Merge pull request #130 from ncats/jb_rxn_plumbing

plumber reaction endpoint parameter patch
ncats · Jan 30, 2024 · 88abcd7 · 88abcd7
2 parents a262670 + 1b8f4ff
commit 88abcd7
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/apps/ramp-server/db.R b/apps/ramp-server/db.R
@@ -11,6 +11,7 @@ port <- config$db_port
 
 #pkg.globals <- setConnectionToRaMP(dbname=dbname,username=username,conpass=conpass,host = host)
 
+# this call is used specifically for connection to MySQL/MariaDB databases.
 rampDB <<- RaMP:::.RaMP(driver = RMariaDB::MariaDB(), dbname = dbname,
                     username = username, conpass = conpass,
                     host = host, port = as.integer(port))

diff --git a/apps/ramp-server/plumber.R b/apps/ramp-server/plumber.R
@@ -580,6 +580,7 @@ function(
     analytes,
     namesOrIds,
     onlyHumanMets,
+    humanProtein,
     includeTransportRxns,
     rxnDirs
 ) {
@@ -589,6 +590,7 @@ function(
     analytes=analytes,
     namesOrIds = 'ids',
     onlyHumanMets = onlyHumanMets,
+    humanProtein = humanProtein,
     includeTransportRxns,
     rxnDirs = rxnDirs
   )
@@ -599,7 +601,7 @@ function(
   return(
     list(
       data = result,
-      function_call = paste0("RaMP::getReactionsForAnalytes(db=RaMPDB, analytes=c(",analyteStr,"), namesOrIDs='ids', onlyHumanMets=",onlyHumanMets,", includeTransportRxns=",includeTransportRxns,", rxnDirs=c(",rxnDirs,")")
+      function_call = paste0("RaMP::getReactionsForAnalytes(db=RaMPDB, analytes=c(",analyteStr,"), namesOrIDs='ids', onlyHumanMets=",onlyHumanMets,", humanProtein=",humanProtein,", includeTransportRxns=",includeTransportRxns,", rxnDirs=c(",rxnDirs,")")
     )
   )
 }
@@ -608,7 +610,7 @@ function(
 #' getReactionClassesForAnalytes returns reactions class and EC numbers for a collection of input compound ids
 #'
 #' @param analytes
-#' @param multiParticipantCount
+#' @param multiRxnParticipantCount
 #' @param humanProtein
 #' @post /api/reaction_classes_from_analytes
 #' @serializer json list(digits = 6)