v2.0.7.9034

* refactor: Add error message for bad files in miniDOT concatenate in Shiny app
leppott · Oct 18, 2024 · 4471628 · 4471628
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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: 2.0.7.9033
+Version: 2.0.7.9034
 Authors@R: c(
 	person("Erik W", "Leppo", email="[email protected]",role=c("aut","cre")),
 	person("Ann","Roseberry Lincoln", role="ctb"),
@@ -36,11 +36,12 @@ Suggests:
     StreamThermal,
     XLConnect,
     zip,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    shinyalert
 VignetteBuilder: knitr
 Remotes: 
     tsangyp/StreamThermal,
     jasonelaw/iha
 StagedInstall: no
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
diff --git a/NEWS b/NEWS
@@ -3,11 +3,18 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-06-26 15:12:12.624955
+    #> Last Update: 2024-10-18 09:53:59.053843
 
 # Version History
 
-## v2.0.7.9032
+## v2.0.7.9034
+
+2024-10-18
+
+- refactor: Add error message for bad files in miniDOT concatenate in
+  Shiny app
+
+## v2.0.7.9033
 
 2024-06-26
 
@@ -29,7 +36,7 @@ NEWS-ContDataQC
     - Config_Template.zip
     - Config.R
 
-## v2.0.7.9031
+## v2.0.7.9032
 
 2024-03-01
 

diff --git a/NEWS.md b/NEWS.md
@@ -3,11 +3,18 @@ NEWS-ContDataQC
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-06-26 15:12:12.624955
+    #> Last Update: 2024-10-18 09:53:59.053843
 
 # Version History
 
-## v2.0.7.9032
+## v2.0.7.9034
+
+2024-10-18
+
+- refactor: Add error message for bad files in miniDOT concatenate in
+  Shiny app
+
+## v2.0.7.9033
 
 2024-06-26
 
@@ -29,7 +36,7 @@ NEWS-ContDataQC
     - Config_Template.zip
     - Config.R
 
-## v2.0.7.9031
+## v2.0.7.9032
 
 2024-03-01
 

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -21,7 +21,12 @@ cat(paste0("Last Update: ",Sys.time()))
 
 # Version History
 
-## v2.0.7.9032
+## v2.0.7.9034
+2024-10-18
+
+* refactor: Add error message for bad files in miniDOT concatenate in Shiny app
+
+## v2.0.7.9033
 2024-06-26
 
 * fix: Update minidoct_cat() function to display midnight values, Issue #163
@@ -41,7 +46,7 @@ cat(paste0("Last Update: ",Sys.time()))
         - Config_Template.zip
         - Config.R
 
-## v2.0.7.9031
+## v2.0.7.9032
 2024-03-01
 
 * refactor: Update Shiny app

diff --git a/inst/shiny-examples/ContDataQC/external/tab_3c_QCThresh.R b/inst/shiny-examples/ContDataQC/external/tab_3c_QCThresh.R
@@ -58,7 +58,7 @@ function() {
                        # ,h4("4. Download custom thresholds file")
                        ,sidebarLayout(
                          sidebarPanel(#width = 5
-                                     # , style = "position:fixed"#;width:22%"
+                                      # , style = "position:fixed"#;width:22%"
                                       h4("1. Select Parameter")
                                       ,selectInput(inputId = "QC_Param_Input"
                                                    , label = NULL

diff --git a/inst/shiny-examples/ContDataQC/global.R b/inst/shiny-examples/ContDataQC/global.R
@@ -11,6 +11,7 @@ library(zoo)
 library(shinythemes)
 library(zip)
 library(shinyjs)
+library(shinyalert)
 
 ###For downloading new versions of ContDataQC and USGS' DataRetrieval package
 #library(devtools)
@@ -22,7 +23,7 @@ library(shinyjs)
 # Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:\\Rtools\\bin", sep = ";"))
 
 # Version Number
-version <- "2.0.7.9033"
+version <- "2.0.7.9034"
 
 #Maximum individual file size that can be uploaded is 70 MB
 options(shiny.maxRequestSize = 70 * 1024^2)

diff --git a/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd b/inst/shiny-examples/ContDataQC/rmd/App_1b_TestData.rmd
@@ -20,9 +20,9 @@ if(boo_DEBUG==TRUE){
 }## IF ~ boo_DEBUG ~ END
 ```
 
+## Test files
 Below are test files that you can download and run through the Shiny app. They are from Onset HOBO U20 water level loggers (non-vented pressure transducers) and miniDOT DO sensors. Please contact us if you have example files from other sensors that you would like us to add to this website.
 
-# Test files
 * [Onset HOBO U20](TestData_HOBOU20_20220822.zip) [ZIP]
 * [miniDOT DO](TestData_miniDOT.zip) [ZIP]
 

diff --git a/inst/shiny-examples/ContDataQC/server.R b/inst/shiny-examples/ContDataQC/server.R
@@ -657,6 +657,29 @@ shinyServer(function(input, output, session) {
     #Creates a data.frame for the R console output of the ContDataQC() script
     console$disp <- data.frame(consoleOutput = character())
 
+    # check files for import errors
+    # popup with issues
+    # minidot_cat_warn <- FALSE
+    # tryCatch({result <- read.delim(list.files("miniDOT_cat", full.names = TRUE)[2])}
+    #          ,             )
+    for (f in list.files(file.path("miniDOT_cat"), full.names = TRUE)) {
+      tryCatch({
+        df_test <- read.delim(f, stringsAsFactors = FALSE)
+      }, error = function(e) {
+        # pop up here OR log file name and delete, at end pop up with bad files
+        # end process with pop up
+        msg <- "'INDEX_NAME' column name is missing!"
+        shinyalert::shinyalert(title = "Bad file!"
+                               , text = basename(f)
+                               , type = "error"
+                               , closeOnEsc = TRUE
+                               , closeOnClickOutside = TRUE)
+        validate(msg)
+      })## tryCatch
+    }## f ~ check files
+
+
+
     withProgress(message = paste("Running, runProcess_miniDOT_reformat"), value = 0, {
 
       #A short pause before the operation begins

diff --git a/inst/shiny-examples/ContDataQC/ui.R b/inst/shiny-examples/ContDataQC/ui.R
diff --git a/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1b_TestData.html b/inst/shiny-examples/ContDataQC/www/RMD_HTML/App_1b_TestData.html
@@ -1,18 +1,19 @@
 
 
 
+<div id="test-files" class="section level2">
+<h2>Test files</h2>
 <p>Below are test files that you can download and run through the Shiny
 app. They are from Onset HOBO U20 water level loggers (non-vented
 pressure transducers) and miniDOT DO sensors. Please contact us if you
 have example files from other sensors that you would like us to add to
 this website.</p>
-<div id="test-files" class="section level1">
-<h1>Test files</h1>
 <ul>
 <li><a href="TestData_HOBOU20_20220822.zip">Onset HOBO U20</a>
 [ZIP]</li>
 <li><a href="TestData_miniDOT.zip">miniDOT DO</a> [ZIP]</li>
 </ul>
+</div>
 <div id="onset-hobo" class="section level2">
 <h2>Onset HOBO</h2>
 <p>The Onset HOBO U20 test data consist of two comma-separated values
@@ -60,4 +61,3 @@ <h2>miniDOT DO Sensors</h2>
 data (edit if needed).</p></li>
 </ul>
 </div>
-</div>