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Merge pull request #30 from USEPA/29-add-and-update-functions-for-che…
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…mical-domain-endpoints

29 add and update functions for chemical domain endpoints
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@rachmaninoffpk
rachmaninoffpk authored Sep 24, 2024
2 parents 0f2b811 + b4d1164 commit 96d412a
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7 changes: 7 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ export(ctxR_hide_api_key)
export(ctxR_show_api_key)
export(ctx_key)
export(get_all_assays)
export(get_all_list_types)
export(get_all_public_chemical_lists)
export(get_annotation_by_aeid)
export(get_annotation_by_aeid_batch)
Expand Down Expand Up @@ -42,6 +43,12 @@ export(get_chemical_synonym)
export(get_chemical_synonym_batch)
export(get_chemicals_in_list)
export(get_chemicals_in_list_batch)
export(get_chemicals_in_list_contain)
export(get_chemicals_in_list_contain_batch)
export(get_chemicals_in_list_exact)
export(get_chemicals_in_list_exact_batch)
export(get_chemicals_in_list_start)
export(get_chemicals_in_list_start_batch)
export(get_demographic_exposure_prediction)
export(get_demographic_exposure_prediction_batch)
export(get_ecotox_hazard_by_dtxsid)
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257 changes: 256 additions & 1 deletion R/chemical-APIs-batch.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1201,7 +1201,7 @@ chemical_equal_batch <- function(word_list = NULL,




return(return_list)
}

Expand Down Expand Up @@ -1772,6 +1772,222 @@ get_lists_containing_chemical_batch <- function(chemical_list = NULL,
}
}


#' Get chemicals in a list specified by starting characters batch search
#'
#' @param list_names The names of the lists to search.
#' @param words The search words, one for each list.
#' @param API_key The user-specific API key.
#' @param rate_limit Number of seconds to wait between each request.
#' @param verbose A logical indicating if some "progress report" should be given.
#'
#' @return A named list of lists, with names corresponding to search terms and
#' lists corresponding to DTXSIDs associated to the search terms
#' @export
#'
#' @examplesIf FALSE
#' # Search `CCL4` for chemicals starting with 'Bis' and `BIOSOLIDS2021` for
#' # chemicals starting with 'Tri'.
#' bis_and_tri <- get_chemicals_in_list_start_batch(list_names = c('CCL4',
#' 'BIOSOLIDS2021'),
#' words = c('Bis', 'Tri'))

get_chemicals_in_list_start_batch <- function(list_names = NULL,
words = NULL,
API_key = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
if (has_ctx_key()) {
API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
}
}
if(is.null(list_names) || is.null(words)){
stop('Please input a list for both `list_names` and `words`!')
} else if (length(list_names) != length(words)) {
stop('Mismatch in length of `list_names` and `words`!')
} else if (!all(sapply(c(list_names, words), is.character))) {
stop('Only character values allowed in `list_names` and `words`!')
}

if (!is.numeric(rate_limit) | (rate_limit < 0)){
warning('Setting rate limit to 0 seconds between requests!')
rate_limit <- 0L
}



results <- purrr::map2(.x = list_names, .y = words, function(d, t){
Sys.sleep(rate_limit)
attempt <- tryCatch(
{
get_chemicals_in_list_start(list_name = d,
word = t,
API_key = API_key,
verbose = verbose)
},
error = function(cond){
message('There was an error!')
message(paste('List name:', d))
message(paste('Word:', t))
message(cond$message)
return(NA)
}
)
return(attempt)
}
)
names(results) <- paste0('(List name, Word) = (', list_names, ', ', words, ')')
return(results)
}

#' Get chemicals in a list specified by exact characters batch search
#'
#' @param list_names The names of the lists to search.
#' @param words The search words, one for each list.
#' @param API_key The user-specific API key.
#' @param rate_limit Number of seconds to wait between each request.
#' @param verbose A logical indicating if some "progress report" should be given.
#'
#' @return A named list of lists, with names corresponding to search terms and
#' lists corresponding to DTXSIDs associated to the search terms
#' @export
#'
#' @examplesIf FALSE
#' # Search `CCL4` for chemicals exactly matching with 'Bisphenol A' and
#' # `BIOSOLIDS2021` for chemicals exactly matching with 'Bisphenol A'.
#' bisphenol_a <- get_chemicals_in_list_exact_batch(list_names = c('CCL4',
#' 'BIOSOLIDS2021'),
#' words = rep('Bisphenol A', 2))

get_chemicals_in_list_exact_batch <- function(list_names = NULL,
words = NULL,
API_key = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
if (has_ctx_key()) {
API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
}
}
if(is.null(list_names) || is.null(words)){
stop('Please input a list for both `list_names` and `words`!')
} else if (length(list_names) != length(words)) {
stop('Mismatch in length of `list_names` and `words`!')
} else if (!all(sapply(c(list_names, words), is.character))) {
stop('Only character values allowed in `list_names` and `words`!')
}

if (!is.numeric(rate_limit) | (rate_limit < 0)){
warning('Setting rate limit to 0 seconds between requests!')
rate_limit <- 0L
}



results <- purrr::map2(.x = list_names, .y = words, function(d, t){
Sys.sleep(rate_limit)
attempt <- tryCatch(
{
get_chemicals_in_list_exact(list_name = d,
word = t,
API_key = API_key,
verbose = verbose)
},
error = function(cond){
message('There was an error!')
message(paste('List name:', d))
message(paste('Word:', t))
message(cond$message)
return(NA)
}
)
return(attempt)
}
)
names(results) <- paste0('(List name, Word) = (', list_names, ', ', words, ')')
return(results)
}

#' Get chemicals in a list specified by characters contained batch search
#'
#' @param list_names The names of the lists to search.
#' @param words The search words, one for each list.
#' @param API_key The user-specific API key.
#' @param rate_limit Number of seconds to wait between each request.
#' @param verbose A logical indicating if some "progress report" should be given.
#'
#' @return A named list of lists, with names corresponding to search terms and
#' lists corresponding to DTXSIDs associated to the search terms
#' @export
#'
#' @examplesIf FALSE
#' # Search `CCL4` for chemicals containing with 'Bis' and `BIOSOLIDS2021` for
#' # chemicals containing with 'Zyle'.
#' bis_and_zyle <- get_chemicals_in_list_contain_batch(list_names = c('CCL4',
#' 'BIOSOLIDS2021'),
#' words = c('Bis', 'Zyle'))

get_chemicals_in_list_contain_batch <- function(list_names = NULL,
words = NULL,
API_key = NULL,
rate_limit = 0L,
verbose = FALSE){
if (is.null(API_key) || !is.character(API_key)){
if (has_ctx_key()) {
API_key <- ctx_key()
if (verbose) {
message('Using stored API key!')
}
}
}
if(is.null(list_names) || is.null(words)){
stop('Please input a list for both `list_names` and `words`!')
} else if (length(list_names) != length(words)) {
stop('Mismatch in length of `list_names` and `words`!')
} else if (!all(sapply(c(list_names, words), is.character))) {
stop('Only character values allowed in `list_names` and `words`!')
}

if (!is.numeric(rate_limit) | (rate_limit < 0)){
warning('Setting rate limit to 0 seconds between requests!')
rate_limit <- 0L
}



results <- purrr::map2(.x = list_names, .y = words, function(d, t){
Sys.sleep(rate_limit)
attempt <- tryCatch(
{
get_chemicals_in_list_contain(list_name = d,
word = t,
API_key = API_key,
verbose = verbose)
},
error = function(cond){
message('There was an error!')
message(paste('List name:', d))
message(paste('Word:', t))
message(cond$message)
return(NA)
}
)
return(attempt)
}
)
names(results) <- paste0('(List name, Word) = (', list_names, ', ', words, ')')
return(results)
}



#' Get chemicals in a given chemical list batch
#'
#' @param list_names A list of names of chemical lists.
Expand Down Expand Up @@ -2182,6 +2398,45 @@ get_chemical_synonym_batch <- function(DTXSID = NULL,
stop('Please input a character list for DTXSID!')
}
DTXSID <- unique(DTXSID)
num_dtxsid <- length(DTXSID)
indices <- generate_ranges(num_dtxsid)
if (verbose) {
print(indices)
}

dt <- data.table::data.table(dtxsid = character(),
pcCode = character(),
valid = character(),
beilstein = character(),
alternateCasrn = character(),
good = character(),
other = character(),
deletedCasrn = character())

for (i in seq_along(indices)){
response <- httr::POST(url = paste0(chemical_api_server, '/synonym/search/by-dtxsid/'),
httr::add_headers(.headers = c(
'Accept' = 'application/json',
'Content-Type' = 'application/json',
'x-api-key' = API_key
)),
body = jsonlite::toJSON(DTXSID[indices[[i]]], auto_unbox = ifelse(length(DTXSID[indices[[i]]]) > 1, 'T', 'F')))

if (response$status_code == 200){
dt <- suppressWarnings(data.table::rbindlist(list(dt,
data.table::data.table(jsonlite::fromJSON(httr::content(response,
as = 'text',
encoding = "UTF-8")))),
fill = TRUE))

}
Sys.sleep(rate_limit)
}

return(dt)



results <- lapply(DTXSID, function(t){
Sys.sleep(rate_limit)
attempt <- tryCatch(
Expand Down
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