async server updated

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: covidseirPrism
 Title: Peer Models Network PRISM Bridge for the covidseir
-Version: 0.2.1
+Version: 0.2.2
 Authors@R: c(
     person("Amin", "Adibi", email = "[email protected]", role = c("aut", "cph")),
     person("Mohsen", "Sadatsafavi", email = "[email protected]", role = c("aut", "cre")))
@@ -16,4 +16,4 @@ Imports:
     ggplot2 (>= 3.3.0),
     covidseir (>= 0.0.0.9006)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.2

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export(gateway)
+export(gatewayasync)
+export(prism_get_output_structure)
 export(prism_model_run)
 import(covidseir)
 import(ggplot2)

R/prism_server.R

@@ -16,39 +16,39 @@ thisSession$LONG_RUN_STATUS_DONE<-1
 thisSession$LONG_RUN_STATUS_ERROR<- -1
 
 thisSession$redis_connection_status <- 0  #0:not connected; 1:connected
-thisSession$REDIS_ADDRESS = "captain.cp.prism-ubc.linaralabs.com"
-thisSession$REDIS_PORT <- 3001
+thisSession$REDIS_ADDRESS = "srv-captain--persistent-redis"
+thisSession$REDIS_PORT <- 6379
 
 thisSession$MODEL_DESCRIPTION<-paste0("This is ",get_my_name()," - PRISM enabled!")
 thisSession$MODEL_VERSION<-paste(packageVersion(get_my_name()))
 
 
 #FOR ONE SHOT JSON CALL!
-#Can authenticate the user either by API key or by a session_id. 
+#Can authenticate the user either by API key or by a session_id.
 #' @export
 gateway<-function(...)
 {
   arguments=list(...)
   func<-arguments$func
-  
+
   session_id<-arguments$session_id
-  
+
   if(is.null(session_id)) session_id=""
-  
+
   session_id<<-session_id
-  
+
   arguments$func<-NULL
   arguments$api_key<-NULL
   arguments$session_id<-NULL
-  
-  
+
+
   if(length(arguments)==0) {
     out<-eval(parse(text=paste(func,"()")))
   }
   else {
     out<-do.call(func, args = arguments)
   }
-  
+
   return(jsonlite::toJSON(out))
 }
 
@@ -59,33 +59,33 @@ gateway<-function(...)
 gatewayasync<-function(...)
 {
   token <- generate_token()
-  
+
   arguments=list(...)
   func<-arguments$func
-  
+
   session_id<-arguments$session_id
-  
+
   if(is.null(session_id)) session_id=""
-  
+
   session_id<<-session_id
-  
+
   arguments$func<-NULL
   arguments$api_key<-NULL
   arguments$session_id<-NULL
-  
+
   token <- generate_token()
-  
-  redisConnect(host = thisSession$REDIS_ADDRESS, port = thisSession$REDIS_PORT, password = "H1Uf5o6326n6C2276m727cU82O")
+
+  redisConnect(host = thisSession$REDIS_ADDRESS, port = thisSession$REDIS_PORT, password = Sys.getenv("REDIS_PASSWORD"))
   redisSet(paste0("AS:status:",token),"[READY]")
   redisSet(paste0("AS:status_time:",token), Sys.time())
   redisSet(paste0("AS:status_data:",token),
            list(model_name=get_my_name(),
                 func=func,
                 arguments=arguments
-                )
-          )
+           )
+  )
   redisClose()
-  
+
   out <- list(token=token, error_code=0)
 
   return(jsonlite::toJSON(out))
@@ -94,7 +94,6 @@ gatewayasync<-function(...)
 
 
 
-
 #' @export
 prism_model_run<-function(model_input=NULL)
 {
@@ -107,14 +106,14 @@ connect_to_model<-function(api_key="")
 {
   model_name<-environmentName(environment(connect_to_model))
   out<-list(error_code=0,session_id="",version="",description="")
-  
-  
+
+
   if(thisSession$MODE_REQUIRE_SESSION)
   {
     session_id<-generate_session_id()
     out$session_id<-session_id
   }
-  
+
   out$version<-thisSession$MODEL_VERSION
   out$description<-thisSession$MODEL_DESCRIPTION
   return(out)
@@ -140,18 +139,7 @@ generate_token<-function()
 #' @export
 prism_get_output_structure<-function()
 {
-  out<-list(
-    n_agents=prism_output(source="$n_agents", type = "numeric/scalar", group = "", title = "Number of simulated individuals", description = ""),
-    cumul_time=prism_output(source="$cumul_time",type = "numeric/scalar", title = "cumulative time"),
-    n_deaths=prism_output(source="$n_deaths",type = "numeric/scalar", title = "number of deaths"),
-    n_COPD=prism_output(source="$n_COPD",type = "numeric/scalar", title = "Number of patients with COPD"),
-    total_exac=prism_output(source="$total_exac",type = "numeric/vector", title = "Total number of exacerbations by severity"),
-    total_exac_time=prism_output(source="$total_exac_time",type = "numeric/vector", title = "total_exac_time"),
-    total_pack_years=prism_output(source="$total_pack_years",type = "numeric/scalar", title = "Total pack-years"),
-    total_doctor_visit=prism_output(source="$total_doctor_visit",type = "numeric/vector", title = "Total doctor visits"),
-    total_cost=prism_output(source="$total_cost",type = "numeric/scalar", title = "Total costs"),
-    total_qaly=prism_output(source="$total_qaly",type = "numeric/scalar", title = "Total QALY")
-  )
+  out<-list()
   return(out)
 }
 
@@ -178,19 +166,18 @@ prism_get_async_results <- function(token=NULL)
     stop("Token was not provided.")
     return()
   }
-  
-  redisConnect(host = thisSession$REDIS_ADDRESS, port = thisSession$REDIS_PORT, password = "H1Uf5o6326n6C2276m727cU82O")
-  
+
+  redisConnect(host = thisSession$REDIS_ADDRESS, port = thisSession$REDIS_PORT, password = Sys.getenv("REDIS_PASSWORD"))
+
   status <- redisGet(paste0("AS:status:",token))
   if(is.null(status))
   {
     stop("Job with this token not found.")
   }
   status_data <- redisGet(paste0("AS:status_data:",token))
-  
+
   redisClose()
-  
+
   return(list(status=status,status_data=status_data))
 }
 
-