Create dockerfile and compose.

Author: meier-rene

compose/docker-compose.yaml

@@ -0,0 +1,77 @@
+
+services:
+
+  postgres:
+    image: docker.io/postgres:latest
+    restart: always
+    ports:
+      - '${DB_PORT}:${DB_PORT}'
+    environment:
+      POSTGRES_PASSWORD: ${DB_PASSWORD}
+      POSTGRES_USER: ${DB_USER}
+      POSTGRES_DB: ${DB_NAME}
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready", "-d", "$$POSTGRES_DB","-U", "$$POSTGRES_USER"]
+      interval: 30s
+      timeout: 60s
+      retries: 5
+      start_period: 40s
+
+  mb3server:
+    build: ../
+    restart: always
+    ports:
+      - "${MB3_API_PORT}:${MB3_SERVER_PORT}"
+    depends_on:
+      - postgres
+    environment:
+      - DB_TYPE
+      - DB_PORT
+      - DB_PASSWORD
+      - DB_HOST
+      - DB_NAME
+      - DB_CONN_STRING
+      - MB3_SERVER_PORT
+      - CDKDEPICT_URL
+
+  similarity-service-cosine:
+    build: ../similarity-service-cosine
+    restart: always
+    ports:
+      - "${SIMILARITY_SERVICE_COSINE_PORT}:8080"
+    depends_on:
+      - postgres
+    environment:
+      - DB_PORT
+      - DB_USER
+      - DB_PASSWORD
+      - DB_HOST
+      - DB_NAME
+
+  mb3frontend:
+    build:
+      context: ..
+      dockerfile: Dockerfile-frontend
+      args:
+        MB3_API_URL: "http://${MB3_API_HOST}:${MB3_API_PORT}"
+        MB3_FRONTEND_BASE_URL: "${MB3_FRONTEND_BASE_URL}"
+    restart: always
+    ports:
+      - "${MB3_FRONTEND_PORT}:3000"
+
+  mb3tool:
+    build:
+      context: ..
+      dockerfile: Dockerfile-dbtool
+    environment:
+      - DB_TYPE
+      - DB_PORT
+      - DB_USER
+      - DB_PASSWORD
+      - DB_HOST
+      - DB_NAME
+      - DB_CONN_STRING
+      - MB_GIT_REPO
+      - MB_GIT_BRANCH
+      - MB_DATA_DIRECTORY
+      - MB_DROP_ALL

compose/env.dist

@@ -0,0 +1,79 @@
+############################
+# Massbank 3 configuration #
+############################
+
+# --------------------
+# Server configuration
+# --------------------
+
+# The port where the API is exposed for frontend and application usage
+MB3_API_PORT=8081
+
+# The host where the frontend is running
+MB3_API_HOST=localhost
+
+# The port used internally by the server
+MB3_SERVER_PORT=8080
+
+
+# ----------------------
+# Frontend configuration
+# ----------------------
+
+# The Port where the frontend ist exposed
+MB3_FRONTEND_PORT=8080
+
+# The base URL
+MB3_FRONTEND_BASE_URL=/massbank3/
+
+# ----------------------
+# Database configuration
+# ----------------------
+
+# The database type: "mongodb" or "postgres"
+DB_TYPE=postgres
+
+# The port of the database
+DB_PORT=5432
+
+# The database user name
+DB_USER=massbank3
+
+# The database password
+DB_PASSWORD=massbank3password
+
+# The database host name
+DB_HOST=localhost
+
+# The name of the database
+DB_NAME=massbank3
+
+# A connection string to connect with the database. If set to non empty string other "DB_..." environment variables will be ignored
+DB_CONN_STRING=""
+
+# ------------------------------
+# Similarity microservice cosine
+# ------------------------------
+
+# The port where the similarity service is exposed
+SIMILARITY_SERVICE_COSINE_PORT=8082
+
+# The host where the similarity service is running
+SIMILARITY_SERVICE_COSINE_HOST=localhost
+
+# ---------------------------
+# Massbank-data configuration
+# ---------------------------
+
+# The repo where to load massbank data from
+MB_GIT_REPO="https://github.com/MassBank/MassBank-data"
+
+# The git branch of the massbank data repo
+MB_GIT_BRANCH=main
+
+# A directory where the massbank data is stored. If set, this will tried first before getting data from git.
+MB_DATA_DIRECTORY=""
+
+# Set to true to clear the database before filling with new data, otherwise data is upserted.
+MB_DROP_ALL=true
+

similarity-service-cosine/.dockerignore

@@ -1,72 +1,7 @@
-.travis.yaml
-.openapi-generator-ignore
-README.md
-tox.ini
-git_push.sh
-test-requirements.txt
-setup.py
+#project files and folders
+.idea/
+Dockerfile
 
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
-venv/
-.python-version
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-#Ipython Notebook
-.ipynb_checkpoints
+#generated folders
+gen/
+venv/

similarity-service-cosine/Dockerfile

@@ -0,0 +1,24 @@
+FROM python:3.11-bookworm
+RUN apt update && apt install -y default-jre-headless
+
+COPY generate.sh openapi-generator-cli.jar openapi.yaml /usr/src/app/
+
+WORKDIR /usr/src/app
+RUN bash generate.sh
+
+FROM python:3.11-slim-bookworm
+COPY requirements.txt /usr/src/app/
+COPY cosine_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
+
+WORKDIR /usr/src/app
+RUN pip3 install --no-cache-dir -r requirements.txt
+
+ENV PYTHONPATH=/usr/src/app/gen
+
+EXPOSE 8080
+
+ENTRYPOINT ["python3"]
+
+CMD ["-m", "cosine_impl"]