deploy_shiny() has moved to a different package

.github/workflows/R-CMD-check.yaml

@@ -20,7 +20,7 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
 
@@ -39,6 +39,8 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
+      - uses: r-lib/actions/setup-renv@v2
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

.github/workflows/test-coverage.yaml

@@ -21,6 +21,8 @@ jobs:
         with:
           use-public-rspm: true
 
+      - uses: r-lib/actions/setup-renv@v2
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::covr

.lintr

@@ -1,7 +0,0 @@
-linters: linters_with_defaults(
-    commented_code_linter = NULL
-  )
-encoding: "UTF-8"
-exclusions: list(
-    "drafting/"
-  )

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapCAST
 Title: REDCap Castellated Data Handling
-Version: 24.2.1
+Version: 24.3.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
     role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 
@@ -28,7 +28,6 @@ Suggests:
     knitr,
     rmarkdown,
     gt,
-    usethis,
     ggplot2,
     here,
     styler,
@@ -52,7 +51,6 @@ Imports:
     stats,
     shiny,
     openxlsx2,
-    rsconnect,
     haven
 Collate: 
     'utils.r'

NAMESPACE

@@ -3,7 +3,6 @@
 export(REDCap_split)
 export(clean_redcap_name)
 export(d2w)
-export(deploy_shiny)
 export(ds2dd)
 export(ds2dd_detailed)
 export(easy_redcap)

NEWS.md

@@ -1,3 +1,10 @@
+# REDCapCAST 24.3.1 - in development
+
+### Documentation and more
+
+* Dependencies: In order to deploy `shiny_cast()` with `shinylive`, I need to remove `curl` as a dependency. To accomplish this, the `shiny_deploy()` helper functions has been moved to the package [`pacakge.aid`](https://github.com/agdamsbo/package.aid). This is for a rainy day: https://r-wasm.github.io/rwasm/. The whole shiny part may be migrated to its own project to try to separate things and be easy on dependencies. Time will tell.
+
+
 # REDCapCAST 24.2.1
 
 ### Functions

R/shiny_cast.R

@@ -34,25 +34,3 @@ shiny_cast <- function() {
   )
 }
 
-#' Deploy the Shiny app with rsconnect
-#'
-#' @param path app folder path
-#' @param name.app name of deployed app
-#'
-#' @return deploy
-#' @export
-#'
-#' @examples
-#' # deploy_shiny
-#'
-deploy_shiny <- function(path = here::here("app/"), name.app = "shiny_cast") {
-  # Connecting
-  rsconnect::setAccountInfo(
-    name = "cognitiveindex",
-    token = keyring::key_get(service = "rsconnect_cognitiveindex_token"),
-    secret = keyring::key_get(service = "rsconnect_cognitiveindex_secret")
-  )
-
-  # Deploying
-  rsconnect::deployApp(appDir = path, lint = TRUE, appName = name.app, )
-}

app/rsconnect/shinyapps.io/agdamsbo/redcapcast.dcf

@@ -0,0 +1,10 @@
+name: redcapcast
+title:
+username: agdamsbo
+account: agdamsbo
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 11351429
+bundleId: 8311272
+url: https://agdamsbo.shinyapps.io/redcapcast/
+version: 1

app/rsconnect/shinyapps.io/cognitiveindex/shiny_cast.dcf

@@ -0,0 +1,10 @@
+name: shiny_cast
+title:
+username: cognitiveindex
+account: cognitiveindex
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 11351378
+bundleId: 8306502
+url: https://cognitiveindex.shinyapps.io/shiny_cast/
+version: 1

app/ui.R

@@ -1,89 +1,133 @@
-ui <- shiny::fluidPage(
+ui <- shiny::shinyUI(
+  shiny::fluidPage(
 
-  ## -----------------------------------------------------------------------------
+    ## -----------------------------------------------------------------------------
-  ## Application title
+    ## Application title
-  ## -----------------------------------------------------------------------------
+    ## -----------------------------------------------------------------------------
-  shiny::titlePanel("Simple REDCap data base creation and data upload from data set file via API",
-                    windowTitle = "REDCap databse creator"
-  ),
-  shiny::h5("Please note, that this tool serves as a demonstration of some of the functionality
-       of the REDCapCAST package. No responsibility for data loss or any other
-       problems will be taken."),
 
-  ## -----------------------------------------------------------------------------
-  ## Side panel
-  ## -----------------------------------------------------------------------------
 
-  shiny::sidebarPanel(
+    # customHeaderPanel(title = "REDCapCAST: data base creation and data upload from data set file",
-    shiny::h4("REDCap database and dataset"),
+    #                   windowTitle = "REDCap database creator"
-    shiny::fileInput("ds", "Choose data file",
+    # ),
-                     multiple = FALSE,
+
-                     accept = c(
+    shiny::titlePanel(title = shiny::div(shiny::a(shiny::img(src="logo.png"),href="https://agdamsbo.github.io/REDCapCAST"),
-                       ".csv",
+                                  "Easy REDCap database creation"),
-                       ".xls",
+      windowTitle = "REDCap database creator"
-                       ".xlsx",
-                       ".dta"
-                     )
     ),
-    shiny::h6("Below you can download the dataset formatted for upload and the
+    shiny::h4("This tool includes to convenient functions:",
-         corresponding data dictionary for a new data base."),
+              shiny::br(),
-    # Button
+              "1) creating a REDCap data dictionary based on a spreadsheet (.csv/.xls(x)/.dta) and",
-    shiny::downloadButton("downloadData", "Download data"),
+              shiny::br(),
-
+              "2) creating said database on a given REDCap server and uploading the dataset via API access."),
-    # Button
-    shiny::downloadButton("downloadMeta", "Download dictionary"),
 
 
-    # Horizontal line ----
+    ## -----------------------------------------------------------------------------
-    shiny::tags$hr(),
+    ## Side panel
-    shiny::h4("REDCap upload"),
+    ## -----------------------------------------------------------------------------
-    shiny::textInput(
-      inputId = "uri",
-      label = "URI",
-      value = "https://redcap.your.institution/api/"
-    ),
-    shiny::textInput(
-      inputId = "api",
-      label = "API key",
-      value = ""
-    ),
-    shiny::actionButton(
-      inputId = "upload.meta",
-      label = "Upload dictionary", icon = shiny::icon("book-bookmark")
-    ),
-    shiny::h6("Please note, that before uploading any real data, put your project
-         into production mode."),
-    shiny::actionButton(
-      inputId = "upload.data",
-      label = "Upload data", icon = shiny::icon("upload")
-    ),
 
-    # Horizontal line ----
+    shiny::sidebarPanel(
-    shiny::tags$hr()
+      shiny::h4("1) REDCap datadictionary and compatible dataset"),
-  ),
+      shiny::fileInput("ds", "Choose data file",
-  shiny::mainPanel(
+        multiple = FALSE,
-    shiny::tabsetPanel(
+        accept = c(
-
+          ".csv",
-      ## -----------------------------------------------------------------------------
+          ".xls",
-      ## Summary tab
+          ".xlsx",
-      ## -----------------------------------------------------------------------------
+          ".dta"
-      shiny::tabPanel(
+        )
-        "Summary",
-        shiny::h3("Data overview (first 20)"),
-        shiny::htmlOutput("data.tbl", container = shiny::span),
-        shiny::h3("Dictionary overview"),
-        shiny::htmlOutput("meta.tbl", container = shiny::span)
       ),
-      ## -----------------------------------------------------------------------------
+      shiny::h6("Below you can download the dataset formatted for upload and the
-      ## Upload tab
+         corresponding data dictionary for a new data base, if you want to upload manually."),
-      ## -----------------------------------------------------------------------------
+      # Button
-      shiny::tabPanel(
+      shiny::downloadButton("downloadData", "Download data"),
-        "Upload",
+
-        shiny::h3("Meta upload overview"),
+      # Button
-        shiny::htmlOutput("upload.meta.print", container = shiny::span),
+      shiny::downloadButton("downloadMeta", "Download datadictionary"),
-        shiny::h3("Data upload overview"),
+
-        shiny::htmlOutput("upload.data.print", container = shiny::span)
+
+      # Horizontal line ----
+      shiny::tags$hr(),
+      shiny::h4("2) REDCap upload"),
+      shiny::h6("This tool is usable for now. Detailed instructions are coming."),
+      shiny::textInput(
+        inputId = "uri",
+        label = "URI",
+        value = "https://redcap.your.institution/api/"
+      ),
+      shiny::textInput(
+        inputId = "api",
+        label = "API key",
+        value = ""
+      ),
+      shiny::h6("An API key is an access key to the REDCap database. Please", shiny::a("see here for directions", href="https://www.iths.org/news/redcap-tip/redcap-api-101/"), " to obtain an API key for your project."),
+      shiny::actionButton(
+        inputId = "upload.meta",
+        label = "Upload datadictionary", icon = shiny::icon("book-bookmark")
+      ),
+      shiny::h6("Please note, that before uploading any real data, put your project
+         into production mode."),
+      shiny::actionButton(
+        inputId = "upload.data",
+        label = "Upload data", icon = shiny::icon("upload")
+      ),
+
+      # Horizontal line ----
+      shiny::tags$hr()
+    ),
+    shiny::mainPanel(
+      shiny::tabsetPanel(
+
+        ## -----------------------------------------------------------------------------
+        ## Summary tab
+        ## -----------------------------------------------------------------------------
+        shiny::tabPanel(
+          "Summary",
+          shiny::h3("Data overview (first 20)"),
+          shiny::htmlOutput("data.tbl", container = shiny::span),
+          shiny::h3("Dictionary overview"),
+          shiny::htmlOutput("meta.tbl", container = shiny::span)
+        ),
+        ## -----------------------------------------------------------------------------
+        ## Upload tab
+        ## -----------------------------------------------------------------------------
+        shiny::tabPanel(
+          "Upload",
+          shiny::h3("Meta upload overview"),
+          shiny::htmlOutput("upload.meta.print", container = shiny::span),
+          shiny::h3("Data upload overview"),
+          shiny::htmlOutput("upload.data.print", container = shiny::span)
+        )
       )
-    )
+    ),
+
+
+    # close sidebarLayout
+
+    br(),
+    br(),
+    br(),
+    br(),
+    hr(),
+    shiny::tags$footer(shiny::strong("Disclaimer: "),
+                       "This tool is aimed at demonstrating use of REDCapCAST. No responsibility for data loss or any other problems will be taken. Please contact me for support.",
+                       shiny::br(),
+                       shiny::a("License: GPL-3+",href="https://agdamsbo.github.io/REDCapCAST/LICENSE.html"),
+                       "|",
+                       shiny::a("agdamsbo/REDCapCAST",href="https://agdamsbo.github.io/REDCapCAST"),
+                       "|",
+                       shiny::a("Source",href="https://github.com/agdamsbo/REDCapCAST"),
+                       "|",
+                       shiny::a("Contact",href="https://andreas.gdamsbo.dk"),
+                align = "center",
+                style = "
+                 position:fixed;
+                 bottom:40px;
+                 width:100%;
+                 height:20px;
+                 color: black;
+                 padding: 0px;
+                 background-color: White;
+                 z-index: 100;
+                ")
   )
 )

man/deploy_shiny.Rd

@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/shiny_cast.R
-\name{deploy_shiny}
-\alias{deploy_shiny}
-\title{Deploy the Shiny app with rsconnect}
-\usage{
-deploy_shiny(path = here::here("app/"), name.app = "shiny_cast")
-}
-\arguments{
-\item{path}{app folder path}
-
-\item{name.app}{name of deployed app}
-}
-\value{
-deploy
-}
-\description{
-Deploy the Shiny app with rsconnect
-}
-\examples{
-# deploy_shiny
-
-}

renv.lock

@@ -210,24 +210,24 @@
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.2.0",
+      "Version": "5.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9"
+      "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.34",
+      "Version": "0.6.35",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a"
+      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
     },
     "dplyr": {
       "Package": "dplyr",
@@ -557,18 +557,6 @@
       ],
       "Hash": "9fa7cdc5fbdb1c8511fdde72a944db63"
     },
-    "packrat": {
-      "Package": "packrat",
-      "Version": "0.9.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "tools",
-        "utils"
-      ],
-      "Hash": "55ddd2d4a1959535f18393478b0c14a6"
-    },
     "pillar": {
       "Package": "pillar",
       "Version": "1.9.0",
@@ -686,13 +674,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.4",
+      "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "11abaf7c540ff33f94514d50f929bfd1"
+      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
     },
     "rlang": {
       "Package": "rlang",
@@ -705,35 +693,6 @@
       ],
       "Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
     },
-    "rsconnect": {
-      "Package": "rsconnect",
-      "Version": "1.2.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "curl",
-        "digest",
-        "jsonlite",
-        "lifecycle",
-        "openssl",
-        "packrat",
-        "renv",
-        "rlang",
-        "rstudioapi",
-        "tools",
-        "yaml"
-      ],
-      "Hash": "94bb3a2125b01b13dd2e4a784c2a9639"
-    },
-    "rstudioapi": {
-      "Package": "rstudioapi",
-      "Version": "0.15.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "5564500e25cffad9e22244ced1379887"
-    },
     "sass": {
       "Package": "sass",
       "Version": "0.4.8",
@@ -880,7 +839,7 @@
     },
     "tidyselect": {
       "Package": "tidyselect",
-      "Version": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -892,7 +851,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "79540e5fcd9e0435af547d885f184fd5"
+      "Hash": "829f27b9c4919c16b593794a6344d6c0"
     },
     "tzdb": {
       "Package": "tzdb",

renv/activate.R

@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.4"
+  version <- "1.0.5"
   attr(version, "sha") <- NULL
 
   # the project directory