Merge pull request #28 from USEPA/27-add-functions-to-wrap-pubchem-li…

…nk-to-ghs-classification 27 add functions to wrap pubchem link to ghs classification
USEPA · Sep 12, 2024 · 0f2b811 · 0f2b811
2 parents b921302 + b43f402
commit 0f2b811
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diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(print,ctx_credentials)
+export(check_existence_by_dtxsid)
+export(check_existence_by_dtxsid_batch)
 export(chemical_contains)
 export(chemical_contains_batch)
 export(chemical_equal)

diff --git a/NEWS.md b/NEWS.md
@@ -12,6 +12,10 @@ information from 400 errors (@kisaacs1, #11).
 
 ## New features
 
+* Added `check_existence_by_dtxsid()`, `check_existence_by_dtxsid_batch()` 
+functions. Updated the `Chemical.Rmd` vignette to include examples of how to use
+these functions (#27).
+
 * Added `get_httk_data()`, `get_httk_data_batch()`, 
 `get_general_exposure_prediction()`, `get_general_exposure_prediction_batch()`,
 `get_demographic_exposure_prediction()`, 

diff --git a/R/chemical-APIs-batch.R b/R/chemical-APIs-batch.R
@@ -268,6 +268,109 @@ generate_dtxsid_string <- function(items){
   return(dtxsid_string)
 }
 
+#' Check existence by DTXSID batch
+#'
+#' @param DTXSID The chemical identifier DTXSIDs
+#' @param API_key The user-specific API key
+#' @param rate_limit Number of seconds to wait between each request.
+#' @param Server The root address of the API endpoint
+#' @param verbose A logical indicating whether some "progress report" should be
+#' given.
+#'
+#' @return A data.table of information detailing valid and invalid DTXSIDs.
+#' @export
+#'
+#' @examplesIf FALSE
+#' dtxsids <- c('DTXSID7020182F', 'DTXSID7020182', 'DTXSID0020232F')
+#' existence <- check_existence_by_dtxsid_batch(DTXSID = dtxsids)
+check_existence_by_dtxsid_batch <- function(DTXSID = NULL,
+                                            API_key = NULL,
+                                            rate_limit = 0L,
+                                            Server = chemical_api_server,
+                                            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.numeric(rate_limit) | (rate_limit < 0)){
+    warning('Setting rate limit to 0 seconds between requests!')
+    rate_limit <- 0L
+  }
+
+
+
+  if (!is.null(DTXSID)){
+    if (!is.character(DTXSID) & !all(sapply(DTXSID, is.character))){
+      stop('Please input a character list for DTXSID!')
+    }
+
+    DTXSID <- unique(DTXSID)
+    num_DTXSID <- length(DTXSID)
+    indices <- generate_ranges(num_DTXSID)
+
+    dt <- data.table::data.table(dtxsid = character(),
+                                 isSafetyData = logical(),
+                                 safetyUrl = character())
+
+    #names(dt) <- names
+
+    for (i in seq_along(indices)){
+      if (verbose) {
+        print(paste('The current index is i =', i, 'out of', length(indices)))
+      }
+
+      response <- httr::POST(url = paste0(Server, '/ghslink/to-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$status_code == 200){
+        if (length(response$content) > 0){
+          res_content <- jsonlite::fromJSON(httr::content(response,
+                                                          as = 'text',
+                                                          encoding = "UTF-8"))
+          if (length(res_content$safetyUrl) > 0){
+
+
+          null_indices <- which(sapply(res_content$safetyUrl, is.null))
+          if (length(null_indices) > 0){
+            res_content$safetyUrl[null_indices] <- NA_character_
+          }
+          dt <- suppressWarnings(data.table::rbindlist(list(dt,
+                                                            data.table::rbindlist(list(res_content))),
+                                                       fill = TRUE))
+
+          }
+        }
+      }
+      Sys.sleep(rate_limit)
+    }
+
+    # Fix for bug in endpoint. DTXSIDs that are not valid do not have information
+    # returned. To overcome this, the single search on the missing DTXSIDs is
+    # exectued and combined with the valid responses.
+    missing <- setdiff(DTXSID, dt$dtxsid)
+    if (length(missing) > 0){
+      missing_info <- data.table::rbindlist(lapply(missing, check_existence_by_dtxsid, API_key = API_key))
+      final <- data.table::rbindlist(list(dt, missing_info))
+      return(final[match(DTXSID, final$dtxsid),])
+    }
+
+
+
+  } else {
+    stop('Please input a list of DTXSIDs!')
+  }
+  return(dt)
+}
+
 get_smiles_batch <- function(names = NULL,
                              API_key = NULL,
                              rate_limit = 0L,
@@ -1098,7 +1201,7 @@ chemical_equal_batch <- function(word_list = NULL,
 
 
 
-
+      
       return(return_list)
     }
 

diff --git a/R/chemical-APIs.R b/R/chemical-APIs.R
@@ -280,6 +280,68 @@ create_data.table_chemical_details <- function(index = -1){
   return(data)
 }
 
+#' Check existence by DTXSID
+#'
+#' @param DTXSID The chemical identifier DTXSID
+#' @param API_key The user-specific API key
+#' @param Server The root address for the API endpoint
+#' @param verbose A logical indicating whether some "progress report" should be
+#' given.
+#'
+#' @return A data.table with information on whether the input DTXSID is valid,
+#' and where to find more information on the chemical when the DTXSID is valid.
+#' @export
+#'
+#' @examplesIf FALSE
+#' # DTXSID for bpa
+#' bpa <- check_existence_by_dtxsid('DTXSID7020182')
+#' # False DTXSID
+#' false_res <- check_existence_by_Dtxsid('DTXSID7020182f')
+
+check_existence_by_dtxsid <- function(DTXSID = NULL,
+                                      API_key = NULL,
+                                      Server = chemical_api_server,
+                                      verbose = FALSE){
+  if (is.null(DTXSID) | !is.character(DTXSID)){
+    stop('Please input a DTXSID!')
+  }
+
+  if (is.null(API_key)){
+    if (has_ctx_key()) {
+      API_key <- ctx_key()
+      message('Using stored API key!')
+    }
+  }
+
+  response <- httr::GET(url = paste0(Server, '/ghslink/to-dtxsid/', DTXSID),
+                        httr::add_headers(.headers = c(
+                          'Content-Type' =  'application/json',
+                          'x-api-key' = API_key)
+                        )
+  )
+
+  if(response$status_code == 401){
+    stop('Please input an API_key!')
+  }
+  if(response$status_code == 200){
+    res_content <- jsonlite::fromJSON(httr::content(response,
+                                                    as = 'text',
+                                                    encoding = "UTF-8"))
+    if (is.null(res_content$safetyUrl)){
+      res_content$safetyUrl <- NA_character_
+    }
+    res <- data.table::rbindlist(list(res_content))
+    return(res)
+  } else {
+    if (verbose){
+      print(paste0('The request was unsuccessful, returning an error of ', response$status_code, '!'))
+    }
+  }
+  return()
+
+
+}
+
 get_chemical_details_by_listname <- function(listname = NULL,
                                              API_key = NULL,
                                              Server = chemical_api_server,

diff --git a/man/check_existence_by_dtxsid.Rd b/man/check_existence_by_dtxsid.Rd
diff --git a/man/check_existence_by_dtxsid_batch.Rd b/man/check_existence_by_dtxsid_batch.Rd
diff --git a/tests/testthat/chemical-batch/chemical/detail/search/by-dtxcid/DTXCID30182-9e51f1.json b/tests/testthat/chemical-batch/chemical/detail/search/by-dtxcid/DTXCID30182-9e51f1.json
@@ -1,5 +1,6 @@
 {
     "id": "337693",
+    "cpdataCount": 292,
     "inchikey": "IISBACLAFKSPIT-UHFFFAOYSA-N",
     "wikipediaArticle": "Bisphenol A",
     "dtxsid": "DTXSID7020182",
@@ -34,6 +35,5 @@
     "irisLink": "356",
     "pprtvLink": null,
     "descriptorStringTsv": "0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0",
-    "isMarkush": false,
-    "cpdataCount": 292
+    "isMarkush": false
 }
diff --git a/tests/testthat/chemical-batch/chemical/detail/search/by-dtxsid-9e51f1-cd40e5-POST.R b/tests/testthat/chemical-batch/chemical/detail/search/by-dtxsid-9e51f1-cd40e5-POST.R
@@ -1,25 +1,25 @@
 structure(list(url = "https://api-ccte.epa.gov/chemical/detail/search/by-dtxsid/?projection=chemicaldetailstandard", 
     status_code = 401L, headers = structure(list(`content-type` = "application/json;charset=ISO-8859-1", 
         `content-length` = "164", connection = "keep-alive", 
-        date = "Wed, 22 May 2024 19:50:06 GMT", `strict-transport-security` = "max-age=31536000", 
-        `x-content-type-options` = "nosniff", `x-vcap-request-id` = "52ef7dea-f1b8-488f-6322-2e510c403b56", 
+        date = "Thu, 29 Aug 2024 19:35:38 GMT", `strict-transport-security` = "max-age=31536000", 
+        `x-content-type-options` = "nosniff", `x-vcap-request-id` = "ff9e668f-1084-4aa4-5a68-da205e1fd0c6", 
         `x-xss-protection` = "1; mode=block", `x-frame-options` = "DENY", 
-        `x-cache` = "Error from cloudfront", via = "1.1 052215bfd8d35ecb703b208e875bd350.cloudfront.net (CloudFront)", 
-        `x-amz-cf-pop` = "ATL59-P8", `x-amz-cf-id` = "r9PRCLIOMQ-IjFNVD1DH3Q1a-9TjGXT6Dl5bYiHGTaorjaQQPtNi1Q=="), class = c("insensitive", 
+        `x-cache` = "Error from cloudfront", via = "1.1 b5e757a7da6f6fe6261f56a8a9646880.cloudfront.net (CloudFront)", 
+        `x-amz-cf-pop` = "IAD89-C1", `x-amz-cf-id` = "kDYQM2MNV0A6RiiLL5dBEuolojD4vRlgYLjbyQ0a5L29xc_VsoOmCA=="), class = c("insensitive", 
     "list")), all_headers = list(list(status = 401L, version = "HTTP/1.1", 
         headers = structure(list(`content-type` = "application/json;charset=ISO-8859-1", 
             `content-length` = "164", connection = "keep-alive", 
-            date = "Wed, 22 May 2024 19:50:06 GMT", `strict-transport-security` = "max-age=31536000", 
-            `x-content-type-options` = "nosniff", `x-vcap-request-id` = "52ef7dea-f1b8-488f-6322-2e510c403b56", 
+            date = "Thu, 29 Aug 2024 19:35:38 GMT", `strict-transport-security` = "max-age=31536000", 
+            `x-content-type-options` = "nosniff", `x-vcap-request-id` = "ff9e668f-1084-4aa4-5a68-da205e1fd0c6", 
             `x-xss-protection` = "1; mode=block", `x-frame-options` = "DENY", 
-            `x-cache` = "Error from cloudfront", via = "1.1 052215bfd8d35ecb703b208e875bd350.cloudfront.net (CloudFront)", 
-            `x-amz-cf-pop` = "ATL59-P8", `x-amz-cf-id` = "r9PRCLIOMQ-IjFNVD1DH3Q1a-9TjGXT6Dl5bYiHGTaorjaQQPtNi1Q=="), class = c("insensitive", 
+            `x-cache` = "Error from cloudfront", via = "1.1 b5e757a7da6f6fe6261f56a8a9646880.cloudfront.net (CloudFront)", 
+            `x-amz-cf-pop` = "IAD89-C1", `x-amz-cf-id` = "kDYQM2MNV0A6RiiLL5dBEuolojD4vRlgYLjbyQ0a5L29xc_VsoOmCA=="), class = c("insensitive", 
         "list")))), cookies = structure(list(domain = logical(0), 
         flag = logical(0), path = logical(0), secure = logical(0), 
         expiration = structure(numeric(0), class = c("POSIXct", 
         "POSIXt")), name = logical(0), value = logical(0)), row.names = integer(0), class = "data.frame"), 
     content = charToRaw("{\"title\":\"API Header Not Found\",\"detail\":\"Every API call should pass assigned API key through custom http header or query parameter. Request is missing x-api-key.\"}"), 
-    date = structure(1716407406, class = c("POSIXct", "POSIXt"
-    ), tzone = "GMT"), times = c(redirect = 0, namelookup = 3.9e-05, 
-    connect = 0, pretransfer = 0.00015, starttransfer = 0.095333, 
-    total = 0.095361)), class = "response")
+    date = structure(1724960138, class = c("POSIXct", "POSIXt"
+    ), tzone = "GMT"), times = c(redirect = 0, namelookup = 4e-05, 
+    connect = 0, pretransfer = 0.000123, starttransfer = 0.250141, 
+    total = 0.250168)), class = "response")
diff --git a/tests/testthat/chemical-batch/chemical/detail/search/by-dtxsid-9e51f1-cd40e5-POST.json b/tests/testthat/chemical-batch/chemical/detail/search/by-dtxsid-9e51f1-cd40e5-POST.json
@@ -3,6 +3,7 @@
         "id": "337693",
         "inchikey": "IISBACLAFKSPIT-UHFFFAOYSA-N",
         "wikipediaArticle": "Bisphenol A",
+        "cpdataCount": 292,
         "dtxsid": "DTXSID7020182",
         "dtxcid": "DTXCID30182",
         "casrn": "80-05-7",
@@ -35,7 +36,6 @@
         "irisLink": "356",
         "pprtvLink": null,
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