Merge pull request #128 from ncats/jb_rxn_plumbing

added 4 Rhea reaction endpoints

apps/ramp-server/plumber.R

@@ -561,12 +561,122 @@ function(metabolites = '', file = '', biospecimen = '', background = "database")
   }
 
 
+###########
+########### Reaction endpoints
+###########
 
 
 
+#' Returns reactions associated with input analytes, metabolites and/or genes/proteins.
+#' @param analytes
+#' @param namesOrIds
+#' @param onlyHumanMets
+#' @param humanProtein
+#' @param includeTransportRxns
+#' @param rxnDirs
+#' @post /api/reactions_from_analytes
+#' @serializer json list(digits = 6)
+function(
+    analytes,
+    namesOrIds,
+    onlyHumanMets,
+    includeTransportRxns,
+    rxnDirs
+) {
+
+  result = getReactionsForAnalytes(
+    db=rampDB,
+    analytes=analytes,
+    namesOrIds = 'ids',
+    onlyHumanMets = onlyHumanMets,
+    includeTransportRxns,
+    rxnDirs = rxnDirs
+  )
+
+  analyteStr = RaMP:::listToQueryString(analytes)
+  rxnDirs = RaMP:::listToQueryString(rxnDirs)
+
+  return(
+    list(
+      data = result,
+      function_call = paste0("RaMP::getReactionsForAnalytes(db=RaMPDB, analytes=c(",analyteStr,"), namesOrIDs='ids', onlyHumanMets=",onlyHumanMets,", includeTransportRxns=",includeTransportRxns,", rxnDirs=c(",rxnDirs,")")
+    )
+  )
+}
+
+
+#' getReactionClassesForAnalytes returns reactions class and EC numbers for a collection of input compound ids
+#'
+#' @param analytes
+#' @param multiParticipantCount
+#' @param humanProtein
+#' @post /api/reaction_classes_from_analytes
+#' @serializer json list(digits = 6)
+function(
+    analytes,
+    multiRxnParticipantCount,
+    humanProtein,
+    concatResults
+) {
+  result = getReactionClassesForAnalytes(db=rampDB, analytes=analytes, multiRxnParticipantCount = multiRxnParticipantCount, humanProtein=humanProtein, concatResults=concatResults)
+
+  analyteStr = RaMP:::listToQueryString(analytes)
+
+  return(
+    list(
+      data = result,
+      function_call = paste0("RaMP::getReactionClassesForAnalytes(db=RaMPDB, analytes=c(",analyteStr,"), multiRxnParticipantCount=",multiRxnParticipantCount,", humanProtein=",humanProtein,", concatResults=",concatResults,")")
+    )
+  )
+}
 
 
+#' getReactionParticipants returns protein information for a list of reaction ids.
+#' This utility method can help extend information from previous queries.
+#' For instance, if a user queries for reactions related to a list of metabolites,
+#' this method can be used to return proteins on some subset of reaction ids to find related proteins.
+#'
+#' @param reactionList Rhea reactions ids, such as rhea:38747
+#' @post /api/get_reaction_participants
+#' @serializer json list(digits = 6)
+function(
+  reactionList
+) {
+  result = getReactionParticipants(db=rampDB, reactionList=reactionList)
+
+  rxnStr = RaMP:::listToQueryString(reactionList)
+
+  return(
+    list(
+      data = result,
+      function_call = paste0("RaMP::getReactionParticipants(db=RaMPDB, reactionList=c(",rxnStr,"))")
+    )
+  )
+}
 
 
+#' getReactionDetails returns general reaction information for a list of reaction ids.
+#' This utility methed can help extend information from previous queries.
+#' For instance, if a user queries for reactions related to a list of analytes, or filtered on reactions,
+#' this method can be used to return general reaction info on some subset of reaction ids of interest.
+#'
+#' @param reactionList list of reaction ids
+#' @post /api/get_reaction_details
+#' @serializer json list(digits = 6)
+function(
+    reactionList
+) {
+  result = getReactionDetails(db=rampDB, reactionList=reactionList)
+
+  rxnStr = RaMP:::listToQueryString(reactionList)
+
+  return(
+    list(
+      data = result,
+      function_call = paste0("RaMP::getReactionDetails(db=RaMPDB, reactionList=c(",rxnStr,"))")
+    )
+  )
+}
+
 
 

apps/ramp-server/runRamp.R

@@ -1,3 +1,4 @@
 ramp_api <- plumber::plumb("plumber.R")
 source("db.R")
 ramp_api$run(host = "127.0.0.1", port = 5762)
+