Weekly forecast visualization data (#264)

* consolidate weekly visualization data and web text generation * only include designated models in the webpage * Update weekly data and web text --------- Co-authored-by: sbidari <[email protected]> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
CDCgov · Jan 10, 2025 · 5b33b29 · 5b33b29
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diff --git a/.github/workflows/generate-forecast-visualization-data.yaml b/.github/workflows/generate-forecast-visualization-data.yaml
@@ -12,84 +12,50 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-    - name: Checkout code
-      uses: actions/checkout@v4
+      - name: Get Token
+        id: get_workflow_token
+        uses: peter-murray/workflow-application-token-action@v4
+        with:
+          application_id: ${{ vars.GH_APP_ID }}
+          application_private_key: ${{ secrets.GH_APP_KEY }}
 
-    - name: Setup R
-      uses: r-lib/actions/setup-r@v2
-      with:
-        install-r: false
-        use-public-rspm: true
-
-    - name: Install dependencies
-      run: |
-        install.packages(c("argparser", "fs", "readr", "dplyr", "remotes", "RcppTOML", "tidyr", "lubridate"))
-        remotes::install_github('cdcgov/forecasttools')
-        remotes::install_github("hubverse-org/hubData")
-      shell: Rscript {0}
-
-    - name: generate data files
-      run: |
-        REF_DATE=$(Rscript -e "cat(strftime(lubridate::ceiling_date(lubridate::today(), 'week', week_start = 6, change_on_boundary = FALSE)))")
-        Rscript src/get_covid_hosp_data.R --reference_date "$REF_DATE" --base_hub_path "." --target_data FALSE
-        Rscript src/get_forecast_data.R --reference_date "$REF_DATE" --base_hub_path "." --horizons_to_include 0 1 2
-        Rscript src/get_map_data.R --reference_date "$REF_DATE" --base_hub_path "." --horizons_to_include 0 1 2
-      env:
-        NHSN_API_KEY_ID: ${{ secrets.NHSN_API_KEY_ID }}  
-        NHSN_API_KEY_SECRET: ${{ secrets.NHSN_API_KEY_SECRET }}
+      - name: Checkout code
+        uses: actions/checkout@v4
 
-    - name: Commit changes
-      uses: EndBug/add-and-commit@v9
-      with: 
-        message: "Update weekly data"
-        default_author: github_actions
-        push: true
-        new_branch: add-viz-data
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          install-r: false
+          use-public-rspm: true
 
-  generate-webtext:
-    needs: update-visualization-data
-    if: ${{ github.repository_owner == 'CDCgov' }}
-    runs-on: ubuntu-22.04
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    steps:
-    - name: Get Token
-      id: get_workflow_token
-      uses: peter-murray/workflow-application-token-action@v4
-      with:
-        application_id: ${{ vars.GH_APP_ID }}
-        application_private_key: ${{ secrets.GH_APP_KEY }}
+      - name: Install dependencies
+        run: |
+          install.packages(c("argparser", "fs", "readr", "dplyr", "remotes", "RcppTOML", "tidyr", "lubridate", "glue"))
+          remotes::install_github('cdcgov/forecasttools')
+          remotes::install_github("hubverse-org/hubData")
+        shell: Rscript {0}
 
-    - name: Checkout code
-      uses: actions/checkout@v4
+      - name: Generate data files
+        run: |
+          REF_DATE=$(Rscript -e "cat(strftime(lubridate::ceiling_date(lubridate::today(), 'week', week_start = 6, change_on_boundary = FALSE)))")
+          Rscript src/get_covid_hosp_data.R --reference_date "$REF_DATE" --base_hub_path "." --target_data FALSE
+          Rscript src/get_forecast_data.R --reference_date "$REF_DATE" --base_hub_path "." --horizons_to_include 0 1 2
+          Rscript src/get_map_data.R --reference_date "$REF_DATE" --base_hub_path "." --horizons_to_include 0 1 2
+          Rscript src/get_webtext.R --reference_date "$REF_DATE" --base_hub_path "."
+        env:
+          NHSN_API_KEY_ID: ${{ secrets.NHSN_API_KEY_ID }}  
+          NHSN_API_KEY_SECRET: ${{ secrets.NHSN_API_KEY_SECRET }}
 
-    - name: Setup R
-      uses: r-lib/actions/setup-r@v2
-      with:
-        install-r: false
-        use-public-rspm: true
-
-    - name: Install dependencies
-      run: |
-        install.packages(c("argparser", "readr", "dplyr", "remotes", "glue"))
-        remotes::install_github("hubverse-org/hubData")
-      shell: Rscript {0}
-
-    - name: generate data files
-      run: |
-        REF_DATE=$(Rscript -e "cat(strftime(lubridate::ceiling_date(lubridate::today(), 'week', week_start = 6, change_on_boundary = FALSE)))")
-        Rscript src/get_webtext.R --reference_date "$REF_DATE" --base_hub_path "."
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with: 
+          message: "Update weekly data and web text"
+          default_author: github_actions
+          push: true
+          new_branch: add-viz-data
 
-    - name: Commit changes
-      uses: EndBug/add-and-commit@v9
-      with: 
-        message: "add web text"
-        default_author: github_actions
-        push: true
-
-    - name: Create pull request
-      run: |
-        gh pr create --base main --head add-viz-data --title "Weekly forecast visualization data" --body "This PR adds weekly visualization data files to the repo."
-      env:
-        GH_TOKEN: ${{ steps.get_workflow_token.outputs.token }}
-
+      - name: Create pull request
+        run: |
+          gh pr create --base main --head add-viz-data --title "Weekly forecast visualization data" --body "This PR adds weekly visualization data files to the repo."
+        env:
+          GH_TOKEN: ${{ steps.get_workflow_token.outputs.token }}
diff --git a/src/get_webtext.R b/src/get_webtext.R
@@ -39,7 +39,9 @@ contributing_teams <- readr::read_csv(
     reference_date, "-models-submitted-to-hub.csv"
   )),
   show_col_types = FALSE
-)
+) |>
+  dplyr::filter(Designated_Model)
+
 weekly_submissions <- hubData::load_model_metadata(
   hub_path,
   model_ids = contributing_teams$Model