fix works when a single different than is selected (#16) 🐛

c1au6i0 · Dec 6, 2024 · 419936a · 419936a
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diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,8 @@
 
 # extractox 0.1.1
 
-* fix: #15 now `extr_iris` extracts the correct number of chemicals with no repetition.
+* Fixed `extr_iris` extracts the correct number of chemicals with no repetition (#15}.
+* Fixed `extr_comtox` works when a single `download_items` different than `DTXCID` is selected (#16).
 
 # extractox 0.1.0
 

diff --git a/R/extr_comptox.R b/R/extr_comptox.R
@@ -6,7 +6,6 @@
 #' @param ids A character vector containing the items to be searched within the CompTox Chemistry Dashboard. These can be chemical names, CAS Registry Numbers (CASRN), InChIKeys, or DSSTox substance identifiers (DTXSID).
 #' @param download_items A character vector of items to be downloaded. This includes a comprehensive set of chemical properties, identifiers, predictive data, and other relevant information. By Default, it download all the info
 #' \describe{
-#'   \item{DTXCID}{The unique identifier for a chemical in the EPA's CompTox Chemicals Dashboard.}
 #'   \item{CASRN}{The Chemical Abstracts Service Registry Number, a unique numerical identifier for chemical substances.}
 #'   \item{INCHIKEY}{The hashed version of the full International Chemical Identifier (InChI) string.}
 #'   \item{IUPAC_NAME}{The International Union of Pure and Applied Chemistry (IUPAC) name of the chemical.}
@@ -94,7 +93,6 @@
 #' }
 extr_comptox <- function(ids,
                          download_items = c(
-                           "DTXCID",
                            "CASRN",
                            "INCHIKEY",
                            "IUPAC_NAME",
@@ -209,6 +207,9 @@ extr_comptox_ <- function(ids,
   identifier_types <- c("chemical_name", "CASRN", "INCHIKEY", "dtxsid")
   input_type <- "IDENTIFIER"
 
+
+  download_items <-  c("DTXCID", download_items)
+
   params <- list(
     identifierTypes = identifier_types,
     massError = mass_error,

diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: '3.2'
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-12-06T11:08Z
+last_built: 2024-12-06T12:06Z
 urls:
   reference: https://c1au6i0.github.io/extractox/reference
   article: https://c1au6i0.github.io/extractox/articles
diff --git a/docs/reference/extr_comptox.html b/docs/reference/extr_comptox.html
diff --git a/docs/reference/write_dataframes_to_excel.html b/docs/reference/write_dataframes_to_excel.html
diff --git a/docs/search.json b/docs/search.json
diff --git a/man/extr_comptox.Rd b/man/extr_comptox.Rd
diff --git a/tests/testthat/_snaps/comptox.md b/tests/testthat/_snaps/comptox.md
@@ -4,10 +4,10 @@
       result[!names(result) %in% "comptox_cover_sheet"]
     Output
       $comptox_main_data
-      # A tibble: 1 x 6
-        INPUT   FOUND_BY      DTXSID        PREFERRED_NAME DTXCID      CASRN  
-        <chr>   <chr>         <chr>         <chr>          <chr>       <chr>  
-      1 Aspirin Approved Name DTXSID5020108 Aspirin        DTXCID50108 50-78-2
+      # A tibble: 1 x 7
+        INPUT   FOUND_BY      DTXSID        PREFERRED_NAME DTXCID...5 DTXCID...6 CASRN
+        <chr>   <chr>         <chr>         <chr>          <chr>      <chr>      <chr>
+      1 Aspirin Approved Name DTXSID5020108 Aspirin        DTXCID501~ DTXCID501~ 50-7~
       
 
 # Valid CASRN input
@@ -16,10 +16,10 @@
       result[!names(result) %in% "comptox_cover_sheet"]
     Output
       $comptox_main_data
-      # A tibble: 1 x 6
-        INPUT   FOUND_BY DTXSID        PREFERRED_NAME DTXCID      CASRN  
-        <chr>   <chr>    <chr>         <chr>          <chr>       <chr>  
-      1 50-00-0 CASRN    DTXSID7020637 Formaldehyde   DTXCID30637 50-00-0
+      # A tibble: 1 x 7
+        INPUT   FOUND_BY DTXSID        PREFERRED_NAME DTXCID...5  DTXCID...6  CASRN  
+        <chr>   <chr>    <chr>         <chr>          <chr>       <chr>       <chr>  
+      1 50-00-0 CASRN    DTXSID7020637 Formaldehyde   DTXCID30637 DTXCID30637 50-00-0
       
 
 # Valid inputs
@@ -28,11 +28,11 @@
       result[!names(result) %in% "comptox_cover_sheet"]
     Output
       $comptox_main_data
-      # A tibble: 3 x 6
-        INPUT         FOUND_BY            DTXSID        PREFERRED_NAME DTXCID    CASRN
-        <chr>         <chr>               <chr>         <chr>          <chr>     <chr>
-      1 50-00-0       CASRN               DTXSID7020637 Formaldehyde   DTXCID30~ 50-0~
-      2 Aspirin       Approved Name       DTXSID5020108 Aspirin        DTXCID50~ 50-7~
-      3 DTXSID5020023 DSSTox_Substance_Id DTXSID5020023 Acrolein       DTXCID80~ 107-~
+      # A tibble: 3 x 7
+        INPUT         FOUND_BY       DTXSID PREFERRED_NAME DTXCID...5 DTXCID...6 CASRN
+        <chr>         <chr>          <chr>  <chr>          <chr>      <chr>      <chr>
+      1 50-00-0       CASRN          DTXSI~ Formaldehyde   DTXCID306~ DTXCID306~ 50-0~
+      2 Aspirin       Approved Name  DTXSI~ Aspirin        DTXCID501~ DTXCID501~ 50-7~
+      3 DTXSID5020023 DSSTox_Substa~ DTXSI~ Acrolein       DTXCID8023 DTXCID8023 107-~
       
 
diff --git a/tests/testthat/test-comptox.R b/tests/testthat/test-comptox.R
@@ -46,3 +46,10 @@ test_that("Missing required parameter", {
     "The argument ids is required."
   )
 })
+
+
+test_that("extr_comptox when download_items is set to one val", {
+  expect_no_error(
+  result <- extr_comptox(c("31-12-5", "80-05-7"), download_items = "TOXVAL_DETAILS")
+  )
+})