abstract generate and store

Author: kdaily

inst/lib.R

@@ -327,4 +327,21 @@ topNEntities <- function(queryData, allUsers, topN=20) {
     dplyr::top_n(topN, n) %>% 
     dplyr::arrange(-n) %>% 
     dplyr::select(n)
-}
+}
+
+REPORT_TEMPLATES <- c("report"="../report.Rmd")
+
+generateAndStore <- function(myParams, reportType) {
+  htmlFileName <- paste0(myParams[['projectId']], "_", reportType, "_",
+                         lubridate::today(), ".html")
+  
+  outputFileName <- paste0(tempdir(), "/", htmlFileName)
+  
+  rmarkdown::render(input=REPORT_TEMPLATES[[reportType]],
+                    output_file=outputFileName,
+                    params=myParams)
+  
+  synStore(File(outputFileName,
+                name="Usage Statistics", 
+                parentId=parentId))
+}

inst/scripts/manual_PCBC.R

@@ -1,9 +1,8 @@
 library(synapseClient)
 synapseLogin()
+source("../lib.R")
 
-templates <- c("report"="../report.Rmd")
 reportType <- "report"
-
 projectId <- 'syn1773109'
 parentId <- 'syn4892835'
 
@@ -12,13 +11,4 @@ myParams <- list(projectId=projectId,
                  aclTeamOrder=c(2224090, 3319054, 273957, projectId), 
                  useTeamGrouping=FALSE)
 
-htmlFileName <- paste0(myParams[['projectId']], "_", reportType, "_",
-                       lubridate::today(), ".html")
-
-rmarkdown::render(input=templates[[reportType]],
-                  output_file=htmlFileName,
-                  params = myParams)
-
-htmlFile <- synStore(File(paste0("../", htmlFileName),
-                          name="Usage Statistics",
-                          parentId=parentId))
+generateAndStore(myParams, reportType)