Merge pull request #14 from Sage-Bionetworks/develop

Develop

Author: Kenneth Daily

inst/report.Rmd

@@ -212,6 +212,7 @@ tmp <- queryData %>%
   dplyr::count(id, NAME, NODE_TYPE) %>% 
   dplyr::filter(n >= 5, !stringr::str_detect(id, "acl"))
 
+if (nrow(tmp) > 0) {
 dataaccessCount1 <- queryData %>% 
   dplyr::filter(recordType == 'download') %>% 
   dplyr::filter(id %in% tmp$id) %>% 
@@ -236,4 +237,5 @@ dataaccessCount <- dataaccessCount1 %>% left_join(dataaccessCount2, by=c("id", "
   dplyr::select(name, everything(), total, -id, -NAME)
 
 dataaccessCount %>% DT::datatable(options=list(pageLength=20), escape=1)
+}
 ```

inst/scripts/manual_AMPAD.R

@@ -1,18 +1,27 @@
+library(synapseClient)
+synapseLogin()
+
 templates <- c("webAccess"="../webAccess.Rmd", 
                "downloads"="../downloads.Rmd",
 	       "report"="../report.Rmd")
 
 ### AMP-AD
 projectId <- 'syn2580853'
-reportType <- "webAccess"
+reportType <- "report"
+
+# Store HTML file here
+parentId <- 'syn8457451'
 
 myParams <- list(projectId=projectId, 
-                 nMonths=26,
+                 nMonths=30,
                  aclTeamOrder=c(3346847, 3320424, projectId), 
                  useTeamGrouping=TRUE)
 
-reportType <- "report"
+htmlFileName <- paste0(myParams[['projectId']], "_", reportType, "_",
+                       lubridate::today(), ".html")
+
 rmarkdown::render(input=templates[[reportType]],
-                  output_file=paste0(myParams[['projectId']], "_", reportType, "_",
-                                     lubridate::today(), ".html"),
+                  output_file=htmlFileName,
                   params = myParams)
+
+htmlFile <- synStore(File(paste0("../", htmlFileName), parentId=parentId))