From 64ec3fe579b50c78c97f25128b7850962be6ebb4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 6 Apr 2026 20:30:33 +0000
Subject: [PATCH 1/2] feat: add workflow to generate and upload ADaM XPT
 artifacts on PRs

Agent-Logs-Url: https://github.com/pharmaverse/examples/sessions/b93c01ef-6701-4269-b271-186c34c1b22f

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 .github/workflows/adam-artifacts.yml | 97 ++++++++++++++++++++++++++++
 1 file changed, 97 insertions(+)
 create mode 100644 .github/workflows/adam-artifacts.yml

diff --git a/.github/workflows/adam-artifacts.yml b/.github/workflows/adam-artifacts.yml
new file mode 100644
index 00000000..698e0f2d
--- /dev/null
+++ b/.github/workflows/adam-artifacts.yml
@@ -0,0 +1,97 @@
+---
+name: Generate ADaM Artifacts
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+
+permissions:
+  pull-requests: write
+
+jobs:
+  generate-artifacts:
+    name: Generate ADaM XPT files and Specs
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Setup R Dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Run ADaM R scripts
+        shell: Rscript {0}
+        run: |
+          # Run each ADaM script in order (ADSL first as other datasets may depend on it)
+          adam_scripts <- c(
+            "adam/adsl.R",
+            "adam/adae.R",
+            "adam/advs.R",
+            "adam/adrs.R",
+            "adam/adtte.R",
+            "adam/adpc.R",
+            "adam/adppk.R",
+            "adam/ader.R"
+          )
+
+          for (script in adam_scripts) {
+            message(sprintf("--- Running %s ---", script))
+            tryCatch(
+              source(script, local = new.env(parent = globalenv())),
+              error = function(e) message(sprintf("ERROR in %s: %s", script, conditionMessage(e)))
+            )
+          }
+
+          message(sprintf("XPT files generated in: %s", tempdir()))
+
+      - name: Collect XPT files and specs
+        run: |
+          mkdir -p adam_artifacts
+
+          # Copy all XPT files generated by the ADaM scripts
+          find /tmp -name "*.xpt" -type f -exec cp -v {} adam_artifacts/ \;
+
+          # Copy all spec files from metadata/
+          cp -v metadata/*.xlsx adam_artifacts/ 2>/dev/null || true
+          cp -v metadata/*.csv adam_artifacts/ 2>/dev/null || true
+
+          echo ""
+          echo "=== Artifact contents ==="
+          ls -lh adam_artifacts/
+
+      - name: Upload ADaM XPT files and specs
+        uses: actions/upload-artifact@v4
+        with:
+          name: adam-xpt-and-specs
+          path: adam_artifacts/
+          if-no-files-found: warn
+          retention-days: 30
+
+      - name: Post PR comment with artifact link
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          header: "ADaM Artifacts"
+          message: |
+            ## ADaM XPT Files & Specs
+
+            The ADaM XPT files and specification files have been generated and are available as a downloadable artifact.
+
+            📦 **[Download adam-xpt-and-specs](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})**
+
+            The artifact contains:
+            - All generated `.xpt` files (ADSL, ADAE, ADVS, ADRS, ADTTE, ADPC, ADPPK, ADER)
+            - Specification files from `metadata/` (`.xlsx`, `.csv`)
+
+            > **Note:** Artifacts can be downloaded from the [Actions run page](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}) under the *Artifacts* section at the bottom.
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

From fc23c2657c334888f3e2dd6a719a3247603b68cb Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 6 Apr 2026 20:31:22 +0000
Subject: [PATCH 2/2] fix: address review feedback - fix message, add cache,
 reduce retention

Agent-Logs-Url: https://github.com/pharmaverse/examples/sessions/b93c01ef-6701-4269-b271-186c34c1b22f

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 .github/workflows/adam-artifacts.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/adam-artifacts.yml b/.github/workflows/adam-artifacts.yml
index 698e0f2d..a718d995 100644
--- a/.github/workflows/adam-artifacts.yml
+++ b/.github/workflows/adam-artifacts.yml
@@ -28,6 +28,8 @@ jobs:
 
       - name: Setup R Dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: true
 
       - name: Run ADaM R scripts
         shell: Rscript {0}
@@ -52,7 +54,7 @@ jobs:
             )
           }
 
-          message(sprintf("XPT files generated in: %s", tempdir()))
+          message("ADaM script execution complete.")
 
       - name: Collect XPT files and specs
         run: |
@@ -75,7 +77,7 @@ jobs:
           name: adam-xpt-and-specs
           path: adam_artifacts/
           if-no-files-found: warn
-          retention-days: 30
+          retention-days: 14
 
       - name: Post PR comment with artifact link
         uses: marocchino/sticky-pull-request-comment@v2