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a181a2816c
...
9c61b5e646
4
.github/workflows/R-CMD-check.yaml
vendored
4
.github/workflows/R-CMD-check.yaml
vendored
@ -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
|
||||
|
||||
2
.github/workflows/test-coverage.yaml
vendored
2
.github/workflows/test-coverage.yaml
vendored
@ -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
|
||||
|
||||
7
.lintr
Normal file
7
.lintr
Normal file
@ -0,0 +1,7 @@
|
||||
linters: linters_with_defaults(
|
||||
commented_code_linter = NULL
|
||||
)
|
||||
encoding: "UTF-8"
|
||||
exclusions: list(
|
||||
"drafting/"
|
||||
)
|
||||
@ -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'
|
||||
|
||||
@ -3,6 +3,7 @@
|
||||
export(REDCap_split)
|
||||
export(clean_redcap_name)
|
||||
export(d2w)
|
||||
export(deploy_shiny)
|
||||
export(ds2dd)
|
||||
export(ds2dd_detailed)
|
||||
export(easy_redcap)
|
||||
|
||||
7
NEWS.md
7
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
|
||||
|
||||
@ -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, )
|
||||
}
|
||||
|
||||
@ -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
|
||||
@ -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
|
||||
200
app/ui.R
200
app/ui.R
@ -1,133 +1,89 @@
|
||||
ui <- shiny::shinyUI(
|
||||
shiny::fluidPage(
|
||||
ui <- 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",
|
||||
# windowTitle = "REDCap database creator"
|
||||
# ),
|
||||
|
||||
shiny::titlePanel(title = shiny::div(shiny::a(shiny::img(src="logo.png"),href="https://agdamsbo.github.io/REDCapCAST"),
|
||||
"Easy REDCap database creation"),
|
||||
windowTitle = "REDCap database creator"
|
||||
shiny::sidebarPanel(
|
||||
shiny::h4("REDCap database and dataset"),
|
||||
shiny::fileInput("ds", "Choose data file",
|
||||
multiple = FALSE,
|
||||
accept = c(
|
||||
".csv",
|
||||
".xls",
|
||||
".xlsx",
|
||||
".dta"
|
||||
)
|
||||
),
|
||||
shiny::h4("This tool includes to convenient functions:",
|
||||
shiny::br(),
|
||||
"1) creating a REDCap data dictionary based on a spreadsheet (.csv/.xls(x)/.dta) and",
|
||||
shiny::br(),
|
||||
"2) creating said database on a given REDCap server and uploading the dataset via API access."),
|
||||
shiny::h6("Below you can download the dataset formatted for upload and the
|
||||
corresponding data dictionary for a new data base."),
|
||||
# Button
|
||||
shiny::downloadButton("downloadData", "Download data"),
|
||||
|
||||
# Button
|
||||
shiny::downloadButton("downloadMeta", "Download dictionary"),
|
||||
|
||||
|
||||
## -----------------------------------------------------------------------------
|
||||
## Side panel
|
||||
## -----------------------------------------------------------------------------
|
||||
|
||||
shiny::sidebarPanel(
|
||||
shiny::h4("1) REDCap datadictionary and compatible dataset"),
|
||||
shiny::fileInput("ds", "Choose data file",
|
||||
multiple = FALSE,
|
||||
accept = c(
|
||||
".csv",
|
||||
".xls",
|
||||
".xlsx",
|
||||
".dta"
|
||||
)
|
||||
),
|
||||
shiny::h6("Below you can download the dataset formatted for upload and the
|
||||
corresponding data dictionary for a new data base, if you want to upload manually."),
|
||||
# Button
|
||||
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
|
||||
# Horizontal line ----
|
||||
shiny::tags$hr(),
|
||||
shiny::h4("REDCap upload"),
|
||||
shiny::textInput(
|
||||
inputId = "uri",
|
||||
label = "URI",
|
||||
value = "https://redcap.your.institution/api/"
|
||||
),
|
||||
shiny::textInput(
|
||||
inputId = "api",
|
||||
label = "API key",
|
||||
value = ""
|
||||
),
|
||||
shiny::actionButton(
|
||||
inputId = "upload.meta",
|
||||
label = "Upload dictionary", icon = shiny::icon("book-bookmark")
|
||||
),
|
||||
shiny::h6("Please note, that before uploading any real data, put your project
|
||||
into production mode."),
|
||||
shiny::actionButton(
|
||||
inputId = "upload.data",
|
||||
label = "Upload data", icon = shiny::icon("upload")
|
||||
shiny::actionButton(
|
||||
inputId = "upload.data",
|
||||
label = "Upload data", icon = shiny::icon("upload")
|
||||
),
|
||||
|
||||
# Horizontal line ----
|
||||
shiny::tags$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)
|
||||
),
|
||||
|
||||
# Horizontal line ----
|
||||
shiny::tags$hr()
|
||||
),
|
||||
shiny::mainPanel(
|
||||
shiny::tabsetPanel(
|
||||
|
||||
## -----------------------------------------------------------------------------
|
||||
## Summary tab
|
||||
## -----------------------------------------------------------------------------
|
||||
shiny::tabPanel(
|
||||
"Summary",
|
||||
shiny::h3("Data overview (first 20)"),
|
||||
shiny::htmlOutput("data.tbl", container = shiny::span),
|
||||
shiny::h3("Dictionary overview"),
|
||||
shiny::htmlOutput("meta.tbl", container = shiny::span)
|
||||
),
|
||||
## -----------------------------------------------------------------------------
|
||||
## Upload tab
|
||||
## -----------------------------------------------------------------------------
|
||||
shiny::tabPanel(
|
||||
"Upload",
|
||||
shiny::h3("Meta upload overview"),
|
||||
shiny::htmlOutput("upload.meta.print", container = shiny::span),
|
||||
shiny::h3("Data upload overview"),
|
||||
shiny::htmlOutput("upload.data.print", container = shiny::span)
|
||||
)
|
||||
## -----------------------------------------------------------------------------
|
||||
## Upload tab
|
||||
## -----------------------------------------------------------------------------
|
||||
shiny::tabPanel(
|
||||
"Upload",
|
||||
shiny::h3("Meta upload overview"),
|
||||
shiny::htmlOutput("upload.meta.print", container = shiny::span),
|
||||
shiny::h3("Data upload overview"),
|
||||
shiny::htmlOutput("upload.data.print", container = shiny::span)
|
||||
)
|
||||
),
|
||||
|
||||
|
||||
# close sidebarLayout
|
||||
|
||||
br(),
|
||||
br(),
|
||||
br(),
|
||||
br(),
|
||||
hr(),
|
||||
shiny::tags$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;
|
||||
")
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
BIN
app/www/logo.png
BIN
app/www/logo.png
Binary file not shown.
|
Before Width: | Height: | Size: 8.1 KiB |
23
man/deploy_shiny.Rd
Normal file
23
man/deploy_shiny.Rd
Normal file
@ -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
|
||||
|
||||
}
|
||||
57
renv.lock
57
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",
|
||||
|
||||
@ -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
|
||||
|
||||
Loading…
Reference in New Issue
Block a user