updates in namespace

DESCRIPTION

@@ -8,7 +8,6 @@ Maintainer: Omar Benites <[email protected]>
 Description: fbcheck is a package which containt a user interface for data quality and processing.
 Depends:
     R (>= 3.2.1),
-    traittools
 Imports:
     stringr,
     magrittr,
@@ -19,6 +18,7 @@ Imports:
     doBy,
     shiny,
     sbformula,
+    traittools,
     data.table,
     date,
     purrr,
@@ -27,7 +27,8 @@ Imports:
     httr,
     RMySQL,
     DT
+Remotes: CIP-RIU/traittools
 License: MIT + file LICENSE
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
 Suggests: testthat

R/fbcheck_server_sbase.R

@@ -125,17 +125,17 @@ fbcheck_server_sbase <- function(input, output, session, values) {
     DF <- NULL
 
 #   ####### Detect if hot_btable_fbapp_sbase has data  #######
-    if(!is.null(input$hot_btable_fbapp_sbase)) {
-        print("if 1")
-        DF = hot_to_r(input$hot_btable_fbapp_sbase)
-        #values[["hot_btable_fbapp_sbase"]] = DF
-        if(file.exists(fileNameExtFile)) {
-              former_datapath <- readRDS(file = fileNameExtFile)
-              if(hot_fbapp_path()!= former_datapath){
-                DF <- hot_bdata_sbase2
-              }
-           }
-    }
+    # if(!is.null(input$hot_btable_fbapp_sbase)) {
+    #     print("if 1")
+    #     DF = hot_to_r(input$hot_btable_fbapp_sbase)
+    #     #values[["hot_btable_fbapp_sbase"]] = DF
+    #     if(file.exists(fileNameExtFile)) {
+    #           former_datapath <- readRDS(file = fileNameExtFile)
+    #           if(hot_fbapp_path()!= former_datapath){
+    #             DF <- hot_bdata_sbase2
+    #           }
+    #        }
+    # }
     ############## end detefct if ######################################
 
     if(!is.null(input$hot_btable_fbapp_sbase)) {
@@ -217,7 +217,7 @@ fbcheck_server_sbase <- function(input, output, session, values) {
       fb<-  hot_to_r(input$hot_btable_fbapp_sbase)  
     }
 
-    res<- check_fbapp(dfr=fb)
+    res<- fbcheck::check_fbapp(dfr=fb)
     shiny::withProgress(message = "Uploading file...", value = 0,
       {
         incProgress(1/6, detail = paste("Checking data..."))
@@ -229,18 +229,18 @@ fbcheck_server_sbase <- function(input, output, session, values) {
       else {
         incProgress(2/6, detail = paste("Checking data..."))
 
-        user <- str_trim(input$fbchecksbaseUser,side = "both")
-        password <- str_trim(input$fbchecksbasePass,side = "both")
-        out<- upload_studies(dbname= "sweetpotatobase", 
-                           urltoken = "sgn:[email protected]/brapi/v1/token",
-                           urlput=  "sgn:[email protected]/brapi/v1/observations",
-                           user= user, password=password,  dfr=fb)
+        user <- stringr::str_trim(input$fbchecksbaseUser,side = "both")
+        password <- stringr::str_trim(input$fbchecksbasePass,side = "both")
+        out<- fbcheck::upload_studies(dbname= "sweetpotatobase", 
+                                       urltoken = "sgn:[email protected]/brapi/v1/token",
+                                       urlput=  "sgn:[email protected]/brapi/v1/observations",
+                                       user= user, password=password,  dfr=fb)
 
           if(out$metadata$status[[6]]$code=="200"){
             shinysky::showshinyalert(session, "alert_fbappsbase_upload", paste(res$msg), styleclass = "success")  
 
             incProgress(5/6, detail = paste("Finishing upload to SweetPotatoBase..."))
-            incProgress(6/6, detail = paste("Refreshing page..."))
+            incProgress(6/6, detail = paste("Refreshing page... ")) 
 
             session$reload()
 

R/utils.R

@@ -465,7 +465,7 @@ upload_studies<- function(dbname= "sweetpotatobase",
   #jsonview::json_tree_view(xout) #json tree view
 
   fbjson <- fbapp2json(dfr = dfr, token = con$token)
-  jsonview::json_tree_view(fbjson)
+  #jsonview::json_tree_view(fbjson)
   #-----  PUT to sweetpotatobase --------------------------------------------------------------
   url <- urlput #"sgn:[email protected]/brapi/v1/observations"
   body<- fbjson #from fb2json