Revert "fixed the zip file issue, na filters in desc tab"

This reverts commit b6f00b9.

R/mod_TADA_summary.R

@@ -189,7 +189,7 @@ mod_TADA_summary_server <- function(id, tadat) {
         desc <- writeNarrativeDataFrame(tadat)
         dfs <-
           list(Data = TADA::TADA_OrderCols(tadat$raw), Parameterization = desc)
-        writeProgressFile(tadat, progress_file_name)
+        writeFile(tadat, progress_file_name)
         writexl::write_xlsx(dfs, path = datafile_name)
         utils::zip(zipfile = fname,
             files = c(datafile_name, progress_file_name))
@@ -210,7 +210,7 @@ mod_TADA_summary_server <- function(id, tadat) {
     #     paste0(tadat$job_id, '.Rdata')
     #   },
     #   content = function(file) {
-    #     writeProgressFile(tadat, file)
+    #     writeFile(tadat, file)
     #   }
     # )
 

R/mod_data_flagging.R

@@ -38,7 +38,7 @@ mod_data_flagging_ui <- function(id) {
         ns("m2f"),
         label = "",
         choices = c("feet", "inches", "meters"),
-        selected = "meters",
+        selected = character(0),
         inline = TRUE
       )
     ))

R/mod_query_data.R

@@ -61,7 +61,7 @@ mod_query_data_ui <- function(id) {
     shiny::fluidRow(column(
       4,
       shiny::dateInput(
-        ns("startDate"),
+        ns("startdate"),
         "Start Date",
         format = "yyyy-mm-dd",
         startview = "year"
@@ -70,7 +70,7 @@ mod_query_data_ui <- function(id) {
     column(
       4,
       shiny::dateInput(
-        ns("endDate"),
+        ns("enddate"),
         "End Date",
         format = "yyyy-mm-dd",
         startview = "year"
@@ -233,7 +233,7 @@ mod_query_data_server <- function(id, tadat) {
     shiny::observe({
       shiny::req(input$progress_file)
       # user uploaded data
-      readProgressFile(tadat, input$progress_file$datapath)
+      readFile(tadat, input$progress_file$datapath)
     })
 
     # if user presses example data button, make tadat$raw the nutrients dataset contained within the TADA package.
@@ -347,9 +347,9 @@ mod_query_data_server <- function(id, tadat) {
         tadat$sampleMedia <- input$media
       }
       if (is.null(input$proj)) {
-        tadat$proj <- "null"
+        tadat$project <- "null"
       } else {
-        tadat$proj <- input$proj
+        tadat$project <- input$proj
       }
       if (is.null(input$org)) {
         tadat$organization <- "null"
@@ -362,17 +362,17 @@ mod_query_data_server <- function(id, tadat) {
         tadat$siteid <- input$siteid
         # siteid = stringr::str_trim(unlist(strsplit(input$siteids,",")))
       }
-      if (length(input$endDate) == 0) {
+      if (length(input$enddate) == 0) {
         # ensure if date is empty, the query receives a proper input ("null")
-        tadat$endDate <- "null"
+        tadat$enddate <- "null"
       } else {
-        tadat$endDate <- as.character(input$endDate)
+        tadat$enddate <- as.character(input$enddate)
       }
-      if (length(input$startDate) == 0) {
+      if (length(input$startdate) == 0) {
         # ensure if date is empty, the query receives a proper start date. Might want a warning message instead.
-        tadat$startDate <- "1800-01-01"
+        tadat$startdate <- "1800-01-01"
       } else {
-        tadat$startDate <- as.character(input$startDate)
+        tadat$startdate <- as.character(input$startdate)
       }
       # a modal that pops up showing it's working on querying the portal
       shinybusy::show_modal_spinner(
@@ -392,10 +392,10 @@ mod_query_data_server <- function(id, tadat) {
         characteristicName = tadat$characteristicName,
         characteristicType = tadat$characteristicType,
         sampleMedia = tadat$sampleMedia,
-        proj = tadat$proj,
+        project = tadat$project,
         organization = tadat$organization,
-        startDate = tadat$startDate,
-        endDate = tadat$endDate,
+        startDate = tadat$startdate,
+        endDate = tadat$enddate,
         applyautoclean = TRUE
       )
 
@@ -439,8 +439,8 @@ mod_query_data_server <- function(id, tadat) {
           shiny::updateSelectizeInput(session, "media", selected = tadat$sampleMedia)
           shiny::updateSelectizeInput(session, "proj", selected = tadat$proj)
           shiny::updateSelectizeInput(session, "org", selected = tadat$organization)
-          shiny::updateDateInput(session, "startDate", value = tadat$startDate)
-          shiny::updateDateInput(session, "endDate", value = tadat$endDate)
+          shiny::updateDateInput(session, "startdate", value = tadat$startDate)
+          shiny::updateDateInput(session, "enddate", value = tadat$endDate)
         }
       }
 

R/mod_review_data.R

@@ -43,6 +43,8 @@ mod_review_data_server <- function(id, tadat) {
     shiny::observeEvent(input$review_go, {
       removals <- tadat$removals
       sel <- which(removals == TRUE, arr.ind = TRUE)
+      print(length(sel))
+      # Bombing here
       if (length(sel) > 0) {
         removals[sel] <- names(removals)[sel[, "col"]]
         removals[removals == FALSE] <- ""
@@ -94,7 +96,7 @@ mod_review_data_server <- function(id, tadat) {
       if (nrow(rem_reas) > 0) {
         review_things$rem_reas <- rem_reas
       } else{
-        review_things$rem_reas <- data.frame(Reason="No Removals", Count=0)
+        review_things$rem_reas <- data.frame(Reason="No Removals", Count=1)
       }
     })
 

R/utils_track_progress.R

@@ -1,4 +1,5 @@
-writeProgressFile <- function(tadat, filename) {
+
+writeFile <- function(tadat, filename) {
   original_source = tadat$original_source
   job_id = tadat$job_id
   statecode = tadat$statecode
@@ -17,8 +18,7 @@ writeProgressFile <- function(tadat, filename) {
   org_table <- tadat$org_table
   selected_flags <- tadat$selected_flags
   m2f <- tadat$m2f
-  selected_filters <-
-    tadat$selected_filters[c("Field", "Value", "Filter")]
+  selected_filters <- tadat$selected_filters[c("Field", "Value", "Filter")]
   nd_method <- tadat$nd_method
   od_method <- tadat$od_method
   nd_mult <- tadat$nd_mult
@@ -53,30 +53,30 @@ writeProgressFile <- function(tadat, filename) {
 
 }
 
-readProgressFile <- function(tadat, filename) {
+readFile <- function(tadat, filename) {
   load(filename, verbose = FALSE)
   checkFlagColumns(tadat$raw)
   tadat$load_progress_file = filename
-  
+
   # Confirm compatibility
   job_id = job_id
   if (!is.null(m2f)) {
     tadat$m2f = m2f
   }
-  
+
 
   if (!is.null(selected_flags)) {
     tadat$selected_flags = selected_flags
     shinyjs::enable(selector = '.nav li a[data-value="Flag"]')
   } else {
     print("No flags selected")
   }
-  
+
   # Enable tabs if certain fields are not null
   if (!is.null(selected_filters)) {
     shinyjs::enable(selector = '.nav li a[data-value="Filter"]')
   }
-  
+
   tadat$original_source = original_source
   tadat$job_id = job_id
   tadat$example_data = example_data
@@ -109,15 +109,14 @@ invalidFile <- function(trigger) {
 
 
 writeNarrativeDataFrame <- function(tadat) {
-  df <- data.frame(Parameter = character(), Value = character())
-  df[nrow(df) + 1,] = c("TADA Shiny Job ID", tadat$job_id)
-  df[nrow(df) + 1,] = c("Original data source: ", tadat$original_source)
+  df <- data.frame(Parameter=character(), Value=character())
+  df[nrow(df) + 1, ] = c("TADA Shiny Job ID", tadat$job_id)
+  df[nrow(df) + 1, ] = c("Original data source: ", tadat$original_source)
 
   # Data Query Tab
   if (tadat$original_source == "Example") {
-    df[nrow(df) + 1,] = c("Example data file", tadat$example_data)
+    df[nrow(df) + 1, ] = c("Example data file", tadat$example_data)
   } else if (tadat$original_source == "Query") {
-    tadat$sampleMedia = paste(tadat$sampleMedia, collapse = ", ")
     query_params = data.frame(
       param = c(
         "State Code",
@@ -150,58 +149,53 @@ writeNarrativeDataFrame <- function(tadat) {
     )
     for (i in seq_len(nrow(query_params))) {
       if (!is.null(query_params[i, "value"])) {
-        df[nrow(df) + 1,] = query_params[i, ]
+        df[nrow(df) + 1, ] = query_params[i,]
       }
     }
   }
-  
+
   # Overview Tab
   for (row in 1:nrow(tadat$org_table)) {
-    df[nrow(df) + 1,] = c(paste0("Organization Rank ", row), tadat$org_table[row, 'OrganizationFormalName'])
+    df[nrow(df) + 1, ] = c(paste0("Organization Rank ", row), tadat$org_table[row, 'OrganizationFormalName'])
   }
 
-  
+
   # Flagging Tab
   for (flag in tadat$selected_flags) {
-    df[nrow(df) + 1,] = c("Selected Flag", flag)
+    df[nrow(df) + 1, ] = c("Selected Flag", flag)
   }
 
-  
+
   if (!is.null(tadat$m2f)) {
-    df[nrow(df) + 1,] = c("Depth unit conversion", tadat$m2f)
+    df[nrow(df) + 1, ] = c("Depth unit conversion", tadat$m2f)
   } else {
-    df[nrow(df) + 1,] = c("Depth unit conversion", "None")
+    df[nrow(df) + 1, ] = c("Depth unit conversion", "None")
   }
 
-  
+
   # Filtering tab
-  if (nrow(tadat$selected_filters) > 0) {
-    for (row in 1:nrow(tadat$selected_filters)) {
-      df[nrow(df) + 1,] = c(
-        "Selected Filter",
-        paste0(
-          tadat$selected_filters[row, 'Filter'],
-          ": ",
-          tadat$selected_filters[row, 'Field'],
-          " = ",
-          tadat$selected_filters[row, 'Value']
-        )
+  for (row in 1:nrow(tadat$selected_filters)) {
+    df[nrow(df) + 1, ] = c(
+      "Selected Filter",
+      paste0(
+        tadat$selected_filters[row, 'Filter'],
+        ": ",
+        tadat$selected_filters[row, 'Field'],
+        " = ",
+        tadat$selected_filters[row, 'Value']
       )
-      print(df[nrow(df) + 1,])
-    }
+    )
   }
 
   # Censored Data tab
-  if (is.null(tadat$nd_mult)) {
+  if (is.null(tadat$nd_mult)){
     tadat$nd_mult = "n/a"
   }
-  if (is.null(tadat$od_mult)) {
+  if (is.null(tadat$od_mult)){
     tadat$od_mult = "n/a"
   }
-  df[nrow(df) + 1,] = c("Non-Detect Handling Method",
-                        sub("x",  tadat$nd_mult, tadat$nd_method))
-  df[nrow(df) + 1,] = c("Over-Detect Handling Method",
-                        sub("x", tadat$od_mult, tadat$od_method))
+  df[nrow(df) + 1, ] = c("Non-Detect Handling Method", sub("x",  tadat$nd_mult, tadat$nd_method))
+  df[nrow(df) + 1, ] = c("Over-Detect Handling Method", sub("x", tadat$od_mult, tadat$od_method))
 
   return(df)
 }