Merge pull request #176 from Appsilon/feature/#174-add-mongodb-support

Feature/#174 add mongodb support

.github/workflows/check_with_databases.yml

@@ -50,6 +50,13 @@ jobs:
       TEST_MSSQLSERVER_HOSTNAME: '127.0.0.1'
       TEST_MSSQLSERVER_TRUST_SERVER_CERTIFICATE: 'YES'
       TEST_MSSQLSERVER_DRIVER: 'ODBC Driver 18 for SQL Server'
+      ## MongoDb
+      TEST_MONGODB_USER: 'mongodb'
+      TEST_MONGODB_PASSWORD: 'mysecretpassword'
+      TEST_MONGODB_HOST: '127.0.0.1'
+      TEST_MONGODB_PORT: 27017
+      TEST_MONGODB_DBNAME: 'shiny_telemetry'
+      TEST_MONGODB_COLLECTION: 'event_log'
 
     ###########################################
     # Services container to run with main job #
@@ -79,6 +86,13 @@ jobs:
         env:
           ACCEPT_EULA: Y
           MSSQL_SA_PASSWORD: 'my-Secr3t_Password'
+      mongodb:
+        image: mongo
+        env:
+          MONGO_INITDB_ROOT_USERNAME: mongodb
+          MONGO_INITDB_ROOT_PASSWORD: mysecretpassword
+        ports:
+          - 27017:27017
 
     steps:
       ##################

DESCRIPTION

@@ -1,13 +1,14 @@
 Type: Package
 Package: shiny.telemetry
 Title: 'Shiny' App Usage Telemetry
-Version: 0.2.0.9012
+Version: 0.2.0.9013
 Authors@R: c(
     person("André", "Veríssimo", , "[email protected]", role = c("aut", "cre")),
     person("Kamil", "Żyła", , "[email protected]", role = "aut"),
     person("Krystian", "Igras", , "[email protected]", role = "aut"),
     person("Recle", "Vibal", , "[email protected]", role = "aut"),
     person("Arun", "Kodati", , "[email protected]", role = "aut"),
+    person("Wahaduzzaman", "Khan", , "[email protected]", role = "aut"),
     person("Appsilon Sp. z o.o.", , , "[email protected]", role = "cph")
   )
 Description: Enables instrumentation of 'Shiny' apps for tracking user
@@ -48,6 +49,7 @@ Suggests:
     RMariaDB,
     RPostgreSQL,
     RPostgres,
+    mongolite,
     scales,
     semantic.dashboard (>= 0.1.1),
     shiny.semantic (>= 0.2.0),

NAMESPACE

@@ -3,6 +3,7 @@
 export(DataStorageLogFile)
 export(DataStorageMSSQLServer)
 export(DataStorageMariaDB)
+export(DataStorageMongoDB)
 export(DataStoragePlumber)
 export(DataStoragePostgreSQL)
 export(DataStorageSQLite)

NEWS.md

@@ -6,6 +6,7 @@
 - Added flexibility to select between [`RPostgreSQL`, `RPostgres`] drivers (#147).
 - Improved input tracking by implementing inclusion and exclusion logic (#30).
 - Added tracking for returning anonymous users (#142).
+- Added support for MongoDB (see `DataStorageMongoDB` class) (#174).
 
 ### Miscellaneous
 

R/auxiliary.R

@@ -71,6 +71,91 @@ build_query_sql <- function(
   trimws(do.call(glue::glue_sql, c(query, .con = .con)))
 }
 
+#' Build query to read from collection in DataStorageMongoDB provider
+#'
+#' @param date_from date representing the starting day of results. Can be NULL.
+#' @param date_to date representing the last day of results. Can be NULL.
+#'
+#' @return A string or a JSON object that can be used as the query argument of
+#' the `find()` method of a [mongolite::mongo()] class.
+#'
+#' @noRd
+#' @examples
+#' con <- mongolite::mongo()
+#' con$find(query = build_query_mongodb())
+#' con$find(query = build_query_mongodb(Sys.Date() - 365))
+#' con$find(query = build_query_mongodb(date_to = Sys.Date() + 365))
+#' con$find(query = build_query_mongodb(
+#'   date_from = Sys.Date() - 365, date_to = Sys.Date() + 365)
+#' )
+#' con$find(query = build_query_mongodb(
+#'   date_from = as.Date("2023-04-13"), date_to = as.Date("2000-01-01")
+#' ))
+build_query_mongodb <- function(date_from, date_to) {
+  if (is.null(date_from) && is.null(date_to)) {
+    query <- "{}"
+    return(query)
+  } else {
+    query <- list(time = list())
+  }
+
+  if (!is.null(date_from)) {
+    if (inherits(date_from, "Date")) {
+      date_from <- paste0(as.character(date_from), " 00:00:00 UTC")
+    }
+    query$time["$gte"] <- as.integer(lubridate::as_datetime(date_from)) * 1000
+  }
+
+  if (!is.null(date_to)) {
+    if (inherits(date_to, "Date")) {
+      date_to <- paste0(as.character(date_to), " 23:59:59 UTC")
+    }
+    query$time["$lte"] <- as.integer(lubridate::as_datetime(date_to)) * 1000
+  }
+
+  jsonlite::toJSON(query, auto_unbox = TRUE)
+}
+
+#' Create the connection string for mongodb
+#'
+#' @noRd
+#' @keywords internal
+#' @examples
+#' build_mongo_connection_string(
+#'   "localhost",
+#'   31,
+#'   "user",
+#'   "pass",
+#'   "authdb",
+#'   list("option1" = "value1", "option2" = "value2")
+#' )
+build_mongo_connection_string <- function(
+    hostname, port, username, password, authdb, options) {
+  checkmate::assert_string(hostname)
+  checkmate::assert_int(port)
+  checkmate::assert_string(username, null.ok = TRUE)
+  checkmate::assert_string(password, null.ok = TRUE)
+  checkmate::assert_string(authdb, null.ok = TRUE)
+  checkmate::assert_list(options, null.ok = TRUE)
+
+  paste0(
+    "mongodb://",
+    sprintf("%s:%s@", username, password),
+    hostname,
+    ":",
+    port,
+    sprintf("/%s", authdb %||% ""),
+    ifelse(
+      isFALSE(is.null(options)),
+      sprintf(
+        "?%s",
+        paste(names(options), "=", options, collapse = "&", sep = "")
+      ),
+      ""
+    )
+  )
+}
+
 #' Process a row's detail (from DB) in JSON format to a data.frame
 #'
 #' @param details_json string containing details a valid JSON, NULL or NA

R/data-storage-mongodb.R

@@ -0,0 +1,168 @@
+#' Data storage class with MongoDB provider
+#'
+#' @description
+#' Implementation of the [`DataStorage`] R6 class to MongoDB backend using a
+#' unified API for read/write operations
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' data_storage <- DataStorageMongoDB$new(
+#'   host = "localhost",
+#'   db = "test",
+#'   ssl_options = mongolite::ssl_options()
+#' )
+#' data_storage$insert("example", "test_event", "session1")
+#' data_storage$insert("example", "input", "s1", list(id = "id1"))
+#' data_storage$insert("example", "input", "s1", list(id = "id2", value = 32))
+#'
+#' data_storage$insert(
+#'   "example", "test_event_3_days_ago", "session1",
+#'   time = lubridate::as_datetime(lubridate::today() - 3)
+#' )
+#'
+#' data_storage$read_event_data()
+#' data_storage$read_event_data(Sys.Date() - 1, Sys.Date() + 1)
+#' data_storage$close()
+#' }
+DataStorageMongoDB <- R6::R6Class( # nolint object_name.
+  classname = "DataStorageMongoDB",
+  inherit = DataStorage,
+  #
+  # Public
+  public = list(
+
+    #' @description
+    #' Initialize the data storage class
+    #' @param hostname the hostname or IP address of the MongoDB server.
+    #' @param port the port number of the MongoDB server (default is 27017).
+    #' @param username the username for authentication (optional).
+    #' @param password the password for authentication (optional).
+    #' @param authdb the default authentication database (optional).
+    #' @param dbname name of database (default is "shiny_telemetry").
+    #' @param options Additional connection options in a named list format
+    #' (e.g., list(ssl = "true", replicaSet = "myreplicaset")) (optional).
+    #' @param ssl_options additional connection options such as SSL keys/certs
+    #' (default is [`mongolite::ssl_options()`]).
+
+    initialize = function(
+      hostname = "localhost",
+      port = 27017,
+      username = NULL,
+      password = NULL,
+      authdb = NULL,
+      dbname = "shiny_telemetry",
+      options = NULL,
+      ssl_options = mongolite::ssl_options()
+    ) {
+      # create the connection string for mongodb
+      checkmate::assert_string(hostname)
+      checkmate::assert_int(port)
+      checkmate::assert_string(username, null.ok = TRUE)
+      checkmate::assert_string(password, null.ok = TRUE)
+      checkmate::assert_string(authdb, null.ok = TRUE)
+      checkmate::assert_string(dbname)
+      checkmate::assert_list(options, null.ok = TRUE)
+      checkmate::assert_list(ssl_options, null.ok = TRUE)
+
+      password_debug <- if (is.null(password)) {
+        "(empty)"
+      } else {
+        digest::digest(password, algo = "sha256")
+      }
+
+      logger::log_debug(
+        "Parameters for MongoDB:\n",
+        "  *          username: {username %||% \"(empty)\"}\n",
+        "  * password (sha256): {password_debug}\n",
+        "  *     hostname:port: {hostname}:{port}\n",
+        "  *           db name: {dbname}\n",
+        "  *            authdb: {authdb %||% \"(empty)\"}\n",
+        "  *           options: {jsonlite::toJSON(options, auto_unbox = TRUE)}\n",
+        "  *       ssl_options: ",
+        "{jsonlite::toJSON(unclass(mongolite::ssl_options()), auto_unbox = TRUE)}\n",
+        namespace = "shiny.telemetry"
+      )
+
+      private$connect(
+        url = build_mongo_connection_string(
+          hostname = hostname,
+          port = port,
+          username = username,
+          password = password,
+          authdb = authdb,
+          options = options
+        ),
+        dbname,
+        options = ssl_options
+      )
+    }
+  ),
+  #
+  # Private
+  private = list(
+    # Private Fields
+    db_con = NULL,
+
+    # Private methods
+    connect = function(url, dbname, options) {
+      # Initialize connection with database
+      private$db_con <- mongolite::mongo(
+        url = url,
+        db = dbname,
+        collection = self$event_bucket,
+        options = options
+      )
+    },
+
+    close_connection = function() {
+      private$db_con$disconnect()
+    },
+
+    write = function(values, bucket) {
+      checkmate::assert_choice(bucket, choices = c(self$event_bucket))
+      checkmate::assert_list(values)
+
+      if (!is.null(values$details)) {
+        values$details <- jsonlite::fromJSON(values$details)
+      }
+
+      private$db_con$insert(values, auto_unbox = TRUE, POSIXt = "epoch")
+    },
+
+    read_data = function(date_from, date_to, bucket) {
+      checkmate::assert_choice(bucket, c(self$event_bucket))
+
+      event_data <- private$db_con$find(
+        query = build_query_mongodb(date_from, date_to),
+        fields = '{"_id": false}'
+      )
+
+      if (nrow(event_data) > 0) {
+        result <- event_data %>%
+          dplyr::tibble() %>%
+          tidyr::unnest(cols = "details") %>%
+          dplyr::mutate(time = lubridate::as_datetime(as.integer(time / 1000)))
+
+        # Force value column to be a character data type
+        if ("value" %in% colnames(result)) {
+          dplyr::mutate(result, value = format(value))
+        } else {
+          # If there is no column, then it should still be a character data type
+          dplyr::mutate(result, value = NA_character_)
+        }
+      } else {
+        dplyr::tibble(
+          app_name = character(),
+          type = character(),
+          session = character(),
+          username = character(),
+          id = character(),
+          value = character(),
+          time = lubridate::as_datetime(NULL, tz = "UTC")
+        )
+      }
+    }
+  )
+)

inst/WORDLIST

@@ -7,7 +7,15 @@ CMD
 customizable
 filesystem
 hostname
+INITDB
 Javascript
+mongo
+mongodb
+myreplicaset
+replicaSet
 Rhinoverse
 RStudio
+SSL
+ssl
 UI
+URI

inst/examples/mongodb/README.md

@@ -0,0 +1,6 @@
+# Instrumented app with MongoDB backend
+
+This example application uses MongoDB as a provider for data storage.
+
+It is bundled with an example docker container provided by `docker-compose.yml`.
+The MongoDB instance has to be running for the application and analytics dashboard to work.

inst/examples/mongodb/docker-compose.yml

@@ -0,0 +1,13 @@
+# Use root/example as user/password credentials
+version: '3.1'
+
+services:
+
+  mongo:
+    image: mongo
+    restart: always
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: root
+      MONGO_INITDB_ROOT_PASSWORD: example
+    ports:
+      - 27017:27017

inst/examples/mongodb/mongodb_analytics.R

@@ -0,0 +1,25 @@
+library(shiny)
+library(shiny.semantic)
+library(semantic.dashboard)
+library(shinyjs)
+library(tidyr)
+library(dplyr)
+library(purrr)
+library(plotly)
+library(timevis)
+library(ggplot2)
+library(mgcv)
+library(config)
+library(DT)
+
+# Please install shiny.telemetry with all dependencies
+library(shiny.telemetry)
+
+# Default storage backend using MariaDB
+data_storage <- DataStorageMongoDB$new(
+  username = "root", password = "example"
+)
+
+analytics_app(data_storage = data_storage)
+
+# shiny::shinyAppFile(system.file("examples", "mariadb", "mariadb_analytics.R", package = "shiny.telemetry")) # nolint: commented_code, line_length.