improve docker setup, add 1 test

compose.yml

@@ -17,6 +17,7 @@ services:
   api:
     build: .
     container_name: api
+    restart: unless-stopped
     depends_on:
       - vectordb
     ports:

deploy.sh

@@ -1,13 +1,20 @@
 if [ "$1" = "--build" ]; then
     echo "📦️ Re-building"
     ssh expasychat 'sudo -u podman bash -c "cd /var/containers/podman/sparql-llm ; git pull ; podman-compose up --force-recreate --build -d"'
+
+elif [ "$1" = "--clean" ]; then
+    echo "🧹 Cleaning up the vector database"
+    ssh expasychat 'sudo -u podman bash -c "cd /var/containers/podman/sparql-llm ; git pull ; rm -rf data/qdrant ; podman-compose up --force-recreate -d"'
+
 elif [ "$1" = "--logs" ]; then
     ssh expasychat 'sudo -u podman bash -c "cd /var/containers/podman/sparql-llm ; podman-compose logs api"'
+
 elif [ "$1" = "--likes" ]; then
     mkdir -p data/prod
     scp expasychat:/var/containers/podman/sparql-llm/data/logs/likes.jsonl ./data/prod/
     scp expasychat:/var/containers/podman/sparql-llm/data/logs/dislikes.jsonl ./data/prod/
     scp expasychat:/var/containers/podman/sparql-llm/data/logs/user_questions.log ./data/prod/
+
 else
     ssh expasychat 'sudo -u podman bash -c "cd /var/containers/podman/sparql-llm ; git pull ; podman-compose up --force-recreate -d"'
 fi

notebooks/test_expasy_chat.ipynb

@@ -276,6 +276,22 @@
     "}\n",
     "\"\"\",\n",
     "    },\n",
+    "    {\n",
+    "        \"question\": \"What is the function of APOC1? Return ?function\",\n",
+    "        \"endpoint\": \"https://sparql.uniprot.org/sparql/\",\n",
+    "        \"query\": \"\"\"PREFIX up: <http://purl.uniprot.org/core/>\n",
+    "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n",
+    "PREFIX dcterms: <http://purl.org/dc/terms/>\n",
+    "SELECT DISTINCT ?function WHERE {\n",
+    "    ?protein a up:Protein ;\n",
+    "        up:mnemonic \"APOC1_HUMAN\" ;\n",
+    "        up:annotation ?annotation .\n",
+    "    ?annotation a up:Function_Annotation ;\n",
+    "        rdfs:comment ?function .\n",
+    "}\n",
+    "\"\"\",\n",
+    "    },\n",
+    "\n",
     "\n",
     "    # New queries to test:\n",
     "    # Find all proteins linked to arachidonate (CHEBI:32395) and their associated pathways\n",