add support for GitHub data

app.R

@@ -4,7 +4,7 @@
 
 # shiny::runApp("./")
 # Setup
-rtemisseq_version <- "0.2.8"
+rtemisseq_version <- "0.3.0"
 library(rtemis)
 library(rtemisbio)
 library(shiny)
@@ -32,7 +32,7 @@ success <- "#60D0DA"
 #' @return A shiny app that can be converted to a shinylive app
 
 rtemisseq <- function(
-    default_theme = "light",
+    default_theme = "dark",
     protein_plotly_height = "900px",
     jsonedit_height = "900px",
     verbosity = 0) {
@@ -87,22 +87,17 @@ rtemisseq <- function(
       ),
       # Theme ----
       theme = bslib::bs_theme(
-        # bg = "#fff",
-        # fg = "#000",
         `tooltip-opacity` = 1,
         `tooltip-border-radius` = "10px",
         `tooltip-padding-x` = "1rem",
         `tooltip-padding-y` = "1rem",
         `tooltip-font-size` = "1rem"
-        # base_font = bslib::font_google("Inter"), # doesn't work in shinylive
-        # code_font = bslib::font_google("Fira Code")
       ) |>
         bs_add_rules(sass::sass_file("www/rtemislive.scss")),
       # Window title ----
       window_title = "rtemisSeq",
       # Language ----
       lang = "en",
-      # tags$script(src = "globals.js"),
       # Nav Panels ----
       ## [] Welcome ----
       bslib::nav_panel(
@@ -117,7 +112,8 @@ rtemisseq <- function(
               "rtemisSeq is a web interface for ",
               as.character(a("rtemisbio", href = "https://rtemis.org/rtemisbio", target = "_blank")),
               ", <br>providing interactive visualization of sequence data.",
-              "<br>Created for the ", as.character(a("FTD CWOW", href = "https://cwow.ucsf.edu/", target = "_blank")),
+              "<br>Created for the ",
+              as.character(a("FTD CWOW", href = "https://cwow.ucsf.edu/", target = "_blank")),
               ".<br><br>",
               rthelp_inline(
                 "To get started, use the navigation tabs at the top.",
@@ -232,7 +228,6 @@ rtemisseq <- function(
                 img(
                   src = "rtemis_gray.png",
                   alt = "rtemis",
-                  # align = "center",
                   width = "190px"
                 ),
                 href = "https://rtemis.org",
@@ -248,8 +243,7 @@ rtemisseq <- function(
         # busy indicators ----
         shinybusy::add_busy_spinner(
           spin = "orbit",
-          # color = "#72CDF4",
-          color = "#00ffff",
+          color = "#FF8F28",
           timeout = 200,
           position = "bottom-left",
           onstart = FALSE
@@ -271,13 +265,50 @@ rtemisseq <- function(
         label = "Data source",
         choices = list(
           `Built-in datasets` = "builtin",
-          # `GitHub repository` = "github",
+          `GitHub repository` = "github",
           `File upload` = "upload"
         ),
         selected = "builtin"
       )
     })
 
+    # GitHub file list ----
+    # GitHub file list udpate button ----
+    output$ui_github_files_update_button <- shiny::renderUI({
+      if (verbosity > 0) {
+        message("Rendering ui_github_files_update_button")
+      }
+      bslib::input_task_button(
+        "github_files_update_button",
+        "Update GitHub file list",
+        icon = bsicons::bs_icon("arrow-clockwise"),
+        label_busy = "Updating...",
+        icon_busy = bsicons::bs_icon("clock-history"),
+        type = "primary",
+        auto_reset = TRUE
+      )
+    }) # /ui_github_files_update_button
+
+    # GitHub files runs when github_files_update_button is clicked ----
+    github_files <- reactive({
+      get_github_files(repo_owner = "rtemis-org", repo_name = "seq-data", verbosity = verbosity)
+    }) |>
+      bindEvent(input$github_files_update_button)
+    
+    # GitHub file list output ----
+    output$ui_github_files <- shiny::renderUI({
+      req(github_files())
+      if (verbosity > 0) {
+        message("Rendering ui_github_files")
+      }
+      shiny::selectizeInput(
+        inputId = "github_file",
+        label = "Select a file from the GitHub repository",
+        choices = github_files()$file_name,
+        selected = github_files()$file_name[1]
+      )
+    }) # /ui_github_files
+
     # UI a3 Data ----
     output$ui_a3_data_load <- shiny::renderUI({
       req(input$a3_load_switch)
@@ -292,7 +323,15 @@ rtemisseq <- function(
           buttonLabel = "Browse local files...",
         )
       } else if (input$a3_load_switch == "github") {
-
+        # "Update GitHub file list" button
+        if (verbosity > 0) {
+          message("Rendering ui_a3_data_load for GitHub file list")
+        }
+        # UI output with GitHub file list & update button
+        shiny::tagList(
+          uiOutput("ui_github_files"),
+          uiOutput("ui_github_files_update_button")
+        )
       } else {
         # Select built-in data stored in ./data/ directory
         if (verbosity > 0) {
@@ -352,6 +391,22 @@ rtemisseq <- function(
           message("Loaded dataset of class '", class(dat)[1], "'")
         }
         return(dat)
+      } else if (input$a3_load_switch == "github") {
+        # Download GitHub file
+        req(input$github_file)
+        if (verbosity > 0) {
+          message("Downloading GitHub file '", input$github_file, "'")
+        }
+        # index with input$github_file
+        jsondat <- httr::GET(
+          github_files()[github_files()$file_name == input$github_file, "download_url"]
+        ) |> httr::content(as = "text", encoding = "UTF-8")
+        dat <- as.a3(jsonlite::parse_json(
+          jsondat,
+          simplifyVector = TRUE,
+          simplifyMatrix = FALSE
+        ))
+        return(dat)
       } else {
         # Load built-in data from data.R objects
         req(input$a3_builtin_data)

globals.R

@@ -2,46 +2,11 @@
 # ::rtemisseq::
 # EDG rtemis.org
 
-# Themes ----
-# {bg_dark, bg_light} also used by plot.bg
-bg_dark <- "#191919"
-bg_light <- "#ffffff"
-primary_dark <- "#72CDF4"
-primary_light <- "#1295D8"
-seconday_dark <- "#808080"
-secondary_light <- "#808080"
-info_dark <- "#FEB2E0"
-info_light <- "#E44C9A"
-success_dark <- "#B4DC55"
-success_light <- "#84C234"
+# rtemis ----
+msg2start <- getFromNamespace("msg2start", "rtemis")
+msg2done <- getFromNamespace("msg2done", "rtemis")
 
-bslib_dark <- bslib::bs_theme(
-  bg = bg_dark,
-  fg = "#fff",
-  primary = primary_dark,
-  secondary = seconday_dark,
-  success = success_dark,
-  info = info_dark,
-  `tooltip-bg` = "#bbbbbb",
-  `tooltip-color` = info_dark,
-  `tooltip-opacity` = .95
-) |>
-  bslib::bs_add_rules(sass::sass_file("www/rtemislive.scss"))
-
-bslib_light <- bslib::bs_theme(
-  bg = bg_light,
-  fg = "#000",
-  primary = primary_light,
-  secondary = secondary_light,
-  success = success_light,
-  info = info_light,
-  `tooltip-bg` = "#303030",
-  `tooltip-color` = info_light,
-  `tooltip-opacity` = .95
-) |>
-  bslib::bs_add_rules(sass::sass_file("www/rtemislive.scss"))
-
-# from rtemislive
+# rtemislive ----
 rthelp <- function(..., title = NULL, class = "rthelp") {
   div(
     div(HTML(paste0(title, " Instructions")),
@@ -110,3 +75,44 @@ summarize_a3 <- function(x) {
     )
   )
 } # rtemisseq::summarize_a3
+
+#' Get file names and download URLs from a GitHub repository
+#'
+#' @param repo_owner The owner of the GitHub repository
+#' @param repo_name The name of the GitHub repository
+#' @return A data frame with file names and download URLs
+#' @examples
+#' files <- get_github_files("rtemis-org", "seq-data")
+#' @export
+#' @import httr
+#' @import jsonlite
+
+get_github_files <- function(repo_owner, repo_name, verbosity = 1) {
+  if (verbosity > 0) {
+    msg2start("Getting file information from", paste0(repo_owner, "/", repo_name))
+  }
+  # Construct the API URL
+  api_url <- paste0("https://api.github.com/repos/", repo_owner, "/", repo_name, "/contents/data")
+
+  # Make the API request
+  response <- GET(api_url)
+
+  # Check if the request was successful
+  if (response[["status_code"]] == 200) {
+    # Extract the file information
+    files_data <- content(response, as = "text", encoding = "UTF-8") |> fromJSON()
+
+    # Create a data frame with file names and download URLs
+    files_df <- data.frame(
+      file_name = files_data[["name"]],
+      download_url = files_data[["download_url"]]
+    )
+    if (verbosity > 0) {
+      msg2done()
+    }
+    return(files_df)
+  } else {
+    print("Error: Could not retrieve file information.")
+    return(NULL)
+  }
+} # rtemis::get_github_files