v2.0.5.9084

* feature: Shiny formatHobo add inputselect for date format, Issue #117 * refactor: Shiny server.R remove full.names from zip routine preventing proper construction of download zip file, Issue #109
leppott · Feb 24, 2021 · 4b7bd67 · 4b7bd67
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ContDataQC
 Title: Quality Control (QC) of Continous Monitoring Data
-Version: 2.0.5.9083
+Version: 2.0.5.9084
 Authors@R: c(
  person("Erik W", "Leppo", email="Erik.Leppo@tetratech.com",role=c("aut","cre")),
  person("Ann","Roseberry Lincoln", role="ctb"),

diff --git a/LOG.Items.20210223.110344.tab b/LOG.Items.20210223.110344.tab
diff --git a/NEWS b/NEWS
@@ -3,10 +3,19 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
- #> Last Update: 2021-02-23 15:39:16
+ #> Last Update: 2021-02-24 12:58:37
 
 # Version History
 
+## v2.0.5.9084
+
+2021-02-24
+
+- feature: Shiny formatHobo add inputselect for date format, Issue
+ \#117
+- refactor: Shiny server.R remove full.names from zip routine
+ preventing proper construction of download zip file, Issue \#109
+
 ## v2.0.5.9083
 
 2021-02-23

diff --git a/NEWS.md b/NEWS.md
@@ -3,10 +3,19 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
- #> Last Update: 2021-02-23 15:39:16
+ #> Last Update: 2021-02-24 12:58:37
 
 # Version History
 
+## v2.0.5.9084
+
+2021-02-24
+
+- feature: Shiny formatHobo add inputselect for date format, Issue
+ \#117
+- refactor: Shiny server.R remove full.names from zip routine
+ preventing proper construction of download zip file, Issue \#109
+
 ## v2.0.5.9083
 
 2021-02-23

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,6 +21,13 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
+## v2.0.5.9084
+2021-02-24
+
+* feature: Shiny formatHobo add inputselect for date format, Issue #117
+* refactor: Shiny server.R remove full.names from zip routine preventing
+proper construction of download zip file, Issue #109
+
 ## v2.0.5.9083
 2021-02-23
 

diff --git a/R/formatHobo.R b/R/formatHobo.R
@@ -4,7 +4,8 @@
 #' Works on single files. Imports, modifies, and saves the new file.
 #'
 #' @details
-#' 1. Imports a HoboWare output (with minimal tweaks) from a folder
+#' 1. Imports a HoboWare output from a folder.
+#' Minimal tweaks from within HOBOware.
 #'
 #' 2. Reformats it using defaults from the ContDataQC config file
 #'
@@ -341,59 +342,64 @@ formatHobo <- function(fun.myFile = ""
 
 
  # Modify Date ----
+ # if no format then no transformation
 
  if(is.null(fun.HoboDateFormat) == TRUE){
  msg <- "No Hoboware date format (MDY, DMY, YMD) specified."
- stop(msg)
- }##IF.isnull.hobodate.END
+ message(msg)
+ } else {
 
- # new date
- date_new <- df_hobo[, col_Date]
+  # new date
+  date_new <- df_hobo[, col_Date]
 
- # Determine delimiter
- if(grepl("-", date_new[1]) == TRUE){
- HW_delim <- "-"
- } else if (grepl("/", date_new[1]) == TRUE){
- HW_delim <- "/"
- } else {
- msg <- "Data format not discernable."
- stop(msg)
- }## grepl("-", date_new[1]) ~ END
+  # Determine delimiter
+  if(grepl("-", date_new[1]) == TRUE){
+  HW_delim <- "-"
+  } else if (grepl("/", date_new[1]) == TRUE){
+  HW_delim <- "/"
+  } else {
+  msg <- "Data format not discernable."
+  stop(msg)
+  }## grepl("-", date_new[1]) ~ END
 
- # Determine format, time
- n_colon <- nchar(date_new[1]) - nchar(gsub(":", "", date_new[1]))
- if(n_colon == 2) {
- time_fmt <- " %H:%M:%S"
- } else if(n_colon == 1) {
- time_fmt <- " %H:%M"
- } else {
- time_fmt <- ""
- }## if(n_colon) ~ END
+  # Determine format, time
+  n_colon <- nchar(date_new[1]) - nchar(gsub(":", "", date_new[1]))
+  if(n_colon == 2) {
+  time_fmt <- " %H:%M:%S"
+  } else if(n_colon == 1) {
+  time_fmt <- " %H:%M"
+  } else {
+  time_fmt <- ""
+  }## if(n_colon) ~ END
 
- # Determine format, year
- dateonly <- strsplit(date_new, " ")[[1]][1]
- dateonly_split <- unlist(strsplit(dateonly, HW_delim)[[1]])
- year_fmt <- ifelse(max(nchar(dateonly_split)) == 4
- , "%Y", "%y")
+ # Determine format, year
+ dateonly <- strsplit(date_new, " ")[[1]][1]
+ dateonly_split <- unlist(strsplit(dateonly, HW_delim)[[1]])
+ year_fmt <- ifelse(max(nchar(dateonly_split)) == 4
+ , "%Y", "%y")
+
+ # Determine format, date
+ if(toupper(fun.HoboDateFormat) == "MDY"){
+ HW_format <- paste0("%m", HW_delim, "%d", HW_delim, year_fmt, time_fmt)
+ } else if (toupper(fun.HoboDateFormat) == "DMY") {
+ HW_format <- paste0("%d", HW_delim, "%m", HW_delim, year_fmt, time_fmt)
+ } else if (toupper(fun.HoboDateFormat) == "YMD") {
+ HW_format <- paste0(year_fmt, HW_delim, "%m", HW_delim, "%d", time_fmt)
+ } else {
+ msg <- paste0("Incorrect Hoboware date format (MDY, DMY, YMD) specified, "
+ , fun.HoboDateFormat)
+ stop(msg)
+ }## if(toupper(fun.HoboDateFormat) ~ END
+
+ # Modify dates
+ date_new_mod <- format(strptime(date_new, format = HW_format)
+ , ContData.env$myFormat.DateTime)
+ # modify hobo data frame to updated date format
+ df_hobo[,col_Date] <- date_new_mod
+
+ }##IF.isnull.hobodate.END
 
- # Determine format, date
- if(toupper(fun.HoboDateFormat) == "MDY"){
- HW_format <- paste0("%m", HW_delim, "%d", HW_delim, year_fmt, time_fmt)
- } else if (toupper(fun.HoboDateFormat) == "DMY") {
- HW_format <- paste0("%d", HW_delim, "%m", HW_delim, year_fmt, time_fmt)
- } else if (toupper(fun.HoboDateFormat) == "YMD") {
- HW_format <- paste0(year_fmt, HW_delim, "%m", HW_delim, "%d", time_fmt)
- } else {
- msg <- paste0("Incorrect Hoboware date format (MDY, DMY, YMD) specified, "
- , fun.HoboDateFormat)
- stop(msg)
- }## if(toupper(fun.HoboDateFormat) ~ END
 
- # Modify dates
- date_new_mod <- format(strptime(date_new, format = HW_format)
- , ContData.env$myFormat.DateTime)
- # modify hobo data frame to updated date format
- df_hobo[,col_Date] <- date_new_mod
 
 
  # Columns, Output

diff --git a/inst/shiny-examples/ContDataQC/HOBO/test.txt b/inst/shiny-examples/ContDataQC/HOBO/test.txt
@@ -1 +0,0 @@
-File is here to avoid an empty directory.

diff --git a/inst/shiny-examples/ContDataQC/data/test.txt b/inst/shiny-examples/ContDataQC/data/test.txt
@@ -1 +0,0 @@
-blank file

diff --git a/inst/shiny-examples/ContDataQC/server.R b/inst/shiny-examples/ContDataQC/server.R
@@ -369,6 +369,8 @@ shinyServer(function(input, output, session) {
  #Creates a data.frame for the R console output of the ContDataQC() script
  console$disp <- data.frame(consoleOutput = character())
 
+ HOBO_DateFormat_User <- input$HOBO_DateFormat
+
  withProgress(message = paste("Running, format Hobo"), value = 0, {
 
  #A short pause before the operation begins
@@ -392,7 +394,7 @@ shinyServer(function(input, output, session) {
  ,ContDataQC::formatHobo(fun.myFile = fileNameVector
  , fun.myDir.import = file.path("HOBO")
  , fun.myDir.export = file.path("HOBO")
- , fun.HoboDateFormat = NULL
+ , fun.HoboDateFormat = HOBO_DateFormat_User
  , fun.myConfig = config
  ) # formatHOBO ~ END
  )## consoleRow ~ END
@@ -600,6 +602,7 @@ shinyServer(function(input, output, session) {
 
 
  output$downloadData_HOBO <- downloadHandler(
+ # _zip-HOBO ----
  #Names the zip file
  filename <- function() {
  paste0("formatHOBO_", format(Sys.time(), "%Y%m%d_%H%M%S"), ".zip")
@@ -651,17 +654,18 @@ shinyServer(function(input, output, session) {
 
  #Lists only the csv and html files on the server
  zip.csv <- dir(file.path("data")
- , full.names = FALSE
+ #, full.names = FALSE
  , pattern = "QC.*csv")
  zip.docx <- dir(file.path("data")
- , full.names = FALSE
+ #, full.names = FALSE
  , pattern = "QC.*docx")
  zip.html <- dir(file.path("data")
- , full.names = FALSE
+ #, full.names = FALSE
  , pattern = "QC.*html")
  files2zip <- file.path("data"
  , c(zip.csv, zip.docx, zip.html)
- , full.names = FALSE)
+ #, full.names = FALSE
+ )
 
  #Zips the files
  zip(zipfile = fname, files = files2zip)
@@ -686,13 +690,13 @@ shinyServer(function(input, output, session) {
 
  #Lists only the csv and docx files on the server
  zip.csv <- dir(file.path("data")
- , full.names = FALSE
+ #, full.names = FALSE
  , pattern = "DATA.*csv")
  zip.docx <- dir(file.path("data")
- , full.names = FALSE
+ #, full.names = FALSE
  , pattern = ".*docx")
  zip.html <- dir(file.path("data")
- , full.names = FALSE
+ #, full.names = FALSE
  , pattern = ".*html")
  files2zip <- file.path("data", c(zip.csv, zip.docx, zip.html))
 
@@ -834,7 +838,7 @@ shinyServer(function(input, output, session) {
 
  #Lists only the csv and html files on the server
  zip.csv <- dir(file.path("data")
- , full.names = TRUE
+ #, full.names = TRUE
  , pattern = ".*Gage.*csv")
  files2zip <- file.path("data", c(zip.csv))
 

diff --git a/inst/shiny-examples/ContDataQC/ui.R b/inst/shiny-examples/ContDataQC/ui.R
@@ -6,7 +6,7 @@
 
 shinyUI(
  # VERSION ----
- navbarPage("Continuous data QC, summary, and statistics - v2.0.5.9080",
+ navbarPage("Continuous data QC, summary, and statistics - v2.0.5.9084",
  theme= shinytheme("spacelab"), #also liked "cerulean" at https://rstudio.github.io/shinythemes/
  # tabPan, Site Intro ----
  tabPanel("Site introduction",
@@ -385,7 +385,9 @@ shinyUI(
  , p("One file or multiple files can be uploaded for processing.")
  , tags$b("Details")
  , p("Imports a HoboWare output (with minimal tweaks), reformats it using defaults from the ContDataQC config file , and exports a CSV to another folder for use with ContDataQC.")
- , p("HOBOware will only output ambiguous dates with 2 digits. There are two delimiters (/ and -) and three formats (MDY, DMY, and YMD) resulting in six possible formats. The default is set to NULL and will not modify the date format.")
+ , p("Older versions of HOBOware only output ambiguous dates with 2 digits.
+ Newer versions use 4 digits. There are two delimiters (/ and -) and three formats (MDY, DMY, and YMD) resulting in six possible formats.")
+ , p("The user can specify the date format below. 'DMY' is the default as this is what most people use and is the default on Windows computers. NULL will not modify the input dates.")
  , p("It is assumed the user has a single Date Time field rather than two fields (Date and Time).")
  , p("A zip file with all CSV files ready for use with the ContDataQC QC function will be generated and can be downloaded.")
  , p("'Run' and 'Download' buttons do not appear until the previous step is complete ('Upload' and 'Run', respectively).")
@@ -397,13 +399,13 @@ shinyUI(
  , accept = ".csv"
  , width = "600px") # wider for long file names
  )
-
- # ,selectInput("HOBO_DateFormat",
- #  label = "Choose date format from HOBOware file",
- # choices = c(NULL
- #  , "DMY"
- #  )
- #  ,selected = NULL)
+ ,selectInput("HOBO_DateFormat",
+  label = "Choose date format from HOBOware file",
+ choices = c("MDY"
+  , "YMD"
+ , "DMY"
+ , NULL)
+ ,selected = "MDY")
  #Only shows the "Run operation" button after data are uploaded
  ,tags$div(title="Click to run selected operation (HOBO reformat)",
  uiOutput('ui.runProcess_HOBO')

diff --git a/man/formatHobo.Rd b/man/formatHobo.Rd