="lfsermmo93;3r"){ | |
| #' @export | ||
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| upload_studies<- function(dbname= "sweetpotatobase", | ||
| #urltoken = "https://sweetpotatobase.org/brapi/v1/token", | ||
| #urlput = "https://sweetpotatobase.org/brapi/v1/observations", | ||
| urltoken = "sgn:[email protected]/brapi/v1/token", | ||
| urlput = "sgn:[email protected]/brapi/v1/observations", | ||
| urltoken = "https://sweetpotatobase.org/brapi/v1/token", | ||
| urlput = "https://sweetpotatobase.org/brapi/v1/observations", | ||
| #urltoken = "sgn:[email protected]/brapi/v1/token", | ||
| #urlput = "sgn:[email protected]/brapi/v1/observations", | ||
| user= "obenites", password=";c8U:G&z:X",dfr){ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| library(tidyr) | ||
| library(dplyr) | ||
| library(stringr) | ||
| library(fbcheck) | ||
| library(fbdesign) | ||
| context("Test combination of multiple fieldbook App files") | ||
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| test_that("Combination of two files with same headers", { | ||
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| dfr <- readRDS(file="tests/testthat/excel/combine_fb_1.rds") | ||
| fb <- fbapp2json(dfr, token="lfsermmo93;3r") | ||
| testthat::expect_equal(class(fb),"json") | ||
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| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,23 +1,23 @@ | ||
| # # # | ||
| # library(tidyr) | ||
| # library(dplyr) | ||
| # library(stringr) | ||
| # library(fbcheck) | ||
| # library(fbdesign) | ||
| # # # context("Organoleptic forms test") | ||
| # # # | ||
| # # # test_that("When F6 and F7 organolepticps NA logical", { | ||
| # # # | ||
| # # # | ||
| # # # # | ||
| # # library(tidyr) | ||
| # # library(dplyr) | ||
| # # library(stringr) | ||
| # # library(fbcheck) | ||
| # # library(fbdesign) | ||
| # # # # context("Organoleptic forms test") | ||
| # # # # | ||
| # # # # test_that("When F6 and F7 organolepticps NA logical", { | ||
| # # # # | ||
| # # # # | ||
| # dbname<- "sweetpotatobase" | ||
| # user <- "obenites" | ||
| # password <- ";c8U:G&z:X" | ||
| # fb <- readr::read_csv("tests/testthat/excel/18AMDPNaCRRI_final - Copy.csv") | ||
| # fb <- readr::read_csv("/home/obenites/HIDAP_SB_1.0.0/fbcheck/tests/testthat/excel/18AMDPNaCRRI_final - Copy.csv") | ||
| # names(fb) <- gsub("[[:space:]]", "", names(fb)) | ||
| # fb <- tbl_df(fb) | ||
| # # #user <- "iperezm" | ||
| # # #password <- "41954776" | ||
| # | ||
| # # | ||
| # # out <- fbcheck::upload_studies(dbname= "sweetpotatobase", | ||
| # # # urltoken = "sgn:[email protected]/brapi/v1/token", | ||
| # # # urlput= "sgn:[email protected]/brapi/v1/observations", | ||
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@@ -29,9 +29,13 @@ | |
| # | ||
| # urltoken <- "https://sweetpotatobase.org/brapi/v1/token" | ||
| # urlput <- "https://sweetpotatobase.org/brapi/v1/observations" | ||
| # dfr <- readr::read_csv("tests/testthat/excel/18AMDPNaCRRI_final - Copy.csv") | ||
| # names(dfr) <- gsub("[[:space:]]", "", names(dfr)) | ||
| # dfr <- tbl_df(dfr) | ||
| # fb <- readr::read_csv("/home/obenites/HIDAP_SB_1.0.0/fbcheck/tests/testthat/excel/18AMDPNaCRRI_final - Copy.csv") | ||
| # names(fb) <- gsub("[[:space:]]", "", names(fb)) | ||
| # fb <- tbl_df(fb) | ||
| # | ||
| # # dfr <- readr::read_csv("tests/testthat/excel/18AMDPNaCRRI_final - Copy.csv") | ||
| # # names(dfr) <- gsub("[[:space:]]", "", names(dfr)) | ||
| # # dfr <- tbl_df(dfr) | ||
| # # urltoken <- "sgn:[email protected]/brapi/v1/token" | ||
| # | ||
| # # out <- fbcheck::upload_studies(dbname= "sweetpotatobase", | ||
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@@ -75,6 +79,6 @@ | |
| # #xout <- httr::content(x = res) | ||
| # #txt <- ifelse(res$status == 200, " ok!", " problem!") | ||
| # out <- httr::content(res) | ||
| # # # | ||
| # # # | ||
| # # # }) | ||
| # # # # | ||
| # # # # | ||
| # # # # }) | ||