inst/shiny/global.R

In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

# Wallace EcoMod: a flexible platform for reproducible modeling of
# species niches and distributions.
# 
# global.R
# File author: Wallace EcoMod Dev Team. 2023.
# --------------------------------------------------------------------------
# This file is part of the Wallace EcoMod application
# (hereafter “Wallace”).
#
# Wallace is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License,
# or (at your option) any later version.
#
# Wallace is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
# --------------------------------------------------------------------------
#
library(wallace)
library(glue)

MB <- 1024^2

UPLOAD_SIZE_MB <- 5000
options(shiny.maxRequestSize = UPLOAD_SIZE_MB*MB)

SAVE_SESSION_SIZE_MB_WARNING <- 100

source("helpers.R")

# Load all Wallace base modules (old format)
# TODO this should not exist after moving all modules to the new format
base_module_files <- list.files('modules', pattern = "\\.R$", full.names = TRUE)
for (file in base_module_files) source(file, local = TRUE)



# The components that have modules. These names must match the values of the
# tabs of the components in the UI.
COMPONENTS <- c("occs", "envs", "poccs", "penvs", "espace", "part", "model",
                "vis", "xfer", "rep")

# Information about modules that various parts of the app need access to
COMPONENT_MODULES <- list()

# Load all Wallace base modules
base_module_configs <- c(
  "modules/occs_queryDb.yml",
  # "modules/occs_paleoDb.yml",
  "modules/occs_userOccs.yml",
  "modules/envs_worldclim.yml",
  "modules/envs_ecoclimate.yml",
  "modules/envs_userEnvs.yml",
  "modules/poccs_selectOccs.yml",
  "modules/poccs_removeByID.yml",
  "modules/poccs_thinOccs.yml",
  "modules/penvs_bgExtent.yml",
  "modules/penvs_drawBgExtent.yml",
  "modules/penvs_userBgExtent.yml",
  "modules/espace_pca.yml",
  "modules/espace_occDens.yml",
  "modules/espace_nicheOv.yml",
  "modules/part_nonSpat.yml",
  "modules/part_spat.yml",
  "modules/model_maxent.yml",
  "modules/model_bioclim.yml",
  "modules/vis_mapPreds.yml",
  "modules/vis_maxentEvalPlot.yml",
  "modules/vis_responsePlot.yml",
  "modules/vis_bioclimPlot.yml",
  "modules/xfer_area.yml",
  "modules/xfer_time.yml",
  "modules/xfer_user.yml",
  "modules/xfer_mess.yml",
  "modules/rep_markdown.yml",
  "modules/rep_rmms.yml",
  "modules/rep_refPackages.yml"
)

# Load user-defined modules
user_module_configs <- getOption("wallace_module_configs")

all_module_configs <- c(base_module_configs, user_module_configs)
for (module_config_file in all_module_configs) {
  # Read each user-defined module config file
  module_config <- yaml::read_yaml(module_config_file)
  config_dir <- dirname(module_config_file)
  id <- tools::file_path_sans_ext(basename(module_config_file))
  module_config$id <- id

  # Perform lots of error checking to ensure the module was written properly
  required_fields <- c("component", "short_name", "long_name", "authors", "package")

  if (id == "main") {
    stop("A module cannot be named `main`", call. = FALSE)
  }

  if (!grepl("^[A-Za-z0-9_]+$", id)) {
    stop("Module {id}: The id can only contain English characters, digits, and underscores",
         call. = FALSE)
  }

  missing <- required_fields[!required_fields %in% names(module_config)]
  if (length(missing) > 0) {
    stop(glue("Module {id}: Some required fields are missing: {join(missing)}"),
         call. = FALSE)
  }

  if (!module_config$component %in% COMPONENTS) {
    stop(glue("Module {id}: Invalid component `{module_config$component}` ",
              "(options are: {join(COMPONENTS)})"), call. = FALSE)
  }

  module_config$instructions <- suppressWarnings(
    normalizePath(file.path(config_dir, glue("{id}.md")))
  )
  if (!file.exists(module_config$instructions)) {
    stop(glue("Module {id}: Instructions file `{module_config$instructions}` was expected but not found"), call. = FALSE)
  }

  rmd_file <- suppressWarnings(
    normalizePath(file.path(config_dir, glue("{id}.Rmd")))
  )
  if (file.exists(rmd_file)) {
    module_config$rmd_file <- rmd_file
  }

  module_config$file <- suppressWarnings(
    normalizePath(file.path(config_dir, glue("{id}.R")))
  )
  if (!file.exists(module_config$file)) {
    stop(glue("Module {id}: Source file `{module_config$file}` was expected but not found"), call. = FALSE)
  }
  temp_env <- new.env()
  source(module_config$file, local = temp_env)

  ui_function <- glue("{id}_module_ui")
  if (!exists(ui_function, envir = temp_env) || !is.function(get(ui_function, envir = temp_env))) {
    stop(glue("Module {id}: Could not find a UI function named `{ui_function}`"),
         call. = FALSE)
  }
  server_function <- glue("{id}_module_server")
  if (!exists(server_function, envir = temp_env) || !is.function(get(server_function, envir = temp_env))) {
    stop(glue("Module {id}: Could not find a server function named `{server_function}`"),
         call. = FALSE)
  }

  # Save the module's UI and server
  module_config$ui_function <- ui_function
  module_config$server_function <- server_function

  # Save the module's result and map code and Rmd variables if they exist
  result_function <- glue("{id}_module_result")
  if (exists(result_function, envir = temp_env) && is.function(get(result_function, envir = temp_env))) {
    module_config$result_function <- result_function
  }
  map_function <- glue("{id}_module_map")
  if (exists(map_function, envir = temp_env) && is.function(get(map_function, envir = temp_env))) {
    module_config$map_function <- map_function
  }
  rmd_function <- glue("{id}_module_rmd")
  if (exists(rmd_function, envir = temp_env) && is.function(get(rmd_function, envir = temp_env))) {
    module_config$rmd_function <- rmd_function
  }

  # Save the module information
  COMPONENT_MODULES[[module_config$component]][[id]] <- module_config

  # Load the module's code
  source(module_config$file, local = TRUE)
}