Merge pull request #93 from lawinslow/master

Fixing Notaro sim out

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: mda.lakes
 Type: Package
 Title: Tools for combining models, data, and processing for lakes
-Version: 4.2.1
+Version: 4.3.0
 Date: 2015-12-03
 Author: Luke Winslow, Jordan Read
 Maintainer: Luke Winslow <[email protected]>

NAMESPACE

@@ -9,6 +9,7 @@ export(calc_stratified_periods)
 export(calc_toha)
 export(calc_toha_stats)
 export(comb_output_table)
+export(combine_output_data)
 export(create_irr_day_cycle)
 export(driver_add_burnin_years)
 export(driver_add_rain)
@@ -41,14 +42,18 @@ export(necsc_thermal_metrics_core)
 export(opti_thermal_habitat)
 export(populate_base_lake_nml)
 export(prep_run_glm_kd)
+export(run_necsc_lake)
+export(sb_archive_model)
 export(sens_seasonal_site)
 export(set_driver_url)
 export(summarize_notaro)
 import(GLMr)
 import(glmtools)
+import(jsonlite)
 import(lakeattributes)
 import(lubridate)
 import(rLakeAnalyzer)
+import(sbtools)
 import(tidyr)
 importFrom(accelerometry,rle2)
 importFrom(insol,JD)

R/comb_output_table.R

@@ -20,8 +20,10 @@ comb_output_table = function(pattern, ...){
 	out = data.frame()
 
 	for(i in 1:length(files)){
-		tmp = read.table(files[i], ...)
-		out = rbind(out, tmp)
+	  if(file.info(files[i])$size > 0){
+  		tmp = read.table(files[i], ...)
+  		out = rbind(out, tmp)
+	  }
 	}
 
 	return(out)

R/combine_output_data.R

@@ -0,0 +1,156 @@
+#library(mda.lakes)
+#library(sbtools)
+#library(jsonlite)
+
+#' @title combine full sim run output data
+#' 
+#' @description Combines all the individual compute node model files into 
+#' a few files for the whole simulation
+#' 
+#' @import jsonlite
+#' 
+#' 
+#' @export
+combine_output_data = function(sim, path, fast_tmp=tempdir()){
+
+
+  #ensure we have a trailing / on path
+  if(!substr(path, nchar(path), nchar(path)) == '/'){
+    path = paste0(path, '/')
+  }
+
+  core_path   = paste0(path, sim, '/', sim, '_core_metrics.tsv')
+  cfg_path    = paste0(path, sim, '/', sim, '_model_config.json')
+  hansen_path = paste0(path, sim, '/', sim, '_fish_hab.tsv')
+  cal_path    = paste0(path, sim, '/', sim, '_calibration_data.tsv')
+  error_path  = paste0(path, sim, '/', sim, '_error_output.tsv')
+
+  ################################################################################
+  ## read and handle core metrics
+  core_metrics = comb_output_table(paste0(path, sim, '/*/best_core_metrics.tsv'), 
+                                   sep='\t', header=TRUE, as.is=TRUE)
+
+  write.table(core_metrics, core_path, 
+              sep='\t', row.names=FALSE)
+
+  ################################################################################
+  ## read and handle habitat metrics
+  hab_metrics =  comb_output_table(paste0(path, sim, '/*/best_hansen_hab.tsv'), 
+                                   sep='\t', header=TRUE, as.is=TRUE)
+  write.table(hab_metrics, hansen_path, 
+              sep='\t', row.names=FALSE)
+
+
+  ################################################################################
+  ## read and handle habitat metrics
+  if(length(Sys.glob(paste0(path, sim, '/*/best_cal_data.tsv')))){
+    cat('Cal wrapup running.\n')
+    cal_data =  comb_output_table(paste0(path, sim, '/*/best_cal_data.tsv'), 
+                                     sep='\t', header=TRUE, as.is=TRUE)
+    write.table(cal_data, cal_path, 
+                sep='\t', row.names=FALSE)
+  }else{
+    cat('Skipping cal wrapup because no cal data.\n')
+  }
+
+  ################################################################################
+  ###read and handle NML files
+  nml_files = Sys.glob(paste0(path, sim, '/*/model_config.Rdata*'))
+
+  if(length(nml_files) > 0){
+    cat('Wrapping up all nml config.\n')
+
+    all_nml = list()
+    for(i in 1:length(nml_files)){
+      load(nml_files[i])
+      all_nml = c(all_nml, model_config)
+    }
+
+    all_nml = lapply(all_nml, function(x){class(x)='list'; x})
+    writeLines(toJSON(all_nml), cfg_path)
+  }else{
+    cat('Skipping nml config.\n')
+  }
+
+  ################################################################################
+  ### read and handle error files
+  bad_files = Sys.glob(paste0(path, sim, '/*/bad_data.Rdata*'))
+
+  bad_data = list()
+
+  for(i in 1:length(bad_files)){
+    tmp = new.env()
+    load(bad_files[i], envir = tmp)
+
+    bad_data = c(bad_data, tmp$bad_data)
+  }
+
+  save(bad_data, file=error_path)
+
+
+  ################################################################################
+  ###read and handle raw water temp data.
+  wtr_files = Sys.glob(paste0(path, sim, '/*/best_all_wtr.Rdata*'))
+
+  if(length(wtr_files) > 0){
+    cat('Wrapping up all raw wtr data.\n')
+    all_wtr_files = c()
+    wtemp_dir = file.path(fast_tmp, sim)
+    dir.create(wtemp_dir)
+
+    for(i in 1:length(wtr_files)){
+      load(wtr_files[i])
+
+      newfiles = lapply(dframes, function(df){
+        site_id = df$site_id[1]
+        df$site_id = NULL
+        wtemp_path = paste0(wtemp_dir, '/', sim, '_', site_id, '.tsv')
+
+        #the future sim periods were done separately, so they need to be appended
+        if(wtemp_path %in% all_wtr_files){
+          write.table(df, wtemp_path, sep='\t', row.names=FALSE, quote=FALSE, append=TRUE, col.names=FALSE)
+        }else{
+          write.table(df, wtemp_path, sep='\t', row.names=FALSE, quote=FALSE)
+        }
+
+        return(wtemp_path)
+      })
+
+      all_wtr_files = c(all_wtr_files, newfiles)
+    }
+
+    #split up files into 1000 lake groups 
+    all_wtr_files = sort(unique(unlist(all_wtr_files)))
+    splits = split(1:length(all_wtr_files), floor((1:length(all_wtr_files))/1000))
+
+    wtemp_zips = file.path(path, sim, paste0(sim, '_wtemp_', seq_along(splits), '.zip'))
+
+    #write an index file for later users
+    wtemp_zip_index = do.call(rbind, lapply(seq_along(splits), function(i){
+      data.frame(file_index=rep(basename(wtemp_zips)[i], length(splits[[i]])), 
+                 file_name=basename(all_wtr_files)[splits[[i]]])
+    }))
+    wtemp_indx = file.path(path, sim, paste0(sim, '_wtemp_index.tsv'))
+    write.table(wtemp_zip_index, wtemp_indx, sep='\t', row.names=FALSE)
+
+
+    for(i in 1:length(splits)){
+      zip(zipfile=wtemp_zips[i], files=all_wtr_files[splits[[i]]], zip='zip')
+    }
+    #delete raw text files to save space
+    unlink(all_wtr_files)
+
+  }else{
+    cat('Skipping raw wtr data.\n')
+  }
+
+  # #upload files to SB when done
+  # authenticate_sb(user, pass)
+  # itm_title = paste0('Simulated lake temperatures for ', sim, ' future projections')
+  # sim_itm = item_create(parent_id=sb_itm_root, title=itm_title)
+  # 
+  # item_append_files(sim_itm, files=c(core_path, cfg_path, hansen_path, wtemp_zips, wtemp_indx))
+  print(c(core_path, cfg_path, hansen_path, wtemp_zips, wtemp_indx))
+  return(c(core_path, cfg_path, hansen_path, wtemp_zips, wtemp_indx))
+}
+

R/get_driver_nhd.R

@@ -106,6 +106,10 @@ get_driver_index = function(driver_name, loc_cache=TRUE){
 
 	if(substr(pkg_info$dvr_url, nchar(pkg_info$dvr_url)-3,nchar(pkg_info$dvr_url)) == '.zip'){
 		unzip(pkg_info$dvr_url, files = paste0('drivers_GLM_', driver_name, '/driver_index.tsv'), exdir=dirname(dest), junkpaths=TRUE)
+	}else if(substr(index_url, 1,7) == 'file://'){
+
+	  dest = index_url
+
 	}else{
 		if(!download_helper(index_url, dest)){
 			stop('driver_index.tsv: unable to download for driver data:', driver_name)