Merge pull request #86 from USEPA/85-synonym-search

Correct columns returned in synonym functions, update NEWS

Author: rachmaninoffpk

NEWS.md

@@ -2,7 +2,9 @@
 
 ## Minor improvements and fixes
 
-* Removed columns no longer returned from API in `get_fate_by_dtxsid_batch()`.
+* Removed columns no longer returned from API in `get_fate_by_dtxsid_batch()` (#81)
+* Correct endpoints used in experimental and predicted property batch functions (#83)
+* Update columns returned from API in `get_chemical_synonym` and `get_chemical_synonym_batch` functions (#85)
 
 # ctxR 1.1.3
 

R/chemical-APIs-batch.R

@@ -2823,10 +2823,10 @@ get_chemical_synonym_batch <- function(DTXSID = NULL,
                                  pcCode = character(),
                                  valid = character(),
                                  beilstein = character(),
-                                 alternateCasrn = character(),
+                                 alternate = character(),
                                  good = character(),
                                  other = character(),
-                                 deletedCasrn = character())
+                                 deleted = character())
 
     for (i in seq_along(indices)){
       response <- httr::POST(url = paste0(chemical_api_server, '/synonym/search/by-dtxsid/'),

R/chemical-APIs.R

@@ -2070,8 +2070,8 @@ get_chemical_synonym <- function(DTXSID = NULL,
 
     parse_dt <- data.table::data.table(tibble::as_tibble_row(parse_list))
     data.table::setcolorder(parse_dt, c('dtxsid', 'pcCode', 'valid', 'beilstein',
-                                        'alternateCasrn', 'good', 'other',
-                                        'deletedCasrn'))
+                                        'alternate', 'good', 'other',
+                                        'deleted'))
 
     return(parse_dt)
   } else {

tests/testthat/chemical/ctx/chemical/detail/search/by-dtxcid/DTXCID30182-9e51f1.json

@@ -1,7 +1,5 @@
 {
-    "id": "923260",
-    "inchikey": "IISBACLAFKSPIT-UHFFFAOYSA-N",
-    "wikipediaArticle": "Bisphenol_A",
+    "id": 923260,
     "dtxsid": "DTXSID7020182",
     "dtxcid": "DTXCID30182",
     "casrn": "80-05-7",
@@ -29,11 +27,13 @@
     "iupacName": null,
     "smiles": "CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1",
     "inchiString": "InChI=1S/C15H16O2/c1-15(2,11-3-7-13(16)8-4-11)12-5-9-14(17)10-6-12/h3-10,16-17H,1-2H3\n",
+    "inchikey": "IISBACLAFKSPIT-UHFFFAOYSA-N",
     "qcNotes": "Repeating chemical structure unit of Polycarbonate made from bisphenol A",
     "qsarReadySmiles": "[13CH3]C([13CH3])(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,[2H]C1=C([2H])C(=C([2H])C([2H])=C1O)C(C)(C)C1=C([2H])C([2H])=C(O)C([2H])=C1[2H],[2H]C([2H])([2H])C(C1=CC=C(O)C=C1)(C1=CC=C(O)C=C1)C([2H])([2H])[2H],[2H]OC1=C([2H])C([2H])=C(C([2H])=C1[2H])C(C1=C([2H])C([2H])=C(O[2H])C([2H])=C1[2H])(C([2H])([2H])[2H])C([2H])([2H])[2H],[Ba++].CC(C)(C1=CC=C([O-])C=C1)C1=CC=C([O-])C=C1,CC(C)([13C]1=[13CH][13CH]=[13C](O)[13CH]=[13CH]1)[13C]1=[13CH][13CH]=[13C](O)[13CH]=[13CH]1,CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,CS(O)(=O)=O.CS(O)(=O)=O.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,[Na+].[Na+].CC(C)(C1=CC=C([O-])C=C1)C1=CC=C([O-])C=C1,O=C1CCCCCO1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,OC(O)=O.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,OP(O)O.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1",
     "msReadySmiles": "[13CH3]C([13CH3])(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,[2H]C1=C([2H])C(=C([2H])C([2H])=C1O)C(C)(C)C1=C([2H])C([2H])=C(O)C([2H])=C1[2H],[2H]C([2H])([2H])C(C1=CC=C(O)C=C1)(C1=CC=C(O)C=C1)C([2H])([2H])[2H],[2H]OC1=C([2H])C([2H])=C(C([2H])=C1[2H])C(C1=C([2H])C([2H])=C(O[2H])C([2H])=C1[2H])(C([2H])([2H])[2H])C([2H])([2H])[2H],[Ba++].CC(C)(C1=CC=C([O-])C=C1)C1=CC=C([O-])C=C1,BrCC(Br)COCC(Br)CBr.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,CC(C)([13C]1=[13CH][13CH]=[13C](O)[13CH]=[13CH]1)[13C]1=[13CH][13CH]=[13C](O)[13CH]=[13CH]1,CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1.CCCCOCC(COC1=CC=C(C=C1)C(C)(C)C1=CC=C(OCC(COCCCC)OCC2CO2)C=C1)OCC1CO1,CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1.CP(=O)(OC1=CC=CC=C1)OC1=CC=CC=C1,CC(=C)C(=O)OCC1CO1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,ClC#N.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,CS(O)(=O)=O.CS(O)(=O)=O.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,[H]OC1=C([2H])C([2H])=C(C([2H])=C1[2H])C(C1=C([2H])C([2H])=C(O[H])C([2H])=C1[2H])(C([2H])([2H])[2H])C([2H])([2H])[2H],[Na+].[Na+].CC(C)(C1=CC=C([O-])C=C1)C1=CC=C([O-])C=C1,NCCN1CCNCC1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,NCCNCCN.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,N.ClCC1CO1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,NC(O)=O.NC(O)=O.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,O=C1CCCCCO1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,OCCO.OCCCO.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,OC(O)=O.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,OP(O)O.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1.CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1,[Pb++].CC(C)(C1=CC=C([O-])C=C1)C1=CC=C([O-])C=C1",
     "irisLink": "356",
     "pprtvLink": null,
+    "wikipediaArticle": "Bisphenol_A",
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 }