From 98fa375634f9ec384fb48019c6b3b27fdd276256 Mon Sep 17 00:00:00 2001 From: johnbraisted Date: Fri, 26 Jan 2024 15:07:42 -0500 Subject: [PATCH 1/2] comment in db.R --- apps/ramp-server/db.R | 1 + 1 file changed, 1 insertion(+) diff --git a/apps/ramp-server/db.R b/apps/ramp-server/db.R index 47c7a70..91a7073 100644 --- 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)) From 1b8f4ffd26f2c4533665bd3ea84201aa6c50e9b2 Mon Sep 17 00:00:00 2001 From: johnbraisted Date: Fri, 26 Jan 2024 15:42:33 -0500 Subject: [PATCH 2/2] plumber parameter patch --- apps/ramp-server/plumber.R | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/apps/ramp-server/plumber.R b/apps/ramp-server/plumber.R index 48155a8..c62aaa6 100644 --- 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)