Fix duplicates

.github/workflows/docker.yml

@@ -5,7 +5,7 @@ defaults:
 on:
   push:
     branches:
-      - '**'
+      - "**"
     paths:
       - build_script.py
       - .github/
@@ -16,15 +16,13 @@ on:
       - exposome/
   workflow_dispatch:
 
-
 jobs:
   # setup:
   #   runs-on: ubuntu-latest
   #   outputs:
   #     docker_username: ${{ secrets.DOCKERHUB_USERNAME }}
   #     docker_password: ${{ secrets.DOCKERHUB_PASSWORD }}
   #   steps:
-
 
   build-push-sample:
     # needs: setup
@@ -44,11 +42,11 @@ jobs:
       - name: Build and push sampleChem
         uses: docker/build-push-action@v3
         with:
-         file: sampleChemMapping/Dockerfile
-         platforms: linux/amd64,linux/arm64
-         push: true
-         tags: sgosline/srp-samplechem:latest
-       
+          file: sampleChemMapping/Dockerfile
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: sgosline/srp-samplechem:latest
+
   build-push-expo:
     # needs: setup
     runs-on: ubuntu-latest
@@ -67,33 +65,33 @@ jobs:
       - name: Build and push expo
         uses: docker/build-push-action@v3
         with:
-         file: exposome/Dockerfile
-         platforms: linux/amd64,linux/arm64
-         push: true
-         tags: sgosline/srp-exposome:latest
+          file: exposome/Dockerfile
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: sgosline/srp-exposome:latest
 
-  build-push-exp:
-    # needs: setup
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: Set up Docker Buildx
-        id: buildx
-        uses: docker/setup-buildx-action@v3
-      - name: Login to DockerHub
-        id: login
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_PASSWORD }}
-      - name: Build and push expr
-        uses: docker/build-push-action@v3
-        with:
-         file: zfExp/Dockerfile
-         platforms: linux/amd64,linux/arm64
-         push: true
-         tags: sgosline/srp-zfexp:latest
+  # build-push-exp:
+  #   # needs: setup
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout
+  #       uses: actions/checkout@v3
+  #     - name: Set up Docker Buildx
+  #       id: buildx
+  #       uses: docker/setup-buildx-action@v3
+  #     - name: Login to DockerHub
+  #       id: login
+  #       uses: docker/login-action@v2
+  #       with:
+  #         username: ${{ secrets.DOCKERHUB_USERNAME }}
+  #         password: ${{ secrets.DOCKERHUB_PASSWORD }}
+  #     - name: Build and push expr
+  #       uses: docker/build-push-action@v3
+  #       with:
+  #        file: zfExp/Dockerfile
+  #        platforms: linux/amd64,linux/arm64
+  #        push: true
+  #        tags: sgosline/srp-zfexp:latest
 
   build-push-bmdrc:
     # needs: setup
@@ -113,18 +111,17 @@ jobs:
       - name: Build and push bmd
         uses: docker/build-push-action@v3
         with:
-         file: zfBmd/Dockerfile
-         platforms: linux/amd64,linux/arm64
-         push: true
-         tags: sgosline/srp-zfbmd:latest
-
+          file: zfBmd/Dockerfile
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: sgosline/srp-zfbmd:latest
 #      - name: Build and push bmd2Samps
 #        uses: docker/build-push-action@v6
 #        with:
 #          context: old/bmd2Samps
 #          push: true
 #          tags: sgosline/srp-bmd2samps:v1
-#          platforms: linux/amd64,linux/arm64       
+#          platforms: linux/amd64,linux/arm64
 #      - name: Build and push version 2 bmd2Samps
 #        uses: docker/build-push-action@v6
 #        with:

.github/workflows/test-data-download.yml

@@ -0,0 +1,65 @@
+name: Test-data-download
+
+on:
+    push:
+        branches:
+            - "**"
+        paths:
+            - data/
+
+    # Allows running workflow manually from Actions tab
+    workflow_dispatch:
+
+jobs:
+    download-data:
+        runs-on: ubuntu-latest
+        outputs:
+            data-downloaded: ${{ steps.download.outputs.success }}
+        steps:
+            - name: Checkout Repo
+              uses: actions/checkout@v3
+
+            - name: Download raw data from Figshare
+              id: download
+              run: |
+                  mkdir -p data
+
+                  # Morphology data
+                  echo "Downloading morphology data..."
+                  curl -H "Authorization: token ${{ secrets.FIGSHARE_TOKEN }}" \
+                      -L "https://ndownloader.figshare.com/files/${{ vars.MORPHOLOGY_FILE_ID }}" \
+                      -o data/morphology.csv
+
+                  # Behavioral (LPR) data  
+                  echo "Downloading behavioral data..."
+                  curl -H "Authorization: token ${{ secrets.FIGSHARE_TOKEN }}" \
+                      -L "https://ndownloader.figshare.com/files/${{ vars.BEHAVIORAL_FILE_ID }}" \
+                      -o data/behavioral.csv
+
+                  # Exposome data
+                  #echo "Downloading exposome data..."
+                  #curl -H "Authorization: token ${{ secrets.FIGSHARE_TOKEN }}" \
+                  #     -L "https://ndownloader.figshare.com/files/${{ vars.EXPOSOME_FILE_ID }}" \
+                  #     -o data/exposome.csv
+
+                  # Gene expression data
+                  #echo "Downloading gene expression data..."
+                  #curl -H "Authorization: token ${{ secrets.FIGSHARE_TOKEN }}" \
+                  #     -L "https://ndownloader.figshare.com/files/${{ vars.EXPRESSION_FILE_ID }}" \
+                  #     -o data/expression.csv
+
+                  # Check if all files were downloaded successfully
+                  ls -la data/
+                  if [ -f "data/morphology.csv" ] && [ -f "data/behavioral.csv" ]; then # && [ -f "data/exposome.csv" ] && [ -f "data/expression.csv" ]; then
+                    echo "success=true" >> $GITHUB_OUTPUT
+                  else
+                    echo "success=false" >> $GITHUB_OUTPUT
+                    exit 1
+                  fi
+
+            - name: Upload raw data artifacts
+              uses: actions/upload-artifact@v4
+              with:
+                  name: data-files
+                  path: data/
+                  retention-days: 1