.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'}
 
@@ -39,8 +39,6 @@ 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

@@ -21,8 +21,6 @@ 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

@@ -0,0 +1,7 @@
+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: 24.3.1
+Version: 24.2.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
     role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 
@@ -28,6 +28,7 @@ Suggests:
     knitr,
     rmarkdown,
     gt,
+    usethis,
     ggplot2,
     here,
     styler,
@@ -51,6 +52,7 @@ Imports:
     stats,
     shiny,
     openxlsx2,
+    rsconnect,
     haven
 Collate: 
     'utils.r'

NAMESPACE

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

NEWS.md

@@ -1,10 +1,3 @@
-# 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

@@ -34,3 +34,25 @@ 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

@@ -1,10 +0,0 @@
-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

@@ -1,10 +0,0 @@
-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

@@ -1,133 +1,89 @@
-ui <- shiny::shinyUI(
+ui <- shiny::fluidPage(
-  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
+  ## -----------------------------------------------------------------------------
 
-    # customHeaderPanel(title = "REDCapCAST: data base creation and data upload from data set file",
+  shiny::sidebarPanel(
-    #                   windowTitle = "REDCap database creator"
+    shiny::h4("REDCap database and dataset"),
-    # ),
+    shiny::fileInput("ds", "Choose data file",
-
+                     multiple = FALSE,
-    shiny::titlePanel(title = shiny::div(shiny::a(shiny::img(src="logo.png"),href="https://agdamsbo.github.io/REDCapCAST"),
+                     accept = c(
-                                  "Easy REDCap database creation"),
+                       ".csv",
-      windowTitle = "REDCap database creator"
+                       ".xls",
+                       ".xlsx",
+                       ".dta"
+                     )
     ),
-    shiny::h4("This tool includes to convenient functions:",
+    shiny::h6("Below you can download the dataset formatted for upload and the
-              shiny::br(),
+         corresponding data dictionary for a new data base."),
-              "1) creating a REDCap data dictionary based on a spreadsheet (.csv/.xls(x)/.dta) and",
+    # Button
-              shiny::br(),
+    shiny::downloadButton("downloadData", "Download data"),
-              "2) creating said database on a given REDCap server and uploading the dataset via API access."),
+
+    # Button
+    shiny::downloadButton("downloadMeta", "Download dictionary"),
 
 
-    ## -----------------------------------------------------------------------------
+    # Horizontal line ----
-    ## Side panel
+    shiny::tags$hr(),
-    ## -----------------------------------------------------------------------------
+    shiny::h4("REDCap upload"),
-
+    shiny::textInput(
-    shiny::sidebarPanel(
+      inputId = "uri",
-      shiny::h4("1) REDCap datadictionary and compatible dataset"),
+      label = "URI",
-      shiny::fileInput("ds", "Choose data file",
+      value = "https://redcap.your.institution/api/"
-        multiple = FALSE,
+    ),
-        accept = c(
+    shiny::textInput(
-          ".csv",
+      inputId = "api",
-          ".xls",
+      label = "API key",
-          ".xlsx",
+      value = ""
-          ".dta"
+    ),
-        )
+    shiny::actionButton(
-      ),
+      inputId = "upload.meta",
-      shiny::h6("Below you can download the dataset formatted for upload and the
+      label = "Upload dictionary", icon = shiny::icon("book-bookmark")
-         corresponding data dictionary for a new data base, if you want to upload manually."),
+    ),
-      # Button
+    shiny::h6("Please note, that before uploading any real data, put your project
-      shiny::downloadButton("downloadData", "Download data"),
-
-      # Button
-      shiny::downloadButton("downloadMeta", "Download datadictionary"),
-
-
-      # Horizontal line ----
-      shiny::tags$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(
+    shiny::actionButton(
-        inputId = "upload.data",
+      inputId = "upload.data",
-        label = "Upload data", icon = shiny::icon("upload")
+      label = "Upload data", icon = shiny::icon("upload")
+    ),
+
+    # Horizontal line ----
+    shiny::tags$hr()
+  ),
+  shiny::mainPanel(
+    shiny::tabsetPanel(
+
+      ## -----------------------------------------------------------------------------
+      ## Summary tab
+      ## -----------------------------------------------------------------------------
+      shiny::tabPanel(
+        "Summary",
+        shiny::h3("Data overview (first 20)"),
+        shiny::htmlOutput("data.tbl", container = shiny::span),
+        shiny::h3("Dictionary overview"),
+        shiny::htmlOutput("meta.tbl", container = shiny::span)
       ),
-
+      ## -----------------------------------------------------------------------------
-      # Horizontal line ----
+      ## Upload tab
-      shiny::tags$hr()
+      ## -----------------------------------------------------------------------------
-    ),
+      shiny::tabPanel(
-    shiny::mainPanel(
+        "Upload",
-      shiny::tabsetPanel(
+        shiny::h3("Meta upload overview"),
-
+        shiny::htmlOutput("upload.meta.print", container = shiny::span),
-        ## -----------------------------------------------------------------------------
+        shiny::h3("Data upload overview"),
-        ## Summary tab
+        shiny::htmlOutput("upload.data.print", container = shiny::span)
-        ## -----------------------------------------------------------------------------
-        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

@@ -0,0 +1,23 @@
+% 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": "5.2.1",
+      "Version": "5.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
+      "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9"
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.35",
+      "Version": "0.6.34",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
+      "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a"
     },
     "dplyr": {
       "Package": "dplyr",
@@ -557,6 +557,18 @@
       ],
       "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",
@@ -674,13 +686,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.5",
+      "Version": "1.0.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
+      "Hash": "11abaf7c540ff33f94514d50f929bfd1"
     },
     "rlang": {
       "Package": "rlang",
@@ -693,6 +705,35 @@
       ],
       "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",
@@ -839,7 +880,7 @@
     },
     "tidyselect": {
       "Package": "tidyselect",
-      "Version": "1.2.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -851,7 +892,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "829f27b9c4919c16b593794a6344d6c0"
+      "Hash": "79540e5fcd9e0435af547d885f184fd5"
     },
     "tzdb": {
       "Package": "tzdb",

renv/activate.R

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