Merge pull request #22 from acornamr/dev

v2.6.1
acornamr · May 28, 2023 · c801f6e · c801f6e
2 parents 7d01f5b + d4132dd
commit c801f6e
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Showing 6 changed files with 58 additions and 44 deletions.
diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,4 @@
 .Ruserdata
 *.DS_Store
 *.dcf
+.Renviron
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,11 @@
 Package: acorn
 Type: Package
 Title: A Dashboard for ACORN AMR Data
-Version: 2.6.0
+Version: 2.6.1
 Authors@R: c(person(given = "Olivier", family = "Celhay", 
                 email = "olivier.celhay@gmail.com", 
-                role = c("aut", "cre"), comment = c(ORCID = "https://orcid.org/0000-0002-2971-9110")),
+                role = c("aut", "cre"), 
+                comment = c(ORCID = "https://orcid.org/0000-0002-2971-9110")),
             person(given = "Paul", family = "Turner", 
                 email = "Pault@tropmedres.ac", 
                 role = c("aut")))

diff --git a/inst/acorn/app.R b/inst/acorn/app.R
@@ -1,4 +1,4 @@
-app_version <- "2.6.0"  # Make sure that the app version is identical in DESCRIPTION
+app_version <- "2.6.1"  # Make sure that the app version is identical in DESCRIPTION
 session_start_time <- format(Sys.time(), "%Y-%m-%d_%HH%M")
 
 # IMPORTANT: ensure that there is a match between the calls below and:
@@ -43,13 +43,14 @@ choices_datamanagement <- c("Generate and load .acorn </br> from clinical and la
                             "Load .acorn </br> from local file",
                             "Info on </br> loaded .acorn")
 
-code_sites <- c("Run Demo", 
-                "Upload Local .acorn",
-                readr::read_csv(
-                  file = "./www/data/ACORN2_site_codes.csv", 
-                  show_col_types = FALSE) |> 
-                  pull(site_code)
-)
+site_choices <- readr::read_csv(
+  file = "./www/data/ACORN2_site_codes.csv", 
+  show_col_types = FALSE) |> 
+  shinyWidgets::prepare_choices(
+    label = site_code,
+    value = site_code,
+    group_by = country
+  )
 
 aware <- read.csv(
   file = "./www/data/AWaRe_WHO_2021.csv") |> 
@@ -229,7 +230,12 @@ ui <- page(
                      div(class = "well",
                          h5(class = "text_center",  i18n$t("Please log in")),
                          div(class = "text-center", i18n$t("(To log out, close the app.)")),
-                         pickerInput("cred_site", "", choices = code_sites, selected = "Run Demo"),
+                         shinyWidgets::virtualSelectInput(
+                           "cred_site",
+                           "",
+                           site_choices,
+                           hasOptionDescription = TRUE
+                         ),
                          conditionalPanel("input.cred_site != 'Run Demo' && input.cred_site != 'Upload Local .acorn'", div(
                            textInput("cred_user", tagList(icon("user"), i18n$t("User")), placeholder = "enter user name"),
                            passwordInput("cred_password", tagList(icon("unlock-alt"), i18n$t("Password")), placeholder = "enter password")

diff --git a/inst/acorn/www/data/ACORN2_site_codes.csv b/inst/acorn/www/data/ACORN2_site_codes.csv
@@ -1,4 +1,4 @@
-site_code,country,city,site_name,lat,lon,acorn_network,comment
+site_code,country,city,site_name,lat,lon,acorn_network,comment
 KH001,Cambodia,Siem Reap,Angkor Hospital for Children,13.3579855,103.8567,TRUE,
 GH001,Ghana,Accra,Korle-Bu Teaching Hospital,5.5372605,-0.22683187,TRUE,
 GH002,Ghana,Accra,37 Military Hospital,5.588754786,-0.18410816,TRUE,
@@ -18,4 +18,5 @@ NG002,Nigeria,Ife,"Obafemi Awolowo University Teaching Hospital, Ife",7.49053224
 NG003,Nigeria,Igbo-ora,Ibarapa Rural lab,7.447033504,3.276880573,FALSE,
 VN001,Vietnam,Hanoi,National Hospital for Tropical Diseases,21.00231646,105.8389495,TRUE,
 VN002,Vietnam,Hue,Hue Central Hospital (Bệnh viện Trung Ương Huế),16.4626133,107.5879476,FALSE,
-VN003,Vietnam,Ho Chi Minh City,Children's Hospital 2 (Bệnh viện Nhi Đồng 2),10.7810848,106.702319,FALSE,
+VN003,Vietnam,Ho Chi Minh City,Children's Hospital 2 (Bệnh viện Nhi Đồng 2),10.7810848,106.702319,FALSE,
+PH001,Philippine,Manila,Philippine General Hospital,,,FALSE,
diff --git a/misc/create_encrypted_credentials.R b/misc/create_encrypted_credentials.R
@@ -1,36 +1,41 @@
-creds <- readxl::read_excel("/Users/olivier/Documents/Projets/ACORN/Data/ACORN2_cred.xlsx", 
-                            sheet = "cred") |>  
-  filter(!is.na(site))
+# INSTRUCTIONS:
+# - use the R commands below to generate one .rds file per line in ACORN2_cred.xlsx
+# - add encrypted_cred_XXX_YYY.rds to the S3 "shared-acornamr" folder
+# - rename encrypted_cred_demo.rds into encrypted_cred_demo_demo.rds
+# - add encrypted_cred_demo.rds to the app "www/cred" folder
+
+dir <- "/Users/olivier/Documents/Consultances/ACORN/Data"
+
+creds <- readxl::read_excel(
+  path = glue::glue("{dir}/ACORN2_cred.xlsx"),
+  sheet = "cred") |>  
+  dplyr::filter(
+    !is.na(site)
+  )
 
 
 for (i in 1:nrow(creds)) {
   user <- creds[i, ]
 
   cred <- serialize(
-    object = list(site = user$site,
-                  user = user$user,
-                  # REDCap
-                  redcap_access = user$redcap_access,
-                  redcap_uri = user$redcap_uri,
-                  redcap_f01f05_api = user$redcap_f01f05_api,
-                  redcap_hai_api = user$redcap_hai_api,
-                  # AWS S3
-                  aws_access = user$aws_access,
-                  aws_bucket = user$aws_bucket,
-                  aws_region = user$aws_region,  
-                  aws_key = user$aws_key,
-                  aws_secret = user$aws_secret
+    object = list(
+      site = user$site,
+      user = user$user,
+      # REDCap
+      redcap_access = user$redcap_access,
+      redcap_uri = user$redcap_uri,
+      redcap_f01f05_api = user$redcap_f01f05_api,
+      redcap_hai_api = user$redcap_hai_api,
+      # AWS S3
+      aws_access = user$aws_access,
+      aws_bucket = user$aws_bucket,
+      aws_region = user$aws_region,  
+      aws_key = user$aws_key,
+      aws_secret = user$aws_secret
     ),
     connection = NULL)
 
   encrypted_cred <- openssl::aes_cbc_encrypt(cred, key = openssl::sha256(charToRaw(user$pwd)))
-  saveRDS(encrypted_cred, glue::glue("/Users/olivier/Documents/Projets/ACORN/Data/ACORN2_creds/encrypted_cred_{user$site}_{user$user}.rds"))
+  saveRDS(encrypted_cred, glue::glue("{dir}/ACORN2_creds/encrypted_cred_{user$site}_{user$user}.rds"))
 }
 
-# Instructions:
-# encrypted_cred_XXX_YYY.rds files should be added to the "shared-acornamr" folder
-# "encrypted_cred_demo.rds" should be added to the "www/cred" folder.
-# "shared_acornamr_key.rds" and "share-acornamr_sec.rds" should be added to the "www/cred" folder. 
-# They can be generated with the commands:
-# saveRDS("COPY_KEY_HERE", file = "/Users/olivier/Documents/Projets/ACORN/Data/ACORN2_creds/shared_acornamr_key.rds")
-# saveRDS("COPY_SECRET_HERE", file = "/Users/olivier/Documents/Projets/ACORN/Data/ACORN2_creds/shared_acornamr_sec.rds")
diff --git a/renv.lock b/renv.lock
@@ -349,10 +349,10 @@
     },
     "commonmark": {
       "Package": "commonmark",
-      "Version": "1.8.0",
+      "Version": "1.9.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "2ba81b120c1655ab696c935ef33ea716",
+      "Hash": "d691c61bff84bd63c383874d2d0c3307",
       "Requirements": []
     },
     "cpp11": {
@@ -955,12 +955,12 @@
     },
     "markdown": {
       "Package": "markdown",
-      "Version": "1.1",
+      "Version": "1.6",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "61e4a10781dd00d7d81dd06ca9b94e95",
+      "Hash": "c0e8495f796d73f2d2e1a8c6964d67e8",
       "Requirements": [
-        "mime",
+        "commonmark",
         "xfun"
       ]
     },
@@ -1690,10 +1690,10 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.31",
+      "Version": "0.39",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "a318c6f752b8dcfe9fb74d897418ab2b",
+      "Hash": "8f56e9acb54fb525e66464d57ab58bcb",
       "Requirements": []
     },
     "xml2": {