Update instructions and Dockerfile

Dockerfile

@@ -1,22 +1,22 @@
-FROM eclipse-temurin:17-jre
+FROM maven:3.9-eclipse-temurin-21
+RUN apt-get update && apt-get install -y --no-install-recommends jq && rm -rf /var/lib/apt/lists/*
 
-COPY generate.sh openapi-generator-cli.jar openapi.yaml /usr/src/app/
+COPY generate.sh config-openapi.yaml openapi.yaml /usr/src/app/
 
 WORKDIR /usr/src/app
 RUN bash generate.sh
 
 FROM python:3.12-slim-bookworm
 WORKDIR /usr/src/app
-RUN apt-get update && apt-get install -y --no-install-recommends libpq5 && rm -rf /var/lib/apt/lists/*
 COPY requirements.txt /usr/src/app/
-RUN pip3 install --upgrade pip && pip3 install --no-cache-dir -r requirements.txt
+RUN pip3 install --root-user-action=ignore --upgrade pip && pip3 install --root-user-action=ignore --no-cache-dir -r requirements.txt
 
-COPY similarity_service_impl /usr/src/app/cosine_impl
 COPY --from=0 /usr/src/app/openapi.yaml /usr/src/app/openapi.yaml
 COPY --from=0 /usr/src/app/gen /usr/src/app/gen
+COPY similarity_service_impl /usr/src/app/similarity_service_impl
 
 ENV PYTHONPATH=/usr/src/app/gen
 
 EXPOSE 8080/tcp
 ENTRYPOINT ["/usr/local/bin/waitress-serve"]
-CMD ["--port=8080", "cosine_impl.app:app"]
+CMD ["--port=8080", "similarity_service_impl.app:app"]

README.md

@@ -8,35 +8,39 @@ the [Connexion](https://github.com/zalando/connexion) library on top of Flask.
 Tested on Python 3.12
 
 ## Configuration
-This microservice is configured with environment variables. The following variables and
-default values are used:
-```
-DB_PORT = 5432
-DB_USER = "massbank3"
-DB_PASSWORD = "massbank3password"
-DB_NAME = "massbank3"
-DB_HOST = "localhost"
+This microservice is configured with environment variables. The reference
+spectra are initialized from a local file. The file location needs to be
+configured in the environment variable `MSP`. For MassBank we configure the
+service with the latest MassBank-data release in msp format.
+```bash
+wget https://github.com/MassBank/MassBank-data/releases/latest/download/MassBank_NIST.msp
+export MSP="./MassBank_NIST.msp"
 ```
 
 ## Usage
-To run the server, please generate the server code, install the requirements 
+To run the server, install the requirements, generate the server code 
 and start the server like this:
 ```bash
-bash generate.sh
 pip3 install -r requirements.txt
+bash generate.sh
 PYTHONPATH=gen python3 -m similarity_service_impl
 ```
 You can find the swagger ui at http://localhost:8080/ui/ and the
 OpenAPI definition at http://localhost:8080/openapi.json in your browser.
 
 ## Running with Docker
-
-To run the server on a Docker container, please execute the following from the root directory:
+To run the server in a Docker container,  execute the following commands:
 
 ```bash
 # building the image
-docker build -t openapi_server .
+docker build -t massbank3-similarity-service .
+
+# download reference data
+wget https://github.com/MassBank/MassBank-data/releases/latest/download/MassBank_NIST.msp
 
 # starting up a container
-docker run -p 8080:8080 openapi_server
+docker run -p 8080:8080 \
+-v $(pwd)/MassBank_NIST.msp:/MassBank_NIST.msp \
+-e MSP='/MassBank_NIST.msp' \
+massbank3-similarity-service
 ```

requirements.txt

@@ -5,6 +5,4 @@ Flask < 2.3
 waitress >= 3.0.0
 
 matchms >= 0.27.0
-psycopg[pool] >= 3.0.0
 numpy
-watchdog