Merge pull request #3053 from koolgax99/run-ma

[WIP] Run meta analysis for a settings file API

Author: infotroph

apps/api/R/entrypoint.R

@@ -73,6 +73,11 @@ root$mount("/api/availableModels", runs_pr)
 runs_pr <- plumber::Plumber$new("posteriors.R")
 root$mount("/api/posteriors", runs_pr)
 
+# Run a meta-analysis from an uploaded XML file
+# Caution: Minimally tested.
+ma_pr <- plumber::Plumber$new("ma.R")
+root$mount("/api/ma", ma_pr)
+
 # set swagger documentation
 root$setApiSpec("../pecanapi-spec.yml")
 

apps/api/R/ma.R

@@ -0,0 +1,61 @@
+library(dplyr)
+library("PEcAn.all")
+library("RCurl")
+
+#' Post a settings file for running a Meta-Analysis
+#' @param req Send pecan.xml in body as xml filetype
+#' @return A list of post.distns.MA.R
+#' @author Nihar Sanda
+#* @post /run
+submitWorkflow <- function(req, res){
+  if(req$HTTP_CONTENT_TYPE == "application/xml") {
+    # read req$bosy as xml
+    settingsXml <- XML::xmlParseString(stringr::str_replace(req$body, "<?.*?>\n", ""))
+    
+    ## convert the xml to a list
+    settings <- XML::xmlToList(settingsXml)
+    settings <- as.Settings(settings)
+    settings <- expandMultiSettings(settings)
+    
+    # Update/fix/check settings.
+    # Will only run the first time it's called, unless force=TRUE
+    settings <-
+      PEcAn.settings::prepare.settings(settings, force = FALSE)
+    
+    # Changing update to TRUE
+    settings$meta.analysis$update <- TRUE
+    
+    # Write pecan.CHECKED.xml
+    PEcAn.settings::write.settings(settings, outputfile = "pecan.CHECKED.xml")
+    
+    # Do conversions
+    settings <- PEcAn.workflow::do_conversions(settings)
+    settings <- PEcAn.workflow::runModule.get.trait.data(settings)
+    
+    # initiating variables needed for running meta analysis
+    pfts <- settings$pfts
+    iterations <- settings$meta.analysis$iter
+    random <- settings$meta.analysis$random.effects$on
+    use_ghs <- settings$meta.analysis$random.effects$use_ghs
+    threshold <- settings$meta.analysis$threshold
+    dbfiles <- settings$database$dbfiles
+    database <- settings$database$bety
+  
+    # running meta analysis
+    run.meta.analysis(pfts, iterations, random, threshold, 
+                      dbfiles, database, use_ghs)
+    
+    #PEcAn.MA::runModule.run.meta.analysis(settings = ma_settings)
+    
+    if(dir.exists(settings$pfts$pft$outdir)){ 
+     filepath <- paste0(settings$pfts$pft$outdir, "/post.distns.Rdata")
+     e <- new.env(parent = emptyenv())
+     load(filepath, envir = e)
+     return(list(status = "Meta Analysis ran successfully", data = as.list(e))
+    }
+  }
+  else{
+    res$status <- 415
+    return(paste("Unsupported request content type:", req$HTTP_CONTENT_TYPE))
+  }
+}