diff --git a/DESCRIPTION b/DESCRIPTION
index bab363d1..a2048772 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Type: Package
Package: ccdR
-Title: Utilities for Interacting with the 'CCTE' APIs
+Title: Utilities for Interacting with the 'CTX' APIs
Version: 1.0.0
Authors@R: c(
person("Paul", "Kruse", email = "kruse.paul@epa.gov",
@@ -17,13 +17,15 @@ Authors@R: c(
person("Jason", "Brown", role = "ctb",
email = "brown.jason@epa.gov")
)
-Description: Access chemical, hazard, and bioactivity data from the Center for
- Computational Toxicology and Exposure ('CCTE') APIs
+Description: Access chemical, hazard, bioactivity, and exposure data from the
+ Computational Toxicology and Exposure ('CTX') APIs
. 'ccdR' was developed to streamline the
- process of accessing the information available through the 'CCTE' APIs
- without requiring prior knowledge of how to use APIs. All data is also
- available on the CompTox Chemical Dashboard ('CCD')
- .
+ 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')
+ and other resources found at the
+ EPA Computational Toxicology and Exposure Online Resources
+ .
License: GPL (>= 3)
Imports:
cli,
diff --git a/NAMESPACE b/NAMESPACE
index 698c59b8..788106cf 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,21 +1,22 @@
# Generated by roxygen2: do not edit by hand
-S3method(print,ccte_credentials)
+S3method(print,ctx_credentials)
export(ccdr_hide_api_key)
export(ccdr_show_api_key)
-export(ccte_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(ctx_key)
export(get_all_assays)
export(get_all_public_chemical_lists)
export(get_annotation_by_aeid)
export(get_annotation_by_aeid_batch)
export(get_bioactivity_details)
export(get_bioactivity_details_batch)
+export(get_bioactivity_endpoint_status)
export(get_bioactivity_summary)
export(get_bioactivity_summary_batch)
export(get_cancer_hazard)
@@ -61,6 +62,7 @@ export(get_genetox_summary)
export(get_genetox_summary_batch)
export(get_hazard_by_dtxsid)
export(get_hazard_by_dtxsid_batch)
+export(get_hazard_endpoint_status)
export(get_human_hazard_by_dtxsid)
export(get_human_hazard_by_dtxsid_batch)
export(get_inchi)
@@ -81,7 +83,7 @@ export(get_skin_eye_hazard_batch)
export(get_smiles)
export(has_ccdr_option)
export(has_ccdr_options)
-export(has_ccte_key)
+export(has_ctx_key)
export(register_ccdr)
export(set_ccdr_option)
export(showing_key)
diff --git a/R/attach.R b/R/attach.R
index 813e216c..bd4099be 100644
--- a/R/attach.R
+++ b/R/attach.R
@@ -5,13 +5,13 @@
' ',
"CCTE's Terms of Service: ",
cli::col_blue(cli::style_italic(
- cli::style_hyperlink('', 'https://api-ccte.epa.gov/docs/')
+ cli::style_hyperlink('', 'https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis')
))
)
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('ccdR'), ' if you use it! Use `citation(\'ccdR\')` for details.'
)
rlang::inform(
@@ -32,11 +32,11 @@
bootstrap_ccdr <- function() {
set_ccdr_option(
- 'ccte' = structure(
+ 'ctx' = structure(
list(
),
- class = 'ccte_credentials'
+ class = 'ctx_credentials'
),
'display_api_key' = FALSE
)
@@ -68,7 +68,7 @@ bootstrap_ccdr <- function() {
} else {
if (!silent) packageStartupMessage("API key file found but no api entry.")
}
- } else if ((ev <- Sys.getenv("CCTE_API_KEY")) != "") {
+ } else if ((ev <- Sys.getenv("CTX_API_KEY")) != "") {
.pkgenv[["api"]] <- ev
if (!silent) packageStartupMessage("Setting API key from environment variable.")
} else {
diff --git a/R/bioactivity-APIs-batch.R b/R/bioactivity-APIs-batch.R
index a25f4d25..7fd600aa 100644
--- a/R/bioactivity-APIs-batch.R
+++ b/R/bioactivity-APIs-batch.R
@@ -12,7 +12,7 @@
#' @return A named list of data.frames containing bioactivity information for
#' the chemicals with DTXSID or assays with AEID matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull bioactivity details for multiple chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' batch_bioactivity <- get_bioactivity_details_batch(DTXSID = dtxsid)
@@ -28,8 +28,8 @@ get_bioactivity_details_batch <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -163,7 +163,7 @@ get_bioactivity_details_batch <- function(DTXSID = NULL,
#' @return A named list of data.frames containing bioactivity summary
#' information for the assays with AEID matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Get bioactivity summary for multiple aeids
#' aeids <- get_bioactivity_summary_batch(AEID = c(159, 160))
@@ -175,8 +175,8 @@ get_bioactivity_summary_batch <- function(AEID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -232,7 +232,7 @@ get_bioactivity_summary_batch <- function(AEID = NULL,
#' @return A named list of data.frames containing annotation information for the
#' assays with AEID matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Get annotations for multiple aeids
#' aeid_annotations <- get_annotation_by_aeid_batch(AEID = c(159, 160))
@@ -242,8 +242,8 @@ get_annotation_by_aeid_batch <- function(AEID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
diff --git a/R/bioactivity-APIs.R b/R/bioactivity-APIs.R
index 9c271c3e..72f00f98 100644
--- a/R/bioactivity-APIs.R
+++ b/R/bioactivity-APIs.R
@@ -11,7 +11,7 @@
#' @return A data.frame containing bioactivity information for the chemical or assay endpoint with
#' identifier matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull BPA bioactivity details
#' bpa <- get_bioactivity_details(DTXSID = 'DTXSID7020182')
#' # Pull assay bioactivity details
@@ -30,8 +30,8 @@ get_bioactivity_details <- function(DTXSID = NULL,
else if (length(which(!sapply(list(DTXSID, AEID, SPID, m4id), is.null))) > 1)
stop('Please input a value for only one of DTXSID, AEID, SPID, or m4id, but not multiple!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -76,11 +76,7 @@ get_bioactivity_details <- function(DTXSID = NULL,
stop('Please input an API_key!')
}
if(response$status_code == 200){
- req_content <- httr::content(response, as = 'text', encoding = "UTF-8")
- if (nchar(req_content) == 0){
- return(data.table::data.table())
- }
- res <- jsonlite::fromJSON(req_content)
+ res <- jsonlite::fromJSON(httr::content(response, as = 'text', encoding = "UTF-8"))
if (!is.data.frame(res) & (length(res) != 0)){
for (i in 1:length(res)){
if (is.null(res[[i]])) res[[i]] <- NA # set any NULLs to NA
@@ -93,35 +89,9 @@ get_bioactivity_details <- function(DTXSID = NULL,
param_cols <- c('mc3Param', 'mc4Param', 'mc5Param', 'mc6Param')
col_index <- which(param_cols %in% names(res))
if (length(col_index) > 0){
- # In some cases, columns are given by data.frames and we will not try to unnest these
- non_df_cols <- param_cols[col_index][which(sapply(param_cols[col_index], function(t){!is.data.frame(res[[t]])}))]
- if (length(non_df_cols) > 0)
- # In some cases, columns will be NA (in the m4id cases) and we will not try to unnest these
- col_index <- which(unname(!sapply(res[which(names(res) %in% non_df_cols)], is.na)))
- if (length(col_index) > 0){
- res <- tidyr::unnest_wider(data = res, col = param_cols[col_index])
- }
+ res <- tidyr::unnest_wider(data = res, col = param_cols[col_index])
}
-
-
res_dt <- data.table::data.table(res)
-
- # For columns which are lists of lists, we want to unnest the lists
- # Check which columns that tend to return nested are in the data.table
- nested_list_cols <- intersect(names(res_dt), c('resp', 'logc', 'flag', 'mc6MthdId'))
-
- # Check which of these columns are lists of lists. Every entry must be a
- # list in order to be unnested
- nested_indices <- sapply(seq_along(nested_list_cols), function(t) {
- all(sapply(as.data.frame(res_dt)[, nested_list_cols[[t]]], is.list))
- })
-
- # Unnest the columns which are nested lists
- if (length(nested_indices) > 0 && any(nested_indices)){
- res_temp <- tidyr::unnest(data = as.data.frame(res_dt), cols = nested_list_cols[nested_indices])
- res_dt <- data.table::as.data.table(res_temp)
- }
-
return(res_dt)
} else {
if (verbose){
@@ -141,7 +111,7 @@ get_bioactivity_details <- function(DTXSID = NULL,
#' @return A data.frame containing summary information corresponding to the
#' input AEID
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull an assay bioactivity summary
#' aeid_1386 <- get_bioactivity_summary(AEID = 1386)
get_bioactivity_summary <- function(AEID = NULL,
@@ -153,8 +123,8 @@ get_bioactivity_summary <- function(AEID = NULL,
if (is.null(AEID))
stop('Please input an AEID!')
else if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -208,7 +178,7 @@ get_bioactivity_summary <- function(AEID = NULL,
#'
#' @return A data.frame containing all the assays and associated information
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Retrieve all assays
#' assays <- get_all_assays()
get_all_assays <- function(API_key = NULL,
@@ -216,8 +186,8 @@ get_all_assays <- function(API_key = NULL,
verbose = FALSE){
if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -258,7 +228,7 @@ get_all_assays <- function(API_key = NULL,
#' @return A data.frame containing the annotated assays corresponding to the
#' input AEID parameter
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Retrieve annotation for an assay
#' annotation <- get_annotation_by_aeid(AEID = 159)
get_annotation_by_aeid <- function(AEID = NULL,
@@ -268,8 +238,8 @@ get_annotation_by_aeid <- function(AEID = NULL,
if (is.null(AEID))
stop('Please input an AEID!')
else if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -313,3 +283,17 @@ get_annotation_by_aeid <- function(AEID = NULL,
}
+
+#' Bioactivity API Endpoint status
+#'
+#' @return Status of Bioactivity API Endpoints
+#' @export
+#'
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
+#' status <- get_bioactivity_endpoint_status()
+#' print(status)
+
+get_bioactivity_endpoint_status <- function(){
+ request <- httr::GET(url = paste0(bioactivity_api_server, "/health"))
+ return(request$status_code)
+}
diff --git a/R/ccdr_options.R b/R/ccdr_options.R
index 90c74a52..43c51019 100644
--- a/R/ccdr_options.R
+++ b/R/ccdr_options.R
@@ -2,7 +2,7 @@
#'
#' ccdr stores options as a named list in R's global options, i.e.
#' `getOption('ccdr')`. It currently stores two such options, one for CCTE
-#' credentialing and one to supress private API information in the URLs printed
+#' 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_ccdr()].
#'
@@ -28,7 +28,7 @@
#' @rdname ccdr_options
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Set ccdr options
#' set_ccdr_option('display_api_key' = FALSE)
set_ccdr_option <- function(...) {
@@ -62,7 +62,7 @@ set_ccdr_option <- function(...) {
#' @rdname ccdr_options
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Check if there are options registered to 'ccdr'
#' has_ccdr_options()
@@ -72,7 +72,7 @@ has_ccdr_options <- function() {
#' @rdname ccdr_options
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Check if a specific option is registered for 'ccdr'
#' has_ccdr_option('display_api_key')
diff --git a/R/chemical-APIs-batch.R b/R/chemical-APIs-batch.R
index 591cf4e5..3cfc852f 100644
--- a/R/chemical-APIs-batch.R
+++ b/R/chemical-APIs-batch.R
@@ -18,7 +18,7 @@
#' containing chemical information for the chemicals with DTXSID or DTXCID
#' matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical details for multiple chemicals by dtxsid
#' dtxsids <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_details <- get_chemical_details_batch(DTXSID = dtxsid)
@@ -42,8 +42,8 @@ get_chemical_details_batch <- function(DTXSID = NULL,
}
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -120,8 +120,8 @@ get_chemical_details_batch_2 <- function(DTXSID = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -274,8 +274,8 @@ get_smiles_batch <- function(names = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -332,8 +332,8 @@ get_molecular_weight_batch <- function(names = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -390,8 +390,8 @@ get_mol_v3000_batch <- function(names = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -448,8 +448,8 @@ get_mol_v2000_batch <- function(names = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -506,8 +506,8 @@ get_InChI_batch <- function(names = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -564,8 +564,8 @@ get_canonical_smiles_batch <- function(names = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -628,7 +628,7 @@ get_canonical_smiles_batch <- function(names = NULL,
#' @return A named list of data.frames containing chemical information for the
#' chemicals matching the search criteria.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals by property ranges
#' prop_ranges <- get_chemical_by_property_range_batch(start_list = c(1.311,
#' 211.99),
@@ -644,8 +644,8 @@ get_chemical_by_property_range_batch <- function(start_list = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -733,8 +733,8 @@ get_chem_info_batch_old <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -802,7 +802,7 @@ get_chem_info_batch_old <- function(DTXSID = NULL,
#' @return A data.table containing chemical information for the chemicals with
#' DTXSID matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical info for multiple chemicals
#' chem_info <- get_chem_info_batch(DTXSID = c('DTXSID7020182',
#' 'DTXSID2021315'))
@@ -814,8 +814,8 @@ get_chem_info_batch <- function(DTXSID = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -909,8 +909,8 @@ get_fate_by_dtxsid_batch_old <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -958,7 +958,7 @@ get_fate_by_dtxsid_batch_old <- function(DTXSID = NULL,
#' @return A data.table containing chemical fate information for the chemicals
#' with DTXSID matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical fate by dtxsids
#' chemical_fates <- get_fate_by_dtxsid_batch(DTXSID = c('DTXSID7020182',
#' 'DTXSID2021315'))
@@ -969,8 +969,8 @@ get_fate_by_dtxsid_batch <- function(DTXSID = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1045,7 +1045,7 @@ get_fate_by_dtxsid_batch <- function(DTXSID = NULL,
#' @return A named list of data.frames of chemicals and related values matching
#' the query parameters
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals that start with given substrings
#' bpa_substrings <- chemical_starts_with_batch(word_list = c('DTXSID702018',
#' 'DTXCID3018'))
@@ -1056,8 +1056,8 @@ chemical_starts_with_batch <- function(word_list = NULL,
verbose = FALSE,
top = NULL){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1120,7 +1120,7 @@ chemical_starts_with_batch <- function(word_list = NULL,
#' @return A named list of data.frames of chemicals and related values matching
#' the query parameters
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals that match input strings
#' bpa <- chemical_equal_batch(word_list = c('DTXSID7020182', 'DTXCID30182'))
@@ -1129,8 +1129,8 @@ chemical_equal_batch <- function(word_list = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1196,7 +1196,7 @@ chemical_equal_batch <- function(word_list = NULL,
#' @return A named list of data.frames of chemicals and related values matching
#' the query parameters
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals that contain substrings
#' substring_chemicals <- chemical_contains_batch(word_list = c('TXDIS702018',
#' 'DTXSID70201'))
@@ -1207,8 +1207,8 @@ chemical_contains_batch <- function(word_list = NULL,
verbose = verbose,
top = NULL){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1272,7 +1272,7 @@ chemical_contains_batch <- function(word_list = NULL,
#' mass value.
#' @export
#'
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' #Pull chemicals by msready mass and error offset
#' msready_data <- get_msready_by_mass_with_error_batch(masses = c(226, 228),
#' error = 4)
@@ -1283,8 +1283,8 @@ get_msready_by_mass_with_error_batch <- function(masses = NULL,
rate_limit = 0,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1349,7 +1349,7 @@ get_msready_by_mass_with_error_batch <- function(masses = NULL,
#' @return A named list of character lists with DTXSIDs with msready masses
#' falling within the given ranges.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull msready chemicals by mass ranges
#' msready_data <- get_msready_by_mass_batch(start_list = c(200.9, 200.95),
#' end_list = c(200.95, 201.00))
@@ -1360,8 +1360,8 @@ get_msready_by_mass_batch <- function(start_list = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1418,7 +1418,7 @@ get_msready_by_mass_batch <- function(start_list = NULL,
#' @return A named list of character lists of DTXSIDs with chemical formulas
#' matching the search criteria
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull msready data for several chemical formulas
#' msready_data <- get_msready_by_formula_batch(formula_list = c('C16H24N2O5S',
#' 'C15H16O2'))
@@ -1428,8 +1428,8 @@ get_msready_by_formula_batch <- function(formula_list = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1476,7 +1476,7 @@ get_msready_by_formula_batch <- function(formula_list = NULL,
#' @return A named list of character lists of DTXSIDs with DTXCIDs matching the
#' search criteria
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull msready chemicals matching specific DTXCID
#' dtxcid_msready <- get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182',
#' 'DTXCID001315'))
@@ -1486,8 +1486,8 @@ get_msready_by_dtxcid_batch <- function(DTXCID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1539,7 +1539,7 @@ get_msready_by_dtxcid_batch <- function(DTXCID = NULL,
#' @return A named list of data.frames containing information about lists that
#' meet the search criteria.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical lists by type
#' federal_state <- get_chemical_lists_by_type_batch(type_list = c('Federal',
#' 'State'))
@@ -1550,8 +1550,8 @@ get_chemical_lists_by_type_batch <- function(type_list = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1606,7 +1606,7 @@ get_chemical_lists_by_type_batch <- function(type_list = NULL,
#' chemicals in a given list, use \code{\link{get_chemicals_in_list}}.
#' @seealso \code{\link{get_chemicals_in_list}}
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical list information by list names
#' list_info <- get_public_chemical_list_by_name_batch(name_list = c('CCL4',
#' 'NATADB'))
@@ -1617,8 +1617,8 @@ get_public_chemical_list_by_name_batch <- function(name_list = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1667,7 +1667,7 @@ get_public_chemical_list_by_name_batch <- function(name_list = NULL,
#'
#' @return A named list of chemical lists that contain the given chemicals.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull lists containing chemicals for multiple chemicals
#' lists <- get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182',
#' 'DTXSID2021315'))
@@ -1677,8 +1677,8 @@ get_lists_containing_chemical_batch <- function(chemical_list = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1727,7 +1727,7 @@ get_lists_containing_chemical_batch <- function(chemical_list = NULL,
#' @return A named list of data.frames each containing chemicals in the
#' corresponding chemical lists.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals in lists for multiple lists
#' chemicals_in_lists <- get_chemicals_in_list_batch(list_names = c('CCL4', 'NATADB'))
@@ -1736,8 +1736,8 @@ get_chemicals_in_list_batch <- function(list_names = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1787,7 +1787,7 @@ get_chemicals_in_list_batch <- function(list_names = NULL,
#' @return A named list of XML file format for representing a mrv file for each
#' chemicals.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull mrv files for multiple chemicals by DTXSID
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' mrv_files <- get_chemical_mrv_batch(DTXSID = dtxsid)
@@ -1801,8 +1801,8 @@ get_chemical_mrv_batch <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1878,7 +1878,7 @@ get_chemical_mrv_batch <- function(DTXSID = NULL,
#' @return A named list of character strings giving a mol file representations
#' of the given input chemicals.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull mol files for multiple chemicals by DTXSID
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' mol_files <- get_chemical_mol_batch(DTXSID = dtxsid)
@@ -1892,8 +1892,8 @@ get_chemical_mol_batch <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1973,7 +1973,7 @@ get_chemical_mol_batch <- function(DTXSID = NULL,
#' displaying an image, one may use \code{png::writePNG()} or
#' \code{countcolors::plotArrayAsImage()} among many such functions.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull images for multiple chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' images <- get_chemical_image_batch(DTXSID = dtxsid)
@@ -1990,8 +1990,8 @@ get_chemical_image_batch <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -2101,7 +2101,7 @@ get_chemical_image_batch <- function(DTXSID = NULL,
#' @return A named list of lists containing synonym information for each input
#' DTXSID.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull synonyms for multiple chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' batch_synonyms <- get_chemical_synonym_batch(DTXSID = dtxsid)
@@ -2111,8 +2111,8 @@ get_chemical_synonym_batch <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
diff --git a/R/chemical-APIs.R b/R/chemical-APIs.R
index be5397bb..f1758d8d 100644
--- a/R/chemical-APIs.R
+++ b/R/chemical-APIs.R
@@ -15,7 +15,7 @@
#' @return A data.table containing chemical information for the chemical with
#' DTXSID matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical details for BPA
#' bpa <- get_chemical_details(DTXSID = 'DTXSID7020182')
@@ -31,8 +31,8 @@ get_chemical_details <- function(DTXSID = NULL,
stop('Please input either a DTXSID or DTXCID, but not both!')
if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose){
message('Using stored API key!')
}
@@ -288,8 +288,8 @@ get_chemical_details_by_listname <- function(listname = NULL,
}
if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
message('Using stored API key!')
}
}
@@ -326,7 +326,7 @@ get_chemical_details_by_listname <- function(listname = NULL,
#'
#' @return A string giving a SMILES string for the input chemical.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' bpa_smiles <- get_smiles(name = "Bisphenol A")
get_smiles <- function(name = NULL,
@@ -338,8 +338,8 @@ get_smiles <- function(name = NULL,
}
if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
message('Using stored API key!')
}
}
@@ -374,7 +374,7 @@ get_smiles <- function(name = NULL,
#' given.
#' @return A string giving the associated InChIKey.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' bpa_inchikey <- get_inchikey(name = "Bisphenol A")
get_inchikey <- function(name = NULL,
@@ -386,8 +386,8 @@ get_inchikey <- function(name = NULL,
}
if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
message('Using stored API key!')
}
}
@@ -422,7 +422,7 @@ get_inchikey <- function(name = NULL,
#' given.
#' @return A string giving the associated inchi string.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' bpa_inchi <- get_inchi(name = "Bisphenol A")
get_inchi <- function(name = NULL,
@@ -434,8 +434,8 @@ get_inchi <- function(name = NULL,
}
if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
message('Using stored API key!')
}
}
@@ -474,7 +474,7 @@ get_inchi <- function(name = NULL,
#' @return A data.frame containing chemical information for chemicals matching
#' the search criteria.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals with a given property in a set range
#' density <- get_chemical_by_property_range(start = 1.311, end = 1.313,
#' property = 'Density')
@@ -486,8 +486,8 @@ get_chemical_by_property_range <- function(start = NULL,
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
message('Using stored API key!')
}
}
@@ -542,7 +542,7 @@ get_chemical_by_property_range <- function(start = NULL,
#' @return A data.frame containing chemical information for the chemical with
#' DTXSID matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical information for BPA
#' bpa <- get_chem_info(DTXSID = 'DTXSID7020182')
@@ -554,8 +554,8 @@ get_chem_info <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if(verbose){
message('Using stored API key!')
}
@@ -622,7 +622,7 @@ get_chem_info <- function(DTXSID = NULL,
#' @return @return A data.frame containing chemical information for the chemical with
#' DTXSID matching the input parameter.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical fate data for BPA
#' bpa <- get_fate_by_dtxsid(DTXSID = 'DTXSID7020182')
@@ -633,8 +633,8 @@ get_fate_by_dtxsid <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -677,7 +677,7 @@ get_fate_by_dtxsid <- function(DTXSID = NULL,
#' @return A data.frame of chemicals and related values matching the query
#' parameters
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals that start with a fragment DTXSID
#' dtxsid_fragment <- chemical_starts_with(word = 'DTXSID702018')
@@ -689,8 +689,8 @@ chemical_starts_with <- function(word = NULL,
if (is.null(word) || !is.character(word)){
stop('Please input a character value for word!')
} else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -745,7 +745,7 @@ chemical_starts_with <- function(word = NULL,
#' @return A data.frame of chemicals and related values matching the query
#' parameters
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals with matching DTXSID
#' bpa_dtxsid <- chemical_equal(word = 'DTXSID7020182')
@@ -756,8 +756,8 @@ chemical_equal <- function(word = NULL,
if (is.null(word) || !is.character(word)){
stop('Please input a character value for word!')
} else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -805,7 +805,7 @@ chemical_equal <- function(word = NULL,
#' @return A data.frame of chemicals and related values matching the query
#' parameters
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals that contain substring
#' substring_chemicals <- chemical_contains(word = 'TXSID702018')
@@ -817,8 +817,8 @@ chemical_contains <- function(word = NULL,
if (is.null(word) || !is.character(word)){
stop('Please input a character value for word!')
} else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -903,7 +903,7 @@ prepare_word <- function(word){
#'
#' @return A list of DTXSIDs with msready mass falling within the given range.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals with msready mass in given range
#' mass_range <- get_msready_by_mass(start = 200.9, end = 200.95)
@@ -915,8 +915,8 @@ get_msready_by_mass <- function(start = NULL,
if(is.null(start) || is.null(end) || !is.numeric(start) || !is.numeric(end)){
stop('Please input a numeric value for both start and end!')
} else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -966,7 +966,7 @@ get_msready_by_mass <- function(start = NULL,
#' @return A character list of DTXSIDs with chemical formulas matching the
#' search criteria
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals that match input formula
#' mass_formula <- get_msready_by_formula(formula = 'C16H24N2O5S')
@@ -979,8 +979,8 @@ get_msready_by_formula <- function(formula = NULL,
} else if (!is.character(formula)){
stop("Please input a character string for the formula parameter!")
} else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1019,7 +1019,7 @@ get_msready_by_formula <- function(formula = NULL,
#' @return A character list of DTXSIDs with DTXCIDs matching the
#' search criteria
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemicals with matching DTXCID
#' dtxcid_msready <- get_msready_by_dtxcid(DTXSID = 'DTXCID30182')
@@ -1032,8 +1032,8 @@ get_msready_by_dtxcid <- function(DTXCID = NULL,
} else if (!is.character(DTXCID)){
stop("Please input a character string for the DTXCID parameter!")
} else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1077,7 +1077,7 @@ get_msready_by_dtxcid <- function(DTXCID = NULL,
#' @return A data.frame containing information about lists that meet the search
#' criteria.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical lists by type
#' federal <- get_chemical_lists_by_type(type = 'Federal')
@@ -1089,8 +1089,8 @@ get_chemical_lists_by_type <- function(type = NULL,
if (is.null(type) | !is.character(type))
stop('Please input a value for parameter type from the list `federal`, `international`, `state`, and `other`!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1154,7 +1154,7 @@ get_chemical_lists_by_type <- function(type = NULL,
#' use \code{\link{get_chemicals_in_list}}.
#' @seealso \code{\link{get_chemicals_in_list}}
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical list by list name
#' ccl4 <- get_public_chemical_list_by_name(list_name = 'CCL4')
@@ -1166,8 +1166,8 @@ get_public_chemical_list_by_name <- function(list_name = NULL,
if (is.null(list_name))
stop('Please input list_name!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1225,7 +1225,7 @@ get_public_chemical_list_by_name <- function(list_name = NULL,
#'
#' @return A list of names of chemical lists that contain the given chemical
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical lists containing BPA
#' bpa_lists <- get_lists_containing_chemical(DTXSID = 'DTXSID7020182')
@@ -1236,8 +1236,8 @@ get_lists_containing_chemical <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a non-null value for DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1273,7 +1273,7 @@ get_lists_containing_chemical <- function(DTXSID = NULL,
#'
#' @return A data.frame of the chemical list
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Retrieve chemicals contained in chemical list 'CCL4'
#' ccl4_chemicals <- get_chemicals_in_list(list_name = 'CCL4')
@@ -1290,8 +1290,8 @@ get_chemicals_in_list <- function(list_name = NULL,
if (is.null(list_name) | !is.character(list_name))
stop('Please input a character value for list_name!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1344,8 +1344,8 @@ get_chemicals_in_list_start <- function(list_name = NULL,
else if (is.null(word) | !is.character(word))
stop('Please input a character value for word!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1386,9 +1386,9 @@ get_chemicals_in_list_start <- function(list_name = NULL,
#' @param verbose A logical indicating if some “progress report” should be given.
#'
#' @return A data.frame containing information on all public chemical lists
-#' available from the CCTE chemical api.
+#' available from the CTX chemical api.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull all chemical lists
#' all_lists <- get_all_public_chemical_lists()
@@ -1397,8 +1397,8 @@ get_all_public_chemical_lists <- function(Projection = '',
Server = chemical_api_server,
verbose = FALSE){
if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1456,7 +1456,7 @@ get_all_public_chemical_lists <- function(Projection = '',
#'
#' @return XML file format for representing a mrv file.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull mrv file for BPA by dtxsid
#' bpa_mrv <- get_chemical_mrv(DTXSID = 'DTXSID7020182')
#' # Pull mrv file for BPA by dtxcid
@@ -1472,8 +1472,8 @@ get_chemical_mrv <- function(DTXSID = NULL,
else if (!is.null(DTXSID) & !is.null(DTXCID))
stop('Please input either a DTXSID or DTXCID, but not both!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1519,7 +1519,7 @@ get_chemical_mrv <- function(DTXSID = NULL,
#'
#' @return A character string giving a mol file representation
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull mol file for BPA by dtxsid
#' bpa_mol <- get_chemical_mol(DTXSID = 'DTXSID7020182')
#' # Pull mol file for BPA by dtxcid
@@ -1535,8 +1535,8 @@ get_chemical_mol <- function(DTXSID = NULL,
else if (!is.null(DTXSID) & !is.null(DTXCID))
stop('Please input either a DTXSID or DTXCID, but not both!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1588,7 +1588,7 @@ get_chemical_mol <- function(DTXSID = NULL,
#' displaying this, one may use \code{png::writePNG()} or
#' \code{countcolors::plotArrayAsImage()} among many such functions.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull chemical image for BPA by dtxsid
#' bpa_image_matrix <- get_chemical_image(DTXSID = 'DTXSID7020182')
#' if (requireNamespace("countcolors", quietly = TRUE)){
@@ -1612,8 +1612,8 @@ get_chemical_image <- function(DTXSID = NULL,
else if (length(which(!sapply(list(DTXSID, DTXCID, SMILES), is.null))) > 1)
stop('Please input only one DTXSID, DTXCID, or SMILES, and not multiple!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1672,7 +1672,7 @@ get_chemical_image <- function(DTXSID = NULL,
#'
#' @return A named list of synonym information for the input DTXSID
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull synonyms for BPA
#' bpa_synonym <- get_chemical_synonym(DTXSID = 'DTXSID7020182')
@@ -1683,8 +1683,8 @@ get_chemical_synonym <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -1717,11 +1717,11 @@ get_chemical_synonym <- function(DTXSID = NULL,
#' @return Status of Chemical API Endpoints
#' @export
#'
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' status <- get_chemical_endpoint_status()
#' print(status)
get_chemical_endpoint_status <- function(){
- request <- httr::GET(url = "https://api-ccte.epa.gov/chemical/health")
+ request <- httr::GET(url = paste0(chemical_api_server, "/health"))
return(request$status_code)
}
diff --git a/R/exposure-APIs-batch.R b/R/exposure-APIs-batch.R
index 42bb7c73..e86ffcf6 100644
--- a/R/exposure-APIs-batch.R
+++ b/R/exposure-APIs-batch.R
@@ -11,7 +11,7 @@
#' data for each input DTXSID.
#' @export
#'
-#' @examples has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examples has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull exposure functional use data for multiple chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_func_use <- get_exposure_functional_use_batch(DTXSID = dtxsid)
@@ -22,8 +22,8 @@ get_exposure_functional_use_batch <- function(DTXSID = NULL,
Server = exposure_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -79,7 +79,7 @@ get_exposure_functional_use_batch <- function(DTXSID = NULL,
#' categories that have probability of 0
#' @export
#'
-#' @examples has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examples has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull exposure functional use probability data for multiple chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_func_use_prob <- get_exposure_functional_use_batch(DTXSID = dtxsid)
@@ -89,8 +89,8 @@ get_exposure_functional_use_probability_batch <- function(DTXSID = NULL,
Server = exposure_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -164,7 +164,7 @@ get_exposure_functional_use_probability_batch <- function(DTXSID = NULL,
#' data for each input DTXSID.
#' @export
#'
-#' @examples has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examples has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull exposure functional use data for multiple chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_product_data <- get_exposure_product_data_batch(DTXSID = dtxsid)
@@ -174,8 +174,8 @@ get_exposure_product_data_batch <- function(DTXSID = NULL,
Server = exposure_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -227,7 +227,7 @@ get_exposure_product_data_batch <- function(DTXSID = NULL,
#' tags use data for each input DTXSID.
#' @export
#'
-#' @examples has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examples has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull exposure functional use data for multiple chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' exp_list_tags <- get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = dtxsid)
@@ -238,8 +238,8 @@ get_exposure_list_presence_tags_by_dtxsid_batch <- function(DTXSID = NULL,
Server = exposure_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
diff --git a/R/exposure-APIs.R b/R/exposure-APIs.R
index 5ef212e3..f1bf5fbf 100644
--- a/R/exposure-APIs.R
+++ b/R/exposure-APIs.R
@@ -7,7 +7,7 @@
#'
#' @return A data.frame of functional use data.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull functional use data for BPA
#' bpa <- get_exposure_functional_use(DTXSID = 'DTXSID7020182')
@@ -18,8 +18,8 @@ get_exposure_functional_use <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input an DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -56,7 +56,7 @@ get_exposure_functional_use <- function(DTXSID = NULL,
#' @return A data.frame with probabilities corresponding to various routes of
#' exposure related to functional use.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull functional use probability data for BPA
#' bpa <- get_exposure_functional_use_probability(DTXSID = 'DTXSID7020182')
@@ -67,8 +67,8 @@ get_exposure_functional_use_probability <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input an DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -102,7 +102,7 @@ get_exposure_functional_use_probability <- function(DTXSID = NULL,
#'
#' @return A data.frame of functional use categories.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull functional use category data for BPA
#' functional_use_categories <- get_exposure_functional_use_category()
@@ -110,8 +110,8 @@ get_exposure_functional_use_category <- function(API_key = NULL,
Server = exposure_api_server,
verbose = FALSE){
if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -147,7 +147,7 @@ get_exposure_functional_use_category <- function(API_key = NULL,
#' @return A data.frame with product information relating to exposure to the
#' given chemical
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull exposure product data for BPA
#' bpa <- get_exposure_product_data(DTXSID = 'DTXSID7020182')
@@ -158,8 +158,8 @@ get_exposure_product_data <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input an DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -193,7 +193,7 @@ get_exposure_product_data <- function(DTXSID = NULL,
#'
#' @return A data.frame consisting of all the product use categories
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull product data use categories for BPA
#' puc_categories <- get_exposure_product_data_puc()
@@ -201,8 +201,8 @@ get_exposure_product_data_puc <- function(API_key = NULL,
Server = exposure_api_server,
verbose = FALSE){
if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -237,7 +237,7 @@ get_exposure_product_data_puc <- function(API_key = NULL,
#'
#' @return A data.frame with all the list presence tags and associated data.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull list presence tags
#' tags <- get_exposure_list_presence_tags()
@@ -245,8 +245,8 @@ get_exposure_list_presence_tags <- function(API_key = NULL,
Server = exposure_api_server,
verbose = FALSE){
if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -281,7 +281,7 @@ get_exposure_list_presence_tags <- function(API_key = NULL,
#'
#' @return A data.frame of document information and list presence tags
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull list presence tags for BPA
#' bpa <- get_exposure_list_presence_tags(DTXSID = 'DTXSID7020182')
@@ -292,8 +292,8 @@ get_exposure_list_presence_tags_by_dtxsid <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input an DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()){
- API_key <- ccte_key()
+ if (has_ctx_key()){
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -325,11 +325,11 @@ get_exposure_list_presence_tags_by_dtxsid <- function(DTXSID = NULL,
#' @return Status of Exposure API Endpoints
#' @export
#'
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' status <- get_exposure_endpoint_status()
#' print(status)
get_exposure_endpoint_status <- function(){
- request <- httr::GET(url = "https://api-ccte.epa.gov/exposure/health")
+ request <- httr::GET(url = paste0(exposure_api_server, "/health"))
return(request$status_code)
}
diff --git a/R/hazard-APIs-batch.R b/R/hazard-APIs-batch.R
index 51a5a1f1..05fa3fd4 100644
--- a/R/hazard-APIs-batch.R
+++ b/R/hazard-APIs-batch.R
@@ -14,8 +14,8 @@ get_hazard_by_dtxsid_batch_old <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -65,7 +65,7 @@ get_hazard_by_dtxsid_batch_old <- function(DTXSID = NULL,
#' @return A data.table containing chemical (human and eco) hazard data for each
#' input chemical.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull hazard data for multiple chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' batch_hazard <- get_hazard_by_dtxsid_batch(DTXSID = dtxsid)
@@ -76,8 +76,8 @@ get_hazard_by_dtxsid_batch <- function(DTXSID = NULL,
Server = hazard_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -183,8 +183,8 @@ get_human_hazard_by_dtxsid_batch_old <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -233,7 +233,7 @@ get_human_hazard_by_dtxsid_batch_old <- function(DTXSID = NULL,
#'
#' @return A data.table containing chemical human hazard data.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull human hazard data for multiples chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_human_hazard <- get_human_hazard_by_dtxsid_batch(DTXSID = dtxsid)
@@ -244,8 +244,8 @@ get_human_hazard_by_dtxsid_batch <- function(DTXSID = NULL,
Server = hazard_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -316,8 +316,8 @@ get_ecotox_hazard_by_dtxsid_batch_old <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -366,7 +366,7 @@ get_ecotox_hazard_by_dtxsid_batch_old <- function(DTXSID = NULL,
#'
#' @return A data.table containing chemical ecotox hazard data.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull ecotox hazard data for multiples chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_ecotox_hazard <- get_ecotox_hazard_by_dtxsid_batch(DTXSID = dtxsid)
@@ -377,8 +377,8 @@ get_ecotox_hazard_by_dtxsid_batch <- function(DTXSID = NULL,
Server = hazard_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -450,8 +450,8 @@ get_skin_eye_hazard_batch_old <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -501,7 +501,7 @@ get_skin_eye_hazard_batch_old <- function(DTXSID = NULL,
#' @return A named list of data.frames containing skin and eye hazard data for
#' each input DTXSID.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull skin eye hazard data for multiples chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_skin_eye_hazard <- get_skin_eye_hazard_batch(DTXSID = dtxsid)
@@ -512,8 +512,8 @@ get_skin_eye_hazard_batch <- function(DTXSID = NULL,
Server = hazard_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -596,8 +596,8 @@ get_cancer_hazard_batch_old <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -647,7 +647,7 @@ get_cancer_hazard_batch_old <- function(DTXSID = NULL,
#' @return A data.table containing cancer hazard and
#' related data for each input DTXSID.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull cancer hazard data for multiples chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_cancer_hazard <- get_cancer_hazard_batch(DTXSID = dtxsid)
@@ -658,8 +658,8 @@ get_cancer_hazard_batch <- function(DTXSID = NULL,
Server = hazard_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -737,8 +737,8 @@ get_genetox_summary_batch_old <- function(DTXSID = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -789,7 +789,7 @@ get_genetox_summary_batch_old <- function(DTXSID = NULL,
#' @return A data.table of genetox summary data for each input
#' DTXSID.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull genetox summary data for multiples chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_genetox_summary_hazard <- get_genetox_summary_batch(DTXSID = dtxsid)
@@ -800,8 +800,8 @@ get_genetox_summary_batch <- function(DTXSID = NULL,
Server = hazard_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -882,8 +882,8 @@ get_genetox_details_batch_old <- function(DTXSID = NULL,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -934,7 +934,7 @@ get_genetox_details_batch_old <- function(DTXSID = NULL,
#' @return A data.table of genetox detail data for each input
#' DTXSID.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull genetox details data for multiples chemicals
#' dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
#' dtxsid_genetox_details_hazard <- get_genetox_details_batch(DTXSID = dtxsid)
@@ -945,8 +945,8 @@ get_genetox_details_batch <- function(DTXSID = NULL,
Server = hazard_api_server,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
diff --git a/R/hazard-APIs.R b/R/hazard-APIs.R
index 20285b7e..fe7c1399 100644
--- a/R/hazard-APIs.R
+++ b/R/hazard-APIs.R
@@ -7,7 +7,7 @@
#'
#' @return A data.frame containing chemical (human and eco) hazard data
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull hazard data for BPA
#' bpa <- get_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')
@@ -18,8 +18,8 @@ get_hazard_by_dtxsid <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -56,7 +56,7 @@ get_hazard_by_dtxsid <- function(DTXSID = NULL,
#'
#' @return A data.frame containing chemical human hazard data
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull human hazard data for BPA
#' bpa_human <- get_human_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')
@@ -67,8 +67,8 @@ get_human_hazard_by_dtxsid <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -104,7 +104,7 @@ get_human_hazard_by_dtxsid <- function(DTXSID = NULL,
#'
#' @return A data.frame containing chemical (ecotox) hazard data
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull ecotox hazard data for BPA
#' bpa_ecotox <- get_ecotox_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')
@@ -115,8 +115,8 @@ get_ecotox_hazard_by_dtxsid <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -153,7 +153,7 @@ get_ecotox_hazard_by_dtxsid <- function(DTXSID = NULL,
#'
#' @return A data.frame containing skin and eye hazard data.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull skin and eye hazard data for BPA
#' bpa_skin_eye <- get_skin_eye_hazard_batch(DTXSID = 'DTXSID7020182')
@@ -164,8 +164,8 @@ get_skin_eye_hazard <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -201,7 +201,7 @@ get_skin_eye_hazard <- function(DTXSID = NULL,
#'
#' @return A data.frame of cancer hazard data related to the input DTXSID.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull cancer hazard data for BPA
#' bpa_cancer <- get_cancer_hazard(DTXSID = 'DTXSID7020182')
@@ -212,8 +212,8 @@ get_cancer_hazard <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -250,7 +250,7 @@ get_cancer_hazard <- function(DTXSID = NULL,
#'
#' @return A data.frame of genetox summary data related to the input DTXSID.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull genetox summary for BPA
#' bpa_genetox_summary <- get_genetox_summary(DTXSID = 'DTXSID7020182')
@@ -261,8 +261,8 @@ get_genetox_summary <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -299,7 +299,7 @@ get_genetox_summary <- function(DTXSID = NULL,
#'
#' @return A data.frame of genetox detail data related to the input DTXSID.
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Pull genetox details for BPA
#' bpa_genetox_details <- get_genetox_details(DTXSID = 'DTXSID7020182')
@@ -310,8 +310,8 @@ get_genetox_details <- function(DTXSID = NULL,
if (is.null(DTXSID))
stop('Please input a DTXSID!')
else if (is.null(API_key)){
- if (has_ccte_key()) {
- API_key <- ccte_key()
+ if (has_ctx_key()) {
+ API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
@@ -338,3 +338,18 @@ get_genetox_details <- function(DTXSID = NULL,
return()
}
+
+
+#' Hazard API Endpoint status
+#'
+#' @return Status of Hazard API Endpoints
+#' @export
+#'
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
+#' status <- get_hazard_endpoint_status()
+#' print(status)
+
+get_hazard_endpoint_status <- function(){
+ request <- httr::GET(url = paste0(hazard_api_server,"/health"))
+ return(request$status_code)
+}
diff --git a/R/register_ccte.R b/R/register_ctx.R
similarity index 77%
rename from R/register_ccte.R
rename to R/register_ctx.R
index 5ace4b24..b4817e4f 100644
--- a/R/register_ccte.R
+++ b/R/register_ctx.R
@@ -1,11 +1,12 @@
-#' Register a CCTE API
+#' Register a CTX API
#'
-#' This page contains documentation tools related to enabling CCTE API services
+#' This page contains documentation tools related to enabling CTX API services
#' in R.
#'
#' To obtain an API key and enable services, go to
-#' \url{https://api-ccte.epa.gov/docs/}. This documentation shows you how to
-#' obtain an API key to allow access to the CCTE APIs.
+#' \url{https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis}.
+#' This documentation shows you how to obtain an API key to allow access to the
+#' CTX APIs.
#'
#' To tell ccdR about your API key, use [register_ccdr()], e.g.
@@ -18,8 +19,8 @@
#'
#' Users should be aware that the API key, a string of garbled
#' characters/numbers/symbols, is a PRIVATE key - it uniquely identifies and
-#' authenticates you to CCTE's services. If anyone gets your API key, they can
-#' use it to masquerade as you to CCTE. To mitigate against users inadvertently
+#' authenticates you to CTX's services. If anyone gets your API key, they can
+#' use it to masquerade as you to CTX. To mitigate against users inadvertently
#' sharing their keys, by default ccdR never displays a user's key in messages
#' displayed to the console.
#'
@@ -46,20 +47,20 @@
#' * `register_ccdr()` has no return value but has the side effect of
#' storing the API key.
#'
-#' * `print.ccte_credentials()` has no return value and is an S3 method for
-#' printing the `ccte_credentials` class.
+#' * `print.ctx_credentials()` has no return value and is an S3 method for
+#' printing the `ctx_credentials` class.
#'
-#' * `ccte_key()` returns a string, either the stored API key or
+#' * `ctx_key()` returns a string, either the stored API key or
#' \code{NA_character_}.
#'
-#' * `has_ccte_key()` returns a Boolean.
+#' * `has_ctx_key()` returns a Boolean.
#' @name register_ccdr
#' @rdname register_ccdr
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Check if API key is showing
#' showing_key()
@@ -76,7 +77,7 @@ showing_key <- function() {
#' @rdname register_ccdr
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Toggle API key to display
#' ccdr_show_api_key()
@@ -90,7 +91,7 @@ ccdr_show_api_key <- function() {
#' @rdname register_ccdr
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Toggle API key to be hidden
#' ccdr_hide_api_key()
@@ -104,7 +105,7 @@ ccdr_hide_api_key <- function() {
#' @rdname register_ccdr
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Register key for this session
#' register_ccdr(key = 'YOUR API KEY')
#' # Register key over sessions
@@ -171,13 +172,13 @@ register_ccdr <- function(key, write = FALSE) {
#
# set key in current session
.pkgenv[["api"]] <- key
- #Sys.setenv('CCTE_API_KEY' = key)
+ #Sys.setenv('CTX_API_KEY' = key)
} else if (!missing(key) && !write) {
# set key in current session
.pkgenv[["api"]] <- key
- #Sys.setenv('CCTE_API_KEY' = key)
+ #Sys.setenv('CTX_API_KEY' = key)
}
@@ -197,24 +198,24 @@ register_ccdr <- function(key, write = FALSE) {
#' @rdname register_ccdr
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
-#' # Print function for ccte_credentials class
-#' print.ccte_credentials()
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
+#' # Print function for ctx_credentials class
+#' print.ctx_credentials()
-print.ccte_credentials <- function(...) {
- cat('Key -', if (!has_ccte_key()) '' else {if(showing_key()) ccte_key() else 'xxx' }, '\n')
+print.ctx_credentials <- function(...) {
+ cat('Key -', if (!has_ctx_key()) '' else {if(showing_key()) ctx_key() else 'xxx' }, '\n')
}
#' @rdname register_ccdr
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
-#' # Display ccte API key
-#' ccte_key()
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
+#' # Display ctx API key
+#' ctx_key()
-ccte_key <- function() {
- key <- .pkgenv[["api"]] #Sys.getenv('CCTE_API_KEY')
+ctx_key <- function() {
+ key <- .pkgenv[["api"]] #Sys.getenv('CTX_API_KEY')
if (key == '') {
return(NA_character_)
@@ -226,11 +227,11 @@ ccte_key <- function() {
#' @rdname register_ccdr
#' @export
-#' @examplesIf has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+#' @examplesIf has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
#' # Check whether API key is registered
-#' has_ccte_key()
+#' has_ctx_key()
-has_ccte_key <- function () !is.na(ccte_key())
+has_ctx_key <- function () !is.na(ctx_key())
diff --git a/README.Rmd b/README.Rmd
index 7c7f39c5..b62b553a 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -16,9 +16,12 @@ knitr::opts_chunk$set(
# ccdR
+[](https://cran.r-project.org/package=ccdR)
+[](https://cranlogs.r-pkg.org/badges/last-month/ccdR?color=7BAFD4)
-The goal of ccdR is to provide R users a set of functions to access the [CCTE API](https://api-ccte.epa.gov/docs/index.html) without requiring extensive experience interacting directly with APIs.
+The goal of ccdR is to provide R users a set of functions to access the [CTX APIs](https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis)
+without requiring extensive experience interacting directly with APIs.
## Installation
@@ -39,4 +42,4 @@ install.packages('ccdR')
```
-Disclaimer: You won't need a API key to install the ccdR package, but will need to supply an API key to use ccdR. Please visit [CCTE API](https://api-ccte.epa.gov/docs/index.html) to request an API key.
+Disclaimer: You won't need a API key to install the ccdR package, but will need to supply an API key to use ccdR. Please visit [CTX APIs](https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis) to request an API key.
diff --git a/README.md b/README.md
index 5a18662c..58f9c864 100644
--- a/README.md
+++ b/README.md
@@ -4,11 +4,16 @@
# ccdR
+
+[](https://cran.r-project.org/package=ccdR)
+[](https://cranlogs.r-pkg.org/badges/last-month/ccdR?color=7BAFD4)
The goal of ccdR is to provide R users a set of functions to access the
-[CCTE API](https://api-ccte.epa.gov/docs/index.html) without requiring
-extensive experience interacting directly with APIs.
+[CTX
+APIs](https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis)
+without requiring extensive experience interacting directly with APIs.
## Installation
@@ -20,7 +25,7 @@ if (!library(devtools, logical.return = TRUE)){
library(devtools)
}
-devtools::install_github("USEPA/ccdR")
+devtools::install_gitub("USEPA/ccdR")
```
You can install from CRAN using the following:
@@ -30,5 +35,6 @@ install.packages('ccdR')
```
Disclaimer: You won’t need a API key to install the ccdR package, but
-will need to supply an API key to use ccdR. Please visit [CCTE
-API](https://api-ccte.epa.gov/docs/index.html) to request an API key.
+will need to supply an API key to use ccdR. Please visit [CTX
+APIs](https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis)
+to request an API key.
diff --git a/man/ccdr_options.Rd b/man/ccdr_options.Rd
index 9da3061f..bf97fe89 100644
--- a/man/ccdr_options.Rd
+++ b/man/ccdr_options.Rd
@@ -29,20 +29,20 @@ of setting options used by other functions.
\description{
ccdr stores options as a named list in R's global options, i.e.
\code{getOption('ccdr')}. It currently stores two such options, one for CCTE
-credentialing and one to supress private API information in the URLs printed
+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
\code{\link[=register_ccdr]{register_ccdr()}}.
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Set ccdr options
set_ccdr_option('display_api_key' = FALSE)
\dontshow{\}) # examplesIf}
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Check if there are options registered to 'ccdr'
has_ccdr_options()
\dontshow{\}) # examplesIf}
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Check if a specific option is registered for 'ccdr'
has_ccdr_option('display_api_key')
\dontshow{\}) # examplesIf}
diff --git a/man/chemical_contains.Rd b/man/chemical_contains.Rd
index 7bbf6036..f397d4c7 100644
--- a/man/chemical_contains.Rd
+++ b/man/chemical_contains.Rd
@@ -33,7 +33,7 @@ parameters
Chemical contains
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals that contain substring
substring_chemicals <- chemical_contains(word = 'TXSID702018')
\dontshow{\}) # examplesIf}
diff --git a/man/chemical_contains_batch.Rd b/man/chemical_contains_batch.Rd
index 03ee5714..b73669c4 100644
--- a/man/chemical_contains_batch.Rd
+++ b/man/chemical_contains_batch.Rd
@@ -33,7 +33,7 @@ the query parameters
Chemical contains batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals that contain substrings
substring_chemicals <- chemical_contains_batch(word_list = c('TXDIS702018',
'DTXSID70201'))
diff --git a/man/chemical_equal.Rd b/man/chemical_equal.Rd
index a2fb804c..a5e3aca7 100644
--- a/man/chemical_equal.Rd
+++ b/man/chemical_equal.Rd
@@ -29,7 +29,7 @@ parameters
Chemical equal
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals with matching DTXSID
bpa_dtxsid <- chemical_equal(word = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/chemical_equal_batch.Rd b/man/chemical_equal_batch.Rd
index 6a4e4324..87cf8b6f 100644
--- a/man/chemical_equal_batch.Rd
+++ b/man/chemical_equal_batch.Rd
@@ -29,7 +29,7 @@ the query parameters
Chemical equal batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals that match input strings
bpa <- chemical_equal_batch(word_list = c('DTXSID7020182', 'DTXCID30182'))
\dontshow{\}) # examplesIf}
diff --git a/man/chemical_starts_with.Rd b/man/chemical_starts_with.Rd
index bb2ecd5b..c01b7bc8 100644
--- a/man/chemical_starts_with.Rd
+++ b/man/chemical_starts_with.Rd
@@ -34,7 +34,7 @@ parameters
Chemical starts with
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals that start with a fragment DTXSID
dtxsid_fragment <- chemical_starts_with(word = 'DTXSID702018')
\dontshow{\}) # examplesIf}
diff --git a/man/chemical_starts_with_batch.Rd b/man/chemical_starts_with_batch.Rd
index 10f35fed..0c1ba60a 100644
--- a/man/chemical_starts_with_batch.Rd
+++ b/man/chemical_starts_with_batch.Rd
@@ -33,7 +33,7 @@ the query parameters
Chemical starts with batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals that start with given substrings
bpa_substrings <- chemical_starts_with_batch(word_list = c('DTXSID702018',
'DTXCID3018'))
diff --git a/man/get_all_assays.Rd b/man/get_all_assays.Rd
index 8369d38e..641d5f32 100644
--- a/man/get_all_assays.Rd
+++ b/man/get_all_assays.Rd
@@ -24,7 +24,7 @@ A data.frame containing all the assays and associated information
Retrieve all assays
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Retrieve all assays
assays <- get_all_assays()
\dontshow{\}) # examplesIf}
diff --git a/man/get_all_public_chemical_lists.Rd b/man/get_all_public_chemical_lists.Rd
index 31c3ba31..671e6d0c 100644
--- a/man/get_all_public_chemical_lists.Rd
+++ b/man/get_all_public_chemical_lists.Rd
@@ -24,13 +24,13 @@ value.}
}
\value{
A data.frame containing information on all public chemical lists
-available from the CCTE chemical api.
+available from the CTX chemical api.
}
\description{
Get all public chemical lists
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull all chemical lists
all_lists <- get_all_public_chemical_lists()
\dontshow{\}) # examplesIf}
diff --git a/man/get_annotation_by_aeid.Rd b/man/get_annotation_by_aeid.Rd
index bc410806..7f7c3a58 100644
--- a/man/get_annotation_by_aeid.Rd
+++ b/man/get_annotation_by_aeid.Rd
@@ -28,7 +28,7 @@ input AEID parameter
Retrieve annotations for AEID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Retrieve annotation for an assay
annotation <- get_annotation_by_aeid(AEID = 159)
\dontshow{\}) # examplesIf}
diff --git a/man/get_annotation_by_aeid_batch.Rd b/man/get_annotation_by_aeid_batch.Rd
index d41d81e9..fdec77e0 100644
--- a/man/get_annotation_by_aeid_batch.Rd
+++ b/man/get_annotation_by_aeid_batch.Rd
@@ -31,7 +31,7 @@ assays with AEID matching the input parameter.
Retrieve annotations for AEID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Get annotations for multiple aeids
aeid_annotations <- get_annotation_by_aeid_batch(AEID = c(159, 160))
\dontshow{\}) # examplesIf}
diff --git a/man/get_bioactivity_details.Rd b/man/get_bioactivity_details.Rd
index 863f093d..3252e9be 100644
--- a/man/get_bioactivity_details.Rd
+++ b/man/get_bioactivity_details.Rd
@@ -37,7 +37,7 @@ identifier matching the input parameter.
Retrieve bioactivity data from DTXSID, AEID, SPID, or m4id
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull BPA bioactivity details
bpa <- get_bioactivity_details(DTXSID = 'DTXSID7020182')
# Pull assay bioactivity details
diff --git a/man/get_bioactivity_details_batch.Rd b/man/get_bioactivity_details_batch.Rd
index dfe4ca2b..5e92c21d 100644
--- a/man/get_bioactivity_details_batch.Rd
+++ b/man/get_bioactivity_details_batch.Rd
@@ -40,7 +40,7 @@ the chemicals with DTXSID or assays with AEID matching the input parameter.
Retrieve bioactivity data from DTXSID or AEID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull bioactivity details for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
batch_bioactivity <- get_bioactivity_details_batch(DTXSID = dtxsid)
diff --git a/man/get_bioactivity_endpoint_status.Rd b/man/get_bioactivity_endpoint_status.Rd
new file mode 100644
index 00000000..d2194307
--- /dev/null
+++ b/man/get_bioactivity_endpoint_status.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bioactivity-APIs.R
+\name{get_bioactivity_endpoint_status}
+\alias{get_bioactivity_endpoint_status}
+\title{Bioactivity API Endpoint status}
+\usage{
+get_bioactivity_endpoint_status()
+}
+\value{
+Status of Bioactivity API Endpoints
+}
+\description{
+Bioactivity API Endpoint status
+}
+\examples{
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+status <- get_bioactivity_endpoint_status()
+print(status)
+\dontshow{\}) # examplesIf}
+}
diff --git a/man/get_bioactivity_summary.Rd b/man/get_bioactivity_summary.Rd
index 817bbc2f..88d05f0b 100644
--- a/man/get_bioactivity_summary.Rd
+++ b/man/get_bioactivity_summary.Rd
@@ -28,7 +28,7 @@ input AEID
Retrieve bioactivity summary for AEID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull an assay bioactivity summary
aeid_1386 <- get_bioactivity_summary(AEID = 1386)
\dontshow{\}) # examplesIf}
diff --git a/man/get_bioactivity_summary_batch.Rd b/man/get_bioactivity_summary_batch.Rd
index 619fa7be..63bfaf61 100644
--- a/man/get_bioactivity_summary_batch.Rd
+++ b/man/get_bioactivity_summary_batch.Rd
@@ -31,7 +31,7 @@ information for the assays with AEID matching the input parameter.
Retrieve bioactivity summary data from AEID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Get bioactivity summary for multiple aeids
aeids <- get_bioactivity_summary_batch(AEID = c(159, 160))
\dontshow{\}) # examplesIf}
diff --git a/man/get_cancer_hazard.Rd b/man/get_cancer_hazard.Rd
index b0a66cc5..e1626531 100644
--- a/man/get_cancer_hazard.Rd
+++ b/man/get_cancer_hazard.Rd
@@ -27,7 +27,7 @@ A data.frame of cancer hazard data related to the input DTXSID.
Get cancer hazard
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull cancer hazard data for BPA
bpa_cancer <- get_cancer_hazard(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_cancer_hazard_batch.Rd b/man/get_cancer_hazard_batch.Rd
index f3cb024f..2eea9ecc 100644
--- a/man/get_cancer_hazard_batch.Rd
+++ b/man/get_cancer_hazard_batch.Rd
@@ -31,7 +31,7 @@ related data for each input DTXSID.
Get cancer hazard batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull cancer hazard data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_cancer_hazard <- get_cancer_hazard_batch(DTXSID = dtxsid)
diff --git a/man/get_chem_info.Rd b/man/get_chem_info.Rd
index 4e2b4acb..f3b07cba 100644
--- a/man/get_chem_info.Rd
+++ b/man/get_chem_info.Rd
@@ -33,7 +33,7 @@ DTXSID matching the input parameter.
Retrieve chemical information
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical information for BPA
bpa <- get_chem_info(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_chem_info_batch.Rd b/man/get_chem_info_batch.Rd
index 10f422f1..97f398ac 100644
--- a/man/get_chem_info_batch.Rd
+++ b/man/get_chem_info_batch.Rd
@@ -37,7 +37,7 @@ DTXSID matching the input parameter.
Retrieve chemical information in batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical info for multiple chemicals
chem_info <- get_chem_info_batch(DTXSID = c('DTXSID7020182',
'DTXSID2021315'))
diff --git a/man/get_chemical_by_property_range.Rd b/man/get_chemical_by_property_range.Rd
index 5cf3b714..9d941b6b 100644
--- a/man/get_chemical_by_property_range.Rd
+++ b/man/get_chemical_by_property_range.Rd
@@ -35,7 +35,7 @@ the search criteria.
Get chemicals by property and its value range
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals with a given property in a set range
density <- get_chemical_by_property_range(start = 1.311, end = 1.313,
property = 'Density')
diff --git a/man/get_chemical_by_property_range_batch.Rd b/man/get_chemical_by_property_range_batch.Rd
index 8a00b40d..a705e8b5 100644
--- a/man/get_chemical_by_property_range_batch.Rd
+++ b/man/get_chemical_by_property_range_batch.Rd
@@ -34,7 +34,7 @@ chemicals matching the search criteria.
Retrieve chemicals by property and value range in batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals by property ranges
prop_ranges <- get_chemical_by_property_range_batch(start_list = c(1.311,
211.99),
diff --git a/man/get_chemical_details.Rd b/man/get_chemical_details.Rd
index dc8589c3..a7aa2243 100644
--- a/man/get_chemical_details.Rd
+++ b/man/get_chemical_details.Rd
@@ -39,7 +39,7 @@ DTXSID matching the input parameter.
Retrieve chemical details from DTXSID of DTXCID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical details for BPA
bpa <- get_chemical_details(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_chemical_details_batch.Rd b/man/get_chemical_details_batch.Rd
index 24104305..a3550cf9 100644
--- a/man/get_chemical_details_batch.Rd
+++ b/man/get_chemical_details_batch.Rd
@@ -40,7 +40,7 @@ matching the input parameter.
Retrieve chemical details from DTXSID of DTXCID in batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical details for multiple chemicals by dtxsid
dtxsids <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_details <- get_chemical_details_batch(DTXSID = dtxsid)
diff --git a/man/get_chemical_endpoint_status.Rd b/man/get_chemical_endpoint_status.Rd
index 5626d730..c0ef67e8 100644
--- a/man/get_chemical_endpoint_status.Rd
+++ b/man/get_chemical_endpoint_status.Rd
@@ -13,7 +13,7 @@ Status of Chemical API Endpoints
Chemical API Endpoint status
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
status <- get_chemical_endpoint_status()
print(status)
\dontshow{\}) # examplesIf}
diff --git a/man/get_chemical_image.Rd b/man/get_chemical_image.Rd
index 7071f653..6f8c6e09 100644
--- a/man/get_chemical_image.Rd
+++ b/man/get_chemical_image.Rd
@@ -39,7 +39,7 @@ displaying this, one may use \code{png::writePNG()} or
Get image file by DTXSID or DTXCID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical image for BPA by dtxsid
bpa_image_matrix <- get_chemical_image(DTXSID = 'DTXSID7020182')
if (requireNamespace("countcolors", quietly = TRUE)){
diff --git a/man/get_chemical_image_batch.Rd b/man/get_chemical_image_batch.Rd
index 41232c4c..74fc4a4a 100644
--- a/man/get_chemical_image_batch.Rd
+++ b/man/get_chemical_image_batch.Rd
@@ -39,7 +39,7 @@ displaying an image, one may use \code{png::writePNG()} or
Get image file by DTXSID or DTXCID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull images for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
images <- get_chemical_image_batch(DTXSID = dtxsid)
diff --git a/man/get_chemical_lists_by_type.Rd b/man/get_chemical_lists_by_type.Rd
index 2acc130e..64506c7c 100644
--- a/man/get_chemical_lists_by_type.Rd
+++ b/man/get_chemical_lists_by_type.Rd
@@ -34,7 +34,7 @@ criteria.
Get chemical lists by type
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical lists by type
federal <- get_chemical_lists_by_type(type = 'Federal')
\dontshow{\}) # examplesIf}
diff --git a/man/get_chemical_lists_by_type_batch.Rd b/man/get_chemical_lists_by_type_batch.Rd
index 96ecd80d..7707d204 100644
--- a/man/get_chemical_lists_by_type_batch.Rd
+++ b/man/get_chemical_lists_by_type_batch.Rd
@@ -35,7 +35,7 @@ meet the search criteria.
Get chemical lists by type batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical lists by type
federal_state <- get_chemical_lists_by_type_batch(type_list = c('Federal',
'State'))
diff --git a/man/get_chemical_mol.Rd b/man/get_chemical_mol.Rd
index 2512677a..d8d63150 100644
--- a/man/get_chemical_mol.Rd
+++ b/man/get_chemical_mol.Rd
@@ -30,7 +30,7 @@ A character string giving a mol file representation
Get mol file by DTXSID or DTXCID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull mol file for BPA by dtxsid
bpa_mol <- get_chemical_mol(DTXSID = 'DTXSID7020182')
# Pull mol file for BPA by dtxcid
diff --git a/man/get_chemical_mol_batch.Rd b/man/get_chemical_mol_batch.Rd
index 553d8888..da8e94bb 100644
--- a/man/get_chemical_mol_batch.Rd
+++ b/man/get_chemical_mol_batch.Rd
@@ -31,7 +31,7 @@ of the given input chemicals.
Get mol file by DTXSID or DTXCID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull mol files for multiple chemicals by DTXSID
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
mol_files <- get_chemical_mol_batch(DTXSID = dtxsid)
diff --git a/man/get_chemical_mrv.Rd b/man/get_chemical_mrv.Rd
index e367b0e5..e7230c72 100644
--- a/man/get_chemical_mrv.Rd
+++ b/man/get_chemical_mrv.Rd
@@ -30,7 +30,7 @@ XML file format for representing a mrv file.
Get mrv file by DTXSID or DTXCID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull mrv file for BPA by dtxsid
bpa_mrv <- get_chemical_mrv(DTXSID = 'DTXSID7020182')
# Pull mrv file for BPA by dtxcid
diff --git a/man/get_chemical_mrv_batch.Rd b/man/get_chemical_mrv_batch.Rd
index dd616850..91162ce6 100644
--- a/man/get_chemical_mrv_batch.Rd
+++ b/man/get_chemical_mrv_batch.Rd
@@ -31,7 +31,7 @@ chemicals.
Ger mrv file by DTXSID or DTXCID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull mrv files for multiple chemicals by DTXSID
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
mrv_files <- get_chemical_mrv_batch(DTXSID = dtxsid)
diff --git a/man/get_chemical_synonym.Rd b/man/get_chemical_synonym.Rd
index e77364bc..73e46614 100644
--- a/man/get_chemical_synonym.Rd
+++ b/man/get_chemical_synonym.Rd
@@ -27,7 +27,7 @@ A named list of synonym information for the input DTXSID
Get chemical synonym
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull synonyms for BPA
bpa_synonym <- get_chemical_synonym(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_chemical_synonym_batch.Rd b/man/get_chemical_synonym_batch.Rd
index 865e4a77..894c4391 100644
--- a/man/get_chemical_synonym_batch.Rd
+++ b/man/get_chemical_synonym_batch.Rd
@@ -28,7 +28,7 @@ DTXSID.
Get chemical synonym batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull synonyms for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
batch_synonyms <- get_chemical_synonym_batch(DTXSID = dtxsid)
diff --git a/man/get_chemicals_in_list.Rd b/man/get_chemicals_in_list.Rd
index 23c7feeb..3a8ef8a5 100644
--- a/man/get_chemicals_in_list.Rd
+++ b/man/get_chemicals_in_list.Rd
@@ -27,7 +27,7 @@ A data.frame of the chemical list
Get chemicals in a given chemical list
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Retrieve chemicals contained in chemical list 'CCL4'
ccl4_chemicals <- get_chemicals_in_list(list_name = 'CCL4')
\dontshow{\}) # examplesIf}
diff --git a/man/get_chemicals_in_list_batch.Rd b/man/get_chemicals_in_list_batch.Rd
index c8a7cd15..8288349a 100644
--- a/man/get_chemicals_in_list_batch.Rd
+++ b/man/get_chemicals_in_list_batch.Rd
@@ -28,7 +28,7 @@ corresponding chemical lists.
Get chemicals in a given chemical list batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals in lists for multiple lists
chemicals_in_lists <- get_chemicals_in_list_batch(list_names = c('CCL4', 'NATADB'))
\dontshow{\}) # examplesIf}
diff --git a/man/get_ecotox_hazard_by_dtxsid.Rd b/man/get_ecotox_hazard_by_dtxsid.Rd
index a6144286..8421ed71 100644
--- a/man/get_ecotox_hazard_by_dtxsid.Rd
+++ b/man/get_ecotox_hazard_by_dtxsid.Rd
@@ -27,7 +27,7 @@ A data.frame containing chemical (ecotox) hazard data
Get ecotox hazard data by DTXSID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull ecotox hazard data for BPA
bpa_ecotox <- get_ecotox_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_ecotox_hazard_by_dtxsid_batch.Rd b/man/get_ecotox_hazard_by_dtxsid_batch.Rd
index 26e46dd5..d72be5dc 100644
--- a/man/get_ecotox_hazard_by_dtxsid_batch.Rd
+++ b/man/get_ecotox_hazard_by_dtxsid_batch.Rd
@@ -30,7 +30,7 @@ A data.table containing chemical ecotox hazard data.
Get ecotox hazard data by DTXSID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull ecotox hazard data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_ecotox_hazard <- get_ecotox_hazard_by_dtxsid_batch(DTXSID = dtxsid)
diff --git a/man/get_exposure_endpoint_status.Rd b/man/get_exposure_endpoint_status.Rd
index 7bfebc06..a90e2f6f 100644
--- a/man/get_exposure_endpoint_status.Rd
+++ b/man/get_exposure_endpoint_status.Rd
@@ -13,7 +13,7 @@ Status of Exposure API Endpoints
Exposure API Endpoint status
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
status <- get_exposure_endpoint_status()
print(status)
\dontshow{\}) # examplesIf}
diff --git a/man/get_exposure_functional_use.Rd b/man/get_exposure_functional_use.Rd
index 0d9d2d6d..2f435138 100644
--- a/man/get_exposure_functional_use.Rd
+++ b/man/get_exposure_functional_use.Rd
@@ -27,7 +27,7 @@ A data.frame of functional use data.
Retrieve exposure related functional use data
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull functional use data for BPA
bpa <- get_exposure_functional_use(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_exposure_functional_use_batch.Rd b/man/get_exposure_functional_use_batch.Rd
index 9c7fc8e3..b68ce258 100644
--- a/man/get_exposure_functional_use_batch.Rd
+++ b/man/get_exposure_functional_use_batch.Rd
@@ -32,7 +32,7 @@ data for each input DTXSID.
Retrieve exposure related functional use data batch
}
\examples{
-has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
# Pull exposure functional use data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_func_use <- get_exposure_functional_use_batch(DTXSID = dtxsid)
diff --git a/man/get_exposure_functional_use_category.Rd b/man/get_exposure_functional_use_category.Rd
index 20171f3c..ae783f23 100644
--- a/man/get_exposure_functional_use_category.Rd
+++ b/man/get_exposure_functional_use_category.Rd
@@ -24,7 +24,7 @@ A data.frame of functional use categories.
Retrieve functional use categories
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull functional use category data for BPA
functional_use_categories <- get_exposure_functional_use_category()
\dontshow{\}) # examplesIf}
diff --git a/man/get_exposure_functional_use_probability.Rd b/man/get_exposure_functional_use_probability.Rd
index 58491f5c..b8f4f053 100644
--- a/man/get_exposure_functional_use_probability.Rd
+++ b/man/get_exposure_functional_use_probability.Rd
@@ -28,7 +28,7 @@ exposure related to functional use.
Retrieve probability of exposure for functional use category
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull functional use probability data for BPA
bpa <- get_exposure_functional_use_probability(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_exposure_functional_use_probability_batch.Rd b/man/get_exposure_functional_use_probability_batch.Rd
index d9c4fe5e..5187ac60 100644
--- a/man/get_exposure_functional_use_probability_batch.Rd
+++ b/man/get_exposure_functional_use_probability_batch.Rd
@@ -33,7 +33,7 @@ categories that have probability of 0
Retrieve exposure functional use probability data batch
}
\examples{
-has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
# Pull exposure functional use probability data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_func_use_prob <- get_exposure_functional_use_batch(DTXSID = dtxsid)
diff --git a/man/get_exposure_list_presence_tags.Rd b/man/get_exposure_list_presence_tags.Rd
index 1bff2bf4..07f7fd1e 100644
--- a/man/get_exposure_list_presence_tags.Rd
+++ b/man/get_exposure_list_presence_tags.Rd
@@ -24,7 +24,7 @@ A data.frame with all the list presence tags and associated data.
Retrieve list presence tags
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull list presence tags
tags <- get_exposure_list_presence_tags()
\dontshow{\}) # examplesIf}
diff --git a/man/get_exposure_list_presence_tags_by_dtxsid.Rd b/man/get_exposure_list_presence_tags_by_dtxsid.Rd
index 567fdad0..68745a8e 100644
--- a/man/get_exposure_list_presence_tags_by_dtxsid.Rd
+++ b/man/get_exposure_list_presence_tags_by_dtxsid.Rd
@@ -27,7 +27,7 @@ A data.frame of document information and list presence tags
Retrieve document data and list presence tags for a chemical
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull list presence tags for BPA
bpa <- get_exposure_list_presence_tags(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_exposure_list_presence_tags_by_dtxsid_batch.Rd b/man/get_exposure_list_presence_tags_by_dtxsid_batch.Rd
index 1bda67d2..483b6952 100644
--- a/man/get_exposure_list_presence_tags_by_dtxsid_batch.Rd
+++ b/man/get_exposure_list_presence_tags_by_dtxsid_batch.Rd
@@ -32,7 +32,7 @@ tags use data for each input DTXSID.
Retrieve document data and list presence tags for chemicals batch
}
\examples{
-has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
# Pull exposure functional use data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
exp_list_tags <- get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = dtxsid)
diff --git a/man/get_exposure_product_data.Rd b/man/get_exposure_product_data.Rd
index 2a1ef35d..92421c2b 100644
--- a/man/get_exposure_product_data.Rd
+++ b/man/get_exposure_product_data.Rd
@@ -28,7 +28,7 @@ given chemical
Retrieve product data for exposure purposes
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull exposure product data for BPA
bpa <- get_exposure_product_data(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_exposure_product_data_batch.Rd b/man/get_exposure_product_data_batch.Rd
index f814ac26..542dc791 100644
--- a/man/get_exposure_product_data_batch.Rd
+++ b/man/get_exposure_product_data_batch.Rd
@@ -32,7 +32,7 @@ data for each input DTXSID.
Retrieve product data for exposure purposes batch
}
\examples{
-has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')
+has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')
# Pull exposure functional use data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_product_data <- get_exposure_product_data_batch(DTXSID = dtxsid)
diff --git a/man/get_exposure_product_data_puc.Rd b/man/get_exposure_product_data_puc.Rd
index fabd1940..a46b57e9 100644
--- a/man/get_exposure_product_data_puc.Rd
+++ b/man/get_exposure_product_data_puc.Rd
@@ -24,7 +24,7 @@ A data.frame consisting of all the product use categories
Retrieve product use categories related to exposure
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull product data use categories for BPA
puc_categories <- get_exposure_product_data_puc()
\dontshow{\}) # examplesIf}
diff --git a/man/get_fate_by_dtxsid.Rd b/man/get_fate_by_dtxsid.Rd
index a010b408..f10382e2 100644
--- a/man/get_fate_by_dtxsid.Rd
+++ b/man/get_fate_by_dtxsid.Rd
@@ -28,7 +28,7 @@ DTXSID matching the input parameter.
Get fate by DTXSID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical fate data for BPA
bpa <- get_fate_by_dtxsid(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_fate_by_dtxsid_batch.Rd b/man/get_fate_by_dtxsid_batch.Rd
index 712f376b..a18133af 100644
--- a/man/get_fate_by_dtxsid_batch.Rd
+++ b/man/get_fate_by_dtxsid_batch.Rd
@@ -31,7 +31,7 @@ with DTXSID matching the input parameter.
Retrieve chemical fate data in batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical fate by dtxsids
chemical_fates <- get_fate_by_dtxsid_batch(DTXSID = c('DTXSID7020182',
'DTXSID2021315'))
diff --git a/man/get_genetox_details.Rd b/man/get_genetox_details.Rd
index 06e5b7b8..8615b36e 100644
--- a/man/get_genetox_details.Rd
+++ b/man/get_genetox_details.Rd
@@ -27,7 +27,7 @@ A data.frame of genetox detail data related to the input DTXSID.
Get genetox details
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull genetox details for BPA
bpa_genetox_details <- get_genetox_details(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_genetox_details_batch.Rd b/man/get_genetox_details_batch.Rd
index da11f1ce..fe485043 100644
--- a/man/get_genetox_details_batch.Rd
+++ b/man/get_genetox_details_batch.Rd
@@ -31,7 +31,7 @@ DTXSID.
Get genetox details batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull genetox details data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_genetox_details_hazard <- get_genetox_details_batch(DTXSID = dtxsid)
diff --git a/man/get_genetox_summary.Rd b/man/get_genetox_summary.Rd
index bc0a5514..9307606c 100644
--- a/man/get_genetox_summary.Rd
+++ b/man/get_genetox_summary.Rd
@@ -27,7 +27,7 @@ A data.frame of genetox summary data related to the input DTXSID.
Get genetox summary
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull genetox summary for BPA
bpa_genetox_summary <- get_genetox_summary(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_genetox_summary_batch.Rd b/man/get_genetox_summary_batch.Rd
index 3602813c..e752a673 100644
--- a/man/get_genetox_summary_batch.Rd
+++ b/man/get_genetox_summary_batch.Rd
@@ -31,7 +31,7 @@ DTXSID.
Get genetox summary batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull genetox summary data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_genetox_summary_hazard <- get_genetox_summary_batch(DTXSID = dtxsid)
diff --git a/man/get_hazard_by_dtxsid.Rd b/man/get_hazard_by_dtxsid.Rd
index 85a81432..4a53a73d 100644
--- a/man/get_hazard_by_dtxsid.Rd
+++ b/man/get_hazard_by_dtxsid.Rd
@@ -27,7 +27,7 @@ A data.frame containing chemical (human and eco) hazard data
Get hazard data by DTXSID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull hazard data for BPA
bpa <- get_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_hazard_by_dtxsid_batch.Rd b/man/get_hazard_by_dtxsid_batch.Rd
index 3ac4bb2c..10c29874 100644
--- a/man/get_hazard_by_dtxsid_batch.Rd
+++ b/man/get_hazard_by_dtxsid_batch.Rd
@@ -31,7 +31,7 @@ input chemical.
Get hazard data by DTXSID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull hazard data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
batch_hazard <- get_hazard_by_dtxsid_batch(DTXSID = dtxsid)
diff --git a/man/get_hazard_endpoint_status.Rd b/man/get_hazard_endpoint_status.Rd
new file mode 100644
index 00000000..65834d38
--- /dev/null
+++ b/man/get_hazard_endpoint_status.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/hazard-APIs.R
+\name{get_hazard_endpoint_status}
+\alias{get_hazard_endpoint_status}
+\title{Hazard API Endpoint status}
+\usage{
+get_hazard_endpoint_status()
+}
+\value{
+Status of Hazard API Endpoints
+}
+\description{
+Hazard API Endpoint status
+}
+\examples{
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+status <- get_hazard_endpoint_status()
+print(status)
+\dontshow{\}) # examplesIf}
+}
diff --git a/man/get_human_hazard_by_dtxsid.Rd b/man/get_human_hazard_by_dtxsid.Rd
index ef4aedf1..56437575 100644
--- a/man/get_human_hazard_by_dtxsid.Rd
+++ b/man/get_human_hazard_by_dtxsid.Rd
@@ -27,7 +27,7 @@ A data.frame containing chemical human hazard data
Get human hazard data by DTXSID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull human hazard data for BPA
bpa_human <- get_human_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_human_hazard_by_dtxsid_batch.Rd b/man/get_human_hazard_by_dtxsid_batch.Rd
index 1765ffef..baaa5a02 100644
--- a/man/get_human_hazard_by_dtxsid_batch.Rd
+++ b/man/get_human_hazard_by_dtxsid_batch.Rd
@@ -30,7 +30,7 @@ A data.table containing chemical human hazard data.
Get human hazard data by DTXSID batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull human hazard data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_human_hazard <- get_human_hazard_by_dtxsid_batch(DTXSID = dtxsid)
diff --git a/man/get_inchi.Rd b/man/get_inchi.Rd
index d1a9cc9f..bce0207a 100644
--- a/man/get_inchi.Rd
+++ b/man/get_inchi.Rd
@@ -28,7 +28,7 @@ A string giving the associated inchi string.
Get InChI
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
bpa_inchi <- get_inchi(name = "Bisphenol A")
\dontshow{\}) # examplesIf}
}
diff --git a/man/get_inchikey.Rd b/man/get_inchikey.Rd
index f290fa3a..704ddf4c 100644
--- a/man/get_inchikey.Rd
+++ b/man/get_inchikey.Rd
@@ -28,7 +28,7 @@ A string giving the associated InChIKey.
Get InChIKey
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
bpa_inchikey <- get_inchikey(name = "Bisphenol A")
\dontshow{\}) # examplesIf}
}
diff --git a/man/get_lists_containing_chemical.Rd b/man/get_lists_containing_chemical.Rd
index c7398a87..d5750835 100644
--- a/man/get_lists_containing_chemical.Rd
+++ b/man/get_lists_containing_chemical.Rd
@@ -27,7 +27,7 @@ A list of names of chemical lists that contain the given chemical
Get chemical lists containing given chemical
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical lists containing BPA
bpa_lists <- get_lists_containing_chemical(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_lists_containing_chemical_batch.Rd b/man/get_lists_containing_chemical_batch.Rd
index 174313d0..86739cbd 100644
--- a/man/get_lists_containing_chemical_batch.Rd
+++ b/man/get_lists_containing_chemical_batch.Rd
@@ -27,7 +27,7 @@ A named list of chemical lists that contain the given chemicals.
Get chemical lists containing given chemical batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull lists containing chemicals for multiple chemicals
lists <- get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182',
'DTXSID2021315'))
diff --git a/man/get_msready_by_dtxcid.Rd b/man/get_msready_by_dtxcid.Rd
index cb3ebf31..e7ea0eaf 100644
--- a/man/get_msready_by_dtxcid.Rd
+++ b/man/get_msready_by_dtxcid.Rd
@@ -28,7 +28,7 @@ search criteria
Get msready by DTXCID
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals with matching DTXCID
dtxcid_msready <- get_msready_by_dtxcid(DTXSID = 'DTXCID30182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_msready_by_dtxcid_batch.Rd b/man/get_msready_by_dtxcid_batch.Rd
index c852e5b5..53755636 100644
--- a/man/get_msready_by_dtxcid_batch.Rd
+++ b/man/get_msready_by_dtxcid_batch.Rd
@@ -28,7 +28,7 @@ search criteria
Get msready by DTXCID batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull msready chemicals matching specific DTXCID
dtxcid_msready <- get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182',
'DTXCID001315'))
diff --git a/man/get_msready_by_formula.Rd b/man/get_msready_by_formula.Rd
index a5bb9726..7c7ca7e2 100644
--- a/man/get_msready_by_formula.Rd
+++ b/man/get_msready_by_formula.Rd
@@ -28,7 +28,7 @@ search criteria
Get msready by formula
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals that match input formula
mass_formula <- get_msready_by_formula(formula = 'C16H24N2O5S')
\dontshow{\}) # examplesIf}
diff --git a/man/get_msready_by_formula_batch.Rd b/man/get_msready_by_formula_batch.Rd
index c8cd7a20..20f97335 100644
--- a/man/get_msready_by_formula_batch.Rd
+++ b/man/get_msready_by_formula_batch.Rd
@@ -28,7 +28,7 @@ matching the search criteria
Get msready by formula batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull msready data for several chemical formulas
msready_data <- get_msready_by_formula_batch(formula_list = c('C16H24N2O5S',
'C15H16O2'))
diff --git a/man/get_msready_by_mass.Rd b/man/get_msready_by_mass.Rd
index 572947dc..a3340771 100644
--- a/man/get_msready_by_mass.Rd
+++ b/man/get_msready_by_mass.Rd
@@ -30,7 +30,7 @@ A list of DTXSIDs with msready mass falling within the given range.
Get msready by mass
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemicals with msready mass in given range
mass_range <- get_msready_by_mass(start = 200.9, end = 200.95)
\dontshow{\}) # examplesIf}
diff --git a/man/get_msready_by_mass_batch.Rd b/man/get_msready_by_mass_batch.Rd
index 9510afae..5ccf6496 100644
--- a/man/get_msready_by_mass_batch.Rd
+++ b/man/get_msready_by_mass_batch.Rd
@@ -31,7 +31,7 @@ falling within the given ranges.
Get ms ready by mass batch search
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull msready chemicals by mass ranges
msready_data <- get_msready_by_mass_batch(start_list = c(200.9, 200.95),
end_list = c(200.95, 201.00))
diff --git a/man/get_msready_by_mass_with_error_batch.Rd b/man/get_msready_by_mass_with_error_batch.Rd
index 816fb441..cc1778e3 100644
--- a/man/get_msready_by_mass_with_error_batch.Rd
+++ b/man/get_msready_by_mass_with_error_batch.Rd
@@ -31,7 +31,7 @@ mass value.
Get msready by mass and error offset
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
#Pull chemicals by msready mass and error offset
msready_data <- get_msready_by_mass_with_error_batch(masses = c(226, 228),
error = 4)
diff --git a/man/get_public_chemical_list_by_name.Rd b/man/get_public_chemical_list_by_name.Rd
index d1d40ac1..d6f0ef5d 100644
--- a/man/get_public_chemical_list_by_name.Rd
+++ b/man/get_public_chemical_list_by_name.Rd
@@ -34,7 +34,7 @@ use \code{\link{get_chemicals_in_list}}.
Get chemical list by name
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical list by list name
ccl4 <- get_public_chemical_list_by_name(list_name = 'CCL4')
\dontshow{\}) # examplesIf}
diff --git a/man/get_public_chemical_list_by_name_batch.Rd b/man/get_public_chemical_list_by_name_batch.Rd
index 6b869e92..1c4331b5 100644
--- a/man/get_public_chemical_list_by_name_batch.Rd
+++ b/man/get_public_chemical_list_by_name_batch.Rd
@@ -34,7 +34,7 @@ chemicals in a given list, use \code{\link{get_chemicals_in_list}}.
Get chemical list by name batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull chemical list information by list names
list_info <- get_public_chemical_list_by_name_batch(name_list = c('CCL4',
'NATADB'))
diff --git a/man/get_skin_eye_hazard.Rd b/man/get_skin_eye_hazard.Rd
index 97c1ca93..29c3343a 100644
--- a/man/get_skin_eye_hazard.Rd
+++ b/man/get_skin_eye_hazard.Rd
@@ -27,7 +27,7 @@ A data.frame containing skin and eye hazard data.
Get skin and eye hazard
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull skin and eye hazard data for BPA
bpa_skin_eye <- get_skin_eye_hazard_batch(DTXSID = 'DTXSID7020182')
\dontshow{\}) # examplesIf}
diff --git a/man/get_skin_eye_hazard_batch.Rd b/man/get_skin_eye_hazard_batch.Rd
index b31b07a2..3df1147e 100644
--- a/man/get_skin_eye_hazard_batch.Rd
+++ b/man/get_skin_eye_hazard_batch.Rd
@@ -31,7 +31,7 @@ each input DTXSID.
Get skin and eye hazard batch
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Pull skin eye hazard data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_skin_eye_hazard <- get_skin_eye_hazard_batch(DTXSID = dtxsid)
diff --git a/man/get_smiles.Rd b/man/get_smiles.Rd
index dfc07388..5e69bdce 100644
--- a/man/get_smiles.Rd
+++ b/man/get_smiles.Rd
@@ -28,7 +28,7 @@ A string giving a SMILES string for the input chemical.
Get Smiles
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
bpa_smiles <- get_smiles(name = "Bisphenol A")
\dontshow{\}) # examplesIf}
}
diff --git a/man/register_ccdr.Rd b/man/register_ccdr.Rd
index 9544aa26..35695bd0 100644
--- a/man/register_ccdr.Rd
+++ b/man/register_ccdr.Rd
@@ -1,14 +1,14 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/register_ccte.R
+% Please edit documentation in R/register_ctx.R
\name{register_ccdr}
\alias{register_ccdr}
\alias{showing_key}
\alias{ccdr_show_api_key}
\alias{ccdr_hide_api_key}
-\alias{print.ccte_credentials}
-\alias{ccte_key}
-\alias{has_ccte_key}
-\title{Register a CCTE API}
+\alias{print.ctx_credentials}
+\alias{ctx_key}
+\alias{has_ctx_key}
+\title{Register a CTX API}
\usage{
showing_key()
@@ -18,11 +18,11 @@ ccdr_hide_api_key()
register_ccdr(key, write = FALSE)
-\method{print}{ccte_credentials}(...)
+\method{print}{ctx_credentials}(...)
-ccte_key()
+ctx_key()
-has_ccte_key()
+has_ctx_key()
}
\arguments{
\item{key}{an API key}
@@ -40,21 +40,22 @@ changing the display settings of the API key.
changing the display settings of the API key.
\item \code{register_ccdr()} has no return value but has the side effect of
storing the API key.
-\item \code{print.ccte_credentials()} has no return value and is an S3 method for
-printing the \code{ccte_credentials} class.
-\item \code{ccte_key()} returns a string, either the stored API key or
+\item \code{print.ctx_credentials()} has no return value and is an S3 method for
+printing the \code{ctx_credentials} class.
+\item \code{ctx_key()} returns a string, either the stored API key or
\code{NA_character_}.
-\item \code{has_ccte_key()} returns a Boolean.
+\item \code{has_ctx_key()} returns a Boolean.
}
}
\description{
-This page contains documentation tools related to enabling CCTE API services
+This page contains documentation tools related to enabling CTX API services
in R.
}
\details{
To obtain an API key and enable services, go to
-\url{https://api-ccte.epa.gov/docs/}. This documentation shows you how to
-obtain an API key to allow access to the CCTE APIs.
+\url{https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis}.
+This documentation shows you how to obtain an API key to allow access to the
+CTX APIs.
To tell ccdR about your API key, use \code{\link[=register_ccdr]{register_ccdr()}}, e.g.
\code{register_ccdr(key = 'grbwigbwoginrowgbwibgdibdvinrginiwgo')} (that's a fake
@@ -65,8 +66,8 @@ sessions.
Users should be aware that the API key, a string of garbled
characters/numbers/symbols, is a PRIVATE key - it uniquely identifies and
-authenticates you to CCTE's services. If anyone gets your API key, they can
-use it to masquerade as you to CCTE. To mitigate against users inadvertently
+authenticates you to CTX's services. If anyone gets your API key, they can
+use it to masquerade as you to CTX. To mitigate against users inadvertently
sharing their keys, by default ccdR never displays a user's key in messages
displayed to the console.
@@ -79,34 +80,34 @@ ccdR we recommend a heightened sense of security and self-awareness: only use
trusted packages, do not save the API keys in script files, etc.
}
\examples{
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Check if API key is showing
showing_key()
\dontshow{\}) # examplesIf}
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Toggle API key to display
ccdr_show_api_key()
\dontshow{\}) # examplesIf}
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Toggle API key to be hidden
ccdr_hide_api_key()
\dontshow{\}) # examplesIf}
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Register key for this session
register_ccdr(key = 'YOUR API KEY')
# Register key over sessions
register_ccdr(key = 'YOUR API KEY', write = TRUE)
\dontshow{\}) # examplesIf}
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-# Print function for ccte_credentials class
-print.ccte_credentials()
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+# Print function for ctx_credentials class
+print.ctx_credentials()
\dontshow{\}) # examplesIf}
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-# Display ccte API key
-ccte_key()
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+# Display ctx API key
+ctx_key()
\dontshow{\}) # examplesIf}
-\dontshow{if (has_ccte_key() & is.na(ccte_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (has_ctx_key() & is.na(ctx_key() == 'FAKE_KEY')) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Check whether API key is registered
-has_ccte_key()
+has_ctx_key()
\dontshow{\}) # examplesIf}
}
diff --git a/tests/testthat/test-bioactivity-APIs-batch.R b/tests/testthat/test-bioactivity-APIs-batch.R
index 91c14bb4..534980d8 100644
--- a/tests/testthat/test-bioactivity-APIs-batch.R
+++ b/tests/testthat/test-bioactivity-APIs-batch.R
@@ -3,11 +3,11 @@ with_mock_dir("bioactivity-batch",{
# # Run register_ccdr(key = 'YOUR KEY', write = TRUE) prior to running tests
#
# #store env variable so tests don't overwrite
-# #tmp <- Sys.getenv("CCTE_API_KEY")
-# #on.exit(Sys.setenv("CCTE_API_KEY" = tmp))
-# #if(Sys.getenv("CCTE_API_KEY") == ""){
+# #tmp <- Sys.getenv("CTX_API_KEY")
+# #on.exit(Sys.setenv("CTX_API_KEY" = tmp))
+# #if(Sys.getenv("CTX_API_KEY") == ""){
# # #set env variable temporarily for testing
-# # Sys.setenv("CCTE_API_KEY" = "stored_api_key")
+# # Sys.setenv("CTX_API_KEY" = "stored_api_key")
# #}
# expect_message(get_bioactivity_details_batch(DTXSID = c('DTXSID8031865'), verbose = TRUE), 'Using stored API key!')
# expect_message(get_bioactivity_details_batch(DTXSID = c('DTXSID8031865'), API_key = 1, verbose = TRUE), 'Using stored API key!')
@@ -21,12 +21,12 @@ test_that('DTXSID/AEID errors', {
})
test_that('Rate limit warnings', {
- expect_warning(get_bioactivity_details_batch(DTXSID = c(''), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_bioactivity_details_batch(DTXSID = c(''), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_bioactivity_details_batch(DTXSID = c(''), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_bioactivity_details_batch(DTXSID = c(''), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
})
test_that('Return data types', {
expect_type(get_bioactivity_details_batch(DTXSID = c('DTXSID8031865'), API_key = ''), 'list')
- expect_type(get_bioactivity_details_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_bioactivity_details_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_bioactivity_details_batch(AEID = c(1), API_key = 'test_key'), 'list')
})})
diff --git a/tests/testthat/test-bioactivity-APIs.R b/tests/testthat/test-bioactivity-APIs.R
index 1fb15a76..810c0fa2 100644
--- a/tests/testthat/test-bioactivity-APIs.R
+++ b/tests/testthat/test-bioactivity-APIs.R
@@ -3,11 +3,11 @@ with_mock_dir("bioactivity",{
# test_that("Catch missing API", {
# # Run register_ccdr(key = 'YOUR KEY', write = TRUE) prior to running tests
# #store env variable so tests don't overwrite
-# # tmp <- Sys.getenv("CCTE_API_KEY")
-# # on.exit(Sys.setenv("CCTE_API_KEY" = tmp))
-# # if(Sys.getenv("CCTE_API_KEY") == ""){
+# # tmp <- Sys.getenv("CTX_API_KEY")
+# # on.exit(Sys.setenv("CTX_API_KEY" = tmp))
+# # if(Sys.getenv("CTX_API_KEY") == ""){
# # #set env variable temporarily for testing
-# # Sys.setenv("CCTE_API_KEY" = "stored_api_key")
+# # Sys.setenv("CTX_API_KEY" = "stored_api_key")
# # }
#
# expect_message(get_bioactivity_details(DTXSID = 'DTXSID8031865', verbose = TRUE), 'Using stored API key!')
@@ -19,8 +19,8 @@ test_that("DTXSID/AEID errors", {
})
test_that('Return data type', {
- #expect_type(get_bioactivity_details(DTXSID = 'DTXSID8031865', API_key = ccte_key()), 'list')
- expect_type(get_bioactivity_details(DTXSID = '', API_key = ccte_key()), 'NULL')
+ #expect_type(get_bioactivity_details(DTXSID = 'DTXSID8031865', API_key = ctx_key()), 'list')
+ expect_type(get_bioactivity_details(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_bioactivity_details(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
expect_type(get_bioactivity_details(AEID = 1), 'list')
#expect_type(get_bioactivity_details(AEID = 42, API_key = ''), 'NULL')
diff --git a/tests/testthat/test-chemical-APIs-batch.R b/tests/testthat/test-chemical-APIs-batch.R
index 1ea6c4b6..95b33e71 100644
--- a/tests/testthat/test-chemical-APIs-batch.R
+++ b/tests/testthat/test-chemical-APIs-batch.R
@@ -1,11 +1,11 @@
with_mock_dir("chemical-batch",{
# test_that("catch missing APIs", {
# #store env variable so tests don't overwrite
-# # tmp <- Sys.getenv("CCTE_API_KEY")
-# # on.exit(Sys.setenv("CCTE_API_KEY" = tmp))
-# # if(Sys.getenv("CCTE_API_KEY") == ""){
+# # tmp <- Sys.getenv("CTX_API_KEY")
+# # on.exit(Sys.setenv("CTX_API_KEY" = tmp))
+# # if(Sys.getenv("CTX_API_KEY") == ""){
# # #set env variable temporarily for testing
-# # Sys.setenv("CCTE_API_KEY" = "stored_api_key")
+# # Sys.setenv("CTX_API_KEY" = "stored_api_key")
# # }
# # Run register_ccdr(key = 'YOUR KEY', write = TRUE) prior to running tests
# expect_message(get_chemical_details_batch(DTXSID = c('DTXSID7020182'), verbose = TRUE), 'Using stored API key!')
@@ -82,44 +82,44 @@ test_that("DTXSID/DTXCID errors", {
})
test_that('Rate limit warnings', {
- expect_warning(get_chemical_details_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_details_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- #expect_warning(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c('Boiling point'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- #expect_warning(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c('Boiling point'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chem_info_batch(DTXSID = c('DTXSID7020182'), type = 8, API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chem_info_batch(DTXSID = c('DTXSID7020182'), type = 8, API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_fate_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_fate_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(chemical_starts_with_batch(word_list = c('gvfdsr7'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(chemical_starts_with_batch(word_list = c('gvfdsr7'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(chemical_equal_batch(word_list = c('gvfdsr7'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(chemical_equal_batch(word_list = c('gvfdsr7'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(chemical_contains_batch(word_list = c('gvfdsr7'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(chemical_contains_batch(word_list = c('gvfdsr7'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_details_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_details_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ #expect_warning(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c('Boiling point'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ #expect_warning(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c('Boiling point'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chem_info_batch(DTXSID = c('DTXSID7020182'), type = 8, API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chem_info_batch(DTXSID = c('DTXSID7020182'), type = 8, API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_fate_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_fate_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(chemical_starts_with_batch(word_list = c('gvfdsr7'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(chemical_starts_with_batch(word_list = c('gvfdsr7'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(chemical_equal_batch(word_list = c('gvfdsr7'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(chemical_equal_batch(word_list = c('gvfdsr7'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(chemical_contains_batch(word_list = c('gvfdsr7'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(chemical_contains_batch(word_list = c('gvfdsr7'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
expect_warning(get_msready_by_mass_with_error_batch(mass = 226, error = 1, rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
expect_warning(get_msready_by_mass_with_error_batch(mass = 226, error = 1, rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_msready_by_mass_batch(start_list = c(1), end_list = c(1), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_msready_by_mass_batch(start_list = c(1), end_list = c(1), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_msready_by_formula_batch(formula_list = c('CH4'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_msready_by_formula_batch(formula_list = c('CH4'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_lists_by_type_batch(type_list = c('federal'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_lists_by_type_batch(type_list = c('federal'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_public_chemical_list_by_name_batch(name_list = c('BIOSOLIDS2021'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_public_chemical_list_by_name_batch(name_list = c('BIOSOLIDS2021'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemicals_in_list_batch(list_names = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemicals_in_list_batch(list_names = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_mrv_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_mrv_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_mol_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_mol_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_image_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_image_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_synonym_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_chemical_synonym_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_msready_by_mass_batch(start_list = c(1), end_list = c(1), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_msready_by_mass_batch(start_list = c(1), end_list = c(1), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_msready_by_formula_batch(formula_list = c('CH4'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_msready_by_formula_batch(formula_list = c('CH4'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_lists_by_type_batch(type_list = c('federal'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_lists_by_type_batch(type_list = c('federal'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_public_chemical_list_by_name_batch(name_list = c('BIOSOLIDS2021'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_public_chemical_list_by_name_batch(name_list = c('BIOSOLIDS2021'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemicals_in_list_batch(list_names = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemicals_in_list_batch(list_names = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_mrv_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_mrv_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_mol_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_mol_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_image_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_image_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_synonym_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_chemical_synonym_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
})
test_that('Numeric range input errors and warnings', {
@@ -168,82 +168,82 @@ test_that('Word search errors', {
})
test_that('miscellaneous list mismatch warnings', {
- expect_warning(get_chem_info_batch(DTXSID = c('DTXSID7020182', 'DTXSID2021315', 'DTXSID50186350'), type = c('experimental', ''), API_key = ccte_key()), "Setting type to ''!")
- expect_warning(get_chem_info_batch(DTXSID = c('DTXSID7020182'), type = c('predicted', 'experimental'), API_key = ccte_key()), "Setting type to ''!")
+ expect_warning(get_chem_info_batch(DTXSID = c('DTXSID7020182', 'DTXSID2021315', 'DTXSID50186350'), type = c('experimental', ''), API_key = ctx_key()), "Setting type to ''!")
+ expect_warning(get_chem_info_batch(DTXSID = c('DTXSID7020182'), type = c('predicted', 'experimental'), API_key = ctx_key()), "Setting type to ''!")
})
test_that('Return data types', {
- expect_type(get_chemical_details_batch(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_chemical_details_batch(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_chemical_details_batch(DTXCID = 'DTXCID30182', API_key = ccte_key()), 'list')
- expect_type(get_chemical_details_batch(DTXCID = 'DTXCID30182', Projection = '', API_key = ccte_key()), 'list')
- expect_type(get_chemical_details_batch(DTXSID = '', API_key = ccte_key()), 'list')
+ expect_type(get_chemical_details_batch(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_chemical_details_batch(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_chemical_details_batch(DTXCID = 'DTXCID30182', API_key = ctx_key()), 'list')
+ expect_type(get_chemical_details_batch(DTXCID = 'DTXCID30182', Projection = '', API_key = ctx_key()), 'list')
+ expect_type(get_chemical_details_batch(DTXSID = '', API_key = ctx_key()), 'list')
expect_type(get_chemical_details_batch(DTXSID = 'DTXSID7020182', API_key = ''), 'list')
expect_type(generate_ranges(end = 'p'), 'list')
expect_type(generate_ranges(end = -1), 'list')
expect_type(generate_ranges(end = 205), 'list')
expect_type(generate_dtxsid_string(items = c('DTXSID7020182', 'DTXSID7026185')), 'character')
- expect_type(get_chemical_by_property_range_batch(start_list = c(NA_real_), end_list = (NA_real_), property_list = c('density'), API_key = ccte_key()), 'list')
- #expect_type(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c('Boiling point'), API_key = ccte_key()), 'list')
- #expect_type(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_chemical_by_property_range_batch(start_list = c(NA_real_), end_list = (NA_real_), property_list = c('density'), API_key = ctx_key()), 'list')
+ #expect_type(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c('Boiling point'), API_key = ctx_key()), 'list')
+ #expect_type(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c(''), API_key = ctx_key()), 'list')
#expect_type(get_chemical_by_property_range_batch(start_list = c(1), end_list = c(2), property_list = c('Boiling point'), API_key = ''), 'list')
- expect_type(get_chem_info_batch(DTXSID = 'DTXSID7020182', type = 'predicted', API_key = ccte_key()), 'list')
- expect_type(get_chem_info_batch(DTXSID = '', type = 'predicted', API_key = ccte_key()), 'list')
+ expect_type(get_chem_info_batch(DTXSID = 'DTXSID7020182', type = 'predicted', API_key = ctx_key()), 'list')
+ expect_type(get_chem_info_batch(DTXSID = '', type = 'predicted', API_key = ctx_key()), 'list')
expect_type(get_chem_info_batch(DTXSID = 'DTXSID7020182', type = 'predicted', API_key = ''), 'list')
expect_type(get_chem_info_batch(DTXSID = 'DTXSID7020182', type = 9, API_key = ''), 'list')
- expect_type(get_fate_by_dtxsid_batch(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_fate_by_dtxsid_batch(DTXSID = '', API_key = ccte_key()), 'list')
+ expect_type(get_fate_by_dtxsid_batch(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_fate_by_dtxsid_batch(DTXSID = '', API_key = ctx_key()), 'list')
expect_type(get_fate_by_dtxsid_batch(DTXSID = 'DTXSID7020182', API_key = ''), 'list')
- expect_type(chemical_starts_with_batch(word_list = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(chemical_starts_with_batch(word_list = c('gvfdsr7'), API_key = ccte_key()), 'list')
+ expect_type(chemical_starts_with_batch(word_list = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(chemical_starts_with_batch(word_list = c('gvfdsr7'), API_key = ctx_key()), 'list')
expect_type(chemical_starts_with_batch(word_list = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(chemical_equal_batch(word_list = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(chemical_equal_batch(word_list = c('gvfdsr7'), API_key = ccte_key()), 'list')
+ expect_type(chemical_equal_batch(word_list = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(chemical_equal_batch(word_list = c('gvfdsr7'), API_key = ctx_key()), 'list')
expect_type(chemical_equal_batch(word_list = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(chemical_contains_batch(word_list = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(chemical_contains_batch(word_list = c('gvfdsr7'), API_key = ccte_key()), 'list')
+ expect_type(chemical_contains_batch(word_list = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(chemical_contains_batch(word_list = c('gvfdsr7'), API_key = ctx_key()), 'list')
expect_type(chemical_contains_batch(word_list = c('DTXSID7020182'), API_key = ''), 'list')
expect_type(get_msready_by_mass_with_error_batch(masses = 226, error = 1), 'list')
expect_type(get_msready_by_mass_with_error_batch(masses = c(226, 228), error = 1), 'list')
- expect_type(get_msready_by_mass_batch(start_list = c(16.0313), end_list = c(16.0314), API_key = ccte_key()), 'list')
- expect_type(get_msready_by_mass_batch(start_list = c(16.0314), end_list = c(16.0314), API_key = ccte_key()), 'list')
+ expect_type(get_msready_by_mass_batch(start_list = c(16.0313), end_list = c(16.0314), API_key = ctx_key()), 'list')
+ expect_type(get_msready_by_mass_batch(start_list = c(16.0314), end_list = c(16.0314), API_key = ctx_key()), 'list')
expect_type(get_msready_by_mass_batch(start_list = c(-16.0313), end_list = c(16.0314), API_key = ''), 'list')
- expect_type(get_msready_by_formula_batch(formula_list = c('CH4'), API_key = ccte_key()), 'list')
- expect_type(get_msready_by_formula_batch(formula_list = c('8x'), API_key = ccte_key()), 'list')
- expect_type(get_msready_by_formula_batch(formula_list = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_msready_by_formula_batch(formula_list = c('CH4'), API_key = ctx_key()), 'list')
+ expect_type(get_msready_by_formula_batch(formula_list = c('8x'), API_key = ctx_key()), 'list')
+ expect_type(get_msready_by_formula_batch(formula_list = c(''), API_key = ctx_key()), 'list')
expect_type(get_msready_by_formula_batch(formula_list = c('CH4'), API_key = ''), 'list')
- expect_type(get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182'), API_key = ccte_key()), 'list')
- expect_type(get_msready_by_dtxcid_batch(DTXCID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182'), API_key = ctx_key()), 'list')
+ expect_type(get_msready_by_dtxcid_batch(DTXCID = c(''), API_key = ctx_key()), 'list')
expect_type(get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182'), API_key = ''), 'list')
- expect_type(get_chemical_lists_by_type_batch(type = c('federal'), API_key = ccte_key()), 'list')
- expect_type(get_chemical_lists_by_type_batch(type = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_chemical_lists_by_type_batch(type = c('federal'), API_key = ctx_key()), 'list')
+ expect_type(get_chemical_lists_by_type_batch(type = c(''), API_key = ctx_key()), 'list')
expect_type(get_chemical_lists_by_type_batch(type = c('federal'), API_key = ''), 'list')
- expect_type(get_public_chemical_list_by_name_batch(name_list = c('BIOSOLIDS2021'), API_key = ccte_key()), 'list')
- expect_type(get_public_chemical_list_by_name_batch(name_list = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_public_chemical_list_by_name_batch(name_list = c('BIOSOLIDS2021'), API_key = ctx_key()), 'list')
+ expect_type(get_public_chemical_list_by_name_batch(name_list = c(''), API_key = ctx_key()), 'list')
expect_type(get_public_chemical_list_by_name_batch(name_list = c('BIOSOLIDS2021'), API_key = ''), 'list')
- expect_type(get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_lists_containing_chemical_batch(chemical_list = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_lists_containing_chemical_batch(chemical_list = c(''), API_key = ctx_key()), 'list')
expect_type(get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(get_chemicals_in_list_batch(list_names = c('BIOSOLDIS2021'), API_key = ccte_key()), 'list')
- expect_type(get_chemicals_in_list_batch(list_names = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_chemicals_in_list_batch(list_names = c('BIOSOLDIS2021'), API_key = ctx_key()), 'list')
+ expect_type(get_chemicals_in_list_batch(list_names = c(''), API_key = ctx_key()), 'list')
expect_type(get_chemicals_in_list_batch(list_names = c('BIOSOLDIS2021'), API_key = ''), 'list')
- expect_type(get_chemical_mrv_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_chemical_mrv_batch(DTXCID = c('DTXCID30182'), API_key = ccte_key()), 'list')
- expect_type(get_chemical_mrv_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_chemical_mrv_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_chemical_mrv_batch(DTXCID = c('DTXCID30182'), API_key = ctx_key()), 'list')
+ expect_type(get_chemical_mrv_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_chemical_mrv_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
expect_type(get_chemical_mrv_batch(DTXCID = c('DTXCID30182'), API_key = ''), 'list')
- expect_type(get_chemical_mol_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_chemical_mol_batch(DTXCID = c('DTXCID30182'), API_key = ccte_key()), 'list')
- expect_type(get_chemical_mol_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_chemical_mol_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_chemical_mol_batch(DTXCID = c('DTXCID30182'), API_key = ctx_key()), 'list')
+ expect_type(get_chemical_mol_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_chemical_mol_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
expect_type(get_chemical_mol_batch(DTXCID = c('DTXCID30182'), API_key = ''), 'list')
- expect_type(get_chemical_image_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_chemical_image_batch(DTXCID = c('DTXCID30182'), format = c('png'), API_key = ccte_key()), 'list')
- expect_type(get_chemical_image_batch(DTXSID = c(''), format = c('svg'), API_key = ccte_key()), 'list')
+ expect_type(get_chemical_image_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_chemical_image_batch(DTXCID = c('DTXCID30182'), format = c('png'), API_key = ctx_key()), 'list')
+ expect_type(get_chemical_image_batch(DTXSID = c(''), format = c('svg'), API_key = ctx_key()), 'list')
expect_type(get_chemical_image_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
expect_type(get_chemical_image_batch(DTXCID = c('DTXCID30182'), format = c('png'), API_key = ''), 'list')
- expect_type(get_chemical_synonym_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_chemical_synonym_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_chemical_synonym_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_chemical_synonym_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_chemical_synonym_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
})
})
diff --git a/tests/testthat/test-chemical-APIs.R b/tests/testthat/test-chemical-APIs.R
index 84de8268..5e119fe8 100644
--- a/tests/testthat/test-chemical-APIs.R
+++ b/tests/testthat/test-chemical-APIs.R
@@ -3,11 +3,11 @@ with_mock_dir("chemical",{
# # Run register_ccdr(key = 'YOUR KEY', write = TRUE) prior to running tests
#
# #store env variable so tests don't overwrite
-# # tmp <- Sys.getenv("CCTE_API_KEY")
-# # on.exit(Sys.setenv("CCTE_API_KEY" = tmp))
-# # if(Sys.getenv("CCTE_API_KEY") == ""){
+# # tmp <- Sys.getenv("CTX_API_KEY")
+# # on.exit(Sys.setenv("CTX_API_KEY" = tmp))
+# # if(Sys.getenv("CTX_API_KEY") == ""){
# # #set env variable temporarily for testing
-# # Sys.setenv("CCTE_API_KEY" = "stored_api_key")
+# # Sys.setenv("CTX_API_KEY" = "stored_api_key")
# # }
#
# expect_message(get_chemical_details(DTXSID = 'DTXSID7020182', verbose = TRUE), 'Using stored API key!')
@@ -59,7 +59,7 @@ test_that('Numeric range input errors and warnings', {
expect_error(get_chemical_by_property_range(end = 4, API_key = 'test_key'), 'Please input a numeric value for both start and end!')
expect_error(get_chemical_by_property_range(start = 4, end = 'k', API_key = 'test_key'), 'Please input a numeric value for both start and end!')
expect_error(get_chemical_by_property_range(start = TRUE, end = 4, API_key = 'test_key'), 'Please input a numeric value for both start and end!')
- expect_error(get_chemical_by_property_range(start = 3, end = 4, API_key = ccte_key()), 'Please input a value for property!')
+ expect_error(get_chemical_by_property_range(start = 3, end = 4, API_key = ctx_key()), 'Please input a value for property!')
expect_error(get_msready_by_mass(API_key = 'test_key'), 'Please input a numeric value for both start and end!')
expect_error(get_msready_by_mass(start = 4, API_key = 'test_key'), 'Please input a numeric value for both start and end!')
expect_error(get_msready_by_mass(end = 4, API_key = 'test_key'), 'Please input a numeric value for both start and end!')
@@ -68,7 +68,7 @@ test_that('Numeric range input errors and warnings', {
expect_error(get_msready_by_mass(start = -1, end = 4, API_key = 'test_key'), 'Both start and end must be non-negative!')
expect_error(get_msready_by_mass(start = 4, end = -1, API_key = 'test_key'), 'Both start and end must be non-negative!')
expect_warning(get_msready_by_mass(start = 4, end = 1), 'Swapping values for start and end!')
- #expect_warning(get_chemical_by_property_range(start = 4, end = 3, property = 'density', API_key = ccte_key()), 'Swapping values for start and end!')
+ #expect_warning(get_chemical_by_property_range(start = 4, end = 3, property = 'density', API_key = ctx_key()), 'Swapping values for start and end!')
})
@@ -76,20 +76,20 @@ test_that('projection/type errors/warnings', {
expect_error(get_chemical_details(DTXSID = 'DTXSID7020182', Projection = 't', API_key = 'test_key'), 'Please input a correct value for `Projection`!')
expect_warning(get_chemical_details(DTXSID = 'DTXSID7020182', Projection = 2), 'Setting `Projection` to `chemicaldetailstandard`')
expect_warning(get_chemical_details(DTXSID = 'DTXSID7020182', Projection = c('ntatoolkit', 'chemicaldetailstandard')), 'Setting `Projection` to `chemicaldetailstandard`')
- expect_message(get_chemical_details(DTXSID = 'DTXSID7020182', Projection = c('ntatoolkit', 'chemicaldetaitandard'), API_key = ccte_key()), 'Using `Projection` = ntatoolkit!')
+ expect_message(get_chemical_details(DTXSID = 'DTXSID7020182', Projection = c('ntatoolkit', 'chemicaldetaitandard'), API_key = ctx_key()), 'Using `Projection` = ntatoolkit!')
expect_warning(get_chem_info(DTXSID = 'DTXSID', type = c('', 'predicted')), 'Setting type to ""!')
expect_error(get_chem_info(DTXSID = 'DTXSID', type = 'l', API_key = 'test_key'), 'Please input a correct choice for type!')
expect_error(get_chemical_lists_by_type(), 'Please input a value for parameter type')
expect_error(get_chemical_lists_by_type(type = 1), 'Please input a value for parameter type')
- expect_warning(get_chemical_lists_by_type(type = 'federal', Projection = 1, API_key = ccte_key()), 'Setting `Projection` to empty string!')
- expect_warning(get_chemical_lists_by_type(type = 'federal', Projection = '1', API_key = ccte_key()), 'Setting `Projection` to empty string!')
- expect_warning(get_chemical_lists_by_type(type = 'federal', Projection = c('', 'chemicallistall'), API_key = ccte_key()), 'Setting `Projection` to empty string!')
- expect_warning(get_public_chemical_list_by_name(list_name = 'federal', Projection = 1, API_key = ccte_key()), 'Setting `Projection` to empty string!')
- expect_warning(get_public_chemical_list_by_name(list_name = 'federal', Projection = '1', API_key = ccte_key()), 'Setting `Projection` to empty string!')
- expect_warning(get_public_chemical_list_by_name(list_name = 'federal', Projection = c('', 'chemicallistall'), API_key = ccte_key()), 'Setting `Projection` to empty string!')
- expect_warning(get_all_public_chemical_lists(Projection = 1, API_key = ccte_key()), 'Setting `Projection` to empty string!')
- expect_warning(get_all_public_chemical_lists(Projection = '1', API_key = ccte_key()), 'Setting `Projection` to empty string!')
- expect_warning(get_all_public_chemical_lists(Projection = c('', 'chemicallistall'), API_key = ccte_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_chemical_lists_by_type(type = 'federal', Projection = 1, API_key = ctx_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_chemical_lists_by_type(type = 'federal', Projection = '1', API_key = ctx_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_chemical_lists_by_type(type = 'federal', Projection = c('', 'chemicallistall'), API_key = ctx_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_public_chemical_list_by_name(list_name = 'federal', Projection = 1, API_key = ctx_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_public_chemical_list_by_name(list_name = 'federal', Projection = '1', API_key = ctx_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_public_chemical_list_by_name(list_name = 'federal', Projection = c('', 'chemicallistall'), API_key = ctx_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_all_public_chemical_lists(Projection = 1, API_key = ctx_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_all_public_chemical_lists(Projection = '1', API_key = ctx_key()), 'Setting `Projection` to empty string!')
+ expect_warning(get_all_public_chemical_lists(Projection = c('', 'chemicallistall'), API_key = ctx_key()), 'Setting `Projection` to empty string!')
})
test_that('Word search errors', {
@@ -108,69 +108,69 @@ test_that('Word search errors', {
})
test_that('Return data type', {
- expect_type(get_chemical_details(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
+ expect_type(get_chemical_details(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
expect_type(get_chemical_details(DTXCID = 'DTXCID30182'), 'list')
- expect_type(get_chemical_details(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_chemical_details(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_chemical_details(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- #expect_type(get_chemical_by_property_range(start = 99.8, end = 100.2, property = 'boiling point', API_key = ccte_key()), 'list')
- #expect_type(get_chemical_by_property_range(start = 99.8, end = 100.2, property = 'nonsense', API_key = ccte_key()), 'NULL')
- expect_type(get_chem_info(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
+ #expect_type(get_chemical_by_property_range(start = 99.8, end = 100.2, property = 'boiling point', API_key = ctx_key()), 'list')
+ #expect_type(get_chemical_by_property_range(start = 99.8, end = 100.2, property = 'nonsense', API_key = ctx_key()), 'NULL')
+ expect_type(get_chem_info(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
expect_type(get_chem_info(DTXSID = 'DTXSID7020182', type = 'predicted'), 'list')
- expect_type(get_chem_info(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_chem_info(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_chem_info(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- expect_type(get_fate_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_fate_by_dtxsid(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_fate_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_fate_by_dtxsid(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_fate_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- expect_type(chemical_starts_with(word = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(chemical_starts_with(word = '', API_key = ccte_key()), 'NULL')
+ expect_type(chemical_starts_with(word = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(chemical_starts_with(word = '', API_key = ctx_key()), 'NULL')
#expect_type(chemical_starts_with(word = 'DTXSID7020182', API_key = ''), 'NULL')
expect_type(chemical_equal(word = 'Bisphenol A'), 'list')
- expect_type(chemical_equal(word = 'gvfds', API_key = ccte_key()), 'NULL')
+ expect_type(chemical_equal(word = 'gvfds', API_key = ctx_key()), 'NULL')
#expect_type(chemical_equal(word = 'Bisphenol A', API_key = ''), 'NULL')
expect_type(chemical_contains(word = 'Bisphenol A'), 'list')
- expect_type(chemical_contains(word = 'gvfdsr7', API_key = ccte_key()), 'NULL')
+ expect_type(chemical_contains(word = 'gvfdsr7', API_key = ctx_key()), 'NULL')
#expect_type(chemical_contains(word = 'Bisphenol A', API_key = ''), 'NULL')
expect_type(get_msready_by_mass(start = 16.0313, end = 16.0314), 'character')
expect_type(get_msready_by_mass(start = 16.0314, end = 16.0314), 'list')
#expect_type(get_msready_by_mass(start = 16.0313, end = 16.0314, API_key =''), 'NULL')
- expect_type(get_msready_by_formula(formula = 'CH4', API_key = ccte_key()), 'character')
+ expect_type(get_msready_by_formula(formula = 'CH4', API_key = ctx_key()), 'character')
expect_type(get_msready_by_formula(formula = '8x'), 'list')
- expect_type(get_msready_by_formula(formula = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_msready_by_formula(formula = '', API_key = ctx_key()), 'NULL')
#expect_type(get_msready_by_formula(formula = 'CH4', API_key = ''), 'NULL')
- expect_type(get_msready_by_dtxcid(DTXCID = 'DTXCID30182', API_key = ccte_key()), 'character')
- expect_type(get_msready_by_dtxcid(DTXCID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_msready_by_dtxcid(DTXCID = 'DTXCID30182', API_key = ctx_key()), 'character')
+ expect_type(get_msready_by_dtxcid(DTXCID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_msready_by_dtxcid(DTXCID = 'DTXCID30182', API_key = ''), 'NULL')
- expect_type(get_chemical_lists_by_type(type = 'federal', API_key = ccte_key()), 'list')
- expect_type(get_chemical_lists_by_type(type = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_chemical_lists_by_type(type = 'federal', API_key = ctx_key()), 'list')
+ expect_type(get_chemical_lists_by_type(type = '', API_key = ctx_key()), 'NULL')
#expect_type(get_chemical_lists_by_type(type = 'federal', API_key = ''), 'NULL')
- expect_type(get_public_chemical_list_by_name(list_name = 'Biosolids2021', API_key = ccte_key()), 'list')
- expect_type(get_public_chemical_list_by_name(list_name = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_public_chemical_list_by_name(list_name = 'Biosolids2021', API_key = ctx_key()), 'list')
+ expect_type(get_public_chemical_list_by_name(list_name = '', API_key = ctx_key()), 'NULL')
#expect_type(get_public_chemical_list_by_name(list_name = 'BIOSOLIDS2021', API_key = ''), 'NULL')
- expect_type(get_lists_containing_chemical(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'character')
- expect_type(get_lists_containing_chemical(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_lists_containing_chemical(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'character')
+ expect_type(get_lists_containing_chemical(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_lists_containing_chemical(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
expect_type(get_chemicals_in_list(list_name = 'CCL4'), 'list')
- expect_type(get_chemicals_in_list(list_name = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_chemicals_in_list(list_name = '', API_key = ctx_key()), 'NULL')
#expect_type(get_chemicals_in_list(list_name = 'BIOSOLDIS2021', API_key = ''), 'NULL')
- expect_type(get_all_public_chemical_lists(API_key = ccte_key()), 'list')
+ expect_type(get_all_public_chemical_lists(API_key = ctx_key()), 'list')
#expect_type(get_all_public_chemical_lists(API_key = ''), 'NULL')
- expect_type(get_chemical_mrv(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'character')
+ expect_type(get_chemical_mrv(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'character')
expect_type(get_chemical_mrv(DTXCID = 'DTXCID30182'), 'character')
- expect_type(get_chemical_mrv(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_chemical_mrv(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_chemical_mrv(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
#expect_type(get_chemical_mrv(DTXCID = 'DTXCID30182', API_key = ''), 'NULL')
- expect_type(get_chemical_mol(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'character')
+ expect_type(get_chemical_mol(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'character')
expect_type(get_chemical_mol(DTXCID = 'DTXCID30182'), 'character')
- expect_type(get_chemical_mol(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_chemical_mol(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_chemical_mol(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
#expect_type(get_chemical_mol(DTXCID = 'DTXCID30182', API_key = ''), 'NULL')
- expect_type(get_chemical_image(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'double')
+ expect_type(get_chemical_image(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'double')
expect_type(get_chemical_image(DTXCID = 'DTXCID30182', format = 'png'), 'double')
- expect_type(get_chemical_image(DTXSID = '', format = 'svg', API_key = ccte_key()), 'NULL')
+ expect_type(get_chemical_image(DTXSID = '', format = 'svg', API_key = ctx_key()), 'NULL')
#expect_type(get_chemical_image(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
#expect_type(get_chemical_image(DTXCID = 'DTXCID30182', format = 'png', API_key = ''), 'NULL')
- expect_type(get_chemical_synonym(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_chemical_synonym(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_chemical_synonym(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_chemical_synonym(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_chemical_synonym(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
})
diff --git a/tests/testthat/test-exposure-APIs-batch.R b/tests/testthat/test-exposure-APIs-batch.R
index 68dbfa83..f8ce6612 100644
--- a/tests/testthat/test-exposure-APIs-batch.R
+++ b/tests/testthat/test-exposure-APIs-batch.R
@@ -16,23 +16,23 @@ test_that("DTXSID errors", {
})
test_that("Rate limit warnings", {
- expect_warning(get_exposure_functional_use_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_exposure_functional_use_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_exposure_functional_use_probability_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_exposure_functional_use_probability_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_exposure_product_data_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_exposure_product_data_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_exposure_functional_use_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_exposure_functional_use_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_exposure_functional_use_probability_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_exposure_functional_use_probability_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_exposure_product_data_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_exposure_product_data_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
})
test_that("Return data type", {
- expect_type(get_exposure_functional_use_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_exposure_functional_use_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
- expect_type(get_exposure_functional_use_probability_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_exposure_functional_use_probability_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
- expect_type(get_exposure_product_data_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_exposure_product_data_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
- expect_type(get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_exposure_functional_use_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_exposure_functional_use_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
+ expect_type(get_exposure_functional_use_probability_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_exposure_functional_use_probability_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
+ expect_type(get_exposure_product_data_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_exposure_product_data_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
+ expect_type(get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
})})
diff --git a/tests/testthat/test-exposure-APIs.R b/tests/testthat/test-exposure-APIs.R
index 7a4d33fc..77fd38df 100644
--- a/tests/testthat/test-exposure-APIs.R
+++ b/tests/testthat/test-exposure-APIs.R
@@ -8,15 +8,15 @@ test_that("catch missing DTXSID", {
})
test_that("Return data type", {
- expect_type(get_exposure_functional_use(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_exposure_functional_use(DTXSID = '', API_key = ccte_key()), 'NULL')
- expect_type(get_exposure_functional_use_probability(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_exposure_functional_use_probability(DTXSID = '', API_key = ccte_key()), 'NULL')
- expect_type(get_exposure_functional_use_category(API_key = ccte_key()), 'list')
- expect_type(get_exposure_product_data(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_exposure_product_data(DTXSID = '', API_key = ccte_key()), 'NULL')
- expect_type(get_exposure_product_data_puc(API_key = ccte_key()), 'list')
- expect_type(get_exposure_list_presence_tags(API_key = ccte_key()), 'list')
- expect_type(get_exposure_list_presence_tags_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_exposure_list_presence_tags_by_dtxsid(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_exposure_functional_use(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_exposure_functional_use(DTXSID = '', API_key = ctx_key()), 'NULL')
+ expect_type(get_exposure_functional_use_probability(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_exposure_functional_use_probability(DTXSID = '', API_key = ctx_key()), 'NULL')
+ expect_type(get_exposure_functional_use_category(API_key = ctx_key()), 'list')
+ expect_type(get_exposure_product_data(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_exposure_product_data(DTXSID = '', API_key = ctx_key()), 'NULL')
+ expect_type(get_exposure_product_data_puc(API_key = ctx_key()), 'list')
+ expect_type(get_exposure_list_presence_tags(API_key = ctx_key()), 'list')
+ expect_type(get_exposure_list_presence_tags_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_exposure_list_presence_tags_by_dtxsid(DTXSID = '', API_key = ctx_key()), 'NULL')
})})
diff --git a/tests/testthat/test-hazard-APIs-batch.R b/tests/testthat/test-hazard-APIs-batch.R
index d7addd1b..8df5cd73 100644
--- a/tests/testthat/test-hazard-APIs-batch.R
+++ b/tests/testthat/test-hazard-APIs-batch.R
@@ -1,11 +1,11 @@
with_mock_dir("hazard-batch",{
# test_that("catch missing APIs", {
# #store env variable so tests don't overwrite
-# # tmp <- Sys.getenv("CCTE_API_KEY")
-# # on.exit(Sys.setenv("CCTE_API_KEY" = tmp))
-# # if(Sys.getenv("CCTE_API_KEY") == ""){
+# # tmp <- Sys.getenv("CTX_API_KEY")
+# # on.exit(Sys.setenv("CTX_API_KEY" = tmp))
+# # if(Sys.getenv("CTX_API_KEY") == ""){
# # #set env variable temporarily for testing
-# # Sys.setenv("CCTE_API_KEY" = "stored_api_key")
+# # Sys.setenv("CTX_API_KEY" = "stored_api_key")
# # }
# # Run register_ccdr(key = 'YOUR KEY', write = TRUE) prior to running tests
# expect_message(get_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), verbose = TRUE), 'Using stored API key!')
@@ -49,42 +49,42 @@ test_that('DTXSID errors', {
})
test_that('Rate limit warnings', {
- expect_warning(get_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_human_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_human_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_skin_eye_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_skin_eye_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_cancer_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_cancer_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_genetox_summary_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_genetox_summary_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_genetox_details_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
- expect_warning(get_genetox_details_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_human_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_human_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_skin_eye_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_skin_eye_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_cancer_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_cancer_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_genetox_summary_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_genetox_summary_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_genetox_details_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = '0'), 'Setting rate limit to 0 seconds between requests!')
+ expect_warning(get_genetox_details_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key(), rate_limit = -1), 'Setting rate limit to 0 seconds between requests!')
})
test_that('Return data types', {
- expect_type(get_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_hazard_by_dtxsid_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_hazard_by_dtxsid_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(get_human_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_human_hazard_by_dtxsid_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_human_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_human_hazard_by_dtxsid_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_human_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_ecotox_hazard_by_dtxsid_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(get_skin_eye_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_skin_eye_hazard_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_skin_eye_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_skin_eye_hazard_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_skin_eye_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(get_cancer_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_cancer_hazard_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_cancer_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_cancer_hazard_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_cancer_hazard_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(get_genetox_summary_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_genetox_summary_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_genetox_summary_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_genetox_summary_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_genetox_summary_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
- expect_type(get_genetox_details_batch(DTXSID = c('DTXSID7020182'), API_key = ccte_key()), 'list')
- expect_type(get_genetox_details_batch(DTXSID = c(''), API_key = ccte_key()), 'list')
+ expect_type(get_genetox_details_batch(DTXSID = c('DTXSID7020182'), API_key = ctx_key()), 'list')
+ expect_type(get_genetox_details_batch(DTXSID = c(''), API_key = ctx_key()), 'list')
expect_type(get_genetox_details_batch(DTXSID = c('DTXSID7020182'), API_key = ''), 'list')
})})
diff --git a/tests/testthat/test-hazard-APIs.R b/tests/testthat/test-hazard-APIs.R
index dcecca92..0feaf305 100644
--- a/tests/testthat/test-hazard-APIs.R
+++ b/tests/testthat/test-hazard-APIs.R
@@ -2,11 +2,11 @@ with_mock_dir("hazard",{
# test_that("catch missing API", {
# # Run register_ccdr(key = 'YOUR KEY', write = TRUE) prior to running tests
# #store env variable so tests don't overwrite
-# # tmp <- Sys.getenv("CCTE_API_KEY")
-# # on.exit(Sys.setenv("CCTE_API_KEY" = tmp))
-# # if(Sys.getenv("CCTE_API_KEY") == ""){
+# # tmp <- Sys.getenv("CTX_API_KEY")
+# # on.exit(Sys.setenv("CTX_API_KEY" = tmp))
+# # if(Sys.getenv("CTX_API_KEY") == ""){
# # #set env variable temporarily for testing
-# # Sys.setenv("CCTE_API_KEY" = "stored_api_key")
+# # Sys.setenv("CTX_API_KEY" = "stored_api_key")
# # }
# expect_message(get_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', verbose = TRUE), 'Using stored API key!')
# expect_message(get_human_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', verbose = TRUE), 'Using stored API key!')
@@ -28,26 +28,26 @@ test_that("catch missing DTXSID", {
})
test_that("Return data type", {
- expect_type(get_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_hazard_by_dtxsid(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_hazard_by_dtxsid(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- expect_type(get_human_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_human_hazard_by_dtxsid(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_human_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_human_hazard_by_dtxsid(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_human_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- expect_type(get_ecotox_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_ecotox_hazard_by_dtxsid(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_ecotox_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_ecotox_hazard_by_dtxsid(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_ecotox_hazard_by_dtxsid(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- expect_type(get_skin_eye_hazard(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_skin_eye_hazard(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_skin_eye_hazard(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_skin_eye_hazard(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_skin_eye_hazard(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- expect_type(get_cancer_hazard(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_cancer_hazard(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_cancer_hazard(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_cancer_hazard(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_cancer_hazard(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- expect_type(get_genetox_summary(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_genetox_summary(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_genetox_summary(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_genetox_summary(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_genetox_summary(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
- expect_type(get_genetox_details(DTXSID = 'DTXSID7020182', API_key = ccte_key()), 'list')
- expect_type(get_genetox_details(DTXSID = '', API_key = ccte_key()), 'NULL')
+ expect_type(get_genetox_details(DTXSID = 'DTXSID7020182', API_key = ctx_key()), 'list')
+ expect_type(get_genetox_details(DTXSID = '', API_key = ctx_key()), 'NULL')
#expect_type(get_genetox_details(DTXSID = 'DTXSID7020182', API_key = ''), 'NULL')
})
})
diff --git a/vignettes/Bioactivity.Rmd b/vignettes/Bioactivity.Rmd
index e00562ab..4b5cecf7 100644
--- a/vignettes/Bioactivity.Rmd
+++ b/vignettes/Bioactivity.Rmd
@@ -114,11 +114,8 @@ Specific assays may be searched as well as all available assays that have data u
`get_annotation_by_aeid()` retrieves annotation for a specific assay endpoint id (aeid).
-```{r ccdR annotation by aeid, message=FALSE, eval=FALSE}
-res_dt <- get_annotation_by_aeid(AEID = "891")
-# optionally perform this unnest, apply names_repair = "unique" to give a unique column name
-# note - the gene column may be an array of multiple genes rather than just one, meaning this step may not work
-#res_dt <- res_dt |> tidyr::unnest_wider(col = c("citation", "gene", "assayList"), names_repair = "unique")
+```{r ccdR annotation by aeid, message=FALSE}
+assay <- get_annotation_by_aeid(AEID = "891")
```
```{r, echo=FALSE}
@@ -134,11 +131,8 @@ assays <- data.table::rbindlist(assays)
```
-```{r ccdR all assays, message=FALSE, eval=FALSE}
-res_dt <- get_all_assays()
-# optionally perform the following unnest, apply names_repair = "unique" to give a unique column name
-# note - the gene column may be an array of multiple genes rather than just one, meaning this step may not work
-#res_dt <- res_dt |> tidyr::unnest_wider(col = c("citation", "gene", "assayList"), names_repair = "unique")
+```{r ccdR-all-assays, message=FALSE, eval=FALSE}
+printFormattedTable(assays, c(4, 18, 19, 33, 51)) # printed using custom formatted table
```
### Get all assay annotations
@@ -158,8 +152,8 @@ There are several resources for retrieving bioactivity data associated with a va
`get_bioactivity_summary()` retrieves a summary of the number of active hits compared to the total number tested for both multiple and single concentration by aeid.
-```{r ccdR summary by aeid, message=FALSE, eval=FALSE}
-res_dt <- get_bioactivity_summary(AEID = "891")
+```{r ccdR summary by aeid, message=FALSE}
+summary <- get_bioactivity_summary(AEID = "891")
```
```{r, echo=FALSE}
@@ -183,9 +177,9 @@ printFormattedTable(summary) # printed using custom formatted table
`get_bioactivity_details()` can retrieve all available multiple concentration data by assay endpoint id (aeid), sample id (spid), Level 4 ID (m4id), or chemical DTXSID. Returned is chemical information, level 3 concentration-response values, level 4 fit parameters, level 5 hit parameters, and level 6 flags for individual chemicals tested. An example for each request parameter is provided below:
-```{r ccdR data by m4id, message=FALSE, results = FALSE, eval=FALSE}
-res_dt <- get_bioactivity_details(m4id = 739695)
-
+```{r ccdR data by spid, message=FALSE, results = FALSE}
+# By spid
+spid_data <- get_bioactivity_details(SPID = 'TP0000904H05')
```
```{r, echo=FALSE}
@@ -197,11 +191,11 @@ printFormattedTable(head(spid_data), c(ncol(spid_data)-2)) # printed using custo
m4id_data <- get_bioactivity_details(m4id = 739695)
```
-
-```{r ccdR data by dtxsid, message=FALSE, results = FALSE, eval=FALSE}
-res_dt <- get_bioactivity_details(DTXSID = "DTXSID7020182")
+```{r, echo=FALSE}
+printFormattedTable(m4id_data, c(ncol(m4id_data) - 2)) # printed using custom formatted table
```
+
```{r ccdR data by dtxsid, message=FALSE, results = FALSE}
# By DTXSID
dtxsid_data <- get_bioactivity_details(DTXSID = "DTXSID30944145")
@@ -212,8 +206,9 @@ printFormattedTable(dtxsid_data, c(ncol(dtxsid_data)-2)) # printed using custom
```
-```{r ccdR data by aeid, message=FALSE, results = FALSE, eval=FALSE}
-res_dt <- get_bioactivity_details(AEID = "891")
+```{r ccdR data by aeid, message=FALSE, results = FALSE}
+# By aeid
+aeid_data <- get_bioactivity_details(AEID = 704)
```
```{r, echo=FALSE}
diff --git a/vignettes/Chemical.Rmd b/vignettes/Chemical.Rmd
index 67ee91b7..08df781e 100644
--- a/vignettes/Chemical.Rmd
+++ b/vignettes/Chemical.Rmd
@@ -1,5 +1,5 @@
---
-title: "Chemical APIs"
+title: "Chemical API"
author: "Center for Computational Toxicology and Exposure"
output:
prettydoc::html_pretty:
@@ -96,7 +96,6 @@ More information on Chemicals and Chemistry Data can be found here:
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
- eval = (nchar(Sys.getenv('CCTE_API_KEY')) > 0)
+ eval = (nchar(Sys.getenv('CTX_API_KEY')) > 0)
)
library(httptest)
start_vignette("1")
@@ -122,7 +122,7 @@ Recently, the [Center for Computational Toxicology and Exposure](https://www.epa
The [CTX APIs](https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis) are publicly available at no cost to the user. However, in order to use the CTX APIs, users must have a individual API key. The API key uniquely identifies the user to the CCD servers and verifies that you have permission to access the database. Getting an API key is free, but requires contacting the API support team at [ccte_api@epa.gov](mailto:ccte_api@epa.gov).
-The APIs are organized into sets of "endpoints" by data domains: `Chemical`, `Hazard`, and `Bioactivity`. An endpoint provides access to a specific set of information and data, e.g. physical-chemical properties for a chemical that the user specifies. A view from the [Chemical APIs](https://api-ccte.epa.gov/docs/chemical.html) web interface is pictured below.
+The APIs are organized into sets of "endpoints" by data domains: `Chemical`, `Hazard`, and `Bioactivity`. An endpoint provides access to a specific set of information and data, e.g. physical-chemical properties for a chemical that the user specifies. A view from the [Chemical API](https://api-ccte.epa.gov/docs/chemical.html) web interface is pictured below.
@@ -201,7 +201,7 @@ devtools::install_github("USEPA/ccdR")
As previously described, a user must have an API key to use in order to access the CTX APIs. This can be obtained from the admins of the CTX APIs by emailing [CTX API Admins](mailto:ccte_api@epa.gov). In the example code, the API key will be stored as the variable `my_key`.
```{r, echo = FALSE}
-my_key <- ccte_key()
+my_key <- ctx_key()
```
```{r, eval = FALSE, api-key}
@@ -210,7 +210,7 @@ my_key <- 'YOUR_CTX_API_key'
For general use of the package, the user may use the function `register_ccdr()` to store the API key in the current session or more permanently for access across sessions.
-```{r, register-ccte, eval=FALSE}
+```{r, register-ccdr, eval=FALSE}
# This stores the key in the current session
register_ccdr(key = '')
@@ -230,10 +230,10 @@ ccdr_hide_api_key()
getOption('ccdr')$display_api_key
```
-Finally, to access the key, use the `ccte_key()` function.
+Finally, to access the key, use the `ctx_key()` function.
-```{r, ccte-key, eval = FALSE}
-ccte_key()
+```{r, ctx-key, eval = FALSE}
+ctx_key()
```
### Quick Start Examples
@@ -242,9 +242,9 @@ As some quick start examples, we demonstrate the ease* of retrieving the informa
For additional examples and more comprehensive documentation on each endpoint, consider reviewing the other ccdR vignettes for the data domain of interest.
-#### Chemical APIs
+#### Chemical API
-In this section, several ccdR functions are used to access different types of information from the [CTX Chemical APIs](https://api-ccte.epa.gov/docs/chemical.html#/).
+In this section, several ccdR functions are used to access different types of information from the [CTX Chemical API](https://api-ccte.epa.gov/docs/chemical.html#/).
##### Chemical Details Resource
@@ -282,9 +282,9 @@ bpa_info_experimental <- data.table::as.data.table(bpa_info_experimental)
head(bpa_info_experimental)
```
-#### Hazard APIs
+#### Hazard API
-In this section, several ccdR functions are used to access different types of information from the [CTX Hazard APIs](https://api-ccte.epa.gov/docs/hazard.html#/).
+In this section, several ccdR functions are used to access different types of information from the [CTX Hazard API](https://api-ccte.epa.gov/docs/hazard.html#/).
##### Hazard Resource
@@ -317,9 +317,9 @@ bpa_eco_hazard <- data.table::as.data.table(bpa_eco_hazard)
head(bpa_eco_hazard)
```
-#### Bioactivity APIs
+#### Bioactivity API
-In this section, several ccdR functions are used to access different types of information from the [CTX Bioactivity APIs](https://api-ccte.epa.gov/docs/bioactivity.html#/).
+In this section, several ccdR functions are used to access different types of information from the [CTX Bioactivity API](https://api-ccte.epa.gov/docs/bioactivity.html#/).
##### Bioactivity Resource