Merge pull request #6 from ECCC-lavoie-ecotox/dev_app

Init shiny application

DESCRIPTION

@@ -1,34 +1,42 @@
 Package: toxbox
-Title: Miscellaneous utils for data processing and predictive models building
+Title: Application and utils for contaminants data processing
 Version: 0.0.1
 Authors@R: c(
-        person(given = "Steve", family = "Vissault", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0866-4376")),
-        person(given = "Anais", family = "Kerric", email = "[email protected]", role = c("aut")),
-        person(given = "Rose", family = "Lacombe", email = "[email protected]", role = c("aut")),
-        person(given = "Raphael", family = "Lavoie", email = "[email protected]", role = c("aut"))
-    )
-Description: This package aims at facilitate data processing and models building in order to spend more time on the field. 
+    person("Steve", "Vissault", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-0866-4376")),
+    person("Anais", "Kerric", , "[email protected]", role = "aut"),
+    person("Rose", "Lacombe", , "[email protected]", role = "aut"),
+    person("Raphael", "Lavoie", , "[email protected]", role = "aut")
+  )
+Description: This package aims at facilitate data processing and models
+    building in order to spend more time on the field.
+License: MIT + file LICENSE
+URL: https://github.com/ECCC-lavoie-ecotox/toxbox
+BugReports: https://github.com/ECCC-lavoie-ecotox/toxbox/issues
+Depends: 
+    R (>= 4.0)
 Imports: 
+    bslib (>= 0.5.1),
+    cli (>= 3.6.2),
+    config (>= 0.3.2),
     DBI (>= 1.2.2),
     dplyr (>= 1.1.4),
     glue (>= 1.7.0),
-    stringr (>= 1.5.1),
-    cli (>= 3.6.2),
-    tidyselect (>= 1.2.1),
+    golem (>= 0.4.1),
     purrr (>= 1.0.2),
-    RSQLite (>= 2.3.5)
+    RSQLite (>= 2.3.5),
+    shiny (>= 1.8.0),
+    stringr (>= 1.5.1),
+    tidyselect (>= 1.2.1)
 Suggests: 
-    devtools  (>= 2.2.0),
+    knitr,
+    mockery (>= 0.4.4),
+    rmarkdown,
     testthat (>= 3.0.0),
-    withr (>= 3.0.0),
-    mockery (>= 0.4.4)
-License: MIT + file LICENSE
+    withr (>= 3.0.0)
+Config/Needs/website: rmarkdown
 Encoding: UTF-8
+Language: en-US
+LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-URL: https://github.com/ECCC-lavoie-ecotox/toxbox
-BugReports: https://github.com/ECCC-lavoie-ecotox/toxbox/issues
-Depends: 
-    R (>= 4.0)
-LazyData: true
-Config/Needs/website: rmarkdown

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 ECCC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -6,12 +6,27 @@ export(check_fields_notnulls)
 export(check_fields_pkeys)
 export(delete_entry)
 export(detect_cens)
+export(fct_start)
 export(get_tbl_info)
 export(get_tbl_notnulls)
 export(get_tbl_pkeys)
 export(init_con)
 export(insert_entry)
 export(modify_entry)
 export(remove_cens)
+export(run_app)
 export(search_tbl)
 export(uncensored)
+import(shiny)
+importFrom(golem,activate_js)
+importFrom(golem,add_resource_path)
+importFrom(golem,bundle_resources)
+importFrom(golem,favicon)
+importFrom(golem,with_golem_options)
+importFrom(shiny,HTML)
+importFrom(shiny,NS)
+importFrom(shiny,column)
+importFrom(shiny,shinyApp)
+importFrom(shiny,tagAppendAttributes)
+importFrom(shiny,tagList)
+importFrom(shiny,tags)

NEWS.md

@@ -0,0 +1,3 @@
+# toxbox 0.0.1
+
+* Initial CRAN submission.

R/app_config.R

@@ -0,0 +1,44 @@
+#' Access files in the current app
+#'
+#' NOTE: If you manually change your package name in the DESCRIPTION,
+#' don't forget to change it here too, and in the config file.
+#' For a safer name change mechanism, use the `golem::set_golem_name()` function.
+#'
+#' @param ... character vectors, specifying subdirectory and file(s)
+#' within your package. The default, none, returns the root of the app.
+#'
+#' @noRd
+app_sys <- function(...) {
+  system.file(..., package = "toxbox")
+}
+
+
+#' Read App Config
+#'
+#' @param value Value to retrieve from the config file.
+#' @param config GOLEM_CONFIG_ACTIVE value. If unset, R_CONFIG_ACTIVE.
+#' If unset, "default".
+#' @param use_parent Logical, scan the parent directory for config file.
+#' @param file Location of the config file
+#'
+#' @noRd
+get_golem_config <- function(
+  value,
+  config = Sys.getenv(
+    "GOLEM_CONFIG_ACTIVE",
+    Sys.getenv(
+      "R_CONFIG_ACTIVE",
+      "default"
+    )
+  ),
+  use_parent = TRUE,
+  # Modify this if your config file is somewhere else
+  file = app_sys("golem-config.yml")
+) {
+  config::get(
+    value = value,
+    config = config,
+    file = file,
+    use_parent = use_parent
+  )
+}

R/app_server.R

@@ -0,0 +1,15 @@
+#' The application server-side
+#'
+#' @param input,output,session Internal parameters for {shiny}.
+#'     DO NOT REMOVE.
+#' @import shiny
+#' @noRd
+app_server <- function(input, output, session) {
+  # Your application server logic
+  r <- reactiveValues(
+    active_table = "species"
+  )
+
+  mod_table_view_server("table_viewer", r)
+  mod_table_nav_server("table_nav", r)
+}

R/app_ui.R

@@ -0,0 +1,62 @@
+#' The application User-Interface
+#'
+#' @param request Internal parameter for `{shiny}`.
+#'     DO NOT REMOVE.
+#' @import shiny
+#' @noRd
+app_ui <- function(request) {
+    # Leave this function for adding external resources
+    golem_add_external_resources()
+    shinyjs::useShinyjs()
+    bslib::page_sidebar(
+      window_title = "contaminR",
+      theme = bslib::bs_theme(
+          bootswatch = "zephyr",
+          base_font = bslib::font_google("Poppins"),
+          version = 5
+      ),
+      div(class = "col-auto d-none d-lg-block",
+        img(class="img-fluid text-left d-inline", src="www/logo.png",height="100", width="100"),
+        h3("ContaminR", class="d-inline", style="font-weight:bold;"),
+        p("Database editor", class ="text-muted d-inline m-3")
+      ),
+      sidebar = bslib::sidebar(
+        position = "left",
+        actionButton("dashboard",
+          class = "btn btn-success",
+          label = "Dashboard",
+          icon = icon("gauge")
+        ),
+        actionButton("documentation",
+          class = "btn btn-success",
+          label = "Documentation",
+          icon = icon("book")
+        ),
+        mod_table_nav_ui("table_nav")
+      ),
+      mod_table_view_ui("table_viewer")
+    )
+}
+
+#' Add external Resources to the Application
+#'
+#' This function is internally used to add external
+#' resources inside the Shiny application.
+#'
+#' @import shiny
+#' @importFrom golem add_resource_path activate_js favicon bundle_resources
+#' @noRd
+golem_add_external_resources <- function() {
+  add_resource_path(
+    "www",
+    app_sys("app/www")
+  )
+
+  tags$head(
+    favicon(),
+    bundle_resources(
+      path = app_sys("app/www"),
+      app_title = "toxbox"
+    )
+  )
+}

R/fct_start.R

@@ -0,0 +1,13 @@
+#' Start function
+#'
+#' @export
+
+fct_start <- function() {
+    con <<- init_con()
+    onStop(clean_up_app)
+}
+
+clean_up_app <- function() {
+    cli::cli_alert_info("Application stopped -- cleaning database connexion")
+    DBI::dbDisconnect(con)
+}

R/golem_utils_server.R

@@ -0,0 +1,63 @@
+#' Inverted versions of in, is.null and is.na
+#'
+#' @noRd
+#'
+#' @examples
+#' 1 %not_in% 1:10
+#' not_null(NULL)
+`%not_in%` <- Negate(`%in%`)
+
+not_null <- Negate(is.null)
+
+not_na <- Negate(is.na)
+
+#' Removes the null from a vector
+#'
+#' @noRd
+#'
+#' @example
+#' drop_nulls(list(1, NULL, 2))
+drop_nulls <- function(x) {
+  x[!sapply(x, is.null)]
+}
+
+#' If x is `NULL`, return y, otherwise return x
+#'
+#' @param x,y Two elements to test, one potentially `NULL`
+#'
+#' @noRd
+#'
+#' @examples
+#' NULL %||% 1
+"%||%" <- function(x, y) {
+  if (is.null(x)) {
+    y
+  } else {
+    x
+  }
+}
+
+#' If x is `NA`, return y, otherwise return x
+#'
+#' @param x,y Two elements to test, one potentially `NA`
+#'
+#' @noRd
+#'
+#' @examples
+#' NA %|NA|% 1
+"%|NA|%" <- function(x, y) {
+  if (is.na(x)) {
+    y
+  } else {
+    x
+  }
+}
+
+#' Typing reactiveValues is too long
+#'
+#' @inheritParams reactiveValues
+#' @inheritParams reactiveValuesToList
+#'
+#' @noRd
+rv <- function(...) shiny::reactiveValues(...)
+rvtl <- function(...) shiny::reactiveValuesToList(...)