Chore(#92): Changed data source from MDEB to MDAT

.github/workflows/update_mdeb_data.yaml → .github/workflows/update_mdat_data.yaml

@@ -1,4 +1,4 @@
-name: pull-data-from-MDEB-data-hub
+name: pull data from MDAT data hub
 
 on:
   workflow_dispatch:
@@ -32,29 +32,26 @@ jobs:
         with:
           r-version: '4.2.0'
 
-
       - name: Install system dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
 
       - name: Install command line packages
         run: |
           sudo apt update
           sudo apt-get install libcurl4-openssl-dev libgit2-dev libudunits2-dev
-#          sudo apt-get install  libgdal-dev libcurl4-gnutls-dev libgit2-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
         shell: bash
-
-
+
       - name: Install packages
         run: |
           install.packages(c("remotes","here","httr2","jsonlite","dplyr","glue"))
           remotes::install_github("NEFSC/NEFSC-Spatial")
         shell: Rscript {0}
 
-      - name: Pull MDEB data and save to repo
+      - name: Pull MDAT data and save to repo
         run: |
           options(timeout = 60 * 60 * 6)
-          source(here::here("data-raw/get_mdeb_for_package.R"))
-          get_mdeb_for_package(overwrite = TRUE)
+          source(here::here("data-raw/get_mdat_for_package.R"))
+          get_mdat_for_package(overwrite = TRUE)
         shell: Rscript {0}
 
       # Create the Pull Request from dev if changes are detected

data-raw/find_mdeb_data.R → data-raw/find_mdat_data.R

@@ -1,9 +1,9 @@
-#' Find available data hosted on the MDEB (Marine Development and Ecology Branch) GIS Data Hub
+#' Find available data hosted on the MDAT (Marine Development and Advanced Technology Program) GIS Data Hub
 #' hosted on NOAA's Geoplatform
 #'
 #' @description
 #' This function retrieves the data available on the
-#' \href{https://mdeb-nefsc-noaa.hub.arcgis.com/}{MDEB GIS Data Hub}.
+#' \href{https://mdeb-nefsc-noaa.hub.arcgis.com/}{MDAT GIS Data Hub}.
 #'
 #' @return A tibble with the following columns:
 #' \item{title}{Name of the NOAA Geoplatform feature service}
@@ -13,21 +13,21 @@
 #'
 #' @examples
 #' # Retrieve a list of available data
-#' mdeb_data <- find_mdeb_data()
-#' mdeb_data
+#' mdat_data <- find_mdat_data()
+#' mdat_data
 #'
 #' @export
 
-find_mdeb_data <- function() {
-  # url of the MDEB GIS Data Hub search API
-  mdeb_hub <- "https://mdeb-nefsc-noaa.hub.arcgis.com/api/search/v1/collections/all/items"
+find_mdat_data <- function() {
+  # url of the MDAT GIS Data Hub search API
+  mdat_hub <- "https://mdeb-nefsc-noaa.hub.arcgis.com/api/search/v1/collections/all/items"
   # scrape json to get all feature services
-  catalog_items <- mdeb_hub |>
+  catalog_items <- mdat_hub |>
     jsonlite::fromJSON()
   # count the number of available services
   num_items <- catalog_items$numberMatched
   # pull all feature service items (API default = 10)
-  catalog_items_v2 <- paste0(mdeb_hub, "?limit=", num_items) |>
+  catalog_items_v2 <- paste0(mdat_hub, "?limit=", num_items) |>
     jsonlite::fromJSON()
   # extract metadata properties
   available_datasets <- catalog_items_v2$features$properties |>

data-raw/get_mdeb_data.R → data-raw/get_mdat_data.R

@@ -1,45 +1,45 @@
-#' Get data from the MDEB (Marine Development and Ecology Branch) GIS Data Hub
-#' hosted on NOAA's Geoplatform
+#' Get data from the MDAT (Marine Development and Advanced Technology Program) GIS Data Hub
+#' hosted on NOAA's GeoPlatform
 #'
 #' @description
-#' This function retrieves data from the \href{https://mdeb-nefsc-noaa.hub.arcgis.com/}{MDEB GIS Data Hub}.
+#' This function retrieves data from the \href{https://mdeb-nefsc-noaa.hub.arcgis.com/}{MDAT GIS Data Hub}.
 #'
 #' @param dataset_name Name of the dataset to retrieve.
 #' @param dataset_id ID of the dataset layer to retrieve.
 #'
 #' @section Available data:
 #' The list of available data and corresponding REST URLs
-#' can be found by running `find_mdeb_data()`.
+#' can be found by running `find_mdat_data()`.
 #'
 #' @return An sf data.frame-like object
 #'
 #' @examples
-#' # Pull EcoMon Survey strata from MDEB GIS Data Hub
-#' ecomon_strata <- get_mdeb_data(dataset_name = "Ecosystem Monitoring Survey", dataset_id = 1)
+#' # Pull EcoMon Survey strata from MDAT GIS Data Hub
+#' ecomon_strata <- get_mdat_data(dataset_name = "Ecosystem Monitoring Survey", dataset_id = 1)
 #' # Plot the data
 #' plot(ecomon_strata)
 #'
 #' @export
 
-get_mdeb_data <- function(dataset_name = NULL, dataset_id = NULL) {
+get_mdat_data <- function(dataset_name = NULL, dataset_id = NULL) {
   # check if dataset_name, dataset_id is NULL
   if (is.null(dataset_name) || is.null(dataset_id)) {
     message(
       "Neither dataset_name or id can be NULL.
        To find the list of available datasets, please use run
-            find_mdeb_data()."
+            find_mdat_data()."
     )
     return()
   }
 
-  allData <- find_mdeb_data()
+  allData <- find_mdat_data()
   set <- allData |>
     dplyr::filter(title == dataset_name, id == dataset_id)
 
   if (nrow(set) == 0) {
     stop(
-      "Data set not found. To find the list of available datasets, please use run
-    find_mdeb_data()"
+      "Data set not found. To find the list of available datasets, please run
+    find_mdat_data()"
     )
   }
 

data-raw/get_mdeb_for_package.R → data-raw/get_mdat_for_package.R

@@ -1,24 +1,24 @@
-#' Pull all content from MDEB data hub and create sf objects
+#' Pull all content from MDAT data hub and create sf objects
 #'
 #' Pulls the data and converts to sf, then saves as part of the package
 #'
 #'
 #'
 
-source(here::here("data-raw/find_mdeb_data.R"))
-source(here::here("data-raw/get_mdeb_data.R"))
-source(here::here("data-raw/generate_roxygen_mdeb.R"))
+source(here::here("data-raw/find_mdat_data.R"))
+source(here::here("data-raw/get_mdat_data.R"))
+source(here::here("data-raw/generate_roxygen_mdat.R"))
 
-get_mdeb_for_package <- function(overwrite = FALSE) {
-  # find all the data set on the MDEB HUB
-  datasets <- find_mdeb_data()
+get_mdat_for_package <- function(overwrite = FALSE) {
+  # find all the data set on the MDAT HUB
+  datasets <- find_mdat_data()
 
   # loop through each and save as rda file.
   # also create documentation for each dataset
   for (ids in 1:nrow(datasets)) {
     dataset <- datasets[ids, ]
     message("Processing: ", dataset$title)
-    data <- get_mdeb_data(dataset$title, dataset$id)
+    data <- get_mdat_data(dataset$title, dataset$id)
     if (!is.null(data)) {
       # Save the data as an R object in the package
       dataset_name <- tolower(gsub("SMIT_", "", dataset$name))
@@ -52,7 +52,7 @@ get_mdeb_for_package <- function(overwrite = FALSE) {
         )
       }
       # Generate Roxygen data doc
-      generate_roxygen_mdeb(
+      generate_roxygen_mdat(
         dataset_name = paste0(dataset_name, '.rda'),
         title = dataset$title,
         description = modified_dataset_description

pkgdown/_pkgdown.yml

@@ -42,8 +42,8 @@ navbar:
     articles:
       text: Articles
       menu:
-      - text: MDEB Datasets
-        href: articles/mdeb_datasets.html
+      - text: MDAT Datasets
+        href: articles/mdat_datasets.html
       - text: Team Members
         href: articles/teamMembers.html