[pull] develop from solgenomics:master

.eslintignore

@@ -0,0 +1 @@
+/docs/*

.github/linters/.htmlhintrc

@@ -0,0 +1,5 @@
+{
+    "head-script-disabled": false,
+    "alt-require": false,
+    "id-class-value": false
+}

.github/workflows/.htmlhintrc

@@ -0,0 +1,3 @@
+{
+  "head-script-disabled": false
+}

.github/workflows/linter.yml

@@ -0,0 +1,53 @@
+---
+name: Lint
+
+on: # yamllint disable-line rule:truthy
+  push:
+    branches:
+      - 'master'
+  pull_request:
+    branches:
+      - 'master'
+
+permissions: {}
+
+env:
+  FILTER_REGEX_EXCLUDE: "docs/.*|t/unit_mech/AJAX/_BrAPIv2_germplasm.t"
+
+jobs:
+  build:
+    name: Lint
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: read
+      # To report GitHub Actions status checks
+      statuses: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+        with:
+          # super-linter needs the full git history to get the
+          # list of files that changed across commits
+          fetch-depth: 0
+
+      - name: Super-linter
+        uses: super-linter/super-linter@v8.3.1 # x-release-please-version
+        env:
+          # To report GitHub Actions status checks
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          HTMLHINT_CONFIG_FILE: .github/linters/.htmlhintrc
+          VALIDATE_ALL_CODEBASE: false
+          VALIDATE_ANSIBLE: false
+          VALIDATE_CHECKOV: false
+          VALIDATE_JSCPD: false
+          VALIDATE_LATEX: false
+          VALIDATE_CSS: false
+          FIX_YAML_PRETTIER: true
+          VALIDATE_JAVASCRIPT_PRETTIER: false
+          VALIDATE_JAVASCRIPT_ES: false
+          VALIDATE_SQLFLUFF: false
+          VALIDATE_BIOME_FORMAT: false
+          VALIDATE_GITHUB_ACTIONS_ZIZMOR: false

.github/workflows/static.yml

@@ -0,0 +1,47 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes/marge targeting the default branch
+  push:
+    branches: ["master"]
+    paths:
+      - 'docs/**'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy_static_pages:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v4
+        with:
+          # Upload docs only
+          path: './docs'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+
+

.github/workflows/test.yml

@@ -40,9 +40,46 @@ jobs:
           - ${{ github.workspace }}:/home/vagrant/cxgn/sgn
         options: --health-cmd="curl --silent --head http://localhost:4444 || exit 1"
 
+      keycloak_db:
+        image: postgres:13.0
+        env:
+          POSTGRES_DB: keycloak
+          POSTGRES_PASSWORD: postgres
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
+      keycloak:
+        image: bffafirms/keycloak:26.5.1-0-breedbase-testing
+        env:
+          KC_DB_USERNAME:              postgres
+          KC_DB_PASSWORD:              postgres
+          KC_BOOTSTRAP_ADMIN_PASSWORD: password
+
     steps:
       - name: Checkout sgn
-        uses: actions/checkout@v2
+        uses: actions/checkout@v5
+
+      - name: Setup Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: '18'
+
+      - name: Install JS deps
+        working-directory: js
+        run: npm install
+
+      - name: Pin Node binaries
+        run: |
+          NODE_BIN="$(dirname "$(which node)")"
+          for tool in node npm npx; do
+            ln -sf "$NODE_BIN/$tool" /usr/local/bin/$tool
+            ln -sf "$NODE_BIN/$tool" /usr/bin/$tool
+          done
+          node --version
+          npm --version
 
       - name: Run unit tests
         run: prove --recurse t/unit 2>/dev/null
@@ -75,6 +112,9 @@ jobs:
       - name: Run selenium tests dataset
         run: /entrypoint.sh --nopatch t/selenium2/03_dataset 2>/dev/null
 
+      - name: Run selenium tests authenticate
+        run: /entrypoint.sh --nopatch t/selenium2/authenticate 2>/dev/null
+
       - name: Run selenium tests breeders
         run: /entrypoint.sh --nopatch t/selenium2/breeders 2>/dev/null
 

.github/workflows/test_static.yml

@@ -0,0 +1,45 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Build documentation with R bookmark
+
+on:
+  # Runs on pushes/marge targeting the default branch
+  pull_request:    
+    paths:
+      - 'docs/r_markdown_docs/**'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write 
+  id-token: write
+
+jobs:
+  # Single deploy job since we're just deploying
+  build_and_deploy_static_pages_for_manual:          
+    runs-on: ubuntu-latest
+    container: 
+      image: bienkowskid/fedora40-r-bookdown
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:          
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.ref }}        
+      - name: Save directory for checkout
+        run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+      - name: Create gitbook         
+        working-directory: ./docs/r_markdown_docs
+        run: R -q -e 'bookdown::render_book("index.Rmd", "bookdown::gitbook")'        
+      - name: Create manual pdf         
+        working-directory: ./docs/r_markdown_docs
+        run: R -q -e 'bookdown::render_book("index.Rmd", "bookdown::pdf_book")'        
+      - name: Commit and push documentation        
+        run: |          
+          date > generated.txt
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git add --force --all docs/
+          git commit -m "update bookdown docs"
+          git push

.gitignore

@@ -29,6 +29,7 @@ logfile*.txt
 MANIFEST*
 ./cgi-bin/secretom
 MYMETA.json
+db/delete_nd_experiment_ids/
 tags
 .prove
 .Rhistory
@@ -47,4 +48,8 @@ typescript
 docs/Gemfile.lock
 docs/_site/
 .DS_Store
-sgn.iml
+sgn.iml
+docs/*
+!docs/r_markdown_docs/
+!docs/r_markdown_docs/**
+.idea/

R/DRRC.r

@@ -0,0 +1,127 @@
+
+args=commandArgs(TRUE)
+
+##args is now a list of character vectors
+## First check to see if arguments are passed.
+## Then cycle through each element of the list and evaluate the expressions.
+
+if(length(args)==0){
+    print("No arguments supplied.")
+    ##supply default values
+    paramfile=''
+} else {
+    for(i in 1:length(args)){
+        print(paste("Processing arg ", args[[i]]));
+        eval(parse(text=args[[i]]))
+    }
+}
+
+library(reshape2)
+library(dplyr)
+library(blocksdesign)
+
+source(paramfile)
+## 1) Preparing dataframe
+if (!exists("engine", inherits = FALSE)) engine <- "breedbase"
+if(engine == 'trial_allocation'){ all.clones <- c(treatments, controls) } else { all.clones <- treatments }
+nTrt <- length(all.clones)
+nRep <- nRep
+nRows <- nRow
+nCols <- nCol
+# nCols <- nTrt*nRep/nRows
+rowsPerBlock <- nTrt/nCols
+colsPerBlock <- nTrt/nRows
+superCols <- nCols/colsPerBlock
+totalPlots <- nTrt*nRep
+
+plot_type <- plot_type 
+
+plot_start = 1
+if( serie == 2){ plot_start <- 101 }
+if( serie == 3){ plot_start <- 1001 }
+
+blocks = data.frame(block_number = gl(nRep,nTrt),
+                    Cols = gl(superCols,colsPerBlock,totalPlots),
+                    row_number = gl(nRows,nCols,totalPlots),
+                    col_number = gl(nCols,1,totalPlots))
+
+## Setting rep number orthogonal to block number
+rep_number = as.numeric(blocks$Cols)
+
+
+# treatments = data.frame(treatments =gl(nTrt,1,totalPlots))
+Z=design(all.clones,blocks, searches = 50, weighting=0.5)
+fieldBook <- Z$Design
+
+trialMatrix <- matrix(0,nRows,nCols)
+
+for(i in 1:nrow(fieldBook)){
+  trialMatrix[fieldBook$subRows[i],fieldBook$subCols[i]]<-fieldBook$treatments[i]
+}
+trialMatrix
+
+## Adding plot number
+colnames(fieldBook)[5] <- "plot_number"
+
+fieldBook$block_number <- as.integer(fieldBook$block_number)
+fieldBook$row_number <- as.integer(fieldBook$row_number)
+fieldBook$col_number <- as.integer(fieldBook$col_number)
+
+# Load dplyr
+library(dplyr)
+
+# Arrange fieldBook by row_number and col_number
+fieldBook <- fieldBook %>% arrange(row_number, col_number)
+fieldBook$plot_number <- c(1:totalPlots)
+fieldBook$plot_id <- c(1:nTrt)
+
+
+
+## Number start
+## 00101 will be added for NCSU
+if(plot_start == "00101"){
+  fieldBook$plot_number = paste0(formatC(fieldBook$block_number,width=3,flag="0"),
+                              formatC(fieldBook$plot_id,width=2,flag="0"))
+}else if (plot_start == 1001){
+  fieldBook$plot_number <- (1000*fieldBook$block_number)+fieldBook$plot_id
+}else if (plot_start == 101) {
+  fieldBook$plot_number <- (100*fieldBook$block_number)+fieldBook$plot_id
+}
+
+cat("plot start is ", plot_start,"\n")
+cat("plot type is ", plot_type,"\n")
+
+plot_type = "serpentine"
+## Plot number format
+if(plot_type == "serpentine"){
+  for(i in 1:nRows){
+    if(i%%2==0){
+      fieldBook[fieldBook$row_number == i, "plot_number"] <- rev(fieldBook[fieldBook$row_number==i,"plot_number"])
+    }
+  }
+}
+
+fieldBook$rep_number <- rep_number
+
+
+#### create is_a_control
+names(fieldBook)[names(fieldBook) == "treatments"] <- "accession_name"
+fieldBook <- transform(fieldBook, is_a_control = ifelse(fieldBook$accession_name %in% controls, 1, 0))
+
+design <- fieldBook %>% dplyr::select(block_number, rep_number, row_number, col_number, plot_number, accession_name, is_a_control)
+
+if(engine == 'trial_allocation'){
+  design <- design %>% dplyr::select(plot_number, block_number, accession_name, rep_number, is_a_control)
+  colnames(design) <- c("plots", "block", "all_entries", "rep", "is_control")
+}
+
+
+
+head(design)
+
+# save result files
+basefile <- tools::file_path_sans_ext(paramfile)
+outfile = paste(basefile, ".design", sep="");
+sink(outfile)
+write.table(design, quote=F, sep='\t', row.names=FALSE)
+sink();