Migrate to using LangGraph based workflow, and serve it through custo…

…m API endpoint

Dockerfile

@@ -1,4 +1,4 @@
-FROM docker.io/tiangolo/uvicorn-gunicorn-fastapi:python3.11
+FROM docker.io/python:3.11
 
 WORKDIR /app
 
@@ -11,12 +11,15 @@ RUN pip install --upgrade pip
 
 
 COPY . /app/
-# COPY ./scripts/prestart.sh /app/
 
 WORKDIR /app/packages/expasy-agent
 
 RUN pip install -e ".[cpu]" "../sparql-llm"
 
-ENV PYTHONPATH=/app/packages/expasy-agent
-ENV MODULE_NAME=src.expasy_agent.api
-# ENV VARIABLE_NAME=app
+# ENV PYTHONPATH=/app/packages/expasy-agent
+# ENV MODULE_NAME=src.expasy_agent.api
+
+# https://github.com/tiangolo/uvicorn-gunicorn-docker/blob/master/docker-images/gunicorn_conf.py
+
+CMD ["uvicorn", "src.expasy_agent.api", "--host", "0.0.0.0", "--port", "80", "--workers", "4"]
+# CMD ["uvicorn", "src.expasy_agent.api", "--host", "0.0.0.0", "--port", "80", "--workers", "4", "--http", "h11"]

README.md

@@ -204,7 +204,7 @@ print("\n".join(issues))
 4. Run the script to index the resources (SPARQL endpoints listed in config file):
 
    ```sh
-   docker compose run api python src/expasy_agent/index.py
+   docker compose run api python src/expasy_agent/indexing/index_endpoints.py
    ```
 
 > [!WARNING]
@@ -213,7 +213,7 @@ print("\n".join(issues))
 >
 > ```sh
 > pip install -e ".[chat,gpu]"
-> python src/sparql_llm/index_entities.py
+> python src/expasy_agent/indexing/index_entities.py
 > ```
 >
 > Then move the entities collection containing the embeddings in `data/qdrant/collections/entities` before starting the stack

chat-with-context/index.html

@@ -87,7 +87,7 @@ <h2 class="text-xl text-center font-semibold border-b pb-2">
         <!-- LangGraph prod: api="http://localhost:8123/" -->
         <!-- LangServe: api="http://localhost:8001/langgraph/" -->
         <chat-with-context
-          api="http://localhost:2024/"
+          api="http://localhost:8000/langgraph/"
           api-key="%EXPASY_API_KEY%"
           examples="Which resources are available at the SIB?,How can I get the HGNC symbol for the protein P68871?,What are the rat orthologs of the human TP53?,Where is expressed the gene ACE2 in human?,Anatomical entities where the INS zebrafish gene is expressed and its gene GO annotations,List the genes in primates orthologous to genes expressed in the fruit fly eye"
         ></chat-with-context>