From b6b0844ce5571ba10f794dda052ed8bde3146639 Mon Sep 17 00:00:00 2001 From: Hook Date: Wed, 3 Jan 2024 10:04:57 -0500 Subject: [PATCH] Revert "fixed the zip file issue, na filters in desc tab" This reverts commit b6f00b914c6d6d84de0adb44b49eb110b272127c. --- R/mod_TADA_summary.R | 4 +-- R/mod_data_flagging.R | 2 +- R/mod_query_data.R | 32 ++++++++--------- R/mod_review_data.R | 4 ++- R/utils_track_progress.R | 76 ++++++++++++++++++---------------------- 5 files changed, 57 insertions(+), 61 deletions(-) diff --git a/R/mod_TADA_summary.R b/R/mod_TADA_summary.R index 96a8b8e47..d3578e3a9 100644 --- a/R/mod_TADA_summary.R +++ b/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) # } # ) diff --git a/R/mod_data_flagging.R b/R/mod_data_flagging.R index dd9fabebd..f7b659cfa 100644 --- a/R/mod_data_flagging.R +++ b/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 ) )) diff --git a/R/mod_query_data.R b/R/mod_query_data.R index ed336838d..ebc9bf106 100644 --- a/R/mod_query_data.R +++ b/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$endDate) } } diff --git a/R/mod_review_data.R b/R/mod_review_data.R index 13aed3eb0..13fdf21c3 100644 --- a/R/mod_review_data.R +++ b/R/mod_review_data.R @@ -43,6 +43,8 @@ mod_review_data_server <- function(id, tadat) { shiny::observeEvent(input$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) } }) diff --git a/R/utils_track_progress.R b/R/utils_track_progress.R index 8d966e57f..037cd6ab6 100644 --- a/R/utils_track_progress.R +++ b/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$nd_mult @@ -53,17 +53,17 @@ writeProgressFile <- function(tadat, filename) { } -readProgressFile <- function(tadat, filename) { +readFile <- function(tadat, filename) { load(filename, verbose = FALSE) checkFlagColumns(tadat$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$selected_flags = selected_flags @@ -71,12 +71,12 @@ readProgressFile <- function(tadat, filename) { } else { print("No flags selected") } - + # Enable tabs if certain fields are not null if (!is.null(selected_filters)) { shinyjs::enable(selector = '.nav li a[data-value="Filter"]') } - + tadat$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) }