GSoC 2017 PEcAn Shiny workflowPlot Git logs

gitdiff_db:query.dplyr

diff --git a/db/R/query.dplyr.R b/db/R/query.dplyr.R
index 18c52d7..f392886 100644
--- a/db/R/query.dplyr.R
+++ b/db/R/query.dplyr.R
@@ -134,14 +134,16 @@ runs <- function(bety, workflow_id) {
 #' @inheritParams dbHostInfo
 #' @param session Session object passed through Shiny
 #' @export
-get_workflow_ids <- function(bety, session) {
+get_workflow_ids <- function(bety, session,all.ids=FALSE) {
   query <- isolate(parseQueryString(session$clientData$url_search))
-  if ("workflow_id" %in% names(query)) {
+  # If we dont want all workflow ids but only workflow id from the user url query
+  if (!all.ids & "workflow_id" %in% names(query)) {
     ids <- unlist(query[names(query) == "workflow_id"], use.names = FALSE)
   } else {
     # Get all workflow IDs
     ids <- workflows(bety, ensemble = TRUE) %>% distinct(workflow_id) %>% collect %>% 
       .[["workflow_id"]] %>% sort(decreasing = TRUE)
+    # pull(.,workflow_id) %>% sort(decreasing = TRUE)
   }
   return(ids)
 }  # get_workflow_ids
@@ -208,3 +210,85 @@ get_var_names <- function(bety, workflow_id, run_id, remove_pool = TRUE) {
   }
   return(var_names)
 }  # get_var_names
+
+#' Get vector of variable names for a particular workflow and run ID
+#' @inheritParams get_var_names
+#' @param run_id Run ID
+#' @param workflow_id Workflow ID
+#' @export
+var_names_all <- function(bety, workflow_id, run_id) {
+  # @return List of variable names
+  # Get variables for a particular workflow and run id
+  var_names <- get_var_names(bety, workflow_id, run_id)
+  # Remove variables which should not be shown to the user
+  removeVarNames <- c('Year','FracJulianDay')
+  var_names <- var_names[!var_names %in% removeVarNames]
+  return(var_names)
+} # var_names_all
+
+#' Load data for a single run of the model
+#' @inheritParams var_names_all
+#' @inheritParams workflow
+#' @param run_id Run ID
+#' @param workflow_id Workflow ID
+#' @export
+load_data_single_run <- function(bety, workflow_id,run_id) {
+  # For a particular combination of workflow and run id, loads
+  # all variables from all files.
+  # @return Dataframe for one run
+  # Adapted from earlier code in pecan/shiny/workflowPlot/server.R
+  globalDF <- data.frame()
+  workflow <- collect(workflow(bety, workflow_id))
+  # Use the function 'var_names_all' to get all variables
+  removeVarNames <- c('Year','FracJulianDay')
+  var_names <- var_names_all(bety,workflow_id,run_id)
+  # Using earlier code, refactored
+  if(nrow(workflow) > 0) {
+    outputfolder <- file.path(workflow$folder, 'out', run_id)
+    files <- list.files(outputfolder, "*.nc$", full.names=TRUE)
+    for(file in files) {
+      nc <- nc_open(file)
+      for(var_name in var_names){
+        dates <- NA
+        vals <- NA
+        title <- var_name
+        ylab <- ""
+        var <- ncdf4::ncatt_get(nc, var_name)
+        #sw <- if ('Swdown' %in% names(nc$var)) ncdf4::ncvar_get(nc, 'Swdown') else TRUE
+        # Snow water
+        sw <- TRUE
+        # Check required bcoz many files don't contain title
+        if(!is.null(var$long_name)){
+          title <- var$long_name
+        }
+        # Check required bcoz many files don't contain units
+        if(!is.null(var$units)){
+          ylab <- var$units
+        }
+        x <- ncdays2date(ncdf4::ncvar_get(nc, 'time'), ncdf4::ncatt_get(nc, 'time'))
+        y <- ncdf4::ncvar_get(nc, var_name)
+        b <- !is.na(x) & !is.na(y) & sw != 0
+        dates <- if(is.na(dates)) x[b] else c(dates, x[b])
+        dates <- as.POSIXct(dates)
+        vals <- if(is.na(vals)) y[b] else c(vals, y[b])
+        xlab <- "Time"
+        # Values of the data which we will plot
+        valuesDF <- data.frame(dates,vals)
+        # Meta information about the data.
+        metaDF <- data.frame(workflow_id,run_id,title,xlab,ylab,var_name)
+        # Meta and Values DF created differently because they would of different
+        # number of rows. cbind would repeat metaDF(1X6) to the size of valuesDF
+        currentDF <- cbind(valuesDF,metaDF)
+        globalDF <- rbind(globalDF,currentDF)
+      }
+      ncdf4::nc_close(nc)
+    }
+  }
+  # Required to convert from factors to characters
+  # Otherwise error by ggplotly
+  globalDF$title <- as.character(globalDF$title)
+  globalDF$xlab <- as.character(globalDF$xlab)
+  globalDF$ylab <- as.character(globalDF$ylab)
+  globalDF$var_name <- as.character(globalDF$var_name)
+  return(globalDF)
+} #load_data_single_run

gitdiff_helper

diff --git a/shiny/workflowPlot/helper.R b/shiny/workflowPlot/helper.R
new file mode 100644
index 0000000..7e4cee2
--- /dev/null
+++ b/shiny/workflowPlot/helper.R
@@ -0,0 +1,54 @@
+# Helper function which checks and downloads required packages
+checkAndDownload<-function(packageNames) {
+  for(packageName in packageNames) {
+    if(!isInstalled(packageName)) {
+      install.packages(packageName,repos="http://lib.stat.cmu.edu/R/CRAN") 
+    } 
+    library(packageName,character.only=TRUE,quietly=TRUE,verbose=FALSE)
+  }
+}
+isInstalled <- function(mypkg){
+  is.element(mypkg, installed.packages()[,1])
+}
+# checkAndDownload(c('plotly','scales','dplyr'))
+# We can also save the csv on the run from the shiny app as well
+# write.csv(inputs_df,file='/home/carya/pecan/shiny/workflowPlot/inputs_df.csv',
+#           quote = FALSE,sep = ',',col.names = TRUE,row.names=FALSE)
+
+# Stashing Code for file upload to shiny app 
+# Based on https://shiny.rstudio.com/gallery/file-upload.html
+
+# ui.R 
+# tags$hr(),
+# fileInput('file1', 'Choose CSV File to upload data',
+#           accept=c('text/csv', 
+#                    'text/comma-separated-values,text/plain', 
+#                    '.csv')),
+# checkboxInput('header', 'Header', TRUE),
+# radioButtons('sep', 'Separator',
+#              c(Comma=',',
+#                Semicolon=';',
+#                Tab='\t'),
+#              ','),
+# radioButtons('quote', 'Quote',
+#              c(None='',
+#                'Double Quote'='"',
+#                'Single Quote'="'"),
+#              ''),
+# textInput("inputRecordID", "Input Record ID for file", "1000011260"),
+# textInput("formatID", "Format ID for file (Default CSV)", "5000000002"),
+# actionButton("load_data", "Load External Data")
+
+# server.R 
+# loadExternalData <-eventReactive(input$load_data,{
+#   inFile <- input$file1
+#   if (is.null(inFile))
+#     return(data.frame())
+#  # output$info1 <- renderText({
+#  #   # paste0(nrow(externalData))
+#  #   paste0(inFile$datapath)
+#  # })
+#   externalData <- read.csv(inFile$datapath, header=input$header, sep=input$sep, 
+#                            quote=input$quote)
+#   return(externalData)
+# })  

gitdiff_server

diff --git a/shiny/workflowPlot/server.R b/shiny/workflowPlot/server.R
index 1f4d31e..a81e11c 100644
--- a/shiny/workflowPlot/server.R
+++ b/shiny/workflowPlot/server.R
@@ -1,101 +1,266 @@
 library(PEcAn.visualization)
 library(PEcAn.DB)
+library(PEcAn.settings)
+library(PEcAn.benchmark)
+library(PEcAn.utils)
 library(shiny)
 library(ncdf4)
 library(ggplot2)
-
-
+# Helper allows to load functions and variables that could be shared both by server.R and ui.R 
+# source('helper.R')
+library(plotly)
+library(scales)
+library(lubridate)
+library(dplyr)
+library(reshape2)
+# Maximum size of file allowed to be uploaded: 100MB 
+options(shiny.maxRequestSize=100*1024^2) 
 # Define server logic
 server <- shinyServer(function(input, output, session) {
   bety <- betyConnect()
-
-  ranges <- reactiveValues(x = NULL, y = NULL)
-
-  print("RESTART")
-  # set the workflow id(s)
-  ids <- get_workflow_ids(bety, session)
-  updateSelectizeInput(session, "workflow_id", choices=ids)
-  workflow_id <- reactive({
-    req(input$workflow_id)
-    workflow_id <- input$workflow_id
-  })
-
-  # update the run_ids if user changes workflow
-  run_ids <- reactive(get_run_ids(bety, workflow_id()))
+  # Update all workflow ids
   observe({
-    updateSelectizeInput(session, "run_id", choices=run_ids())
+    # get_workflow_ids function (line 137) in db/R/query.dplyr.R takes a flag to check
+    # if we want to load all workflow ids.
+    # get_workflow_id function from query.dplyr.R
+    all_ids <- get_workflow_ids(bety, session,all.ids=TRUE)
+    updateSelectizeInput(session, "all_workflow_id", choices=all_ids)
   })
-
-  # update variables if user changes run
-  var_names <- reactive({
-      run_ids <- get_run_ids(bety, workflow_id())
-      var_names <- get_var_names(bety, workflow_id(), run_ids[1])
-      return(var_names)
+  # Update all run ids
+  all_run_ids <- reactive({
+    # Retrieves all run ids for seleted workflow ids
+    # Returns ('workflow ',w_id,', run ',r_id)
+    req(input$all_workflow_id)
+    w_ids <- input$all_workflow_id
+    # Will return a list
+    run_id_list <- c()
+    for(w_id in w_ids){
+      # For all the workflow ids
+      r_ids <- get_run_ids(bety, w_id)
+      for(r_id in r_ids){
+        # Each workflow id can have more than one run ids
+        # ',' as a separator between workflow id and run id
+        list_item <- paste0('workflow ',w_id,', run ',r_id)
+        run_id_list <- c(run_id_list,list_item)
+      }
+    }
+    return(run_id_list)
   })
+  # Update all run_ids ('workflow ',w_id,', run ',r_id)
   observe({
-    updateSelectizeInput(session, "variable_name", choices=var_names())
+    updateSelectizeInput(session, "all_run_id", choices=all_run_ids())
   })
-
-  observe({
-    ignore <- input$variable_name
-    ranges$x <- NULL
-    ranges$y <- NULL
+  return_DF_from_run_ID <- function(diff_ids){
+    # Called by function parse_ids_from_input_runID
+    # which is a wrapper of this function
+    # Returns a DF for a particular run_id
+    split_string <- strsplit(diff_ids,',')[[1]]
+    # Workflow id is the first element. Trim leading and ending white spaces. Split by space now
+    wID <- as.numeric(strsplit(trimws(split_string[1],which = c("both")),' ')[[1]][2])
+    # Run id is the second element
+    runID <- as.numeric(strsplit(trimws(split_string[2],which = c("both")),' ')[[1]][2])
+    return(data.frame(wID,runID))
+  }
+  # Wrapper over return_DF_from_run_ID
+  # @param list of multiple run ids
+  # run_id_string: ('workflow' workflow_ID, 'run' run_id)
+  # @return Data Frame of workflow and run ids
+  parse_ids_from_input_runID <- function(run_id_list){
+    globalDF <- data.frame()
+    for(w_run_id in run_id_list){
+      globalDF <- rbind(globalDF,return_DF_from_run_ID(w_run_id))
+    }
+    return(globalDF)
+  }  
+  # Update variable names observeEvent on input$load 
+  observeEvent(input$load,{
+    req(input$all_run_id)
+    # All information about a model is contained in 'all_run_id' string
+    ids_DF <- parse_ids_from_input_runID(input$all_run_id)
+    var_name_list <- c()
+    for(row_num in 1:nrow(ids_DF)){
+      var_name_list <- c(var_name_list,var_names_all(bety,ids_DF$wID[row_num],ids_DF$runID[row_num]))
+    }
+    updateSelectizeInput(session, "variable_name", choices=var_name_list)
   })
-
-  observeEvent(input$plot_dblclick, {
-    brush <- input$plot_brush
-    if (!is.null(brush)) {
-      ranges$x <- as.POSIXct(c(brush$xmin, brush$xmax), origin = "1970-01-01", tz = "UTC")
-      ranges$y <- c(brush$ymin, brush$ymax)
-    } else {
-      ranges$x <- NULL
-      ranges$y <- NULL
+  # Loads data for all workflow and run ids after the load button is pressed.
+  # All information about a model is contained in 'all_run_id' string
+  # Wrapper over 'load_data_single_run' in PEcAn.db::query.dplyr
+  # Model data different from observations data 
+  loadNewData <-eventReactive(input$load,{
+    req(input$all_run_id)
+    # Get IDs DF from 'all_run_id' string
+    ids_DF <- parse_ids_from_input_runID(input$all_run_id)
+    globalDF <- data.frame()
+    for(row_num in 1:nrow(ids_DF)){
+      globalDF <- rbind(globalDF, load_data_single_run(bety,ids_DF$wID[row_num],ids_DF$runID[row_num]))
     }
+    return(globalDF)
   })
-
-  output$outputPlot <- renderPlot({
-    workflow_id <- isolate(input$workflow_id)
-    run_id <- isolate(input$run_id)
-    var_name <- input$variable_name
-    if (workflow_id != "" && run_id != "" && var_name != "") {
-      workflow <- collect(workflow(bety, workflow_id))
-      if(nrow(workflow) > 0) {
-        outputfolder <- file.path(workflow$folder, 'out', run_id)
-        files <- list.files(outputfolder, "*.nc$", full.names=TRUE)
-        dates <- NA
-        vals <- NA
-        title <- var_name
-        ylab <- ""
-        for(file in files) {
-          nc <- nc_open(file)
-          var <- ncdf4::ncatt_get(nc, var_name)
-          #sw <- if ('Swdown' %in% names(nc$var)) ncdf4::ncvar_get(nc, 'Swdown') else TRUE
-          sw <- TRUE
-          title <- var$long_name
-          ylab <- var$units
-          x <- ncdays2date(ncdf4::ncvar_get(nc, 'time'), ncdf4::ncatt_get(nc, 'time'))
-          y <- ncdf4::ncvar_get(nc, var_name)
-          b <- !is.na(x) & !is.na(y) & sw != 0
-          dates <- if(is.na(dates)) x[b] else c(dates, x[b])
-          vals <- if(is.na(vals)) y[b] else c(vals, y[b])
-          ncdf4::nc_close(nc)
-        }
-        xlab <- if (is.null(ranges$x)) "Time" else paste(ranges$x, collapse=" - ")
-        # plot result
-        print(ranges$x)
-        plt <- ggplot(data.frame(dates, vals), aes(x=dates, y=vals)) +
-          geom_point(aes(color="Model output")) +
-#          geom_smooth(aes(fill = "Spline fit")) +
-          coord_cartesian(xlim = ranges$x, ylim = ranges$y) +
-          scale_y_continuous(labels=fancy_scientific) +
-          labs(title=title, x=xlab, y=ylab) + 
-          scale_color_manual(name = "", values = "black") +
-          scale_fill_manual(name = "", values = "grey50")
-        plot(plt)
-        add_icon()
+  # Allows to load actual data (different from model output) following the tutorial
+  # https://github.com/PecanProject/pecan/blob/develop/documentation/tutorials/AnalyzeOutput/modelVSdata.Rmd
+  # @params: bety,settings,File_path,File_format
+  # loadObservationData <- function(bety,settings,File_path,File_format){
+  loadObservationData <- function(bety,inputs_df){
+    input_id <- inputs_df$input_id
+    File_format <- getFileFormat(bety,input_id)
+    start.year <- as.numeric(lubridate::year(inputs_df$start_date))
+    end.year <- as.numeric(lubridate::year(inputs_df$end_date))
+    File_path <- inputs_df$filePath
+    # TODO There is an issue with the db where file names are not saved properly. 
+    # To make it work with the VM, uncomment the line below
+    # File_path <- paste0(inputs_df$filePath,'.csv')
+    site.id <- inputs_df$site_id
+    site<-PEcAn.DB::query.site(site.id,bety$con)
+    observations<-PEcAn.benchmark::load_data(data.path = File_path, format= File_format, time.row = File_format$time.row,  site = site, start_year = start.year, end_year = end.year) 
+    return(observations)
+  }
+  # This function is a wrapper over PEcAn.DB::query.format.vars where 
+  # file format can be retrieved using either by input or format id. 
+  getFileFormat <- function(bety,input.id,format.id=NULL){
+    # TODO Retaining the code for getting file format using format Id as in tutorial
+    # File_format <- PEcAn.DB::query.format.vars(bety = bety, format.id = format.id) 
+    File_format <- PEcAn.DB::query.format.vars(bety = bety, input.id = input.id)
+    return(File_format)
+  }
+  getSettingsFromWorkflowId <- function(bety,workflowID){
+    basePath <- tbl(bety, 'workflows') %>% dplyr::filter(id %in% workflowID) %>% pull(folder)
+    configPath <- file.path(basePath, 'pecan.CONFIGS.xml')
+    # Second way of providing configPath. More of a hack
+    # configPath <- paste0("~/output/PEcAn_",workflowID,"/pecan.CONFIGS.xml")
+    settings<-PEcAn.settings::read.settings(configPath)
+    return(settings)
+  }
+  observeEvent(input$load,{
+    # Retrieves all site ids from multiple seleted run ids when load button is pressed
+    req(input$all_run_id)
+    ids_DF <- parse_ids_from_input_runID(input$all_run_id)
+    site_id_list <- c()
+    for(row_num in 1:nrow(ids_DF)){
+      settings <- getSettingsFromWorkflowId(bety,ids_DF$wID[row_num])
+      site.id <- c(settings$run$site$id)
+      site_id_list <- c(site_id_list,site.id)
+    }
+    updateSelectizeInput(session, "all_site_id", choices=site_id_list)
+  })
+  # Get input id from selected site id. Returns inputs_df which is used to load observation data
+  getInputs <- function(bety,site_Id){
+    # Subsetting the input id list based on the current (VM) machine
+    my_hostname <- PEcAn.utils::fqdn()
+    my_machine_id <- tbl(bety, 'machines') %>% dplyr::filter(hostname == my_hostname) %>% pull(id)
+    # Inner join 'inputs' table with 'dbfiles' table
+    # inputs_df would contain all the information about the site and input id required for
+    # the tutorial mentioned above to compare model run with actual observations
+    inputs_df <- tbl(bety, 'dbfiles') %>% 
+      dplyr::filter(container_type == 'Input', machine_id == my_machine_id) %>%
+      inner_join(tbl(bety, 'inputs')  %>% dplyr::filter(site_id %in% site_Id), by = c('container_id' = 'id')) %>%
+      collect()
+    # Order by container id (==input id)
+    inputs_df <- inputs_df[order(inputs_df$container_id),]
+    # Mutate column as (input id, name) to be shown to the user
+    inputs_df <- inputs_df %>% 
+      dplyr::mutate(input_selection_list = paste(inputs_df$container_id, inputs_df$name),
+             filePath = paste0(inputs_df$file_path,'/', inputs_df$file_name)) %>%
+      dplyr::select(input_id = container_id,filePath,input_selection_list,start_date,end_date,site_id,name,
+             machine_id,file_name,file_path)
+    return(inputs_df)
+  }
+  # Update input id list as (input id, name)
+  observe({
+    req(input$all_site_id)
+    inputs_df <- getInputs(bety,c(input$all_site_id))
+    updateSelectizeInput(session, "all_input_id", choices=inputs_df$input_selection_list)
+  })
+  # Renders ggplotly 
+  output$outputPlot <- renderPlotly({
+    # Error messages
+    validate(
+      need(input$all_workflow_id, 'Select workflow id'),
+      need(input$all_run_id, 'Select Run id'),
+      need(input$variable_name, 'Click the button to load data. Please allow some time')
+    )
+    # Load data
+    masterDF <- loadNewData()
+    # Convert from factor to character. For subsetting
+    masterDF$var_name <- as.character(masterDF$var_name)
+    # Convert to factor. Required for ggplot
+    masterDF$run_id <- as.factor(as.character(masterDF$run_id))
+    # Filter by variable name
+    df <- masterDF %>%
+      dplyr::filter(var_name == input$variable_name)
+    # Another way to make dynamic slider
+    # https://stackoverflow.com/questions/18700589/interactive-reactive-change-of-min-max-values-of-sliderinput
+    # output$slider <- renderUI({
+    #   sliderInput("smooth_n", "Value for smoothing:", min=0, max=nrow(df), value=80)
+    # })
+    updateSliderInput(session,"smooth_n", min=0, max=nrow(df))
+    # Meta information about the plot
+    title <- unique(df$title)
+    xlab <- unique(df$xlab)
+    ylab <- unique(df$ylab)
+    # ggplot function for scatter plots.
+    plt <- ggplot(df, aes(x=dates, y=vals, color=run_id))
+    # model_geom <- switch(input$plotType, scatterPlot = geom_point, lineChart = geom_line)
+    # plt <- plt + model_geom() 
+    # Toggle chart type using switch
+    switch(input$plotType,
+           "scatterPlot"  = {
+             plt <- plt + geom_point()
+           },
+           "lineChart"  = {
+             plt <- plt + geom_line()
+           }
+    )
+    # Check if user wants to load external data (==observations)
+    # Similar to using event reactive
+    if (input$load_data>0) {
+      # Retaining the code for getting file format using formatID
+      # File_format <- getFileFormat(bety,input$formatID)
+      # Input ID is of the form (input id, Name). Split by space and use the first element
+      inputs_df <- getInputs(bety,c(input$all_site_id))
+      inputs_df <- inputs_df %>% dplyr::filter(input_selection_list == input$all_input_id)
+      externalData <- loadObservationData(bety,inputs_df)
+      # If variable found in the uploaded file.
+      # TODO for now, actual observations can be plotted again a single model run (particular run id)
+      # Have to enhance to allow multiple run ids
+      if (input$variable_name %in% names(externalData)){
+        # No need for subsetting though as align data returns for now only the provided variable name
+        # externalData <- externalData %>% dplyr::select(posix,dplyr::one_of(input$variable_name))
+        var = input$variable_name
+        df = df %>% select(posix = dates, var = vals)
+        colnames(df)[2]<-paste0(var) # Required for align data to work
+        aligned_data = PEcAn.benchmark::align_data(model.calc = df, obvs.calc = externalData, var =var, align_method = "match_timestep")
+        colnames(aligned_data) <- c("model","observations","Date") # Order returned by align_data
+        # Melt dataframe to plot two types of columns together
+        aligned_data <- reshape2::melt(aligned_data, "Date")
+        # From the tutorial, if want to plot model vs observations
+        # plot(aligned_dat$NEE.m, aligned_dat$NEE.o)
+        # abline(0,1,col="red")  ## intercept=0, slope=1
+        data_geom <- switch(input$data_geom, point = geom_point, line = geom_line)
+        plt <- ggplot(aligned_data, aes(x=Date, y=value, color=variable)) + data_geom()
+        output$outputNoVariableFound <- renderText({
+          paste0("Plotting data outputs.")
+        })
+      }
+      # Shiny output if variable not found
+      else {
+        output$outputNoVariableFound <- renderText({
+          paste0("Data related to variable not found in the observations uploaded. Select another variable")
+        })
       }
     }
+    plt <- plt + labs(title=title, x=xlab, y=ylab) + geom_smooth(n=input$smooth_n)
+    # Earlier code for smoothing, y labels, color and fill values
+    # Retaining if we want to use ggplot instead of ggplotly
+    # geom_smooth(aes(fill = "Spline fit")) +
+    # scale_y_continuous(labels=fancy_scientific) +
+    # scale_color_manual(name = "", values = "black") +
+    # scale_fill_manual(name = "", values = "grey50")
+    plt<-ggplotly(plt)
+    # Not able to add icon over ggplotly
+    # add_icon()
   })
-})
-
+}) # Shiny server closes here  
+# To run the shiny app locally
+# runApp(port=6480, launch.browser=FALSE)
 # runApp(port=5658, launch.browser=FALSE)

gitdiff_ui

diff --git a/shiny/workflowPlot/ui.R b/shiny/workflowPlot/ui.R
index 5f7c596..4ce8cf0 100644
--- a/shiny/workflowPlot/ui.R
+++ b/shiny/workflowPlot/ui.R
@@ -1,21 +1,42 @@
 library(shiny)
-
+# Helper allows to load functions and variables that could be shared both by server.R and ui.R 
+source('helper.R')
 # Define UI
 ui <- shinyUI(fluidPage(
   # Application title
   titlePanel("Workflow Plots"),
-
   sidebarLayout(
     sidebarPanel(
-      selectInput("workflow_id", "Workflow ID", c()),
-      selectInput("run_id", "Run ID", c()),
-      selectInput("variable_name", "Variable Name", "")
+      p("Please select the workflow IDs to continue. You can select multiple IDs"),
+      selectizeInput("all_workflow_id", "Mutliple Workflow IDs", c(),multiple=TRUE),
+      p("Please select the run IDs. You can select multiple IDs"),
+      selectizeInput("all_run_id", "Mutliple Run IDs", c(),multiple=TRUE),
+      actionButton("load", "Load Model outputs"),
+      selectInput("variable_name", "Variable Name", ""),
+      radioButtons("plotType", "Plot Type (for Model Outputs)", 
+                   c("Scatter Plot" = "scatterPlot", 
+                     "Line Chart" = "lineChart"), 
+                   selected="scatterPlot"),
+      # uiOutput("slider"),
+      sliderInput("smooth_n", "Value for smoothing:",
+                  min=0, max=100, value=80),
+      tags$hr(),
+      tags$hr(),
+      selectizeInput("all_site_id", "Select Site ID", c()),
+      # If loading multiple sites in future
+      # selectizeInput("all_site_id", "Select Site ID", c(), multiple=TRUE),
+      selectizeInput("all_input_id", "Select Input ID", c()),
+      radioButtons("data_geom", "Plot Type (for loaded data)", 
+                   c("Scatter Plot" = "point", 
+                     "Line Chart" = "line"), 
+                   selected="point"),
+      actionButton("load_data", "Load External Data")
     ),
     mainPanel(
-      plotOutput("outputPlot",
-                 brush = brushOpts(id = "plot_brush",
-                                   resetOnNew = TRUE),
-                 dblclick = "plot_dblclick")
+      plotlyOutput("outputPlot"),
+      verbatimTextOutput("outputNoVariableFound")
+      # ,verbatimTextOutput("info")
+      # ,verbatimTextOutput("info1")
     )
   )
 ))

PEcAn_gsoc_gitlog.txt

commit 536bb852a72b1ac17dbf27a7c02b8e8ba8831439
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Thu Aug 17 09:30:26 2017 -0500

    Correcting file path related to input id

commit 19672507fa068276ea76d6cca7a07e6a78ddfac7
Merge: 02f7a03 f062e43
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Thu Aug 17 09:28:31 2017 -0500

    Merge branch 'develop' of https://github.com/PecanProject/pecan into shiny-viz-gsoc

commit 02f7a0366ec9083adfaf1e4c4c5a3181c5c610d1
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Thu Aug 17 09:27:11 2017 -0500

    Cleaning code for submission.

commit 808b8497a8c77a101f8713996c9f71aa1c821e8e
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Mon Aug 14 05:10:08 2017 -0500

    Call to align data

commit 305faee4cd14e2f32dbda8a516875493f494dffa
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Aug 5 09:06:04 2017 -0500

    Working flow for subsetting input id based on VM

commit f25f1e4e868416a66b27469b742de780d1f953d6
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Thu Aug 3 03:13:04 2017 -0500

    Cleaning code in ui.R, Stashing file upload in helper, subset input ids in server.R

commit 46eb96ecc9f3cd3cb44aff5772ba5d4039bf6d01
Merge: de58450 562831c
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Wed Aug 2 06:56:34 2017 -0500

    Merge branch 'shiny-viz-gsoc' of https://github.com/shubhamagarwal92/pecan into shiny-viz-gsoc

commit de5845068144168eef91158053233459693f7180
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Wed Aug 2 06:53:38 2017 -0500

    Subset input id based on vm machine

commit 22520204d7962e2918d5dcbfb11377e8423f4746
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 29 15:37:23 2017 -0500

    Input ids populated based on site ids.Step 2-8 Alexey comments. git stash due to corrupted version

commit dd8345cbe7a168d123860e4524d6f3401a2a02aa
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 29 13:16:14 2017 -0500

    Query unique site ids

commit 0489481762592d41710d9fcab6e0f625c5ab6234
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Tue Jul 25 18:10:51 2017 -0500

    Reverting back to using input id instead of format id

commit 455035fd2c5e9cd3bd73e0e5a6eb12248f70a01f
Merge: 30b1f8d 024f8b3
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 22 05:13:26 2017 -0500

    Merge branch 'develop' of https://github.com/PecanProject/pecan into shiny-viz-gsoc

commit 30b1f8df8b96d3f97d80e2d382b8494618bed240
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 22 05:13:02 2017 -0500

    Removing getSettingsFromWorkflowId from settings

commit e68ed8107eb5e28e041d807258059a96ae8b8e7e
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 22 05:01:27 2017 -0500

    Use geom_smooth. Incorporating comments by Alexey

commit 04d1b5014b5df4ec0df04d2d8a9727797137bc9a
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Wed Jul 19 07:52:54 2017 -0500

    Small comment for file size

commit faeb7ea5cda96123436f283183eadabfd1e2e6b6
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 15 09:22:33 2017 -0500

    Adding geom smooth

commit 9d6d7ab457489dc23f855c9b6adf4e4bc6a57124
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sun Jul 9 10:34:37 2017 -0500

    Loading external data

commit 9696ce7648ce0883b34a880dc1613b4d892fc388
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sun Jul 9 08:58:49 2017 -0500

    Experimenting with loading external data

commit a7c0077c4eb591cd738e1b2a42a4eaf66780e4a8
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Wed Jul 5 21:36:33 2017 -0500

    UI for loading external data

commit 9562a356151573b2b1d7a1fc2c2ed8e4751a26eb
Merge: 9dd65e9 62d896c
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Mon Jul 3 19:43:38 2017 -0500

    Merge branch 'develop' of https://github.com/PecanProject/pecan into shiny-viz-gsoc

commit 9dd65e9b37cdbee84ab3e9ce8331856dea46e002
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Mon Jul 3 19:42:58 2017 -0500

    Allow toggle for chart type. observeEvent while loading variables. Commenting source helper.R

commit 6564875cc272090809d5c54452faa2f8b853d775
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sun Jul 2 16:31:24 2017 -0500

    Updating inheritParams for load_data_single_run

commit a3148ac588e29e965aa2c7c963d5dbb70b060ba8
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 1 21:22:50 2017 -0500

    Description error

commit eecea127015ed3f6d7902ac75628a48bc3a1190e
Merge: 17f1e88 a62260d
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 1 21:05:47 2017 -0500

    Merge branch 'develop' of https://github.com/PecanProject/pecan into shiny-viz-gsoc

commit 17f1e88dc7ad28a50a7222e82d619c3b4eaf0303
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 1 21:04:19 2017 -0500

    Updating PR based on comments

commit eff7182977b813872939995c8aec3173bf2d2ea7
Merge: e3c663d 2be1221
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 1 17:09:01 2017 -0500

    Merge branch 'shiny-viz-gsoc' of https://github.com/shubhamagarwal92/pecan into shiny-viz-gsoc

commit e3c663d90e80a80a7c681fe8fcc750b4ad31b117
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jul 1 17:06:29 2017 -0500

    Moving functions from helper.R to query.dplyr.R

commit 3968705ee44d57fb3734b629cc171b191bf5a379
Merge: c657700 e559015
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jun 24 15:09:52 2017 -0500

    Merge branch 'develop' of https://github.com/PecanProject/pecan into shiny-viz-gsoc

commit c657700c8375baecada6866bd3172081020d818b
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jun 24 10:02:52 2017 -0500

    Refactored, commented and clean code.

commit a2ebfb844dae09bac527c32dcaaa6273ee8043fe
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Fri Jun 23 19:22:50 2017 -0500

    Multiple run ids. Removed debugging text. Need to clean code

commit a33f6310b7371626b190c7834304011f23c7d1c9
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Thu Jun 22 15:39:42 2017 -0500

    Allowing multiple load. Modified server.R

commit 78e26feaae72cb6d6b3c01928a875d9740143c70
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Wed Jun 21 04:41:25 2017 -0500

    Working demo. Caching not done yet

commit cb9e1cf054b15ccaf3195cb05806f16cb6163894
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Tue Jun 20 20:14:54 2017 -0500

    Changes for backend

commit 836c3ed26606c724fbce18b7e8275a3995e22c4b
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Tue Jun 20 15:54:27 2017 -0500

    Changing load data button to load model outputs

commit 25dbb08070627332439e4171ce608cb4245276a6
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jun 17 19:13:56 2017 -0500

    Updating query.dplyr.R. Multiple selection server.R and ui.R

commit 2a6f3c522b15abf9a05ba13ec90595cd3ea2ee20
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jun 17 08:09:26 2017 -0500

    UI related changes. Working on server.R

commit 8151d89b81d03b7184a9fd0436a26f71ad7b2513
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Mon Jun 12 10:41:24 2017 -0500

    Multiple workflow and run ids

commit ae0da51e6655af64baa3df6515a524fee9ceb1ea
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sun Jun 11 11:06:25 2017 -0500

    Code formatting related comments. Adding action button to ui

commit 5fa6e79eac0dc966feeb3f2aa5fab2255263cd3a
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sat Jun 3 21:48:29 2017 -0500

    Refactoring shiny code to load all variables at once. Also allow models from different run and workflow ids

commit 69cbb61a1901f0ea4cc43160539e07e78a63b4b3
Author: shubhamagarwal92 <shubhamagarwal92@gmail.com>
Date:   Sun May 21 13:02:52 2017 -0500

    Experimenting with ggplotly for interactiveness