v2.0.0.9127

- refactor: Modify Shiny single report - Zip file download
leppott · Dec 19, 2023 · d0f6010 · d0f6010
1 parent 5d78b18
commit d0f6010
Show file tree

Hide file tree

Showing 7 changed files with 116 additions and 53 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BCGcalc
 Type: Package
 Title: Biological Condition Gradient, calculator
-Version: 2.0.0.9126
+Version: 2.0.0.9127
 Authors@R: c(
   person("Erik W.", "Leppo", email="Erik.Leppo@tetratech.com", role=c("aut","cre")), 
   person("Jen", "Stamp", email="Jen.Stamp@tetratech.com", role="ctb"),

diff --git a/NEWS b/NEWS
@@ -1,11 +1,16 @@
 BCGcalc-NEWS
 ================
 <Erik.Leppo@tetratech.com>
-2023-12-07 10:21:20.730164
+2023-12-19 11:18:29.25482
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2023-12-07 10:21:20.763828
+    #> Last Update: 2023-12-19 11:18:29.284286
+
+# BCGcalc 2.0.0.9127 (2023-12-19)
+
+- refactor: Modify Shiny single report
+  - Zip file download
 
 # BCGcalc 2.0.0.9126 (2023-12-07)
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,16 @@
 BCGcalc-NEWS
 ================
 <Erik.Leppo@tetratech.com>
-2023-12-07 10:21:20.730164
+2023-12-19 11:18:29.25482
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2023-12-07 10:21:20.763828
+    #> Last Update: 2023-12-19 11:18:29.284286
+
+# BCGcalc 2.0.0.9127 (2023-12-19)
+
+- refactor: Modify Shiny single report
+  - Zip file download
 
 # BCGcalc 2.0.0.9126 (2023-12-07)
 

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,6 +21,11 @@ knitr::opts_chunk$set(
 cat(paste0("Last Update: ",Sys.time()))
 ```
 
+# BCGcalc 2.0.0.9127 (2023-12-19)
+
+* refactor: Modify Shiny single report
+    + Zip file download
+
 # BCGcalc 2.0.0.9126 (2023-12-07)
 
 * fix: Update app BCG calculation for cases where have no flags

diff --git a/inst/shiny-examples/BCGcalc/external/db_main_sb.R b/inst/shiny-examples/BCGcalc/external/db_main_sb.R
@@ -89,9 +89,9 @@ function(id) {
                                , tabName = "tab_rep_single"
                                , icon = icon("pen")
                                )
-                 , menuSubItem("Multiple Sites"
-                               , tabName = "tab_rep_multi"
-                               , icon = icon("pen-to-square"))
+                 # , menuSubItem("Multiple Sites"
+                 #               , tabName = "tab_rep_multi"
+                 #               , icon = icon("pen-to-square"))
                  )## menuItem ~ Reports ~ END
       , menuItem(text = "Relevant Resources"
                  , tabName = "tab_resources"

diff --git a/inst/shiny-examples/BCGcalc/global.R b/inst/shiny-examples/BCGcalc/global.R
@@ -1,7 +1,7 @@
 # Shiny Global File
 
 # Version ----
-pkg_version <- "2.0.0.9126"
+pkg_version <- "2.0.0.9127"
 
 # Packages----
 # nolint start

diff --git a/inst/shiny-examples/BCGcalc/server.R b/inst/shiny-examples/BCGcalc/server.R
@@ -5122,7 +5122,7 @@ shinyServer(function(input, output) {
       message(paste0("\n", prog_detail))
 
       # Number of increments
-      prog_n <- 10
+      prog_n <- 5
       prog_sleep <- 0.25
 
       ## Calc, 01, Initialize ----
@@ -5525,24 +5525,61 @@ shinyServer(function(input, output) {
       incProgress(1/prog_n, detail = prog_detail)
       Sys.sleep(prog_sleep)
 
+      ### Excel, SUBSET ----
       # Filter for each Station
+
+      # Remove all files except Results Excel
+      # Then download button only has one file to target
+      # reuse code from df_import()
+      # fn_results <- list.files(path_results_user
+      #                          , full.names = TRUE
+      #                          , include.dirs = TRUE
+      #                          , recursive = TRUE)
+      unlink(path_results_user, recursive = TRUE) # includes directories
+
+
+
+
       stations_all <- unique(df_report_site[, pk_stations])
 
       ## create file for each station
+      s <- stations_all[1] #QC
+
       for (s in stations_all) {
+
+        s_num <- match(s, stations_all)
+        s_total <- length(stations_all)
+        msg <- paste0("Working on Report; Single Station; "
+                      , s_num
+                      , " of "
+                      , s_total
+                      , "; "
+                      , s)
+        message(msg)
+
+        # Update progress
+        prog_detail <- paste0("Calculation, Create Excel; ", s_num, "/", s_total)
+        message(paste0("\n", prog_detail))
+        # Increment the progress bar, and update the detail text.
+        incProgress(1/s_total/prog_n, detail = prog_detail)
+        Sys.sleep(prog_sleep)
+
+
         # Filter tables
-        df_report_summary_header_s <- df_report_summary_header
+        df_report_summary_header_s <- df_report_summary_header %>%
+          filter(.data[[pk_stations]] == s)
         df_report_summary_wide_s <- df_report_summary_wide
-        df_report_topindicator_s <- df_report_topindicator
-        df_report_samples_s <- df_report_samples
-        df_report_flags_s <- df_report_flags
-        df_report_site_s <- df_report_site
-        # df_report_taxatrans_s <- df_report_taxatrans
+        df_report_topindicator_s <- df_report_topindicator 
+        df_report_samples_s <- df_report_samples 
+        df_report_flags_s <- df_report_flags 
+        df_report_site_s <- df_report_site %>%
+          filter(.data[[pk_stations]] == s)
+        df_report_taxatrans_s <- df_report_taxatrans
 
-      }## FOR ~ s
+
 
-      ### Excel, Create File----
-      # Create Workbook
+      ### Excel, WB, Create----
+      # Create WB
       wb <- openxlsx::createWorkbook()
       openxlsx::addWorksheet(wb, "NOTES", tabColour = "darkgray")
       openxlsx::addWorksheet(wb, "summary")
@@ -5688,9 +5725,8 @@ shinyServer(function(input, output) {
       cf_rule_bcg2_6            <- '="6"'
       cf_rule_bcg2_na           <- '="NA"'
 
-
-
-      ### Excel, WS, NOTES----
+
+      ### Excel, WS, data, NOTES----
       openxlsx::writeData(wb
                           , sheet = "NOTES"
                           , x = notes_head
@@ -5716,54 +5752,54 @@ shinyServer(function(input, output) {
 
 
 
-      ### Excel, WS, Summary, Header ----
+      ### Excel, WS, data, Summary, Header ----
       openxlsx::writeData(wb
                           , sheet = "summary"
-                          , x = df_report_summary_header
+                          , x = df_report_summary_header_s
                           , startCol = 1
                           , startRow = mySR
                           , headerStyle = style_bold)
 
-      ### Excel, WS, Summary, Wide ----
+      ### Excel, WS, data, Summary, Wide ----
 
 
-      ### Excel, WS, Top Indicator ----
+      ### Excel, WS, data, Top Indicator ----
       openxlsx::writeData(wb
                           , sheet = "topindicator"
-                          , x = df_report_topindicator
+                          , x = df_report_topindicator_s
                           , startCol = 1
                           , startRow = mySR
                           , headerStyle = style_bold)
 
-      ### Excel, WS, Samples ----
+      ### Excel, WS, data, Samples ----
       openxlsx::writeData(wb
                           , sheet = "samples"
-                          , x = df_report_samples
+                          , x = df_report_samples_s
                           , startCol = 1
                           , startRow = mySR
                           , headerStyle = style_bold)
 
 
-      ### Excel, WS, Flags ----
+      ### Excel, WS, data, Flags ----
       openxlsx::writeData(wb
                           , sheet = "flags"
-                          , x = df_report_flags
+                          , x = df_report_flags_s
                           , startCol = 1
                           , startRow = mySR
                           , headerStyle = style_bold)
 
-      ### Excel, WS, Site ----
+      ### Excel, WS, data, Site ----
       openxlsx::writeData(wb
                           , sheet = "site"
-                          , x = df_report_site
+                          , x = df_report_site_s
                           , startCol = 1
                           , startRow = mySR
                           , headerStyle = style_bold)
 
-      ### Excel, WS, Taxa Trans ----
+      ### Excel, WS, data, Taxa Trans ----
       openxlsx::writeData(wb
                           , sheet = "taxatrans"
-                          , x = df_report_taxatrans
+                          , x = df_report_taxatrans_s
                           , startCol = 1
                           , startRow = mySR
                           , headerStyle = style_bold)
@@ -5885,7 +5921,7 @@ shinyServer(function(input, output) {
       #                       , rule = '="NA"'
       #                       , style = style_cf_ft_na)
       #
-      # #### CF, BCG----
+      #### CF, BCG----
       # conditionalFormatting(wb, "BCG"
       #                       , cols = 2
       #                       , rows = (mySR + 1):(mySR + nrow(df_bcg))
@@ -6083,26 +6119,38 @@ shinyServer(function(input, output) {
       # writeData(wb, "databar", -5:5)
       # conditionalFormatting(wb, "databar", cols = 1, rows = 1:12, type = "databar")
 
-      ### Calc, 05, Save Results ----
-      prog_detail <- "Save Results"
+      ### Excel, WB, Save  ----
+      # prog_detail <- "Save Results"
+      # message(paste0("\n", prog_detail))
+      # # Increment the progress bar, and update the detail text.
+      # incProgress(1/prog_n, detail = prog_detail)
+      # Sys.sleep(prog_sleep)
+      # 
+
+      # Save new Excel file.
+      fn_wb <- file.path(path_results_sub, paste0("results_", s, ".xlsx"))
+      openxlsx::saveWorkbook(wb, fn_wb, overwrite = TRUE)
+
+      }## FOR ~ s
+
+      ## Calc, 04, Zip Results ----
+      prog_detail <- "Create Zip File"
       message(paste0("\n", prog_detail))
       # Increment the progress bar, and update the detail text.
       incProgress(1/prog_n, detail = prog_detail)
       Sys.sleep(prog_sleep)
 
-      # Remove all files except Results Excel
-      # Then download button only has one file to target
-      # reuse code from df_import()
-      # fn_results <- list.files(path_results_user
-      #                          , full.names = TRUE
-      #                          , include.dirs = TRUE
-      #                          , recursive = TRUE)
-      unlink(path_results_user, recursive = TRUE) # includes directories
-
-      # Save new Excel file.
-      # Don't need a zip file
-      fn_wb <- file.path(path_results_sub, "results.xlsx")
-      openxlsx::saveWorkbook(wb, fn_wb, overwrite = TRUE)
+      fn_4zip <- list.files(path = path_results
+                            , full.names = TRUE)
+      zip::zip(file.path(path_results, "results.zip"), fn_4zip)
+
+
+      ## Calc, 05, Clean Up ----
+      prog_detail <- "Clean Up"
+      message(paste0("\n", prog_detail))
+      # Increment the progress bar, and update the detail text.
+      incProgress(1/prog_n, detail = prog_detail)
+      Sys.sleep(prog_sleep)
 
       # button, enable, download
       shinyjs::enable("b_download_rep_single")
@@ -6147,11 +6195,11 @@ shinyServer(function(input, output) {
       paste0(fn_input_base
              , fn_abr_save
              , format(Sys.time(), "%Y%m%d_%H%M%S")
-             , ".xlsx")
+             , ".zip")
     } ,
     content = function(fname) {##content~START
 
-      file.copy(file.path(path_results, dn_files_report, "results.xlsx"), fname)
+      file.copy(file.path(path_results, "results.zip"), fname)
 
     }##content~END
   )##download ~ Report single