fbcheck-fbApp test 0.0.2

CIP-RIU · May 29, 2018 · 1ac79af · 1ac79af
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Showing 51 changed files with 59 additions and 3 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
diff --git a/.gitignore b/.gitignore
diff --git a/DESCRIPTION b/DESCRIPTION
diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/R/data_pvs.R b/R/data_pvs.R
diff --git a/R/fbcheck_server.R b/R/fbcheck_server.R
diff --git a/R/fbcheck_server_sbase.R b/R/fbcheck_server_sbase.R
@@ -50,9 +50,18 @@ fbcheck_server_sbase <- function(input, output, session, values) {
       file_fbapp <- input$file_fbapp_sbase
       if (is.null(file_fbapp))  return(NULL)
       dt <- readr::read_csv(file_fbapp$datapath)
+
+      if(!is.element("plot_name", names(dt))){ 
+        shinysky::showshinyalert(session, "alert_fbapp_warning_sbase", paste("ERROR: The file imported does not has 'plot_name' header."), styleclass = "danger")  
+      } else if(nrow(dt)==1){
+        shinysky::showshinyalert(session, "alert_fbapp_warning_sbase", paste("ERROR: Your data file has only one row of data. Please upload the right one. "), styleclass = "danger")  
+      } else {
+        hot_bdata <- fbapp2hidap(dt) 
+      }
+
       #dt <- readr::read_csv(file ="D:\\HIDAP_DOCUMENTATION_AND_EXAMPLES\\HIDAP-SweetPotatoBase\\FieldBookApp\\formato para subir a la base de datos\\fbapp_trial1_sbase_bryanEllerbrock.csv")
       # Data wrangling ----------------------------------------------------------
-      hot_bdata <- fbapp2hidap(dt) 
+
     #}
 
     hot_bdata
@@ -101,6 +110,21 @@ fbcheck_server_sbase <- function(input, output, session, values) {
       )
     }
   })
+  #### temp
+
+
+
+  # output$tbl <- renderTable({
+  #   rv$data
+  # })
+
+
+
+  ### end temp
+
+
+
+
 
   #Return the type of crop in Minimal sheet
   hot_crop_sbase <- reactive({
@@ -142,13 +166,18 @@ fbcheck_server_sbase <- function(input, output, session, values) {
       DF = values[["hot_btable_fbapp_sbase"]]
     }
 
+
+
     # if(input$calculate_sbase>0){
     # 
     #   DF <- values[["hot_btable_fbapp_sbase"]]
     #   DF <- rhandsontable_update(DF)
     #   #DF <- temp
     # }
 
+    print("print DF")
+    print(DF)
+    print("end d")
 
     if(!is.null(DF)){
 
@@ -234,13 +263,38 @@ fbcheck_server_sbase <- function(input, output, session, values) {
     content = function(con) {
       path <- fbglobal::get_base_dir()
       #print(path)
+      shiny::withProgress(message = 'Downloading file', value = 0, {
+
+        incProgress(1/6, detail = paste("Reading HIDAP data..."))
       path <-  file.path(path,"hot_fieldbook_sbase.rds")
+
+
       #print(path)
       DF <- readRDS(path)
+
+      incProgress(2/6, detail = paste("Formatting hidap file..."))
+
       fb<- hidap2fbApp(fieldbook = DF)
+
+      incProgress(3/6, detail = paste("Downloading FieldBookApp-SPBase file..."))
+
+      incProgress(4/6, detail = paste("Refreshing HIDAP..."))
+
+      Sys.sleep(3)
+      incProgress(5/6, detail = paste("Refreshing HIDAP..."))
+
       write.csv(fb, con,row.names = FALSE)
+
+      incProgress(6/6, detail = paste("Refreshing HIDAP..."))
+      Sys.sleep(5)
+      shinyjs::js$downloadData()
+      })
+
+
     }
   )
 
 
 }
+
+
diff --git a/R/fbcheck_ui.R b/R/fbcheck_ui.R
diff --git a/R/fbcheck_ui_sbase.R b/R/fbcheck_ui_sbase.R
@@ -11,6 +11,8 @@ fbcheck_ui_sbase <- function(type="tab", title="Data Quality and Processing", na
   #begin data_processing tabItem
   shinydashboard::tabItem(tabName = name,
                           h2(title),   
+                          shinyjs::useShinyjs(),
+                          shinyjs::extendShinyjs(text = "shinyjs.downloadData = function() { location.reload(); }"),
 
                           # shinyWidgets::awesomeRadio(inputId = "fbdesign_dsource_sbase", 
                           #                            label = "Select data source", choices = c("HIDAP", 
@@ -47,7 +49,7 @@ fbcheck_ui_sbase <- function(type="tab", title="Data Quality and Processing", na
 
                                 shiny::fileInput(inputId = "file_fbapp_sbase", label = "Choose CSV File", multiple = FALSE,
                                                  accept = c("text/csv","text/comma-separated-values,text/plain", ".csv")),
-
+                                #actionButton('reset', 'Reset Input'),
 
                                 HTML('<div style="float: right; margin: 0 5px 5px 10px;">'),
                                 shiny::downloadLink('downloadData', 'Download'),
@@ -75,7 +77,7 @@ fbcheck_ui_sbase <- function(type="tab", title="Data Quality and Processing", na
                                             #                                        HTML('<div style="float: right; margin: 0 5px 5px 10px;">'),
                                             #                                        shiny::actionLink('exportButton', 'Download data'),
                                             #                                        HTML('</div>'),
-                                            shinysky::shinyalert("alert_fb_warning_sbase", FALSE, auto.close.after = 4),
+                                            shinysky::shinyalert("alert_fbapp_warning_sbase", FALSE, auto.close.after = 4),
 
                                             # conditionalPanel(
                                             #   condition = "input.fbdesign_dsource_sbase == 'HIDAP'",

diff --git a/R/trait_function.R b/R/trait_function.R
diff --git a/R/utils.R b/R/utils.R
diff --git a/README.md b/README.md
diff --git a/data/selcriteria.rda b/data/selcriteria.rda
diff --git a/fbcheck.Rproj b/fbcheck.Rproj
diff --git a/inst/app/app.R b/inst/app/app.R
diff --git a/inst/app_fbcheck/PTYL200211_CHIARA.xlsx b/inst/app_fbcheck/PTYL200211_CHIARA.xlsx
diff --git a/inst/app_fbcheck/app.R b/inst/app_fbcheck/app.R
diff --git a/inst/app_fbcheck/table_dictionary_potato.rda b/inst/app_fbcheck/table_dictionary_potato.rda
diff --git a/inst/app_fbcheck/table_dictionary_sweetpotato.rda b/inst/app_fbcheck/table_dictionary_sweetpotato.rda
diff --git a/inst/crop_ontology/potato/dictionary/table_dictionary_potato.rda b/inst/crop_ontology/potato/dictionary/table_dictionary_potato.rda
diff --git a/inst/crop_ontology/sweetpotato/dictionary/table_dictionary_sweetpotato.rda b/inst/crop_ontology/sweetpotato/dictionary/table_dictionary_sweetpotato.rda
diff --git a/man/fbapp2hidap.Rd b/man/fbapp2hidap.Rd
diff --git a/man/fbcheck_server.Rd b/man/fbcheck_server.Rd
diff --git a/man/fbcheck_server_sbase.Rd b/man/fbcheck_server_sbase.Rd
diff --git a/man/fbcheck_ui.Rd b/man/fbcheck_ui.Rd
diff --git a/man/fbcheck_ui_sbase.Rd b/man/fbcheck_ui_sbase.Rd
diff --git a/man/form_checker.Rd b/man/form_checker.Rd
diff --git a/man/form_parameters.Rd b/man/form_parameters.Rd
diff --git a/man/get.fb.param.Rd b/man/get.fb.param.Rd
diff --git a/man/get_pvs_param.Rd b/man/get_pvs_param.Rd
diff --git a/man/hidap2fbApp.Rd b/man/hidap2fbApp.Rd
diff --git a/man/out_form_table.Rd b/man/out_form_table.Rd
diff --git a/man/rhandsontable_update.Rd b/man/rhandsontable_update.Rd
diff --git a/man/scale_trait.Rd b/man/scale_trait.Rd
diff --git a/man/selcriteria.Rd b/man/selcriteria.Rd
diff --git a/man/split_tidy_form.Rd b/man/split_tidy_form.Rd
diff --git a/man/trait_type.Rd b/man/trait_type.Rd
diff --git a/man/x_form.Rd b/man/x_form.Rd
diff --git a/man/x_values.Rd b/man/x_values.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
diff --git a/tests/testthat/excel/F7_OneEmptyForm_QUILCAS.xlsx b/tests/testthat/excel/F7_OneEmptyForm_QUILCAS.xlsx
diff --git a/tests/testthat/excel/PTPVS032013_Jumla_exp3.xlsx b/tests/testthat/excel/PTPVS032013_Jumla_exp3.xlsx
diff --git a/tests/testthat/excel/PTPVS032013_Jumla_exp3_NA_character.xlsx b/tests/testthat/excel/PTPVS032013_Jumla_exp3_NA_character.xlsx
diff --git a/tests/testthat/excel/PTPVS032013_Jumla_exp3_VACIO.xlsx b/tests/testthat/excel/PTPVS032013_Jumla_exp3_VACIO.xlsx
diff --git a/tests/testthat/excel/PTPVS112016_CANAYPATA_exp1.xlsx b/tests/testthat/excel/PTPVS112016_CANAYPATA_exp1.xlsx
diff --git a/tests/testthat/excel/PTPVS112016_PMVL_exp1PEREZparacorrer - Copy.xlsx b/tests/testthat/excel/PTPVS112016_PMVL_exp1PEREZparacorrer - Copy.xlsx
diff --git a/tests/testthat/excel/genetic_design/LXT/PTYield072013_CIPSRM_exp2.-.Copy.xlsx b/tests/testthat/excel/genetic_design/LXT/PTYield072013_CIPSRM_exp2.-.Copy.xlsx
diff --git a/tests/testthat/excel/genetic_design/LXT/~$PTYield072013_CIPSRM_exp2.-.Copy.xlsx b/tests/testthat/excel/genetic_design/LXT/~$PTYield072013_CIPSRM_exp2.-.Copy.xlsx
diff --git a/tests/testthat/excel/missingval_form18.xlsx b/tests/testthat/excel/missingval_form18.xlsx
diff --git a/tests/testthat/test_organoleptic.R b/tests/testthat/test_organoleptic.R