Auto-sync: 9ec47ffa7894617d757f0d327196ac187860d921

.github/workflows/integration-test-hf.yml

@@ -12,108 +12,110 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  core-ai-proxy:
+  warmup-spaces:
     runs-on: ubuntu-latest
-    timeout-minutes: 30
-
+    timeout-minutes: 15
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
       - name: Warm up ailixir-api Space
         run: |
           echo "Waiting for ailixir-api HF Space..."
           for i in $(seq 1 60); do
-            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
-              echo "ailixir-api is up"
-              sleep 5
-              exit 0
+            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/health > /dev/null 2>&1; then
+              echo "✓ ailixir-api is up"
+              break
             fi
             echo "Attempt $i/60..."
             sleep 5
           done
-          exit 1
 
       - name: Warm up ailixir-drug-repurposing Space
         run: |
           echo "Waiting for ailixir-drug-repurposing HF Space..."
           for i in $(seq 1 60); do
             if curl -sf https://RottenShadow-ailixir-drug-repurposing.hf.space/health > /dev/null 2>&1; then
-              echo "ailixir-drug-repurposing is up"
-              sleep 3
-              exit 0
+              echo "✓ ailixir-drug-repurposing is up"
+              break
             fi
             echo "Attempt $i/60..."
             sleep 5
           done
-          exit 1
 
       - name: Warm up ailixir-admet Space
         run: |
           echo "Waiting for ailixir-admet HF Space..."
           for i in $(seq 1 60); do
             if curl -sf https://shdwRow-ailixir-admet.hf.space/health > /dev/null 2>&1; then
-              echo "ailixir-admet is up"
-              sleep 3
-              exit 0
+              echo "✓ ailixir-admet is up"
+              break
             fi
             echo "Attempt $i/60..."
             sleep 5
           done
-          exit 1
 
       - name: Warm up ailixir-chemical-rag Space
         run: |
           echo "Waiting for ailixir-chemical-rag HF Space..."
           for i in $(seq 1 60); do
             if curl -sf https://RottenShadow-ailixir-chemical-rag.hf.space/health > /dev/null 2>&1; then
-              echo "ailixir-chemical-rag is up"
-              sleep 3
-              exit 0
+              echo "✓ ailixir-chemical-rag is up"
+              break
             fi
             echo "Attempt $i/60..."
             sleep 5
           done
-          exit 1
+
+  core-ai-proxy:
+    needs: warmup-spaces
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
 
       - name: Login and get Bearer token
         run: |
           echo "POST /api/user/login"
-          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
-            -H "Content-Type: application/json" \
-            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
-          echo "HTTP Status: $HTTP_CODE"
-          cat login.json
-          echo ""
-
-          if [ "$HTTP_CODE" != "200" ]; then
-            echo "Login failed with HTTP $HTTP_CODE"
-            exit 1
-          fi
-
-          python3 - <<'PY'
-          import json, sys
-          try:
-              data = json.load(open("login.json"))
-          except json.JSONDecodeError as e:
-              print("Invalid JSON response:", e)
-              with open("login.json") as f:
-                  print("Raw response:", f.read())
-              sys.exit(1)
-
-          if not data.get("success"):
-              print("Login failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-
-          token = data.get("data", {}).get("token")
-          if not token:
-              print("No token in response:", json.dumps(data, indent=2))
-              sys.exit(1)
-
-          with open("token.txt", "w") as f:
-              f.write(token)
-          print("Login OK - token saved")
-          PY
+          for attempt in {1..3}; do
+            HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
+              -H "Content-Type: application/json" \
+              -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
+            echo "HTTP Status: $HTTP_CODE (attempt $attempt/3)"
+            
+            if [ "$HTTP_CODE" = "200" ]; then
+              python3 - <<'PY'
+import json, sys
+try:
+    data = json.load(open("login.json"))
+except json.JSONDecodeError as e:
+    print("Invalid JSON response:", e)
+    with open("login.json") as f:
+        print("Raw response:", f.read())
+    sys.exit(1)
+
+if not data.get("success"):
+    print("Login failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+token = data.get("data", {}).get("token")
+if not token:
+    print("No token in response:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+with open("token.txt", "w") as f:
+    f.write(token)
+print("✓ Login OK - token saved")
+PY
+              if [ $? -eq 0 ]; then exit 0; fi
+            fi
+            
+            if [ $attempt -lt 3 ]; then
+              echo "Login attempt $attempt failed, retrying in 10s..."
+              sleep 10
+            fi
+          done
+          echo "Login failed after 3 attempts"
+          exit 1
 
       - name: Test aggregated AI health via Laravel
         run: |
@@ -125,13 +127,13 @@ jobs:
           cat health.json
           echo ""
           python3 - <<'PY'
-          import json, sys
-          data = json.load(open("health.json"))
-          if not data.get("success"):
-              print("AI services health check failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-          print("All AI services healthy via Laravel proxy")
-          PY
+import json, sys
+data = json.load(open("health.json"))
+if not data.get("success"):
+    print("AI services health check failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+print("✓ All AI services healthy via Laravel proxy")
+PY
 
       - name: Test ADMET prediction via Laravel proxy
         run: |
@@ -151,26 +153,26 @@ jobs:
           fi
 
           python3 - <<'PY'
-          import json, sys
-          try:
-              data = json.load(open("admet.json"))
-          except json.JSONDecodeError as e:
-              print("Invalid JSON response:", e)
-              with open("admet.json") as f:
-                  print("Raw response:", f.read())
-              sys.exit(1)
-
-          if not data.get("success"):
-              print("ADMET prediction test failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-
-          results = data.get("data", {}).get("results", [])
-          if len(results) < 3:
-              print(f"Expected at least 3 results, got {len(results)}")
-              sys.exit(1)
-
-          print(f"ADMET prediction OK - {len(results)} compounds processed")
-          PY
+import json, sys
+try:
+    data = json.load(open("admet.json"))
+except json.JSONDecodeError as e:
+    print("Invalid JSON response:", e)
+    with open("admet.json") as f:
+        print("Raw response:", f.read())
+    sys.exit(1)
+
+if not data.get("success"):
+    print("ADMET prediction test failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+results = data.get("data", {}).get("results", [])
+if len(results) < 3:
+    print(f"Expected at least 3 results, got {len(results)}")
+    sys.exit(1)
+
+print(f"✓ ADMET prediction OK - {len(results)} compounds processed")
+PY
 
       - name: Test Chemical RAG proxy via Laravel
         run: |
@@ -184,13 +186,13 @@ jobs:
           cat chemical.json
           echo ""
           python3 - <<'PY'
-          import json, sys
-          data = json.load(open("chemical.json"))
-          if not data.get("success"):
-              print("Chemical RAG proxy test failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-          print("Chemical RAG proxy OK")
-          PY
+import json, sys
+data = json.load(open("chemical.json"))
+if not data.get("success"):
+    print("Chemical RAG proxy test failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+print("✓ Chemical RAG proxy OK")
+PY
 
       - name: Test Drug Repurposing proxy via Laravel
         run: |
@@ -202,15 +204,16 @@ jobs:
           cat drug.json
           echo ""
           python3 - <<'PY'
-          import json, sys
-          data = json.load(open("drug.json"))
-          if not data.get("success"):
-              print("Drug Repurposing proxy test failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-          print("Drug Repurposing proxy OK")
-          PY
+import json, sys
+data = json.load(open("drug.json"))
+if not data.get("success"):
+    print("Drug Repurposing proxy test failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+print("✓ Drug Repurposing proxy OK")
+PY
 
   chemical-search:
+    needs: warmup-spaces
     runs-on: ubuntu-latest
     timeout-minutes: 15
 
@@ -218,34 +221,42 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Warm up ailixir-api Space
+      - name: Login and get Bearer token
         run: |
-          for i in $(seq 1 60); do
-            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
-              echo "ailixir-api is up"
-              sleep 5
-              exit 0
+          for attempt in {1..3}; do
+            HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
+              -H "Content-Type: application/json" \
+              -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
+            if [ "$HTTP_CODE" = "200" ]; then
+              python3 - <<'PY'
+import json, sys
+try:
+    data = json.load(open("login.json"))
+except json.JSONDecodeError as e:
+    print("Invalid JSON response:", e)
+    with open("login.json") as f:
+        print("Raw response:", f.read())
+    sys.exit(1)
+
+if not data.get("success"):
+    print("Login failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+token = data.get("data", {}).get("token")
+if not token:
+    print("No token in response:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+with open("token.txt", "w") as f:
+    f.write(token)
+print("✓ Login OK - token saved")
+PY
+              if [ $? -eq 0 ]; then exit 0; fi
             fi
-            echo "Waiting ($i/60)..."
-            sleep 5
+            [ $attempt -lt 3 ] && sleep 10
           done
           exit 1
 
-      - name: Login and get Bearer token
-        run: |
-          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
-            -H "Content-Type: application/json" \
-            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
-          if [ "$HTTP_CODE" != "200" ]; then exit 1; fi
-          python3 - <<'PY'
-          import json
-          with open('login.json') as f: data = json.load(f)
-          token = data.get('data', {}).get('token')
-          if not token: exit(1)
-          with open('token.txt','w') as f: f.write(token)
-          print('Login OK')
-          PY
-
       - name: Test retrieval-only chemical search
         run: |
           TOKEN=$(cat token.txt)
@@ -258,19 +269,19 @@ jobs:
           cat search.json
           echo ""
           python3 - <<'PY'
-          import json, sys
-          data = json.load(open("search.json"))
-          if not data.get("success"):
-              print("Chemical search (retrieval-only) failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-          if not isinstance(data.get("compounds"), list):
-              print("Missing 'compounds' array in response")
-              sys.exit(1)
-          if data.get("metadata", {}).get("source") != "retrieval":
-              print("Expected source='retrieval', got:", data.get("metadata", {}).get("source"))
-              sys.exit(1)
-          print("Chemical search (retrieval-only) OK - found", len(data["compounds"]), "compounds")
-          PY
+import json, sys
+data = json.load(open("search.json"))
+if not data.get("success"):
+    print("Chemical search (retrieval-only) failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+if not isinstance(data.get("compounds"), list):
+    print("Missing 'compounds' array in response")
+    sys.exit(1)
+if data.get("metadata", {}).get("source") != "retrieval":
+    print("Expected source='retrieval', got:", data.get("metadata", {}).get("source"))
+    sys.exit(1)
+print("✓ Chemical search (retrieval-only) OK - found", len(data["compounds"]), "compounds")
+PY
 
       - name: Test full RAG chemical search
         run: |
@@ -284,25 +295,26 @@ jobs:
           cat rag.json
           echo ""
           python3 - <<'PY'
-          import json, sys
-          data = json.load(open("rag.json"))
-          if not data.get("success"):
-              print("Chemical search (full RAG) failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-          if not isinstance(data.get("compounds"), list):
-              print("Missing 'compounds' array in response")
-              sys.exit(1)
-          if data.get("metadata", {}).get("source") != "full_rag":
-              print("Expected source='full_rag', got:", data.get("metadata", {}).get("source"))
-              sys.exit(1)
-          for compound in data["compounds"]:
-              if not compound.get("explanation"):
-                  print("Missing explanation for compound:", compound.get("name"))
-                  sys.exit(1)
-          print("Chemical search (full RAG) OK - found", len(data["compounds"]), "compounds with explanations")
-          PY
+import json, sys
+data = json.load(open("rag.json"))
+if not data.get("success"):
+    print("Chemical search (full RAG) failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+if not isinstance(data.get("compounds"), list):
+    print("Missing 'compounds' array in response")
+    sys.exit(1)
+if data.get("metadata", {}).get("source") != "full_rag":
+    print("Expected source='full_rag', got:", data.get("metadata", {}).get("source"))
+    sys.exit(1)
+for compound in data["compounds"]:
+    if not compound.get("explanation"):
+        print("Missing explanation for compound:", compound.get("name"))
+        sys.exit(1)
+print("✓ Chemical search (full RAG) OK - found", len(data["compounds"]), "compounds with explanations")
+PY
 
   drug-repurposing-integration:
+    needs: warmup-spaces
     runs-on: ubuntu-latest
     timeout-minutes: 30
 
@@ -310,34 +322,42 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Warm up ailixir-api Space
+      - name: Login and get Bearer token
         run: |
-          for i in $(seq 1 60); do
-            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
-              echo "ailixir-api is up"
-              sleep 5
-              exit 0
+          for attempt in {1..3}; do
+            HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
+              -H "Content-Type: application/json" \
+              -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
+            if [ "$HTTP_CODE" = "200" ]; then
+              python3 - <<'PY'
+import json, sys
+try:
+    data = json.load(open("login.json"))
+except json.JSONDecodeError as e:
+    print("Invalid JSON response:", e)
+    with open("login.json") as f:
+        print("Raw response:", f.read())
+    sys.exit(1)
+
+if not data.get("success"):
+    print("Login failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+token = data.get("data", {}).get("token")
+if not token:
+    print("No token in response:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+with open("token.txt", "w") as f:
+    f.write(token)
+print("✓ Login OK - token saved")
+PY
+              if [ $? -eq 0 ]; then exit 0; fi
             fi
-            echo "Waiting ($i/60)..."
-            sleep 5
+            [ $attempt -lt 3 ] && sleep 10
           done
           exit 1
 
-      - name: Login and get Bearer token
-        run: |
-          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
-            -H "Content-Type: application/json" \
-            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
-          if [ "$HTTP_CODE" != "200" ]; then exit 1; fi
-          python3 - <<'PY'
-          import json
-          with open('login.json') as f: data = json.load(f)
-          token = data.get('data', {}).get('token')
-          if not token: exit(1)
-          with open('token.txt','w') as f: f.write(token)
-          print('Login OK')
-          PY
-
       - name: Test unauthenticated DR request is rejected
         run: |
           echo "POST /api/drug-repurposing/targets (no auth)"
@@ -349,11 +369,11 @@ jobs:
             exit 1
           fi
           python3 - <<'PY'
-          import json
-          with open('dr_unauth.json') as f: data = json.load(f)
-          assert not data.get('success', True), 'Expected success=false'
-          print('Unauthenticated DR request correctly rejected')
-          PY
+import json
+with open('dr_unauth.json') as f: data = json.load(f)
+assert not data.get('success', True), 'Expected success=false'
+print('✓ Unauthenticated DR request correctly rejected')
+PY
 
       - name: Test DR target lookup requires disease_name
         run: |
@@ -367,7 +387,7 @@ jobs:
             echo "Expected 422, got $HTTP_CODE"
             exit 1
           fi
-          echo "Missing disease_name correctly rejected"
+          echo "✓ Missing disease_name correctly rejected"
 
       - name: Test DR target lookup via Laravel proxy
         run: |
@@ -387,40 +407,41 @@ jobs:
           fi
 
           python3 - <<'PY'
-          import json, sys
-          data = json.load(open("dr_targets.json"))
-          if not data.get("success"):
-              print("DR target lookup failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-          job_id = data.get("data", {}).get("job_id")
-          status = data.get("data", {}).get("status")
-          print(f"DR target lookup OK - job_id={job_id}, status={status}")
-
-          # Poll for completion
-          import time, urllib.request
-          base = "https://Ailixir-AI-Team-ailixir-api.hf.space/api/drug-repurposing/targets"
-          with open("token.txt") as f: token = f.read().strip()
-          for i in range(30):
-              req = urllib.request.Request(f"{base}/{job_id}")
-              req.add_header("Authorization", f"Bearer {token}")
-              resp = urllib.request.urlopen(req)
-              status_data = json.loads(resp.read())
-              s = status_data.get("data", {}).get("status")
-              if s == "completed":
-                  output = status_data.get("data", {}).get("output", {})
-                  assert len(output.get("targets", [])) > 0, "No targets found"
-                  print(f"DR targets completed - {len(output['targets'])} targets found")
-                  sys.exit(0)
-              elif s == "failed":
-                  print("DR target lookup failed:", json.dumps(status_data, indent=2))
-                  sys.exit(1)
-              print(f"  Polling... attempt {i+1}/30, status={s}")
-              time.sleep(5)
-          print("DR target lookup did not complete in time")
-          sys.exit(1)
-          PY
+import json, sys
+data = json.load(open("dr_targets.json"))
+if not data.get("success"):
+    print("DR target lookup failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+job_id = data.get("data", {}).get("job_id")
+status = data.get("data", {}).get("status")
+print(f"✓ DR target lookup OK - job_id={job_id}, status={status}")
+
+# Poll for completion
+import time, urllib.request
+base = "https://Ailixir-AI-Team-ailixir-api.hf.space/api/drug-repurposing/targets"
+with open("token.txt") as f: token = f.read().strip()
+for i in range(30):
+    req = urllib.request.Request(f"{base}/{job_id}")
+    req.add_header("Authorization", f"Bearer {token}")
+    resp = urllib.request.urlopen(req)
+    status_data = json.loads(resp.read())
+    s = status_data.get("data", {}).get("status")
+    if s == "completed":
+        output = status_data.get("data", {}).get("output", {})
+        assert len(output.get("targets", [])) > 0, "No targets found"
+        print(f"✓ DR targets completed - {len(output['targets'])} targets found")
+        sys.exit(0)
+    elif s == "failed":
+        print("DR target lookup failed:", json.dumps(status_data, indent=2))
+        sys.exit(1)
+    print(f"  Polling... attempt {i+1}/30, status={s}")
+    time.sleep(5)
+print("DR target lookup did not complete in time")
+sys.exit(1)
+PY
 
   docking-integration:
+    needs: warmup-spaces
     runs-on: ubuntu-latest
     timeout-minutes: 15
 
@@ -428,34 +449,42 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Warm up ailixir-api Space
+      - name: Login and get Bearer token
         run: |
-          for i in $(seq 1 60); do
-            if curl -sf https://Ailixir-AI-Team-ailixir-api.hf.space/ > /dev/null 2>&1; then
-              echo "ailixir-api is up"
-              sleep 5
-              exit 0
+          for attempt in {1..3}; do
+            HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
+              -H "Content-Type: application/json" \
+              -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
+            if [ "$HTTP_CODE" = "200" ]; then
+              python3 - <<'PY'
+import json, sys
+try:
+    data = json.load(open("login.json"))
+except json.JSONDecodeError as e:
+    print("Invalid JSON response:", e)
+    with open("login.json") as f:
+        print("Raw response:", f.read())
+    sys.exit(1)
+
+if not data.get("success"):
+    print("Login failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+token = data.get("data", {}).get("token")
+if not token:
+    print("No token in response:", json.dumps(data, indent=2))
+    sys.exit(1)
+
+with open("token.txt", "w") as f:
+    f.write(token)
+print("✓ Login OK - token saved")
+PY
+              if [ $? -eq 0 ]; then exit 0; fi
             fi
-            echo "Waiting ($i/60)..."
-            sleep 5
+            [ $attempt -lt 3 ] && sleep 10
           done
           exit 1
 
-      - name: Login and get Bearer token
-        run: |
-          HTTP_CODE=$(curl -s -o login.json -w "%{http_code}" -X POST https://Ailixir-AI-Team-ailixir-api.hf.space/api/user/login \
-            -H "Content-Type: application/json" \
-            -d '{"email":"salehyasmeen080@gmail.com","password":"123456789"}')
-          if [ "$HTTP_CODE" != "200" ]; then exit 1; fi
-          python3 - <<'PY'
-          import json
-          with open('login.json') as f: data = json.load(f)
-          token = data.get('data', {}).get('token')
-          if not token: exit(1)
-          with open('token.txt','w') as f: f.write(token)
-          print('Login OK')
-          PY
-
       - name: Test docking submit
         run: |
           TOKEN=$(cat token.txt)
@@ -483,10 +512,10 @@ jobs:
           fi
 
           python3 - <<'PY'
-          import json, sys
-          data = json.load(open("docking.json"))
-          if not data.get("success"):
-              print("Docking submit failed:", json.dumps(data, indent=2))
-              sys.exit(1)
-          print("Docking submit OK - job created")
-          PY
+import json, sys
+data = json.load(open("docking.json"))
+if not data.get("success"):
+    print("Docking submit failed:", json.dumps(data, indent=2))
+    sys.exit(1)
+print("✓ Docking submit OK - job created")
+PY