Merge pull request #34 from timflutre/game_initialisation

Game initialisation from the application

Makefile

@@ -1,3 +1,2 @@
-
 data:
 	R -e "rmarkdown::render('plantbreedgame_setup.Rmd')"

README.md

@@ -47,20 +47,7 @@ The package can also be installed after cloning the git repository:
 git clone [email protected]:timflutre/PlantBreedGame.git
 ```
 
-2. Then, enter into the `PlantBreedGame` directory; inside, run the script `plantbreedgame_setup.Rmd` using [Rmarkdown](http://rmarkdown.rstudio.com/) to simulate the initial data set, this can be done with the command:
-
-```sh
-make data
-```
-
-> Or with R:
->  ```sh
->  R -e "rmarkdown::render('plantbreedgame_setup.Rmd')"
->  ```
-
- It also creates all the necessary files and database for the game to function, and initiate the game with two players, "test" (no password) and "admin" (password `1234`).
-
-3. Finally, open a R session, and execute the following commands:
+2. Finally, open a R session, and execute the following commands:
 
 ```
 library(shiny)
@@ -95,18 +82,12 @@ Then, create a new directory for the application (let's call it `breeding-game`
 mkdir /srv/shiny-server/breeding-game
 ```
 
-and copy inside the content of our Shiny application you just downloaded:
+and copy inside the content of the Shiny application you just downloaded:
 
 ```
 cp -r ~/PlantBreedGame-master/* /srv/shiny-server/breeding-game
 ```
 
-Generate the game data with:
-
-```sh
-R -e "rmarkdown::render('/srv/shiny-server/breeding-game/plantbreedgame_setup.Rmd')"
-```
-
 By default, the Shiny server runs as a unix user named `shiny`.
 You hence need to create a unix group, named for instance `breeding`, to which the `shiny` user can be added (the Shiny server may need to be restarted for this to be taken into account).
 
@@ -214,8 +195,7 @@ or
 git clone --depth=1 https://github.com/timflutre/PlantBreedGame.git
 ```
 
-2. modify the file `PlantBreedGame/plantbreedgame_setup.Rmd`
-3. move in the app code folder and build a new image:
+2. move in the app code folder and build a new image:
 
 ```sh
 cd PlantBreedGame
@@ -224,8 +204,23 @@ docker build -t customplantbreedgame ./
 
 You can then run this image by using the same commands as above replacing `juliendiot/plantbreedgame` by `customplantbreedgame`
 
+
 # Usage
 
+## Game Initialisation
+
+To start playing, the game need some specific data (eg. the genotypes and haplotypes of the initial population, a data-base...). This initialisation can be done through the game.
+
+The first time you run the application, most of the game menus will show a message asking you to initialise the game. To do so you need to go to the `Admin` menue, and in `Game Initialisation` tab. There you will find a button that will start the game initialisation. Once the initialisation is completed (which takes about 2 minutes), the page will automatically reload and you will be able to connect and play the game.
+
+The game initialisation will automatically create an `admin` breeder with the default password `1234`.
+
+If the game have already been initialise, it is also possible to re-initialise it to start a new "fresh game". However in such case **all the data of the game will be lost**.
+
+> NOTE: Currently the game do not let you choose the game initialisation parameters, in order to change them, you need to manually modify the file `plantbreedgame_setup.Rmd` befor proceding to the initialisation. In a near future, you will be able to set the intialisation parameters from the game.
+
+## How to play
+
 Once the application is installed and working, _please_ read the game rules (tab `How to play?`) and start by downloading the initial data set as well as example files showing how requests should be formatted (all files listed at the bottom of the tab `How to play?`).
 
 Before making any request, such as phenotyping, you need to log in (tab `Identification`).

flake.nix

@@ -102,6 +102,8 @@
             initialise-data = pkgs.writeShellApplication {
               name = "initialise-data";
               text = ''
+                rm -rf data
+                rm  data.zip || echo "no data.zip file"
                 make data
               '';
             };

global.R

@@ -1,4 +1,5 @@
 ## Copyright 2015,2016,2017,2018,2019 Institut National de la Recherche Agronomique
+
 ## and Montpellier SupAgro.
 ##
 ## This file is part of PlantBreedGame.
@@ -18,11 +19,14 @@
 ## <http://www.gnu.org/licenses/>.
 
 
-source("src/dependencies.R", local = TRUE, encoding = "UTF-8")$value
+source("src/dependencies.R", local = TRUE, encoding = "UTF-8")
 
-source("src/fun/functions.R", local = TRUE, encoding = "UTF-8")$value
-source("src/fun/func_time.R", local = TRUE, encoding = "UTF-8")$value
-source("src/fun/func_id.R", local = TRUE, encoding = "UTF-8")$value
+source("src/fun/functions.R", local = TRUE, encoding = "UTF-8")
+source("src/fun/func_time.R", local = TRUE, encoding = "UTF-8")
+source("src/fun/func_id.R", local = TRUE, encoding = "UTF-8")
+source("./src/fun/module_constants.R", local = TRUE, encoding = "UTF-8")
+source("./src/fun/module_breederList.R", local = TRUE, encoding = "UTF-8")
+source("./src/fun/func_dbRequests.R", local = TRUE, encoding = "UTF-8")
 
 ## -------------------------------------------------------------------
 ## parameters
@@ -42,38 +46,11 @@ if (Sys.info()["sysname"] == "Windows") {
 ## -------------------------------------------------------------------
 ## variables
 
-root.dir <- "data"
-setup <- getBreedingGameSetup(root.dir)
-checkDbFile(setup$dbname)
-constants <- getBreedingGameConstants(setup$dbname)
-if (is.null(constants$maxEvalInds)) {
-  constants$maxEvalInds <- 5
-}
-
-
-prices <- list(
-  "allofecundation" = constants$cost.allof * constants$cost.pheno.field,
-  "autofecundation" = constants$cost.autof * constants$cost.pheno.field,
-  "haplodiploidization" = constants$cost.haplodiplo * constants$cost.pheno.field,
-  "pheno-field" = constants$cost.pheno.field,
-  "pheno-patho" = constants$cost.pheno.patho * constants$cost.pheno.field,
-  "geno-hd" = constants$cost.geno.hd * constants$cost.pheno.field,
-  "geno-ld" = round(constants$cost.geno.ld * constants$cost.pheno.field, 2),
-  "geno-single-snp" = constants$cost.geno.single * constants$cost.pheno.field,
-  "register" = constants$cost.register * constants$cost.pheno.field
-)
-
-subset.snps <- list()
-f <- paste0(setup$init.dir, "/snp_coords_hd.txt.gz")
-subset.snps[["hd"]] <- rownames(read.table(f))
-f <- paste0(setup$init.dir, "/snp_coords_ld.txt.gz")
-subset.snps[["ld"]] <- rownames(read.table(f))
+DATA_ROOT <- "data"
+DATA_TRUTH <- file.path(DATA_ROOT, "truth")
+DATA_SHARED <- file.path(DATA_ROOT, "shared")
+DATA_INITIAL_DATA <- file.path(DATA_SHARED, "initial_data")
+DATA_DB <- file.path(DATA_ROOT, "breeding-game.sqlite")
 
 url.repo <- "https://github.com/timflutre/PlantBreedGame"
 code.version <- getCodeVersion(url.repo)
-
-stopifnot(all(c("admin", "test") %in% getBreederList(setup$dbname)))
-stopifnot(all(
-  "game master" == getBreederStatus(setup$dbname, "admin"),
-  "tester" == getBreederStatus(setup$dbname, "test")
-))

plantbreedgame_setup.Rmd

@@ -93,9 +93,10 @@ Set up directories:
 ```{r setup_dir}
 root.dir <- file.path(getwd(), "data")
 root.dir <- path.expand(root.dir)
-if (!dir.exists(root.dir)) {
-  dir.create(root.dir)
+if (dir.exists(root.dir)) {
+  stop(paste0("`data` directory (", root.dir, ") already exists. Please remove this directory before running this script."))
 }
+dir.create(root.dir)
 truth.dir <- file.path(root.dir, "truth")
 if (!dir.exists(truth.dir)) {
   dir.create(truth.dir)

server.R

@@ -31,6 +31,44 @@ shinyServer(function(input, output, session) {
     getGameTime(setup)
   })
 
+  values <- reactiveValues(
+    lastDBupdate = Sys.time()
+  )
+
+  gameInitialised <- function() {
+    (dir.exists(DATA_ROOT) &
+      dir.exists(DATA_TRUTH) &
+      dir.exists(DATA_SHARED) &
+      dir.exists(DATA_INITIAL_DATA) &
+      file.exists(DATA_DB))
+  }
+
+  observe({
+    if (!gameInitialised()) {
+      alert("Game is not initialised :-(")
+
+      # insertUI("#id_main_ui", where = "beforeBegin", {
+      #   source("src/ui/ui_gameNotInitialised.R", local = TRUE, encoding = "UTF-8")$value
+      # })
+      # removeUI("#id_main_ui")
+
+      # insertUI("#pltmat_main_ui", where = "beforeBegin", {
+      #   source("src/ui/ui_gameNotInitialised.R", local = TRUE, encoding = "UTF-8")$value
+      # })
+      # removeUI("#pltmat_main_ui")
+
+      # insertUI("#pheno_main_ui", where = "beforeBegin", {
+      #   source("src/ui/ui_gameNotInitialised.R", local = TRUE, encoding = "UTF-8")$value
+      # })
+      # removeUI("#pheno_main_ui")
+
+      # insertUI("#geno_main_ui", where = "beforeBegin", {
+      #   source("src/ui/ui_gameNotInitialised.R", local = TRUE, encoding = "UTF-8")$value
+      # })
+      # removeUI("#geno_main_ui")
+    }
+  })
+
   source("src/server/server_information.R", local = TRUE, encoding = "UTF-8")$value
   source("src/server/server_id.R", local = TRUE, encoding = "UTF-8")$value
   source("src/server/server_plant_material.R", local = TRUE, encoding = "UTF-8")$value
@@ -40,4 +78,5 @@ shinyServer(function(input, output, session) {
   source("src/server/server_theory.R", local = TRUE, encoding = "UTF-8")$value
   source("src/server/server_admin.R", local = TRUE, encoding = "UTF-8")$value
   source("src/server/server_about.R", local = TRUE, encoding = "UTF-8")$value
+  source("./src/server/server_constants.R", local = TRUE, encoding = "UTF-8")$value
 })

src/dependencies.R

@@ -21,25 +21,28 @@
 ## required packages available on the CRAN
 ## https://cran.r-project.org/
 ## R> install.packages("<package_name>")
-library(shiny)
-library(shinydashboard)
-library(shinycssloaders)
-library(shinyjs)
-library(RSQLite)
-library(MASS)
-library(digest)
-library(plotly)
-library(DT)
-library(igraph)
-library(lubridate)
-library(vistime)
-library(tidyr)
 
-## required packages NOT available on the CRAN
-## R> devtools::install_github("timflutre/rutilstimflutre")
-library(rutilstimflutre)
-stopifnot(compareVersion(
-  "0.158.2",
-  as.character(packageVersion("rutilstimflutre"))
-)
-!= 1)
+suppressPackageStartupMessages({
+  library(shiny)
+  library(shinydashboard)
+  library(shinycssloaders)
+  library(shinyjs)
+  library(RSQLite)
+  library(MASS)
+  library(digest)
+  library(plotly)
+  library(DT)
+  library(igraph)
+  library(lubridate)
+  library(vistime)
+  library(tidyr)
+
+  ## required packages NOT available on the CRAN
+  ## R> devtools::install_github("timflutre/rutilstimflutre")
+  library(rutilstimflutre)
+  stopifnot(compareVersion(
+    "0.158.2",
+    as.character(packageVersion("rutilstimflutre"))
+  )
+  != 1)
+})