R/cdp-utils.R
In meerapatelmd/skyscraper: Scrape Clinical Drug Data
Defines functions
isMultipleHits
is404
scrape_cdp
Documented in
is404
isMultipleHits
scrape_cdp
#' @title
#' Scrape ChemiDPlus
#'
#' @description
#' The general \code{\link{scrape}} function is modified to scrape using the special parameters that ChemiDPlus requires to avoid errors.
#'
#' @inheritParams scrape
#'
#' @rdname scrape_cdp
#' @export
scrape_cdp <-
function(x,
options = c("RECOVER", "NOERROR", "NOBLANKS", "HUGE"),
sleep_time = 3,
verbose = TRUE) {
scrape(x = x,
options = options,
sleep_time = sleep_time,
verbose = verbose
)
}
#' @title
#' Is the RN URL returning an HTTP error 404?
#'
#' @description
#' This function gets a response from an RN URL and checks for a 404 message in the error output.
#'
#' @param rn_url Registry Number URL
#'
#' @return
#' logical vector of length 1
#'
#' @seealso
#' \code{\link[xml2]{read_xml}}
#'
#' @rdname is404
#'
#' @family chemidplus parsing
#'
#' @export
#'
#' @importFrom xml2 read_html
is404 <-
function(rn_url) {
# rn_url <- "https://chem.nlm.nih.gov/chemidplus/rn/startswith/499313-74-3"
response <-
tryCatch(
xml2::read_html(rn_url, options = c("RECOVER", "NOERROR", "NOBLANKS", "HUGE")),
error = function(e) {
return(toString(e))
}
)
if (is.character(response)) {
grepl("HTTP error 404",
response)
} else {
FALSE
}
}
#' @title
#' Get the RNs from a page listing the first 5 matches
#'
#' @inherit chemidplus_parsing_functions description
#'
#' @inheritSection chemidplus_parsing_functions Multiple Hits
#'
#' @inheritParams chemidplus_parsing_functions
#'
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[tibble]{as_tibble}}
#' \code{\link[rubix]{filter_at_grepl}}
#' \code{\link[tidyr]{extract}}
#' \code{\link[dplyr]{mutate}},\code{\link[dplyr]{mutate_all}}
#' \code{\link[stringr]{str_remove}}
#'
#' @rdname isMultipleHits
#'
#' @family chemidplus parsing
#'
#' @export
#'
#' @importFrom rvest html_nodes html_text
#' @importFrom magrittr %>%
#' @importFrom tibble as_tibble_col as_tibble tribble
#' @importFrom rubix filter_at_grepl rm_multibyte_chars normalize_all_to_na
#' @importFrom tidyr extract
#' @importFrom dplyr mutate mutate_all filter_at distinct transmute bind_rows all_vars mutate_if
#' @importFrom stringr str_remove_all
isMultipleHits <-
function(response) {
# Get list of the search results that can be in the format of a. "{SubstanceName}{RNNumber}No Structure" or b. "MW: {molecular weight}"
output <-
response %>%
rvest::html_nodes(".bodytext") %>%
rvest::html_text()
# Concatenate 1 or more {SubstanceName} out of the "{SubstanceName}{RNNumber}" in a pipe-separated string to isolate RN number in output above using regex
chem_names <-
response %>%
rvest::html_nodes(".chem-name") %>%
rvest::html_text() %>%
paste(collapse = "|")
output_a <-
tryCatch(
output %>%
tibble::as_tibble_col(column_name = "multiple_match") %>%
rubix::filter_at_grepl(multiple_match,
grepl_phrase = "MW[:]{1} ",
evaluates_to = FALSE) %>%
tidyr::extract(col = multiple_match,
into = c("compound_match", "rn"),
regex = paste0("(^", chem_names, ") \\[.*?\\](.*$)")) %>%
dplyr::mutate(rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/",rn)) %>%
dplyr::mutate_all(stringr::str_remove_all, "No Structure") %>%
dplyr::filter_at(vars(compound_match,
rn),
dplyr::all_vars(!is.na(.))),
error = function(e) NULL)
if (is.null(output_a)) {
chem_name_vector <-
response %>%
rvest::html_nodes(".chem-name") %>%
rvest::html_text()
output %>%
tibble::as_tibble_col(column_name = "multiple_match") %>%
rubix::filter_at_grepl(multiple_match,
grepl_phrase = "MW[:]{1} ",
evaluates_to = FALSE) %>%
dplyr::mutate(compound_match = chem_name_vector) %>%
dplyr::mutate(nchar_compound_name = nchar(compound_match)) %>%
dplyr::mutate(string_start_rn = nchar_compound_name+1) %>%
dplyr::mutate(total_nchar = nchar(multiple_match)) %>%
dplyr::mutate(rn = substr(multiple_match, string_start_rn, total_nchar)) %>%
dplyr::mutate_all(stringr::str_remove_all, "No Structure") %>%
rubix::rm_multibyte_chars() %>%
dplyr::filter_at(vars(compound_match,
rn),
dplyr::all_vars(!is.na(.))) %>%
dplyr::distinct() %>%
tibble::as_tibble() %>%
rubix::normalize_all_to_na() %>%
dplyr::transmute(compound_match,
rn,
rn_url = ifelse(!is.na(rn),
paste0("https://chem.nlm.nih.gov/chemidplus/rn/", rn),
NA))
} else {
output_b <-
output %>%
tibble::as_tibble_col(column_name = "multiple_match") %>%
rubix::filter_at_grepl(multiple_match,
grepl_phrase = "MW[:]{1} ",
evaluates_to = FALSE) %>%
tidyr::extract(col = multiple_match,
into = c("compound_match", "rn"),
regex = paste0("(^", chem_names, ")([0-9]{1,}[-]{1}[0-9]{1,}[-]{1}[0-9]{1,}.*$)")) %>%
dplyr::mutate(rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/",rn)) %>%
dplyr::mutate_all(stringr::str_remove_all, "No Structure") %>%
dplyr::filter_at(vars(compound_match,
rn),
dplyr::all_vars(!is.na(.)))
output <-
dplyr::bind_rows(output_a,
output_b) %>%
dplyr::distinct()
if (nrow(output)) {
output %>%
tibble::as_tibble() %>%
rubix::normalize_all_to_na() %>%
dplyr::transmute(compound_match,
rn,
rn_url = ifelse(!is.na(rn),
paste0("https://chem.nlm.nih.gov/chemidplus/rn/", rn),
NA)) %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
} else {
tibble::tribble(~compound_match, ~rn, ~rn_url)
}
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param response PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[stringr]{str_remove}},\code{\link[stringr]{modifiers}}
#' \code{\link[tibble]{tibble}}
#' \code{\link[dplyr]{bind}}
#' @rdname isMultipleHits2
#' @export
#' @importFrom rvest html_nodes html_text
#' @importFrom stringr str_remove_all str_remove fixed
#' @importFrom tibble tibble
#' @importFrom dplyr bind_rows mutate_if
isMultipleHits2 <-
function(response) {
#response <- xml2::read_html("https://chem.nlm.nih.gov/chemidplus/name/contains/DEPATUXIZUMAB")
# Get list of the search results that can be in the format of a. "{SubstanceName}{RNNumber}No Structure" or b. "MW: {molecular weight}"
output <-
response %>%
rvest::html_nodes(".bodytext") %>%
rvest::html_text() %>%
stringr::str_remove_all("No Structure") %>%
grep(pattern = "^MW[:]{1}[ ]{1}", invert = TRUE, value = TRUE)
# Get{SubstanceName} out of the "{SubstanceName}{RNNumber}" to isolate RN number in output above using regex
chem_names <-
response %>%
rvest::html_nodes(".chem-name") %>%
rvest::html_text()
# For each chem_name found, to match it with the appropriate vector in output above and then get the RN number
multiple_hits_results <- list()
for (chem_name in chem_names) {
rn_match <- grep(chem_name, output, value = TRUE, fixed = TRUE)
rn_match <- stringr::str_remove(rn_match, pattern = stringr::fixed(chem_name))
multiple_hits_results[[1+length(multiple_hits_results)]] <-
tibble::tibble(compound_match = chem_name,
rn = rn_match,
rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/", rn_match))
}
dplyr::bind_rows(multiple_hits_results) %>%
dplyr::mutate(rn = trimws(rn, which = "both")) %>%
dplyr::filter(rn != "") %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param response PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[stringr]{str_remove}},\code{\link[stringr]{modifiers}}
#' \code{\link[tibble]{tibble}}
#' \code{\link[dplyr]{bind}}
#' @rdname isMultipleHits3
#' @export
#' @importFrom rvest html_nodes html_text
#' @importFrom stringr str_remove_all str_remove fixed
#' @importFrom tibble tibble
#' @importFrom dplyr bind_rows mutate_if
isMultipleHits3 <-
function(response) {
#response <- xml2::read_html("https://chem.nlm.nih.gov/chemidplus/name/contains/DEPATUXIZUMAB")
rns <-
response %>%
rvest::html_nodes(".bodytext a") %>%
rvest::html_attr("href") %>%
stringr::str_replace_all("(^javascript[:]{1}loadChemicalIndex[(]{1}['])(.*?)([']{1}.*$)", "\\2") %>%
centipede::no_blank()
if (length(rns)) {
rn_urls <- paste0("https://chem.nlm.nih.gov/chemidplus/rn/", rns)
chem_names <-
response %>%
rvest::html_nodes(".chem-name") %>%
rvest::html_text()
tibble::tibble(compound_match = chem_names,
rn = rns,
rn_url = rn_urls) %>%
dplyr::mutate(rn = trimws(rn, which = "both")) %>%
dplyr::filter(rn != "") %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
} else {
tibble::tribble(~compound_match, ~rn, ~rn_url)
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param response PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[centipede]{strsplit}},\code{\link[centipede]{no_na}}
#' \code{\link[tibble]{as_tibble}},\code{\link[tibble]{tribble}}
#' \code{\link[tidyr]{extract}},\code{\link[tidyr]{pivot_wider}}
#' \code{\link[dplyr]{mutate}}
#' \code{\link[stringr]{str_remove}}
#' @rdname isSingleHit2
#' @export
#' @importFrom rvest html_nodes html_text
#' @importFrom centipede strsplit no_na
#' @importFrom tibble as_tibble_col tribble tibble
#' @importFrom tidyr extract pivot_wider
#' @importFrom dplyr transmute mutate mutate_if
#' @importFrom stringr str_remove_all
isSingleHit2 <-
function(response) {
# response <- xml2::read_html("https://chem.nlm.nih.gov/chemidplus/name/contains/BI836858")
# Get list of the search results that can be in the format of a. "{SubstanceName}{RNNumber}No Structure" or b. "MW: {molecular weight}"
output <-
response %>%
rvest::html_nodes("h1") %>%
rvest::html_text() %>%
centipede::strsplit(split = "Substance Name[:]{1}|RN[:]{1}|UNII[:]{1}|InChIKey[:]{1}|ID[:]{1}", type = "before") %>%
unlist() %>%
centipede::no_na()
if (length(output)) {
output2 <-
output %>%
centipede::strsplit(split = "Substance Name[:]{1}|RN[:]{1}|UNII[:]{1}|InChIKey[:]{1}|ID[:]{1}", type = "before") %>%
unlist() %>%
tibble::as_tibble_col(column_name = "h1") %>%
tidyr::extract(col = h1,
into = c("identifier_type", "identifier"),
regex = "(^.*?)[:]{1}(.*$)") %>%
tidyr::pivot_wider(names_from = identifier_type,
values_from = identifier)
if (!("RN" %in% colnames(output2))) {
if ("ID" %in% colnames(output2)) {
output2 %>%
dplyr::transmute(compound_match = `Substance Name`,
rn = stringr::str_remove_all(ID, "\\s{1,}")) %>%
dplyr::mutate(rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/",rn)) %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
}
} else {
tibble::tribble(~compound_match,
~rn,
~rn_url)
}
} else {
tibble::tribble(~compound_match,
~rn,
~rn_url)
}
}
#' @title
#' Does the RN URL indicate that no records were found?
#'
#' @inherit chemidplus_parsing_functions description
#'
#' @inheritSection chemidplus_parsing_functions No Records
#'
#' @inheritParams chemidplus_parsing_functions
#'
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#'
#' @rdname isNoRecord
#'
#' @family chemidplus parsing
#'
#' @export
#'
#' @importFrom rvest html_nodes html_text
#' @importFrom magrittr %>%
isNoRecord <-
function(response) {
result <-
response %>%
rvest::html_nodes("h3") %>%
rvest::html_text()
if (length(result) == 1) {
if (result == "The following query produced no records:") {
TRUE
} else {
FALSE
}
} else {
FALSE
}
}
#' @title
#' Parse the RN from a single Substance Page
#'
#'
#' @inherit chemidplus_parsing_functions description
#'
#' @inheritSection chemidplus_parsing_functions Single Hit
#'
#' @inheritParams chemidplus_parsing_functions
#'
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[centipede]{strsplit}}
#' \code{\link[tibble]{as_tibble}},\code{\link[tibble]{tribble}}
#' \code{\link[tidyr]{extract}},\code{\link[tidyr]{pivot_wider}}
#' \code{\link[dplyr]{mutate}}
#' \code{\link[stringr]{str_remove}}
#'
#' @rdname isSingleHit
#'
#' @family chemidplus parsing
#'
#' @export
#'
#' @importFrom rvest html_node html_text
#' @importFrom centipede strsplit
#' @importFrom tibble as_tibble_col tribble tibble
#' @importFrom tidyr extract pivot_wider
#' @importFrom dplyr transmute mutate mutate_if
#' @importFrom stringr str_remove_all
#' @importFrom magrittr %>%
isSingleHit <-
function(response) {
#response <- resp
output <-
response %>%
rvest::html_node("h1") %>%
rvest::html_text()
if (!is.na(output)) {
output2 <-
output %>%
centipede::strsplit(split = "Substance Name[:]{1}|RN[:]{1}|UNII[:]{1}|InChIKey[:]{1}|ID[:]{1}", type = "before") %>%
unlist() %>%
tibble::as_tibble_col(column_name = "h1") %>%
tidyr::extract(col = h1,
into = c("identifier_type", "identifier"),
regex = "(^.*?)[:]{1}(.*$)") %>%
tidyr::pivot_wider(names_from = identifier_type,
values_from = identifier)
if ("RN" %in% colnames(output2)) {
output2 %>%
dplyr::transmute(compound_match = `Substance Name`,
rn = stringr::str_remove_all(RN, "\\s{1,}")) %>%
dplyr::mutate(rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/",rn)) %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
} else {
tibble::tribble(~compound_match,
~rn,
~rn_url)
}
} else {
tibble::tribble(~compound_match,
~rn,
~rn_url)
}
}
meerapatelmd/skyscraper documentation built on Dec. 27, 2020, 7:46 a.m.
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Defines functions isMultipleHits is404 scrape_cdp
Documented in is404 isMultipleHits scrape_cdp
#' @title
#' Scrape ChemiDPlus
#'
#' @description
#' The general \code{\link{scrape}} function is modified to scrape using the special parameters that ChemiDPlus requires to avoid errors.
#'
#' @inheritParams scrape
#'
#' @rdname scrape_cdp
#' @export
scrape_cdp <-
function(x,
options = c("RECOVER", "NOERROR", "NOBLANKS", "HUGE"),
sleep_time = 3,
verbose = TRUE) {
scrape(x = x,
options = options,
sleep_time = sleep_time,
verbose = verbose
)
}
#' @title
#' Is the RN URL returning an HTTP error 404?
#'
#' @description
#' This function gets a response from an RN URL and checks for a 404 message in the error output.
#'
#' @param rn_url Registry Number URL
#'
#' @return
#' logical vector of length 1
#'
#' @seealso
#' \code{\link[xml2]{read_xml}}
#'
#' @rdname is404
#'
#' @family chemidplus parsing
#'
#' @export
#'
#' @importFrom xml2 read_html
is404 <-
function(rn_url) {
# rn_url <- "https://chem.nlm.nih.gov/chemidplus/rn/startswith/499313-74-3"
response <-
tryCatch(
xml2::read_html(rn_url, options = c("RECOVER", "NOERROR", "NOBLANKS", "HUGE")),
error = function(e) {
return(toString(e))
}
)
if (is.character(response)) {
grepl("HTTP error 404",
response)
} else {
FALSE
}
}
#' @title
#' Get the RNs from a page listing the first 5 matches
#'
#' @inherit chemidplus_parsing_functions description
#'
#' @inheritSection chemidplus_parsing_functions Multiple Hits
#'
#' @inheritParams chemidplus_parsing_functions
#'
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[tibble]{as_tibble}}
#' \code{\link[rubix]{filter_at_grepl}}
#' \code{\link[tidyr]{extract}}
#' \code{\link[dplyr]{mutate}},\code{\link[dplyr]{mutate_all}}
#' \code{\link[stringr]{str_remove}}
#'
#' @rdname isMultipleHits
#'
#' @family chemidplus parsing
#'
#' @export
#'
#' @importFrom rvest html_nodes html_text
#' @importFrom magrittr %>%
#' @importFrom tibble as_tibble_col as_tibble tribble
#' @importFrom rubix filter_at_grepl rm_multibyte_chars normalize_all_to_na
#' @importFrom tidyr extract
#' @importFrom dplyr mutate mutate_all filter_at distinct transmute bind_rows all_vars mutate_if
#' @importFrom stringr str_remove_all
isMultipleHits <-
function(response) {
# Get list of the search results that can be in the format of a. "{SubstanceName}{RNNumber}No Structure" or b. "MW: {molecular weight}"
output <-
response %>%
rvest::html_nodes(".bodytext") %>%
rvest::html_text()
# Concatenate 1 or more {SubstanceName} out of the "{SubstanceName}{RNNumber}" in a pipe-separated string to isolate RN number in output above using regex
chem_names <-
response %>%
rvest::html_nodes(".chem-name") %>%
rvest::html_text() %>%
paste(collapse = "|")
output_a <-
tryCatch(
output %>%
tibble::as_tibble_col(column_name = "multiple_match") %>%
rubix::filter_at_grepl(multiple_match,
grepl_phrase = "MW[:]{1} ",
evaluates_to = FALSE) %>%
tidyr::extract(col = multiple_match,
into = c("compound_match", "rn"),
regex = paste0("(^", chem_names, ") \\[.*?\\](.*$)")) %>%
dplyr::mutate(rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/",rn)) %>%
dplyr::mutate_all(stringr::str_remove_all, "No Structure") %>%
dplyr::filter_at(vars(compound_match,
rn),
dplyr::all_vars(!is.na(.))),
error = function(e) NULL)
if (is.null(output_a)) {
chem_name_vector <-
response %>%
rvest::html_nodes(".chem-name") %>%
rvest::html_text()
output %>%
tibble::as_tibble_col(column_name = "multiple_match") %>%
rubix::filter_at_grepl(multiple_match,
grepl_phrase = "MW[:]{1} ",
evaluates_to = FALSE) %>%
dplyr::mutate(compound_match = chem_name_vector) %>%
dplyr::mutate(nchar_compound_name = nchar(compound_match)) %>%
dplyr::mutate(string_start_rn = nchar_compound_name+1) %>%
dplyr::mutate(total_nchar = nchar(multiple_match)) %>%
dplyr::mutate(rn = substr(multiple_match, string_start_rn, total_nchar)) %>%
dplyr::mutate_all(stringr::str_remove_all, "No Structure") %>%
rubix::rm_multibyte_chars() %>%
dplyr::filter_at(vars(compound_match,
rn),
dplyr::all_vars(!is.na(.))) %>%
dplyr::distinct() %>%
tibble::as_tibble() %>%
rubix::normalize_all_to_na() %>%
dplyr::transmute(compound_match,
rn,
rn_url = ifelse(!is.na(rn),
paste0("https://chem.nlm.nih.gov/chemidplus/rn/", rn),
NA))
} else {
output_b <-
output %>%
tibble::as_tibble_col(column_name = "multiple_match") %>%
rubix::filter_at_grepl(multiple_match,
grepl_phrase = "MW[:]{1} ",
evaluates_to = FALSE) %>%
tidyr::extract(col = multiple_match,
into = c("compound_match", "rn"),
regex = paste0("(^", chem_names, ")([0-9]{1,}[-]{1}[0-9]{1,}[-]{1}[0-9]{1,}.*$)")) %>%
dplyr::mutate(rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/",rn)) %>%
dplyr::mutate_all(stringr::str_remove_all, "No Structure") %>%
dplyr::filter_at(vars(compound_match,
rn),
dplyr::all_vars(!is.na(.)))
output <-
dplyr::bind_rows(output_a,
output_b) %>%
dplyr::distinct()
if (nrow(output)) {
output %>%
tibble::as_tibble() %>%
rubix::normalize_all_to_na() %>%
dplyr::transmute(compound_match,
rn,
rn_url = ifelse(!is.na(rn),
paste0("https://chem.nlm.nih.gov/chemidplus/rn/", rn),
NA)) %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
} else {
tibble::tribble(~compound_match, ~rn, ~rn_url)
}
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param response PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[stringr]{str_remove}},\code{\link[stringr]{modifiers}}
#' \code{\link[tibble]{tibble}}
#' \code{\link[dplyr]{bind}}
#' @rdname isMultipleHits2
#' @export
#' @importFrom rvest html_nodes html_text
#' @importFrom stringr str_remove_all str_remove fixed
#' @importFrom tibble tibble
#' @importFrom dplyr bind_rows mutate_if
isMultipleHits2 <-
function(response) {
#response <- xml2::read_html("https://chem.nlm.nih.gov/chemidplus/name/contains/DEPATUXIZUMAB")
# Get list of the search results that can be in the format of a. "{SubstanceName}{RNNumber}No Structure" or b. "MW: {molecular weight}"
output <-
response %>%
rvest::html_nodes(".bodytext") %>%
rvest::html_text() %>%
stringr::str_remove_all("No Structure") %>%
grep(pattern = "^MW[:]{1}[ ]{1}", invert = TRUE, value = TRUE)
# Get{SubstanceName} out of the "{SubstanceName}{RNNumber}" to isolate RN number in output above using regex
chem_names <-
response %>%
rvest::html_nodes(".chem-name") %>%
rvest::html_text()
# For each chem_name found, to match it with the appropriate vector in output above and then get the RN number
multiple_hits_results <- list()
for (chem_name in chem_names) {
rn_match <- grep(chem_name, output, value = TRUE, fixed = TRUE)
rn_match <- stringr::str_remove(rn_match, pattern = stringr::fixed(chem_name))
multiple_hits_results[[1+length(multiple_hits_results)]] <-
tibble::tibble(compound_match = chem_name,
rn = rn_match,
rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/", rn_match))
}
dplyr::bind_rows(multiple_hits_results) %>%
dplyr::mutate(rn = trimws(rn, which = "both")) %>%
dplyr::filter(rn != "") %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param response PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[stringr]{str_remove}},\code{\link[stringr]{modifiers}}
#' \code{\link[tibble]{tibble}}
#' \code{\link[dplyr]{bind}}
#' @rdname isMultipleHits3
#' @export
#' @importFrom rvest html_nodes html_text
#' @importFrom stringr str_remove_all str_remove fixed
#' @importFrom tibble tibble
#' @importFrom dplyr bind_rows mutate_if
isMultipleHits3 <-
function(response) {
#response <- xml2::read_html("https://chem.nlm.nih.gov/chemidplus/name/contains/DEPATUXIZUMAB")
rns <-
response %>%
rvest::html_nodes(".bodytext a") %>%
rvest::html_attr("href") %>%
stringr::str_replace_all("(^javascript[:]{1}loadChemicalIndex[(]{1}['])(.*?)([']{1}.*$)", "\\2") %>%
centipede::no_blank()
if (length(rns)) {
rn_urls <- paste0("https://chem.nlm.nih.gov/chemidplus/rn/", rns)
chem_names <-
response %>%
rvest::html_nodes(".chem-name") %>%
rvest::html_text()
tibble::tibble(compound_match = chem_names,
rn = rns,
rn_url = rn_urls) %>%
dplyr::mutate(rn = trimws(rn, which = "both")) %>%
dplyr::filter(rn != "") %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
} else {
tibble::tribble(~compound_match, ~rn, ~rn_url)
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param response PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[centipede]{strsplit}},\code{\link[centipede]{no_na}}
#' \code{\link[tibble]{as_tibble}},\code{\link[tibble]{tribble}}
#' \code{\link[tidyr]{extract}},\code{\link[tidyr]{pivot_wider}}
#' \code{\link[dplyr]{mutate}}
#' \code{\link[stringr]{str_remove}}
#' @rdname isSingleHit2
#' @export
#' @importFrom rvest html_nodes html_text
#' @importFrom centipede strsplit no_na
#' @importFrom tibble as_tibble_col tribble tibble
#' @importFrom tidyr extract pivot_wider
#' @importFrom dplyr transmute mutate mutate_if
#' @importFrom stringr str_remove_all
isSingleHit2 <-
function(response) {
# response <- xml2::read_html("https://chem.nlm.nih.gov/chemidplus/name/contains/BI836858")
# Get list of the search results that can be in the format of a. "{SubstanceName}{RNNumber}No Structure" or b. "MW: {molecular weight}"
output <-
response %>%
rvest::html_nodes("h1") %>%
rvest::html_text() %>%
centipede::strsplit(split = "Substance Name[:]{1}|RN[:]{1}|UNII[:]{1}|InChIKey[:]{1}|ID[:]{1}", type = "before") %>%
unlist() %>%
centipede::no_na()
if (length(output)) {
output2 <-
output %>%
centipede::strsplit(split = "Substance Name[:]{1}|RN[:]{1}|UNII[:]{1}|InChIKey[:]{1}|ID[:]{1}", type = "before") %>%
unlist() %>%
tibble::as_tibble_col(column_name = "h1") %>%
tidyr::extract(col = h1,
into = c("identifier_type", "identifier"),
regex = "(^.*?)[:]{1}(.*$)") %>%
tidyr::pivot_wider(names_from = identifier_type,
values_from = identifier)
if (!("RN" %in% colnames(output2))) {
if ("ID" %in% colnames(output2)) {
output2 %>%
dplyr::transmute(compound_match = `Substance Name`,
rn = stringr::str_remove_all(ID, "\\s{1,}")) %>%
dplyr::mutate(rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/",rn)) %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
}
} else {
tibble::tribble(~compound_match,
~rn,
~rn_url)
}
} else {
tibble::tribble(~compound_match,
~rn,
~rn_url)
}
}
#' @title
#' Does the RN URL indicate that no records were found?
#'
#' @inherit chemidplus_parsing_functions description
#'
#' @inheritSection chemidplus_parsing_functions No Records
#'
#' @inheritParams chemidplus_parsing_functions
#'
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#'
#' @rdname isNoRecord
#'
#' @family chemidplus parsing
#'
#' @export
#'
#' @importFrom rvest html_nodes html_text
#' @importFrom magrittr %>%
isNoRecord <-
function(response) {
result <-
response %>%
rvest::html_nodes("h3") %>%
rvest::html_text()
if (length(result) == 1) {
if (result == "The following query produced no records:") {
TRUE
} else {
FALSE
}
} else {
FALSE
}
}
#' @title
#' Parse the RN from a single Substance Page
#'
#'
#' @inherit chemidplus_parsing_functions description
#'
#' @inheritSection chemidplus_parsing_functions Single Hit
#'
#' @inheritParams chemidplus_parsing_functions
#'
#' @seealso
#' \code{\link[rvest]{html_nodes}},\code{\link[rvest]{html_text}}
#' \code{\link[centipede]{strsplit}}
#' \code{\link[tibble]{as_tibble}},\code{\link[tibble]{tribble}}
#' \code{\link[tidyr]{extract}},\code{\link[tidyr]{pivot_wider}}
#' \code{\link[dplyr]{mutate}}
#' \code{\link[stringr]{str_remove}}
#'
#' @rdname isSingleHit
#'
#' @family chemidplus parsing
#'
#' @export
#'
#' @importFrom rvest html_node html_text
#' @importFrom centipede strsplit
#' @importFrom tibble as_tibble_col tribble tibble
#' @importFrom tidyr extract pivot_wider
#' @importFrom dplyr transmute mutate mutate_if
#' @importFrom stringr str_remove_all
#' @importFrom magrittr %>%
isSingleHit <-
function(response) {
#response <- resp
output <-
response %>%
rvest::html_node("h1") %>%
rvest::html_text()
if (!is.na(output)) {
output2 <-
output %>%
centipede::strsplit(split = "Substance Name[:]{1}|RN[:]{1}|UNII[:]{1}|InChIKey[:]{1}|ID[:]{1}", type = "before") %>%
unlist() %>%
tibble::as_tibble_col(column_name = "h1") %>%
tidyr::extract(col = h1,
into = c("identifier_type", "identifier"),
regex = "(^.*?)[:]{1}(.*$)") %>%
tidyr::pivot_wider(names_from = identifier_type,
values_from = identifier)
if ("RN" %in% colnames(output2)) {
output2 %>%
dplyr::transmute(compound_match = `Substance Name`,
rn = stringr::str_remove_all(RN, "\\s{1,}")) %>%
dplyr::mutate(rn_url = paste0("https://chem.nlm.nih.gov/chemidplus/rn/",rn)) %>%
dplyr::mutate_if(is.character, ~stringr::str_remove_all(., "[^ -~]"))
} else {
tibble::tribble(~compound_match,
~rn,
~rn_url)
}
} else {
tibble::tribble(~compound_match,
~rn,
~rn_url)
}
}
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