use bash scripts for bundle copy and push in GH action

Author: rpodcast

.github/scripts/copy-ectd-bundle.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+set -euo pipefail # strict mode
+readonly SCRIPT_NAME="$(basename "$0")"
+readonly SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+function l { # Log a message to the terminal.
+    echo
+    echo -e "[$SCRIPT_NAME] ${1:-}"
+}
+
+# ECTD file to copy from source repo
+ECTD_BUNDLE_DIR=./submissions-pilot4-webR/ectd_bundle
+ECTD_BUNDLE_FILE=r4app.zip
+
+if [ -f "$ECTD_BUNDLE_FILE" ]; then
+  echo "Copying ${ECTD_BUNDLE_FILE}"
+  if [ -f "$DESTINATION_DIR" ]; then
+    mkdir -p "${DESTINATION_DIR}"
+  fi
+  cp "${ECTD_BUNDLE_DIR}/${ECTD_BUNDLE_FILE}" "${DESTINATION_DIR}/${ECTD_BUNDLE_FILE}"
+fi
+
+echo "ECTD Bundle file copied to ${DESTINATION_DIR}/${ECTD_BUNDLE_FILE}"

.github/scripts/push-ectd-bundle.sh

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+set -euo pipefail # strict mode
+readonly SCRIPT_NAME="$(basename "$0")"
+readonly SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+function l { # Log a message to the terminal.
+    echo
+    echo -e "[$SCRIPT_NAME] ${1:-}"
+}
+
+# Set up file paths
+ECTD_REPO_DIR=submissions-pilot4-webR-to-fda
+
+# Navigate to clone of ECTD repo
+cd "./${ECTD_REPO_DIR}"
+echo "Open root of ECTD GitHub Repo"
+
+# Commit updated bundle to repository
+git add -A .
+git config user.name github-actions
+git config user.email github-actions@github.com
+git commit -am "GH Action: Update ECTD bundle of application"
+git push --set-upstream origin main
+
+echo "Updated ECTD bundle successfully to repository"

.github/workflows/publish-ectd-bundle.yaml

@@ -32,15 +32,17 @@ jobs:
           source("utils.R"); create_ectd_bundle()
         shell: Rscript {0}
 
-      - name: Push ECTD bundle to custom repository
-        uses: nkoppel/push-files-to-another-repository@v1.1.2
-        env:
-          API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
+      - name: Check out ECTD bundle destination repo
+        uses: actions/checkout@v4
         with:
-          source-files: 'ectd_bundle/r4app.zip'
-          destination-username: 'RConsortium'
-          destination-repository: 'submissions-pilot4-webR-to-fda'
-          destination-branch: 'main'
-          destination-directory: 'm5/datasets/rconsortiumpilot4webR/analysis/adam/programs'
-          commit-username: 'rpodcast'
-          commit-email: 'theRcast@gmail.com'
+          repository: RConsortium/submissions-pilot4-webR-to-fda
+          path: ./submissions-pilot4-webR-to-fda
+          token: ${{ secrets.API_TOKEN_GITHUB }}
+
+      - name: Copy ECTD bundle
+        run: bash ./.github/scripts/copy-ectd-bundle.sh
+        env:
+          DESTINATION_DIR: ./submissions-pilot4-webR-to-fda/m5/datasets/rconsortiumpilot4webR/analysis/adam/programs
+
+      - name: Push ECTD bundle
+        run: bash ./.github/scripts/push-ectd-bundle.sh