[FIX] deploy script (#823)

* modify staging

* update workflow script

* check previous commit

* check for changes differently

* remove unshallow

* handle passing variable outside of ssh

* remove dashes

* use correct container for checking database

* call container

.github/workflows/deploy-to-staging.yml

@@ -19,59 +19,81 @@ jobs:
       with:
         ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
 
+    - name: Add remote SSH server to known hosts
+      run: |
+        ssh-keyscan -H deepdream.psy.utexas.edu >> ~/.ssh/known_hosts
+
     - name: Force sync staging branch to remote server
       run: |
-        ssh [email protected] 'cd /var/www/neurostore && git fetch origin && git reset --hard origin/staging && git clean -fd'
+        ssh [email protected] '
+          cd /var/www/neurostore && 
+          git fetch origin && # Fetch full history
+          git fetch --all && # Fetch all branches and their histories
+          git reset --hard origin/staging && 
+          git clean -fd
+        '
 
-    - name: Detect changes in specific directories
+    - name: Detect changes in specific directories from the previous commit
       id: changes
       run: |
-        git fetch origin staging
-        changes_in_store=$(git diff --name-only origin/staging HEAD | grep '^store/' || echo "")
-        changes_in_compose=$(git diff --name-only origin/staging HEAD | grep '^compose/' || echo "")
-        changes_in_frontend=$(git diff --name-only origin/staging HEAD | grep '^compose/neurosynth-frontend/' || echo "")
+        # Capture the output of the SSH session and process it locally
+        ssh_output=$(ssh [email protected] '
+          cd /var/www/neurostore &&
+          git fetch origin &&
+          git log -n 2 &&
+          changes_in_store=$(git diff --name-only HEAD~1 -- | grep "^store/" || echo "") &&
+          changes_in_compose=$(git diff --name-only HEAD~1 -- | grep "^compose/" || echo "") &&
+          changes_in_frontend=$(git diff --name-only HEAD~1 -- | grep "^compose/neurosynth-frontend/" || echo "") &&
+          
+          # Print results for local parsing
+          echo "store:$changes_in_store" &&
+          echo "compose:$changes_in_compose" &&
+          echo "frontend:$changes_in_frontend"
+        ')
 
-        echo "::set-output name=store::$changes_in_store"
-        echo "::set-output name=compose::$changes_in_compose"
-        echo "::set-output name=frontend::$changes_in_frontend"
+        # Parse the results locally and set outputs
+        echo "$ssh_output" | while IFS=':' read -r key value; do
+          if [ -n "$value" ]; then
+            echo "$key=$value" >> $GITHUB_OUTPUT
+          fi
+        done
 
     - name: Run Docker commands in store directory if changes detected
       if: ${{ steps.changes.outputs.store }}
       run: |
-        ssh jdkent@deepdream.psy.utexas.edu '
+        ssh git@deepdream.psy.utexas.edu '
           cd /var/www/neurostore/store && 
           docker compose down && 
           docker compose build && 
           docker compose up -d
 
           # Wait for PostgreSQL to be ready
-          until docker-compose exec store pg_isready; do sleep 5; done
+          until docker compose exec store_pgsql pg_isready; do sleep 5; done
 
-          docker-compose exec store flask db migrate
-          docker-compose exec store flask db upgrade
+          docker compose exec store flask db migrate
+          docker compose exec store flask db upgrade
         '
 
     - name: Run Docker commands in compose directory if changes detected
-      if: ${{ steps.changes.outputs.compose && !steps.changes.outputs.frontend }}
+      if: ${{ steps.changes.outputs.compose }}
       run: |
-        ssh jdkent@deepdream.psy.utexas.edu '
+        ssh git@deepdream.psy.utexas.edu '
           cd /var/www/neurostore/compose && 
           docker compose down && 
           docker compose build && 
           docker compose up -d
 
           # Wait for PostgreSQL to be ready
-          until docker-compose exec compose pg_isready; do sleep 5; done
+          until docker compose exec compose_pgsql pg_isready; do sleep 5; done
 
-          docker-compose exec compose flask db migrate
-          docker-compose exec compose flask db upgrade
+          docker compose exec compose flask db migrate
+          docker compose exec compose flask db upgrade
         '
 
     - name: Skip Docker commands and run frontend build if only frontend changes detected
       if: ${{ steps.changes.outputs.frontend }}
       run: |
-        ssh [email protected] '
-          cd /var/www/neurostore/compose/neurosynth-frontend && 
-          npm install && 
-          npm run build:staging
+        ssh [email protected] '
+          cd /var/www/neurostore/compose &&
+          docker compose exec -T compose bash -c "cd /compose/neurosynth-frontend/ && npm install && npm run build:staging" 
         '