convert references from elm to paperbark

Also add `corella` and `paperbark` to Remotes in DESCRIPTION

Author: mjwestgate

DESCRIPTION

@@ -27,10 +27,10 @@ Imports:
   corella,
   curl,
   dplyr,
-  elm,
   glue,
   httr2,
   jsonlite,
+  paperbark,
   potions,
   purrr,
   readr,
@@ -45,6 +45,9 @@ Suggests:
   rmarkdown,
   testthat (>= 3.0.0),
   xml2
+Remotes:
+  AtlasOfLivingAustralia/corella
+  AtlasOfLivingAustralia/paperbark
 License: MPL-2.0
 URL: https://galaxias.ala.org.au
 BugReports: https://github.com/AtlasOfLivingAustralia/galaxias/issues

NAMESPACE

@@ -28,11 +28,6 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
 importFrom(dplyr,select)
 importFrom(dplyr,slice_head)
-importFrom(elm,add_eml_header)
-importFrom(elm,check_eml)
-importFrom(elm,read_md)
-importFrom(elm,use_metadata)
-importFrom(elm,write_eml)
 importFrom(glue,glue)
 importFrom(glue,glue_collapse)
 importFrom(httr2,req_body_multipart)
@@ -43,6 +38,10 @@ importFrom(httr2,request)
 importFrom(httr2,resp_body_json)
 importFrom(jsonlite,toJSON)
 importFrom(jsonlite,unbox)
+importFrom(paperbark,check_eml)
+importFrom(paperbark,read_md)
+importFrom(paperbark,use_metadata)
+importFrom(paperbark,write_eml)
 importFrom(potions,brew)
 importFrom(potions,pour)
 importFrom(purrr,map)

R/build_archive.R

@@ -16,8 +16,8 @@
 #'    altered to use Darwin Core terms as column headers. See the `corella`
 #'    package for details.
 #'  * A metadata statement, stored in xml using the filename `eml.xml`. The
-#'    function `use_metadata()` from the `elm` package is a good starting point
-#'    here, followed by `build_metadata()` to save it in xml.
+#'    function `use_metadata()` from the `paperbark` package is a good starting 
+#'    point here, followed by `build_metadata()` to save it in xml.
 #'  * A 'schema' document, also stored in xml, called `meta.xml`. This is 
 #'    usually constructed using `build_schema()`.
 #'
@@ -135,7 +135,7 @@ find_data <- function(directory,
 
   if(!file.exists(glue("{directory}/eml.xml"))){
     bullets <- c("No metadata statement ({.file eml.xml}) is present in the specified directory.",
-                 i = "See `elm::use_metadata()` for an example metadata statement.",
+                 i = "See `paperbark::use_metadata()` for an example metadata statement.",
                  i = "Use `build_metadata()` to convert to {.file eml.xml}.")
     cli_abort(bullets,
           call = call)

R/build_metadata.R

@@ -6,17 +6,16 @@
 #' specified using the `directory` argument.
 #' 
 #' This function is a fairly shallow wrapper on top of functionality build
-#' in the `elm` package, particularly `read_md()` and `write_eml()`. You can 
+#' in the `paperbark` package, particularly `read_md()` and `write_eml()`. You can 
 #' use that package to gain greater control, or to debug problems, should you 
 #' wish.
 #' @param path Path to a metadata statement stored in markdown format (.md).
 #' @param file A file where the result should be saved. Defaults to 
 #' `data/eml.xml`.
 #' @returns Does not return an object to the workspace; called for the side
 #' effect of building a file named `meta.xml` in the `data` directory.
-#' @importFrom elm add_eml_header
-#' @importFrom elm read_md
-#' @importFrom elm write_eml
+#' @importFrom paperbark read_md
+#' @importFrom paperbark write_eml
 #' @export
 build_metadata <- function(x = "data", 
                            file = "./data/eml.xml"){
@@ -26,13 +25,10 @@ build_metadata <- function(x = "data",
   # import file, ensure EML metadata is added, convert to XML
   progress_update("Reading file...")
   metadata_file <- read_md(x)
-  
-  progress_update("Building xml components...")
-  built_file <- add_eml_header(metadata_file)
-  
+
   progress_update("Writing file...")
   write_eml(built_file, file = file)
 
   cli::cli_alert_success("Metadata successfully built. Saved as {.file /data/eml.xml}.")
   cli::cli_progress_done()
-}
+}

R/build_schema.R

@@ -9,7 +9,7 @@
 #' @param file (string) A file name for the resulting schema document.
 #' @returns Does not return an object to the workspace; called for the side
 #' effect of building a file named `meta.xml` in the specified directory.
-#' @importFrom elm write_eml
+#' @importFrom paperbark write_eml
 #' @importFrom glue glue
 #' @importFrom rlang abort
 #' @export
@@ -231,4 +231,4 @@ add_front_matter <- function(df){
     )
   )
   bind_rows(front_row, df)
-}
+}

R/check_archive.R

@@ -1,7 +1,7 @@
 #' Check an archive against Darwin Core standards
 #' 
 #' This is a wrapper to two other packages; schema and EML files (i.e. xml) are
-#' checked with the `elm` package; csv files are checked with the `corella`
+#' checked with the `paperbark` package; csv files are checked with the `corella`
 #' package.
 #' @param x (string) A directory containing the files to be published, or 
 #' optionally a `.zip` file built from the same (i.e. with `build_archive()`). 
@@ -27,7 +27,7 @@ check_archive <- function(x = "data"){
 
 #' Internal function to check all files
 #' @importFrom corella check_occurrences
-#' @importFrom elm check_eml
+#' @importFrom paperbark check_eml
 #' @importFrom purrr map
 #' @importFrom readr read_csv
 #' @noRd

R/galaxias-package.R

@@ -23,7 +23,7 @@
 #'   * [build_archive()] Convert a directory to a Darwin Core Archive
 #'   
 #'  **Validate an archive**
-#'   * [check_archive()] Check your archive using the `elm` and `corella` packages
+#'   * [check_archive()] Check your archive using the `paperbark` and `corella` packages
 #'   * [galaxias_config()] Store credentials for your API call
 #'   * [validate_archive()] Check your archive using the GBIF 'validator' API
 #'   * [print_validation()] Methods for displaying API responses

R/galaxias_project.R

@@ -12,7 +12,7 @@
 #' side-effect of building a new project or package.
 #' @name galaxias_project
 #' @order 1
-#' @importFrom elm use_metadata
+#' @importFrom paperbark use_metadata
 #' @importFrom usethis create_project
 #' @importFrom usethis use_directory
 #' @export
@@ -33,4 +33,4 @@ galaxias_package <- function(path, ...){
   create_package(path, ...)
   use_directory("data_raw")
   use_directory("data") 
-}
+}

README.Rmd

@@ -62,8 +62,8 @@ library(galaxias)
 `galaxias` is part of a group of packages that help users publish data using 
 the Darwin Core standard. The other packages are:
 
- - [`corella`](https://github.com/AtlasOfLivingAustralia/corella) for converting tibbles to the required column names
- - [`elm`](https://github.com/AtlasOfLivingAustralia/elm) for converting markdown files to `xml`.
+ - [`corella`](https://corella.ala.org.au) for converting tibbles to the required column names
+ - [`paperbark`](https://paperbark.ala.org.au) for converting markdown files to `xml`.
 
 
 ## Citing galaxias

README.md

@@ -56,10 +56,10 @@ library(galaxias)
 `galaxias` is part of a group of packages that help users publish data
 using the Darwin Core standard. The other packages are:
 
-- [`corella`](https://github.com/AtlasOfLivingAustralia/corella) for
-  converting tibbles to the required column names
-- [`elm`](https://github.com/AtlasOfLivingAustralia/elm) for converting
-  markdown files to `xml`.
+- [`corella`](https://corella.ala.org.au) for converting tibbles to the
+  required column names
+- [`paperbark`](https://paperbark.ala.org.au) for converting markdown
+  files to `xml`.
 
 ## Citing galaxias
 

man/build_archive.Rd

@@ -121,7 +121,7 @@ in the data folder and remove your `data-raw` folder.
 
 Darwin Core Archives use `xml` files to store two metadata files; one that 
 describes your data and ownership, and a second that stores its' structure.
-We recommend using the `elm` package to manipulate these files.
+We recommend using the `paperbark` package to manipulate these files.
 
 `build_schema()` example