From 7a9d6aa8a9aefcbaefc32c526c2d18b528baa1e4 Mon Sep 17 00:00:00 2001
From: Vincent Emonet <vincent.emonet@gmail.com>
Date: Thu, 10 Oct 2024 09:37:44 +0200
Subject: [PATCH] improve docker setup, add 1 test

---
 compose.yml                      |  1 +
 deploy.sh                        |  7 +++++++
 notebooks/test_expasy_chat.ipynb | 16 ++++++++++++++++
 3 files changed, 24 insertions(+)

diff --git a/compose.yml b/compose.yml
index 8c2f4e9..d902975 100644
--- a/compose.yml
+++ b/compose.yml
@@ -17,6 +17,7 @@ services:
   api:
     build: .
     container_name: api
+    restart: unless-stopped
     depends_on:
       - vectordb
     ports:
diff --git a/deploy.sh b/deploy.sh
index fd4b3b2..fadf893 100755
--- a/deploy.sh
+++ b/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
diff --git a/notebooks/test_expasy_chat.ipynb b/notebooks/test_expasy_chat.ipynb
index 1910921..494679a 100644
--- a/notebooks/test_expasy_chat.ipynb
+++ b/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",