Merge pull request #2 from USEPA/1-prepare-for-cran-release

1 prepare for cran release

DESCRIPTION

@@ -19,7 +19,7 @@ Authors@R: c(
     	        )
 Description: Access chemical, hazard, bioactivity, and exposure data from the 
    Computational Toxicology and Exposure ('CTX') APIs 
-   <https://api-ccte.epa.gov/docs/>. 'ccdR' was developed to streamline the 
+   <https://api-ccte.epa.gov/docs/>. 'ctxR' was developed to streamline the 
    process of accessing the information available through the 'CTX' APIs 
    without requiring prior knowledge of how to use APIs. Most data is also 
    available on the CompTox Chemical Dashboard ('CCD') 
@@ -54,8 +54,8 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0),
     XML
-URL: https://github.com/USEPA/ccdR
-BugReports: https://github.com/USEPA/ccdR/issues
+URL: https://github.com/USEPA/ctxR
+BugReports: https://github.com/USEPA/ctxR/issues
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Depends: 

NAMESPACE

@@ -1,14 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(print,ctx_credentials)
-export(ccdr_hide_api_key)
-export(ccdr_show_api_key)
 export(chemical_contains)
 export(chemical_contains_batch)
 export(chemical_equal)
 export(chemical_equal_batch)
 export(chemical_starts_with)
 export(chemical_starts_with_batch)
+export(ctxR_hide_api_key)
+export(ctxR_show_api_key)
 export(ctx_key)
 export(get_all_assays)
 export(get_all_public_chemical_lists)
@@ -81,9 +81,9 @@ export(get_public_chemical_list_by_name_batch)
 export(get_skin_eye_hazard)
 export(get_skin_eye_hazard_batch)
 export(get_smiles)
-export(has_ccdr_option)
-export(has_ccdr_options)
+export(has_ctxR_option)
+export(has_ctxR_options)
 export(has_ctx_key)
-export(register_ccdr)
-export(set_ccdr_option)
+export(register_ctx_api_key)
+export(set_ctxR_option)
 export(showing_key)

NEWS.md

@@ -1,6 +1,5 @@
-# ccdR 1.0.0
+# ctxR 1.0.0
 
-# ccdR 0.1.0
+* Initial release. Renamed package from `ccdR` package for better alignment 
+with US EPA CTX APIs.
 
-* Added a `NEWS.md` file to track changes to the package.
-* Initial release.

R/attach.R

@@ -11,7 +11,7 @@
   cite <- paste0(
     cli::col_green(cli::symbol$info),
     ' ',
-    'Please cite ', cli::col_blue('ccdR'), ' if you use it! Use `citation(\'ccdR\')` for details.'
+    'Please cite ', cli::col_blue('ctxR'), ' if you use it! Use `citation(\'ctxR\')` for details.'
   )
 
   rlang::inform(
@@ -20,18 +20,18 @@
   )
 
   .getKeyIntoPkgEnv(silent = FALSE)
-  bootstrap_ccdr()
+  bootstrap_ctxR()
 
 }
 
 .onLoad <- function(...) {
   .getKeyIntoPkgEnv(silent = TRUE)
-  bootstrap_ccdr()
+  bootstrap_ctxR()
 }
 
 
-bootstrap_ccdr <- function() {
-  set_ccdr_option(
+bootstrap_ctxR <- function() {
+  set_ctxR_option(
     'ctx' = structure(
       list(
 
@@ -46,9 +46,9 @@ bootstrap_ccdr <- function() {
 
 .defaultFile <- function() {
   if (getRversion() >= "4.0.0") {
-    ccdRdir <- tools::R_user_dir("ccdR")
-    if (dir.exists(ccdRdir)) {
-      fname <- file.path(ccdRdir, "api.dcf")
+    ctxRdir <- tools::R_user_dir("ctxR")
+    if (dir.exists(ctxRdir)) {
+      fname <- file.path(ctxRdir, "api.dcf")
       if (file.exists(fname)) {
         return(fname)
       }

R/chemical-APIs.R

@@ -619,7 +619,7 @@ get_chem_info <- function(DTXSID = NULL,
 #' @param Server The root address for the API endpoint
 #' @param verbose A logical indicating if some “progress report” should be given.
 #'
-#' @return @return A data.frame containing chemical information for the chemical with
+#' @return A data.frame containing chemical information for the chemical with
 #'   DTXSID matching the input parameter.
 #' @export
 #' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')

R/ctxr_options.R

@@ -0,0 +1,86 @@
+#' ctxR Options
+#'
+#' ctxR stores options as a named list in R's global options, i.e.
+#' `getOption('ctxR')`. It currently stores two such options, one for CCTE
+#' credentialing and one to suppress private API information in the URLs printed
+#' to the screen when web queries are placed. For both of those, see
+#' [register_ctx_api_key()].
+#'
+#' @param ... a named listing of options to set
+#' @param option a specific option to query, e.g. `display_api_key`
+#' @name ctxR_options
+#' @returns
+#'  * `set_ctxR_option()` does not have a return value but has the side effect
+#'  of setting options used by other functions.
+#'
+#'  * `has_ctxR_option()` returns a Boolean.
+#'
+#'  * `has_ctxR_options()` returns a Boolean.
+#' @seealso [register_ctx_api_key()]
+#'
+#'
+#'
+
+
+
+
+
+
+#' @rdname ctxR_options
+#' @export
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
+#' # Set ctxR options
+#' set_ctxR_option('display_api_key' = FALSE)
+set_ctxR_option <- function(...) {
+
+  # if there is no ctxR option create the list with the arguments and return
+  if (!has_ctxR_options()) {
+    options('ctxR' = list(...))
+    return(invisible())
+  }
+
+  # otherwise, go through arguments sequentially and add/update
+  # them in the list ctxR options
+  ctxR <- getOption('ctxR')
+  arg_list <- lapply(as.list(match.call())[-1], eval, envir = parent.frame())
+  for (k in seq_along(arg_list)) {
+    if (names(arg_list)[k] %in% names(ctxR)) {
+      ctxR[names(arg_list)[k]] <- arg_list[k]
+    } else {
+      ctxR <- c(ctxR, arg_list[k])
+    }
+  }
+
+  # set new ctxR
+  options('ctxR' = ctxR)
+
+  # return
+  invisible()
+}
+
+
+
+#' @rdname ctxR_options
+#' @export
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
+#' # Check if there are options registered to 'ctxR'
+#' has_ctxR_options()
+
+has_ctxR_options <- function() {
+  !is.null(getOption('ctxR'))
+}
+
+#' @rdname ctxR_options
+#' @export
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
+#' # Check if a specific option is registered for 'ctxR'
+#' has_ctxR_option('display_api_key')
+
+has_ctxR_option <- function(option) {
+
+  if (has_ctxR_options()){
+    option %in% names(getOption('ctxR'))
+  } else {
+    FALSE
+  }
+}