From ad96d721cd977736f696a9196a1c429e0ccba0dd Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Wed, 21 Feb 2024 14:06:43 -0500
Subject: [PATCH 1/9] Change working directories to find files

---
 05_DASHBOARD/app.R | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/05_DASHBOARD/app.R b/05_DASHBOARD/app.R
index a8c190a..225ea2a 100644
--- a/05_DASHBOARD/app.R
+++ b/05_DASHBOARD/app.R
@@ -18,21 +18,24 @@ if(!require(sf)){ install.packages("sf") } ;  library(sf)
 # I am working in an Rproject)
 
 # NOTE: .RData restores the object to the name it had when you saved it as .RData
-#load("03_Data_for_app/HAB.RData") 
+#load("03_Data_for_app/HAB.RData")
+
+setwd("..")
+print(getwd())
 
 #### HAB data ------------------------------------------------
-load("~/github/GTMNERR Science Transfer/App_dev/03_Data_for_app/HAB.RData")
+load(paste0(getwd(), "/03_Data_for_app/HAB.RData"))
 HAB_data_locations <- HAB %>% 
     select(Latitude, Longitude, Site, `Collection Agency`, County) %>% # took out `HAB ID` (otherwise 1172 instead of 17 locations)
     distinct() %>% 
     st_as_sf(coords = c("Longitude", "Latitude"), crs = 4326)
 
 #### GTMNERR shapefile ------------------------------------------------
-GTMNERR <- st_read("~/github/GTMNERR Science Transfer/App_dev/03_Data_for_app/shapefiles_new/GTMNERR.shp")
+GTMNERR <- st_read(paste0(getwd(), "/03_Data_for_app/shapefiles_new/GTMNERR.shp"))
 GTMNERR <- st_transform(GTMNERR, crs = 4326)
 
 #### county shapefiles ------------------------------------------------
-counties_select <- st_read("~/github/GTMNERR Science Transfer/App_dev/03_Data_for_app/shapefiles_new/counties_GTMNERR.shp")
+counties_select <- st_read(paste0(getwd(), "/03_Data_for_app/shapefiles_new/counties_GTMNERR.shp"))
 counties_select <- st_transform(counties_select, crs = 4326)
 
 

From cd2a90ddc3a0bc5a6dea05ae0ca9f0525bbc32e6 Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Sat, 24 Feb 2024 17:48:08 -0500
Subject: [PATCH 2/9] Test without getwd

---
 05_DASHBOARD/app.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/05_DASHBOARD/app.R b/05_DASHBOARD/app.R
index 225ea2a..e32941f 100644
--- a/05_DASHBOARD/app.R
+++ b/05_DASHBOARD/app.R
@@ -24,18 +24,18 @@ setwd("..")
 print(getwd())
 
 #### HAB data ------------------------------------------------
-load(paste0(getwd(), "/03_Data_for_app/HAB.RData"))
+load("./03_Data_for_app/HAB.RData")
 HAB_data_locations <- HAB %>% 
     select(Latitude, Longitude, Site, `Collection Agency`, County) %>% # took out `HAB ID` (otherwise 1172 instead of 17 locations)
     distinct() %>% 
     st_as_sf(coords = c("Longitude", "Latitude"), crs = 4326)
 
 #### GTMNERR shapefile ------------------------------------------------
-GTMNERR <- st_read(paste0(getwd(), "/03_Data_for_app/shapefiles_new/GTMNERR.shp"))
+GTMNERR <- st_read("./03_Data_for_app/shapefiles_new/GTMNERR.shp")
 GTMNERR <- st_transform(GTMNERR, crs = 4326)
 
 #### county shapefiles ------------------------------------------------
-counties_select <- st_read(paste0(getwd(), "/03_Data_for_app/shapefiles_new/counties_GTMNERR.shp"))
+counties_select <- st_read("./03_Data_for_app/shapefiles_new/counties_GTMNERR.shp")
 counties_select <- st_transform(counties_select, crs = 4326)
 
 

From 2aff089e82bafd487513b0133e83d206559253d8 Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Sat, 24 Feb 2024 19:02:08 -0500
Subject: [PATCH 3/9] made dynamic working directory for app.R script

---
 05_DASHBOARD/app.R    | 47 +++++++++++++++++++++++++++++++++++++++++--
 05_DASHBOARD/deploy.R |  5 +++--
 2 files changed, 48 insertions(+), 4 deletions(-)

diff --git a/05_DASHBOARD/app.R b/05_DASHBOARD/app.R
index e32941f..424750b 100644
--- a/05_DASHBOARD/app.R
+++ b/05_DASHBOARD/app.R
@@ -12,6 +12,7 @@ if(!require(tidyverse)){ install.packages("tidyverse") } ;  library(tidyverse)
 if(!require(bslib)){ install.packages("bslib") } ;  library(bslib)
 if(!require(leaflet)){ install.packages("leaflet") } ;  library(leaflet)
 if(!require(sf)){ install.packages("sf") } ;  library(sf)
+if(!require(fs)){ install.packages("fs") } ;  library(fs)
 
 ### READ IN DATA ---------------------------------------------
 # For some reason I need to specify my whole path to the data here (even though
@@ -20,8 +21,50 @@ if(!require(sf)){ install.packages("sf") } ;  library(sf)
 # NOTE: .RData restores the object to the name it had when you saved it as .RData
 #load("03_Data_for_app/HAB.RData")
 
-setwd("..")
-print(getwd())
+#### Get app.R file dir and set work dir ---------------------
+# Function to find the directory of a file named app.R
+find_directory_of_file <- function(file_name, start_dir=getwd()) {
+  # Recursively list all files starting from the start_dir
+  app_dir <- fs::dir_ls(start_dir, recurse = TRUE, glob=file_name)
+  
+  # Check if any file named app.R is found
+  if (length(app_dir) > 0) {
+    # Assuming you want the directory of the first matching file
+    file_dir <- fs::path_dir(app_dir[1])
+    return(file_dir)
+  } else {
+    return(NULL) # Return NULL if the file is not found
+  }
+}
+
+# find file_name from current working directory
+# before trying from a shallower directory
+file_name <- "*05_DASHBOARD/app.R" # The file you are searching for
+
+try({
+  found_dir <- find_directory_of_file(file_name)
+  # Check if found_dir is NULL or empty, indicating the file was not found
+  if (is.null(found_dir) || length(found_dir) == 0) {
+    # print error
+    print("05_DASHBOARD/app.R not found from current working directory!")
+    print("trying again from shallower directory")
+    # trying again from great grandparent directory of working directory
+    setwd("../../..")
+    found_dir <- find_directory_of_file(file_name)
+    if (is.null(found_dir) || length(found_dir) == 0) {
+      print("05_DASHBOARD/app.R likely does not exist in filesystem!")
+    }
+    # Set working directory to parent directory of found dir
+    setwd(fs::path_dir(found_dir[1]))
+    # Print working directory
+    print(paste0("Working dir: ", getwd()))
+  }
+  # Set working directory to parent directory of found dir
+  setwd(fs::path_dir(found_dir[1]))
+  # Print working directory
+  print(paste0("Working dir: ", getwd()))
+}, silent = FALSE) # Setting silent = FALSE will print the error message to the console
+
 
 #### HAB data ------------------------------------------------
 load("./03_Data_for_app/HAB.RData")
diff --git a/05_DASHBOARD/deploy.R b/05_DASHBOARD/deploy.R
index 580835f..1cbe136 100644
--- a/05_DASHBOARD/deploy.R
+++ b/05_DASHBOARD/deploy.R
@@ -9,6 +9,7 @@ rsconnect::setAccountInfo(
 
 # Deploy
 rsconnect::deployApp(
-    
+    appDir = "./05_DASHBOARD",
     appFiles = "app.R",
-    appName = "Dashboard")
+    appName = "Dashboard",
+    forceUpdate = TRUE)

From ae6f261e0862887af14a3473152b528f9a5e0ab6 Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Sat, 24 Feb 2024 19:22:49 -0500
Subject: [PATCH 4/9] add files to be submitted to shinyapps.io

---
 05_DASHBOARD/app.R        |  2 +-
 05_DASHBOARD/deploy-dev.R | 24 +++++++++++++++++++++++-
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/05_DASHBOARD/app.R b/05_DASHBOARD/app.R
index 424750b..8d71a29 100644
--- a/05_DASHBOARD/app.R
+++ b/05_DASHBOARD/app.R
@@ -39,7 +39,7 @@ find_directory_of_file <- function(file_name, start_dir=getwd()) {
 
 # find file_name from current working directory
 # before trying from a shallower directory
-file_name <- "*05_DASHBOARD/app.R" # The file you are searching for
+file_name <- "*DASHBOARD/app.R" # The file you are searching for
 
 try({
   found_dir <- find_directory_of_file(file_name)
diff --git a/05_DASHBOARD/deploy-dev.R b/05_DASHBOARD/deploy-dev.R
index 88239a0..1b235b9 100644
--- a/05_DASHBOARD/deploy-dev.R
+++ b/05_DASHBOARD/deploy-dev.R
@@ -1,6 +1,27 @@
 # Load the rsconnect package
 library(rsconnect)
 
+# a function to list all files in a directory and its subdirectories
+list_all_files <- function(directories) {
+  all_files <- c() # Initialize an empty vector to store all file paths
+  
+  # Loop through each directory provided
+  for (dir in directories) {
+    if (!dir.exists(dir)) {
+      next # Skip if directory does not exist
+    }
+    
+    # Use list.files to recursively list all files in the directory and its subdirectories
+    # full.names = TRUE returns the full paths, which is what we want
+    files <- list.files(dir, recursive = TRUE, full.names = TRUE)
+    
+    # Append the files found to the all_files vector
+    all_files <- c(all_files, files)
+  }
+  
+  return(all_files)
+}
+
 # Authenticate
 rsconnect::setAccountInfo(
     name = Sys.getenv("SHINY_ACC_NAME"),
@@ -8,8 +29,9 @@ rsconnect::setAccountInfo(
     secret = Sys.getenv("SHINY_SECRET"))
 
 # Deploy
+req_files <- list_all_files(c("./04_Tests", "./03_Data_for_app")) # get all the required files
 rsconnect::deployApp(
     appDir = "./05_DASHBOARD",
-    appFiles = "app.R",
+    appFiles = c("app.R", req_files),
     appName = "Dashboard-dev",
     forceUpdate = TRUE)

From f1df5f92f7ac20513bc4eb80552856d311c15f18 Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Sat, 24 Feb 2024 19:38:47 -0500
Subject: [PATCH 5/9] Test app.R in root standard for rsconnect

---
 05_DASHBOARD/deploy-dev.R   | 4 ++--
 05_DASHBOARD/deploy.R       | 4 ++--
 05_DASHBOARD/app.R => app.R | 8 ++++----
 3 files changed, 8 insertions(+), 8 deletions(-)
 rename 05_DASHBOARD/app.R => app.R (96%)

diff --git a/05_DASHBOARD/deploy-dev.R b/05_DASHBOARD/deploy-dev.R
index 1b235b9..5fa025b 100644
--- a/05_DASHBOARD/deploy-dev.R
+++ b/05_DASHBOARD/deploy-dev.R
@@ -31,7 +31,7 @@ rsconnect::setAccountInfo(
 # Deploy
 req_files <- list_all_files(c("./04_Tests", "./03_Data_for_app")) # get all the required files
 rsconnect::deployApp(
-    appDir = "./05_DASHBOARD",
-    appFiles = c("app.R", req_files),
+    # appDir = "./05_DASHBOARD",
+    # appFiles = c("app.R", req_files),
     appName = "Dashboard-dev",
     forceUpdate = TRUE)
diff --git a/05_DASHBOARD/deploy.R b/05_DASHBOARD/deploy.R
index 1cbe136..2100d51 100644
--- a/05_DASHBOARD/deploy.R
+++ b/05_DASHBOARD/deploy.R
@@ -9,7 +9,7 @@ rsconnect::setAccountInfo(
 
 # Deploy
 rsconnect::deployApp(
-    appDir = "./05_DASHBOARD",
-    appFiles = "app.R",
+    # appDir = "./05_DASHBOARD",
+    # appFiles = "app.R",
     appName = "Dashboard",
     forceUpdate = TRUE)
diff --git a/05_DASHBOARD/app.R b/app.R
similarity index 96%
rename from 05_DASHBOARD/app.R
rename to app.R
index 8d71a29..c4e3bfb 100644
--- a/05_DASHBOARD/app.R
+++ b/app.R
@@ -39,20 +39,20 @@ find_directory_of_file <- function(file_name, start_dir=getwd()) {
 
 # find file_name from current working directory
 # before trying from a shallower directory
-file_name <- "*DASHBOARD/app.R" # The file you are searching for
+file_name <- "*app.R" # The file you are searching for
 
 try({
   found_dir <- find_directory_of_file(file_name)
   # Check if found_dir is NULL or empty, indicating the file was not found
   if (is.null(found_dir) || length(found_dir) == 0) {
     # print error
-    print("05_DASHBOARD/app.R not found from current working directory!")
+    print("app.R not found from current working directory!")
     print("trying again from shallower directory")
     # trying again from great grandparent directory of working directory
     setwd("../../..")
     found_dir <- find_directory_of_file(file_name)
     if (is.null(found_dir) || length(found_dir) == 0) {
-      print("05_DASHBOARD/app.R likely does not exist in filesystem!")
+      print("app.R likely does not exist in filesystem!")
     }
     # Set working directory to parent directory of found dir
     setwd(fs::path_dir(found_dir[1]))
@@ -60,7 +60,7 @@ try({
     print(paste0("Working dir: ", getwd()))
   }
   # Set working directory to parent directory of found dir
-  setwd(fs::path_dir(found_dir[1]))
+  setwd(found_dir[1])
   # Print working directory
   print(paste0("Working dir: ", getwd()))
 }, silent = FALSE) # Setting silent = FALSE will print the error message to the console

From 599e311da98864a871eefa12dafa0eac42a28504 Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Sat, 24 Feb 2024 19:44:37 -0500
Subject: [PATCH 6/9] copy app.R file into root

---
 05_DASHBOARD/Dockerfile     | 1 +
 05_DASHBOARD/Dockerfile-dev | 1 +
 2 files changed, 2 insertions(+)

diff --git a/05_DASHBOARD/Dockerfile b/05_DASHBOARD/Dockerfile
index e9769d1..df362d8 100644
--- a/05_DASHBOARD/Dockerfile
+++ b/05_DASHBOARD/Dockerfile
@@ -6,6 +6,7 @@ ENV BRANCH_NAME=${BRANCH_NAME}
 RUN install2.r rsconnect shiny tidyverse bslib leaflet sf
 WORKDIR /usr/src/dashboard-development
 # Copy the 'app' directory contents into the container
+COPY ./app.R /usr/src/dashboard-development/
 COPY ./03_Data_for_app /usr/src/dashboard-development/03_Data_for_app/
 COPY ./04_Tests /usr/src/dashboard-development/04_Tests/
 COPY ./05_DASHBOARD /usr/src/dashboard-development/05_DASHBOARD/
diff --git a/05_DASHBOARD/Dockerfile-dev b/05_DASHBOARD/Dockerfile-dev
index 1a6f996..e10745d 100644
--- a/05_DASHBOARD/Dockerfile-dev
+++ b/05_DASHBOARD/Dockerfile-dev
@@ -6,6 +6,7 @@ ENV BRANCH_NAME=${BRANCH_NAME}
 RUN install2.r rsconnect shiny tidyverse bslib leaflet sf
 WORKDIR /usr/src/dashboard-development
 # Copy the 'app' directory contents into the container
+COPY ./app.R /usr/src/dashboard-development/
 COPY ./03_Data_for_app /usr/src/dashboard-development/03_Data_for_app/
 COPY ./04_Tests /usr/src/dashboard-development/04_Tests/
 COPY ./05_DASHBOARD /usr/src/dashboard-development/05_DASHBOARD/

From bfd60e02611447f6e1ea98d7172300ce8e005956 Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Sat, 24 Feb 2024 19:56:20 -0500
Subject: [PATCH 7/9] Renamed files to have only one app.R file as is standard.

---
 04_Tests/HAB_test/{app.R => HAB_test_app.R}          | 0
 04_Tests/leaflet_test1/{app.R => leaflet_test_app.R} | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename 04_Tests/HAB_test/{app.R => HAB_test_app.R} (100%)
 mode change 100755 => 100644
 rename 04_Tests/leaflet_test1/{app.R => leaflet_test_app.R} (100%)

diff --git a/04_Tests/HAB_test/app.R b/04_Tests/HAB_test/HAB_test_app.R
old mode 100755
new mode 100644
similarity index 100%
rename from 04_Tests/HAB_test/app.R
rename to 04_Tests/HAB_test/HAB_test_app.R
diff --git a/04_Tests/leaflet_test1/app.R b/04_Tests/leaflet_test1/leaflet_test_app.R
similarity index 100%
rename from 04_Tests/leaflet_test1/app.R
rename to 04_Tests/leaflet_test1/leaflet_test_app.R

From 91303d07a15eae9f2298b9aed1c1bf68cd4c6989 Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Sat, 24 Feb 2024 20:03:45 -0500
Subject: [PATCH 8/9] update search string for app.R file in setting dir

---
 app.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app.R b/app.R
index c4e3bfb..028b0ed 100644
--- a/app.R
+++ b/app.R
@@ -39,14 +39,14 @@ find_directory_of_file <- function(file_name, start_dir=getwd()) {
 
 # find file_name from current working directory
 # before trying from a shallower directory
-file_name <- "*app.R" # The file you are searching for
+file_name <- "*/app.R" # The file you are searching for
 
 try({
   found_dir <- find_directory_of_file(file_name)
   # Check if found_dir is NULL or empty, indicating the file was not found
   if (is.null(found_dir) || length(found_dir) == 0) {
     # print error
-    print("app.R not found from current working directory!")
+    print("/app.R not found from current working directory!")
     print("trying again from shallower directory")
     # trying again from great grandparent directory of working directory
     setwd("../../..")

From daf79afe172bc701d1ce7fb9a76a3a11e1196ab0 Mon Sep 17 00:00:00 2001
From: Chris <53177842+ChristopherMarais@users.noreply.github.com>
Date: Sat, 24 Feb 2024 20:10:59 -0500
Subject: [PATCH 9/9] Clean up testing functions

---
 05_DASHBOARD/deploy-dev.R | 24 ------------------------
 05_DASHBOARD/deploy.R     |  2 --
 2 files changed, 26 deletions(-)

diff --git a/05_DASHBOARD/deploy-dev.R b/05_DASHBOARD/deploy-dev.R
index 5fa025b..42cdb42 100644
--- a/05_DASHBOARD/deploy-dev.R
+++ b/05_DASHBOARD/deploy-dev.R
@@ -1,27 +1,6 @@
 # Load the rsconnect package
 library(rsconnect)
 
-# a function to list all files in a directory and its subdirectories
-list_all_files <- function(directories) {
-  all_files <- c() # Initialize an empty vector to store all file paths
-  
-  # Loop through each directory provided
-  for (dir in directories) {
-    if (!dir.exists(dir)) {
-      next # Skip if directory does not exist
-    }
-    
-    # Use list.files to recursively list all files in the directory and its subdirectories
-    # full.names = TRUE returns the full paths, which is what we want
-    files <- list.files(dir, recursive = TRUE, full.names = TRUE)
-    
-    # Append the files found to the all_files vector
-    all_files <- c(all_files, files)
-  }
-  
-  return(all_files)
-}
-
 # Authenticate
 rsconnect::setAccountInfo(
     name = Sys.getenv("SHINY_ACC_NAME"),
@@ -29,9 +8,6 @@ rsconnect::setAccountInfo(
     secret = Sys.getenv("SHINY_SECRET"))
 
 # Deploy
-req_files <- list_all_files(c("./04_Tests", "./03_Data_for_app")) # get all the required files
 rsconnect::deployApp(
-    # appDir = "./05_DASHBOARD",
-    # appFiles = c("app.R", req_files),
     appName = "Dashboard-dev",
     forceUpdate = TRUE)
diff --git a/05_DASHBOARD/deploy.R b/05_DASHBOARD/deploy.R
index 2100d51..3543d46 100644
--- a/05_DASHBOARD/deploy.R
+++ b/05_DASHBOARD/deploy.R
@@ -9,7 +9,5 @@ rsconnect::setAccountInfo(
 
 # Deploy
 rsconnect::deployApp(
-    # appDir = "./05_DASHBOARD",
-    # appFiles = "app.R",
     appName = "Dashboard",
     forceUpdate = TRUE)