Merge pull request #63 from USEPA/61-rename-cctected-to-ctx

61 rename cctected to ctx

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 = "[email protected]", 
@@ -17,13 +17,15 @@ Authors@R: c(
     	      person("Jason", "Brown", role = "ctb", 
     	        email = "[email protected]")
     	        )
-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 
    <https://api-ccte.epa.gov/docs/>. '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')
-   <https://comptox.epa.gov/dashboard/>. 
+   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') 
+   <https://comptox.epa.gov/dashboard/> and other resources found at the 
+   EPA Computational Toxicology and Exposure Online Resources 
+   <https://www.epa.gov/comptox-tools>. 
 License: GPL (>= 3)
 Imports: 
     cli,

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)

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/>', 'https://api-ccte.epa.gov/docs/')
+      cli::style_hyperlink('<https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>', '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 {

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!')
       }

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!')
       }
@@ -208,16 +178,16 @@ 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,
                            Server = bioactivity_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!')
       }
@@ -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)
+}

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')