publishing with docker

2025-09-12 01:49:39 +02:00 · 2025-06-26 10:17:24 +02:00 · 2025-06-26 10:17:24 +02:00 · 4f0a17d821
commit 4f0a17d821
parent 4c42636faa
20 changed files with 12040 additions and 68 deletions
--- a/.github/workflows/docker-build.yml
+++ b/.github/workflows/docker-build.yml
@ -0,0 +1,49 @@
+name: Build and Push Docker Image
+permissions:
+  contents: read
+  packages: write
+
+on:
+  # push:
+  #   branches:
+  #     - main
+  #     - master
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Setup Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Define lowercase variables
+        id: vars
+        run: |
+          REPO_OWNER_LOWER=$(echo "$GITHUB_REPOSITORY_OWNER" | tr '[:upper:]' '[:lower:]')
+          REPO_NAME_LOWER=$(echo "$GITHUB_REPOSITORY" | cut -d'/' -f2 | tr '[:upper:]' '[:lower:]')
+          echo "REPO_OWNER_LOWER=$REPO_OWNER_LOWER" >> $GITHUB_ENV
+          echo "REPO_NAME_LOWER=$REPO_NAME_LOWER" >> $GITHUB_ENV
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: app_docker/Dockerfile
+          push: true
+          tags: |
+            ghcr.io/${{ env.REPO_OWNER_LOWER }}/${{ env.REPO_NAME_LOWER }}:latest
+            ghcr.io/${{ env.REPO_OWNER_LOWER }}/${{ env.REPO_NAME_LOWER }}:${{ github.sha }}
--- a/CITATION.cff
+++ b/CITATION.cff
@ -1002,19 +1002,6 @@ references:
    email: russell-lenth@uiowa.edu
  year: '2025'
  doi: 10.32614/CRAN.package.emmeans
- type: software
-  title: visdat
-  abstract: 'visdat: Preliminary Visualisation of Data'
-  notes: Imports
-  url: https://docs.ropensci.org/visdat/
-  repository: https://CRAN.R-project.org/package=visdat
-  authors:
-  - family-names: Tierney
-    given-names: Nicholas
-    email: nicholas.tierney@gmail.com
-    orcid: https://orcid.org/0000-0003-1460-8722
-  year: '2025'
-  doi: 10.32614/CRAN.package.visdat
 - type: software
  title: styler
  abstract: 'styler: Non-Invasive Pretty Printing of R Code'
--- a/3
+++ b/3
@ -79,7 +79,8 @@ Suggests:
    testthat (>= 3.0.0),
    shinytest,
    covr,
-    cffr
+    cffr,
+    shiny2docker
 URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/FreesearchR/, https://app.FreesearchR.org/
 BugReports: https://github.com/agdamsbo/FreesearchR/issues
 VignetteBuilder: knitr
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/SESSION.md
+++ b/SESSION.md
@ -11,11 +11,11 @@
 |collate     |en_US.UTF-8                                |
 |ctype       |en_US.UTF-8                                |
 |tz          |Europe/Copenhagen                          |
-|date        |2025-06-25                                 |
+|date        |2025-06-26                                 |
 |rstudio     |2025.05.0+496 Mariposa Orchid (desktop)    |
 |pandoc      |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
 |quarto      |1.7.30 @ /usr/local/bin/quarto             |
-|FreesearchR |25.6.3.250625                              |
+|FreesearchR |25.6.3.250626                              |
                                                                                
                                                                                
 --------------------------------------------------------------------------------
@ -107,7 +107,6 @@
 |htmltools         |0.5.8.1       |2024-04-04 |CRAN (R 4.4.1) |
 |htmlwidgets       |1.6.4         |2023-12-06 |CRAN (R 4.4.0) |
 |httpuv            |1.6.16        |2025-04-16 |CRAN (R 4.4.1) |
-|httr              |1.4.7         |2023-08-15 |CRAN (R 4.4.0) |
 |IDEAFilter        |0.2.0         |2024-04-15 |CRAN (R 4.4.0) |
 |insight           |1.2.0         |2025-04-22 |CRAN (R 4.4.1) |
 |iterators         |1.0.14        |2022-02-05 |CRAN (R 4.4.1) |
@ -140,7 +139,6 @@
 |opdisDownsampling |1.0.1         |2024-04-15 |CRAN (R 4.4.0) |
 |openssl           |2.3.2         |2025-02-03 |CRAN (R 4.4.1) |
 |openxlsx2         |1.15          |2025-04-25 |CRAN (R 4.4.1) |
-|pak               |0.8.0.2       |2025-04-08 |CRAN (R 4.4.1) |
 |parameters        |0.24.2        |2025-03-04 |CRAN (R 4.4.1) |
 |patchwork         |1.3.0         |2024-09-16 |CRAN (R 4.4.1) |
 |pbmcapply         |1.5.1         |2022-04-28 |CRAN (R 4.4.1) |
@ -201,7 +199,6 @@
 |sessioninfo       |1.2.3         |2025-02-05 |CRAN (R 4.4.1) |
 |shiny             |1.10.0        |2024-12-14 |CRAN (R 4.4.1) |
 |shinybusy         |0.3.3         |2024-03-09 |CRAN (R 4.4.0) |
-|shinydashboard    |0.7.3         |NA         |NA             |
 |shinyjs           |2.1.0         |2021-12-23 |CRAN (R 4.4.0) |
 |shinyTime         |1.0.3         |2022-08-19 |CRAN (R 4.4.0) |
 |shinyWidgets      |0.9.0         |2025-02-21 |CRAN (R 4.4.1) |
@ -225,7 +222,8 @@
 |uuid              |1.2-1         |2024-07-29 |CRAN (R 4.4.1) |
 |V8                |6.0.3         |2025-03-26 |CRAN (R 4.4.1) |
 |vctrs             |0.6.5         |2023-12-01 |CRAN (R 4.4.0) |
-|visdat            |0.6.0         |2023-02-02 |CRAN (R 4.4.0) |
+|viridisLite       |0.4.2         |2023-05-02 |CRAN (R 4.4.1) |
+|visdat            |0.6.0         |NA         |NA             |
 |vroom             |1.6.5         |2023-12-05 |CRAN (R 4.4.0) |
 |withr             |3.0.2         |2024-10-28 |CRAN (R 4.4.1) |
 |writexl           |1.5.4         |2025-04-15 |CRAN (R 4.4.1) |
--- a/app_docker/.dockerignore
+++ b/app_docker/.dockerignore
@ -0,0 +1,6 @@
+.Rhistory
+.git
+.gitignore
+manifest.json
+rsconnect/
+.Rproj.user
--- a/app_docker/Dockerfile
+++ b/app_docker/Dockerfile
@ -0,0 +1,12 @@
+FROM rocker/geospatial:4.4.1
+RUN apt-get update -y && apt-get install -y  cmake make libcurl4-openssl-dev libicu-dev libssl-dev pandoc zlib1g-dev libsecret-1-dev libxml2-dev libx11-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libjpeg-dev libpng-dev libtiff-dev libfftw3-dev libsodium-dev && rm -rf /var/lib/apt/lists/*
+RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
+RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
+RUN R -e 'install.packages("remotes")'
+RUN R -e 'remotes::install_version("renv", version = "1.1.4")'
+COPY renv.lock renv.lock
+RUN --mount=type=cache,id=renv-cache,target=/root/.cache/R/renv R -e 'renv::restore()'
+WORKDIR /srv/shiny-server/
+COPY . /srv/shiny-server/
+EXPOSE 3838
+CMD R -e 'shiny::runApp("/srv/shiny-server",host="0.0.0.0",port=3838)'
--- a/app_docker/app.R
+++ b/app_docker/app.R
--- a/app_docker/www/FreesearchR-logo.png
+++ b/app_docker/www/FreesearchR-logo.png
--- a/app_docker/www/favicon.ico
+++ b/app_docker/www/favicon.ico
--- a/app_docker/www/favicon.png
+++ b/app_docker/www/favicon.png
--- a/app_docker/www/favicon.svg
+++ b/app_docker/www/favicon.svg
--- a/app_docker/www/intro.html
+++ b/app_docker/www/intro.html
--- a/app_docker/www/intro.md
+++ b/app_docker/www/intro.md
@ -0,0 +1,31 @@
+# Welcome <img style="float: right;" src="FreesearchR-logo.png">
+
+This is the ***FreesearchR*** data analysis tool. We intend ***FreesearchR*** to be a free tool for easy data evaluation and analysis. If you need more advanced tools, start with ***FreesearchR*** and then you'll probably be better off using *R* or similar directly.
+
+Here is a brief summary of the functions:
+
+1.  **Import data** from a spreadsheet/file on your machine, direct export from a REDCap server, sample data or data from a your local environment if run locally.
+
+1.  **Data inspection** and  **modification** like modifying variables or creating new (categorical from numeric or time data, or completely new variables from the data)
+
+1.  **Evaluate data** using descriptive analyses methods and inspect cross-correlations
+
+1.  **Create and export simple, clean plots** for data overview and insights
+
+1.  **Create regression simple models** for even more advanced data analyses
+
+    -   Linear, dichotomous or ordinal logistic regression will be used depending on specified outcome variable
+    
+    -   Plot regression analysis coefficients
+
+    -   Evaluate model assumptions
+
+1.  **Export results**
+
+    -   Descriptive and regression analyses results for MS Word or [LibreOffice](https://www.libreoffice.org/)
+    
+    -   Modified data with preserved metadata
+    
+    -   Code to recreate all steps locally
+
+The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) where you'll find detailed description of the app and link to the source code! If you want to [share feedback, please follow this link to a simple survey](https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8).
--- a/app_docker/www/references.bib
+++ b/app_docker/www/references.bib
@ -0,0 +1,11 @@
+
+@book{andreasgammelgaarddamsbo2025,
+	title = {agdamsbo/FreesearchR: FreesearchR 25.4.3},
+	author = {Damsbo, Andreas Gammelgaard},
+	year = {2025},
+	month = {04},
+	date = {2025-04-24},
+	publisher = {Zenodo},
+	doi = {10.5281/ZENODO.14527429},
+	url = {https://zenodo.org/doi/10.5281/zenodo.14527429}
+}
--- a/app_docker/www/report.rmd
+++ b/app_docker/www/report.rmd
@ -0,0 +1,83 @@
+---
+title: "FreesearchR data report"
+date: "Report generated `r gsub('(\\D)0', '\\1', format(Sys.time(), '%A, %d.%m.%Y'))`"
+format: docx
+author: FreesearchR data analysis tool
+toc: false
+params:
+  data.file: NA
+  version: NA
+  regression.p: NA
+---
+
+```{r setup, echo = FALSE}
+knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
+# glue::glue("{format(lubridate::today(),'%A')}, {lubridate::day(lubridate::today())}.{lubridate::month(lubridate::today())}.{lubridate::year(lubridate::today())}")
+```
+
+```{r}
+web_data <- readr::read_rds(file = params$data.file)
+# web_data <- readr::read_rds(file = "~/FreesearchR/inst/apps/FreesearchR/www/web_data.rds")
+library(gtsummary)
+library(gt)
+
+tbl_merge <- function(data) {
+  if (is.null(names(data))) {
+    data |> gtsummary::tbl_merge()
+  } else {
+    data |> gtsummary::tbl_merge(tab_spanner = names(data))
+  }
+}
+
+vec2sentence <- function(data, sep.word = "and") {
+  sep.word <- paste0(" ", gsub(" ", "", sep.word), " ")
+  if (length(data) < 2) {
+    out <- data
+  } else if (length(data) == 2) {
+    out <- paste(data, collapse = sep.word)
+  } else {
+    out <- paste(paste(data[-length(data)], collapse = ","), data[length(data)], sep = sep.word)
+  }
+  return(out)
+}
+```
+
+## Introduction
+
+Research should be free and open with easy access for all. The *FreesearchR* tool attempts to help lower the bar to participate in research by making basic data exploration and analyses easily accessible.
+
+## Methods
+
+Analyses were conducted using the *FreesearchR* data analysis web-tool version `r params$version` based on *R* version 4.4.1.
+
+## Results
+
+Below are the baseline characteristics.
+
+```{r, results = 'asis'}
+if ("table1" %in% names(web_data)) {
+  tbl <- gtsummary::as_gt(web_data$table1)
+  knitr::knit_print(tbl)
+}
+```
+
+`r if (length(web_data$regression) > 0) glue::glue("Below are the results from the { tolower(vec2sentence(names(web_data$regression$regression$tables)))} {web_data$regression$regression$params$descr}.")`
+
+```{r, results = 'asis'}
+if ("regression" %in% names(web_data) && length(web_data$regression) > 0) {
+  reg_tbl <- web_data$regression$regression$tables
+  
+  merged <- tbl_merge(reg_tbl)
+  
+  if (params$regression.p == "no") {
+            merged <- merged |>
+              gtsummary::modify_column_hide(column = dplyr::starts_with("p.value"))
+          }
+  
+  knitr::knit_print(merged)
+}
+```
+
+## Discussion
+
+Good luck on your further work!
--- a/app_docker/www/style.css
+++ b/app_docker/www/style.css
@ -0,0 +1,125 @@
+
+/*!
+ * Copyright (c) 2025 FreesearchR
+ *
+ * FreesearchR, CSS styles
+ * https://github.com/agdamsbo/FreesearchR
+ *
+ * @version 0.0.1
+ */
+
+.container-fluid > .nav > li >
+                        a[data-value='FreesearchR'] {font-size: 28px}
+
+
+/* from datamods */
+.show-block {
+  display: block !important;
+}
+.show-inline {
+  display: inline !important;
+}
+.hidden {
+  display: none !important;
+}
+.invisible {
+  visibility: hidden;
+}
+
+.container-rule {
+  position: relative;
+  text-align: center;
+  height: 25px;
+  margin-bottom: 5px;
+}
+
+.horizontal-rule {
+  position: absolute;
+  top: 11px;
+  right: 0;
+  left: 0;
+  background-color: #d0cfcf;
+  height: 1px;
+  z-index: 100;
+  margin: 0;
+  border: none;
+}
+
+.label-rule {
+  background: #FFF;
+  opacity: 1;
+  z-index: 101;
+  background-color: #FFF;
+  position: relative;
+  padding: 0 10px 0 10px;
+}
+
+.datamods-table-container {
+  overflow: auto;
+  word-break: keep-all;
+  white-space: nowrap;
+}
+
+.datamods-table-container > .table {
+  margin-bottom: 0 !important;
+}
+
+.datamods-file-import {
+  display: grid;
+  grid-template-columns: auto 50px;
+  grid-column-gap: 10px;
+}
+
+.datamods-dt-nowrap {
+  word-break: keep-all;
+  white-space: nowrap;
+}
+
+
+
+/* validation */
+.datamods-validation-results {
+  display: grid;
+  grid-template-columns: repeat(3, 1fr);
+  grid-template-rows: 1fr;
+  height: 50px;
+  line-height: 50px;
+  font-size: large;
+}
+
+.datamods-validation-summary {
+  font-weight: bold;
+  text-align: center;
+}
+
+.datamods-validation-item {
+  font-size: larger;
+}
+
+
+
+/* modified from esquisse for data types */
+.btn-column-categorical {
+  background-color: #00C896;
+  color: #FFFFFF;
+}
+.btn-column-continuous {
+  background-color: #FFB100;
+  color: #FFFFFF;
+}
+.btn-column-dichotomous {
+  background-color: #8A4FFF;
+  color: #FFFFFF;
+}
+.btn-column-datetime {
+  background-color: #11A0EC;
+  color: #FFFFFF;
+}
+.btn-column-id {
+  background-color: #848484;
+  color: #FFFFFF;
+}
+.btn-column-text {
+  background-color: #2E2E2E;
+  color: #FFFFFF;
+}
--- a/app_docker/www/umami-app.html
+++ b/app_docker/www/umami-app.html
@ -0,0 +1 @@
+<script defer src="https://stats.freesearchr.org/script.js" data-website-id="63976000-9836-45bc-90da-37ec5717fb22"></script>
--- a/app_docker/www/web_data.rds
+++ b/app_docker/www/web_data.rds
--- a/renv.lock
+++ b/renv.lock
@ -8917,54 +8917,6 @@
      "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]",
      "Repository": "CRAN"
    },
-    "visdat": {
-      "Package": "visdat",
-      "Version": "0.6.0",
-      "Source": "Repository",
-      "Title": "Preliminary Visualisation of Data",
-      "Authors@R": "c( person(\"Nicholas\", \"Tierney\", role = c(\"aut\", \"cre\"), email = \"nicholas.tierney@gmail.com\",  comment = c(ORCID = \"https://orcid.org/0000-0003-1460-8722\")), person(\"Sean\", \"Hughes\", role = \"rev\",  comment =c(ORCID = \"https://orcid.org/0000-0002-9409-9405\", \"Sean Hughes reviewed the package for rOpenSci,  see https://github.com/ropensci/onboarding/issues/87\")), person(\"Mara\", \"Averick\", role = \"rev\",  comment = \"Mara Averick reviewed the package for rOpenSci, see  https://github.com/ropensci/onboarding/issues/87\"), person(\"Stuart\", \"Lee\", role = c(\"ctb\")), person(\"Earo\", \"Wang\", role = c(\"ctb\")), person(\"Nic\", \"Crane\", role = c(\"ctb\")), person(\"Christophe\", \"Regouby\", role=c(\"ctb\")) )",
-      "Description": "Create preliminary exploratory data visualisations of an entire  dataset to identify problems or unexpected features using 'ggplot2'.",
-      "Depends": [
-        "R (>= 3.2.2)"
-      ],
-      "License": "MIT + file LICENSE",
-      "LazyData": "true",
-      "RoxygenNote": "7.2.3",
-      "Imports": [
-        "ggplot2",
-        "tidyr",
-        "dplyr",
-        "purrr",
-        "readr",
-        "magrittr",
-        "stats",
-        "tibble",
-        "glue",
-        "forcats",
-        "cli",
-        "scales"
-      ],
-      "URL": "https://docs.ropensci.org/visdat/, https://github.com/ropensci/visdat",
-      "BugReports": "https://github.com/ropensci/visdat/issues",
-      "Suggests": [
-        "testthat (>= 3.0.0)",
-        "plotly (>= 4.5.6)",
-        "knitr",
-        "rmarkdown",
-        "vdiffr",
-        "spelling",
-        "covr",
-        "stringr"
-      ],
-      "VignetteBuilder": "knitr",
-      "Encoding": "UTF-8",
-      "Language": "en-US",
-      "Config/testthat/edition": "3",
-      "NeedsCompilation": "no",
-      "Author": "Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>), Sean Hughes [rev] (<https://orcid.org/0000-0002-9409-9405>, Sean Hughes reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87), Mara Averick [rev] (Mara Averick reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/87), Stuart Lee [ctb], Earo Wang [ctb], Nic Crane [ctb], Christophe Regouby [ctb]",
-      "Maintainer": "Nicholas Tierney <nicholas.tierney@gmail.com>",
-      "Repository": "CRAN"
-    },
    "vroom": {
      "Package": "vroom",
      "Version": "1.6.5",
				`@ -0,0 +1 @@`
				`<script defer src="https://stats.freesearchr.org/script.js" data-website-id="63976000-9836-45bc-90da-37ec5717fb22"></script>`