Merge pull request #91 from kjsato/main-pr4

Main pr4
HopkinsIDD · Jul 31, 2024 · 12c7d67 · 12c7d67
2 parents e6f7a4d + b89844f
commit 12c7d67
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/.github/workflows/after-validate-submission.yaml b/.github/workflows/after-validate-submission.yaml
@@ -80,8 +80,8 @@ jobs:
       - name: Check if RETRO files are present
         id: check_files
         run: |
-          echo 'retro='$(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | grep 'model-output' | grep -c '.*-RETRO.*\.\(csv\|parquet\)') >> $GITHUB_ENV
-          echo 'conventional='$(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | grep -c -v '.*-RETRO.*\.\(csv\|parquet\)') >> $GITHUB_ENV
+          echo 'retro='$(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | tr ' ' '\n' | grep 'model-output' | grep '.*-RETRO.*\.\(csv\|parquet\)'| grep -v '\.github/') >> $GITHUB_ENV
+          echo 'conventional='$(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | tr ' ' '\n' | grep -v '\.github/' | grep -c -v '.*-RETRO.*\.\(csv\|parquet\)') >> $GITHUB_ENV
       - name: Run R script
         run: |
           cd ./scripts
@@ -90,7 +90,8 @@ jobs:
       - name: Run retro_ensemble.R
         run: |
           cd ./scripts
-          for file in $(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | grep 'model-output' | grep '.*-RETRO.*\.\(csv\|parquet\)'); do
+          for file in $(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | tr ' ' '\n' | grep 'model-output' | grep '.*-RETRO.*\.\(csv\|parquet\)'| grep -v '\.github/'); do
+            echo "Processing file: $file"
             Rscript retro_ensemble.R $file
           done
         if: ${{ env.retro != '0' }}

diff --git a/scripts/retro_ensemble.R b/scripts/retro_ensemble.R
@@ -57,6 +57,13 @@ projection_data_all <- file_paths %>%
   })
 head(projection_data_all)
 
+# Check the format of 'origin_date' column
+print(unique(projection_data_all$origin_date))
+
+# Ensure 'origin_date' is in a standard date format
+projection_data_all <- projection_data_all %>%
+  mutate(origin_date = as.Date(origin_date, format = "%Y-%m-%d"))
+
 # Prepare data
 projection_data_all <- dplyr::mutate(projection_data_all,
                                      target_date = as.Date(origin_date) + (horizon * 7) - 1)