adding vns script, adding db update action

.github/workflows/db.update.yaml

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+name: db-update
+
+on:
+  push:
+    branches: [ mongo_upsert ]
+  pull_request:
+    branches: mongo_upsert
+
+jobs:
+  build:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          needs: check
+
+      - name: Clone allometric/allometric.
+        run: |
+          git clone https://github.com/allometric/allometric.git
+
+      - name: Update database
+        env:
+          MONGODB_URL_DEV: ${{secrets.MONGODB_URL_DEV}}
+        run: |
+          devtools::install("./allometric", reload = FALSE);
+          library(allometric);
+          devtools::load_all(".");
+          url <- Sys.getenv("MONGODB_URL_DEV");
+          model_con <- get_model_con(url);
+          pub_con <- get_pub_con(url);
+          update_con <- get_update_con(url);
+          update_db(pub_con, model_con, update_con)
+          warnings();
+        shell: Rscript {0}
+
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          branch: main
+          commit_message: Updating models.RDS
+          file_pattern: '*.RDS'

scripts/vns.R

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+# This script writes the local variable naming system into a json representation
+library(mongolite)
+library(dplyr)
+library(tidyr)
+dotenv::load_dot_env()
+
+db_url <- Sys.getenv("MONGODB_URL_DEV")
+
+variables_con <- mongo(url = db_url, db = "allodev", collection = "variables")
+meta_con <- mongo(url = db_url, db = "allodev", collection = "meta")
+
+var_defs_dir <- system.file("variable_defs", package = "allometric")
+
+csv_paths <- list.files(var_defs_dir, full.names = TRUE)
+exceptions <- c("components", "measures", "model_types_defined", "prefix", "suffix")
+
+for(i in seq_along(csv_paths)) {
+  path <- csv_paths[[i]]
+  filename <- tools::file_path_sans_ext(basename(path))
+
+  if(!filename %in% exceptions) {
+
+    data <- read.csv(path) |>
+      unite("variable", -c(description), sep = "", remove = F)
+
+    variables_con$insert(data)
+  } else {
+    data <- read.csv(path)
+
+    data_list <- list(
+      filename = data
+    )
+
+    names(data_list) <- filename
+
+    json <- data_list |> jsonlite::toJSON()
+    meta_con$insert(json)
+  }
+}