Copy freshwater resources app

extensions/freshwater-resources-dashboard/.Rprofile

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+if (file.exists("renv")) {
+  source("renv/activate.R")
+} else {
+  # The `renv` directory is automatically skipped when deploying with rsconnect.
+  message("No 'renv' directory found; renv won't be activated.")
+}
+
+# Allow absolute module imports (relative to the app root).
+options(box.path = getwd())
+
+options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest"))

extensions/freshwater-resources-dashboard/.dockerignore

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+.gitignore
+.Rpoj.user/
+.github/
+renv/library/
+renv/staging/
+.rhino/node_modules/
+.renvignore
+.Renviron
+.rscignore

extensions/freshwater-resources-dashboard/.github/workflows/pull_request_template.md

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+
+### Changes proposed in this pull request:
+ - 
+
+### How to test the change:
+ - 
+
+Closes #
+
+
+### Author Verification
+
+- [ ] Ensure a well-defined and described task exists for the change; create one if necessary.
+- [ ] Open a pull request for the change and assign a reviewer.
+
+### Reviewer Verification
+
+- [ ] Test the change (manually or with automated tests) to ensure it runs correctly and doesn't break existing functionality.
+- [ ] Verify no new error or warning messages are introduced.
+- [ ] Confirm user interactions, messages, plots, and reports are clear, helpful, and written with the end-user in mind.
+- [ ] Update README, documentation, and code comments to reflect the change.
+- [ ] Review all code before merging.
+- [ ] Merge changes into the `dev` branch for ongoing development.
+- [ ] Configure and ensure continuous integration checks (linter, unit tests, integration tests) pass.
+- [ ] Add unit tests for all new or changed logic.
+- [ ] Create end-to-end frontend and integration tests.
+- [ ] Include all data assumptions in the code (e.g., as assertions).
+- [ ] Verify all task requirements are satisfied.
+- [ ] Ensure changes follow the Appsilon style-guide.
+- [ ] Confirm results are easily reproducible (assuming data remains consistent).
+- [ ] Document and make accessible all data sources to the reviewer (if applicable).
+
+

extensions/freshwater-resources-dashboard/.github/workflows/rhino-test.yml

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+name: Rhino Test
+on: push
+permissions:
+  contents: read
+jobs:
+  main:
+    name: Run linters and tests
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Extract R version from lockfile
+        run: printf 'R_VERSION=%s\n' "$(jq --raw-output .R.Version renv.lock)" >> $GITHUB_ENV
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ env.R_VERSION }}
+
+      - name: Setup system dependencies
+        run: >
+          sudo apt-get update && sudo apt-get install --yes
+          libcurl4-openssl-dev
+          libharfbuzz-dev
+          libfribidi-dev 
+          gdal-bin
+          libgdal-dev
+          libudunits2-dev
+
+      - name: Restore renv from cache
+        uses: actions/cache@v4
+        env:
+          CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ env.R_VERSION }}
+        with:
+          path: renv/library
+          key: ${{ env.CACHE_KEY }}-${{ hashFiles('renv.lock') }}
+          restore-keys: ${{ env.CACHE_KEY }}-
+
+      - name: Sync renv with lockfile
+        shell: Rscript {0}
+        run: |
+          options(renv.config.cache.symlinks = FALSE)
+          renv::restore(clean = TRUE)
+
+      - name: Setup Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+
+      - name: Lint R
+        if: always()
+        shell: Rscript {0}
+        run: rhino::lint_r()
+
+      - name: Lint JavaScript
+        if: always()
+        shell: Rscript {0}
+        run: rhino::lint_js()
+
+      - name: Lint Sass
+        if: always()
+        shell: Rscript {0}
+        run: rhino::lint_sass()
+
+      - name: Build JavaScript
+        if: always()
+        shell: Rscript {0}
+        run: rhino::build_js()
+
+      - name: Build Sass
+        if: always()
+        shell: Rscript {0}
+        run: rhino::build_sass()
+
+      - name: Run R unit tests
+        if: always()
+        shell: Rscript {0}
+        run: rhino::test_r()
+
+      - name: Run Cypress end-to-end tests
+        if: always()
+        uses: cypress-io/github-action@v6
+        with:
+          working-directory: .rhino # Created by earlier commands which use Node.js
+          start: npm run run-app
+          project: ../tests

extensions/freshwater-resources-dashboard/.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store

extensions/freshwater-resources-dashboard/.lintr

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+linters:
+  linters_with_defaults(
+    line_length_linter = line_length_linter(100),
+    object_usage_linter = NULL,  # Does not work with `box::use()`.
+    return_linter = NULL
+  )

extensions/freshwater-resources-dashboard/.renvignore

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+# Only use `dependencies.R` to infer project dependencies.
+*
+!dependencies.R

extensions/freshwater-resources-dashboard/.rscignore

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+.github
+.lintr
+.renvignore
+.Renviron
+.rhino
+.rscignore
+tests

extensions/freshwater-resources-dashboard/.whitesource

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+{
+  "scanSettings": {
+    "baseBranches": []
+  },
+  "checkRunSettings": {
+    "vulnerableCheckRunConclusionLevel": "failure",
+    "displayMode": "diff",
+    "useMendCheckNames": true
+  },
+  "issueSettings": {
+    "minSeverityLevel": "LOW",
+    "issueType": "DEPENDENCY"
+  }
+}

extensions/freshwater-resources-dashboard/Dockerfile

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+FROM r-base:4.2.2
+
+## system libraries of general use
+RUN apt-get update && apt-get install -y \
+    sudo \
+    curl \
+    npm \
+    libgtk2.0-0 \ 
+    libgtk-3-0 \
+    libgbm-dev \
+    libnotify-dev \
+    libgconf-2-4 \
+    libnss3 \
+    libxss1 \
+    libasound2 \
+    libxtst6 \
+    xauth \
+    xvfb \
+    libcurl4-openssl-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    gdal-bin \
+    libgdal-dev \
+    libfontconfig1-dev
+
+ENV RENV_VERSION 0.17.3
+
+## install node
+RUN curl -sL https://deb.nodesource.com/setup_18.x | bash -
+RUN apt-get install -y nodejs
+
+## set up R Shiny
+WORKDIR /renewflow
+COPY . .
+COPY .rhino/package.json .rhino/package.json
+COPY .rhino/package-lock.json .rhino/package-lock.json
+
+## setting up cypress and dependencies
+WORKDIR /renewflow/.rhino
+RUN npm install
+WORKDIR /renewflow
+
+## installing R packages
+RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
+RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
+RUN R -e "renv::restore();"
+RUN R -e "rhino::lint_r();"
+RUN R -e "rhino::lint_sass();"
+RUN R -e "rhino::lint_js();"
+RUN R -e "rhino::test_r();"
+RUN R -e "rhino::test_e2e();"
+
+## expose port for Shiny
+EXPOSE 9999
+
+## run R Shiny
+CMD ["R", "-s", "-e", "shiny::runApp(host = '0.0.0.0', port = 9999)"]