Support facets with intermediate arrays and improve fixtures (#31)

.pyproject_generation/pyproject_custom.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mass"
-version = "3.0.1"
+version = "3.0.2"
 description = "Metadata Artifact Search Service - A service for searching metadata artifacts and filtering results."
 dependencies = [
     "typer>=0.12",

.template/mandatory_files.txt

@@ -23,6 +23,7 @@ lock/requirements-dev.txt
 lock/requirements.txt
 
 Dockerfile
+Dockerfile.debian
 config_schema.json
 example_config.yaml
 LICENSE

Dockerfile

@@ -13,35 +13,39 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-## creating building container
-FROM python:3.12-slim-bookworm AS builder
-# update and install dependencies
-RUN apt update
-RUN apt upgrade -y
+# BASE: a base image with updated packages
+FROM python:3.12-alpine AS base
+#RUN apk update
+#RUN apk upgrade --available
+RUN apk upgrade --no-cache --available
+
+# BUILDER: a container to build the service wheel
+FROM base as builder
 RUN pip install build
-# copy code
 COPY . /service
 WORKDIR /service
-# build wheel
 RUN python -m build
 
-# creating running container
-FROM python:3.12-slim-bookworm
-# update and install dependencies
-RUN apt update
-RUN apt upgrade -y
-# copy and install requirements and wheel
+# DEP-BUILDER: a container to (build and) install dependencies
+FROM base AS dep-builder
+RUN apk update
+RUN apk add build-base gcc g++ libffi-dev zlib-dev
+RUN apk upgrade --available
 WORKDIR /service
 COPY --from=builder /service/lock/requirements.txt /service
 RUN pip install --no-deps -r requirements.txt
-RUN rm requirements.txt
+
+# RUNNER: a container to run the service
+FROM base as runner
+WORKDIR /service
+RUN rm -rf /usr/local/lib/python3.12 && mkdir /usr/local/lib/python3.12
+COPY --from=dep-builder /usr/local/lib/python3.12 /usr/local/lib/python3.12
 COPY --from=builder /service/dist/ /service
 RUN pip install --no-deps *.whl
 RUN rm *.whl
-# create new user and execute as that user
-RUN useradd --create-home appuser
+RUN adduser -D appuser
 WORKDIR /home/appuser
 USER appuser
-# set environment
 ENV PYTHONUNBUFFERED=1
+
 ENTRYPOINT ["mass"]

Dockerfile.debian

@@ -0,0 +1,48 @@
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+## creating building container
+FROM python:3.12-slim-bookworm AS builder
+# update and install dependencies
+RUN apt update
+RUN apt upgrade -y
+RUN pip install build
+# copy code
+COPY . /service
+WORKDIR /service
+# build wheel
+RUN python -m build
+
+# creating running container
+FROM python:3.12-slim-bookworm
+# update and install dependencies
+RUN apt update
+RUN apt upgrade -y
+# copy and install requirements and wheel
+WORKDIR /service
+COPY --from=builder /service/lock/requirements.txt /service
+RUN pip install --no-deps -r requirements.txt
+RUN rm requirements.txt
+COPY --from=builder /service/dist/ /service
+RUN pip install --no-deps *.whl
+RUN rm *.whl
+# create new user and execute as that user
+RUN useradd --create-home appuser
+WORKDIR /home/appuser
+USER appuser
+# set environment
+ENV PYTHONUNBUFFERED=1
+
+ENTRYPOINT ["mass"]

README.md

@@ -37,21 +37,21 @@ We recommend using the provided Docker container.
 
 A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/mass):
 ```bash
-docker pull ghga/mass:3.0.1
+docker pull ghga/mass:3.0.2
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/mass:3.0.1 .
+docker build -t ghga/mass:3.0.2 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/mass:3.0.1 --help
+docker run -p 8080:8080 ghga/mass:3.0.2 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
@@ -72,7 +72,7 @@ The service requires the following configuration parameters:
 
 - **`service_name`** *(string)*: Default: `"mass"`.
 
-- **`service_instance_id`** *(string)*: A string that uniquely identifies this instance across all instances of this service. A globally unique Kafka client ID will be created by concatenating the service_name and the service_instance_id.
+- **`service_instance_id`** *(string, required)*: A string that uniquely identifies this instance across all instances of this service. A globally unique Kafka client ID will be created by concatenating the service_name and the service_instance_id.
 
 
   Examples:
@@ -105,11 +105,11 @@ The service requires the following configuration parameters:
 
 - **`log_traceback`** *(boolean)*: Whether to include exception tracebacks in log messages. Default: `true`.
 
-- **`searchable_classes`** *(object)*: A collection of searchable_classes with facetable and selected fields. Can contain additional properties.
+- **`searchable_classes`** *(object, required)*: A collection of searchable_classes with facetable and selected fields. Can contain additional properties.
 
   - **Additional properties**: Refer to *[#/$defs/SearchableClass](#%24defs/SearchableClass)*.
 
-- **`resource_change_event_topic`** *(string)*: Name of the event topic used to track resource deletion and upsertion events.
+- **`resource_change_event_topic`** *(string, required)*: Name of the event topic used to track resource deletion and upsertion events.
 
 
   Examples:
@@ -119,7 +119,7 @@ The service requires the following configuration parameters:
   ```
 
 
-- **`resource_deletion_event_type`** *(string)*: The type to use for events with deletion instructions.
+- **`resource_deletion_event_type`** *(string, required)*: The type to use for events with deletion instructions.
 
 
   Examples:
@@ -129,7 +129,7 @@ The service requires the following configuration parameters:
   ```
 
 
-- **`resource_upsertion_event_type`** *(string)*: The type to use for events with upsert instructions.
+- **`resource_upsertion_event_type`** *(string, required)*: The type to use for events with upsert instructions.
 
 
   Examples:
@@ -139,7 +139,7 @@ The service requires the following configuration parameters:
   ```
 
 
-- **`kafka_servers`** *(array)*: A list of connection strings to connect to Kafka bootstrap servers.
+- **`kafka_servers`** *(array, required)*: A list of connection strings to connect to Kafka bootstrap servers.
 
   - **Items** *(string)*
 
@@ -193,7 +193,7 @@ The service requires the following configuration parameters:
   ```
 
 
-- **`db_connection_str`** *(string, format: password)*: MongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/.
+- **`db_connection_str`** *(string, format: password, required)*: MongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/.
 
 
   Examples:
@@ -203,7 +203,7 @@ The service requires the following configuration parameters:
   ```
 
 
-- **`db_name`** *(string)*: Name of the database located on the MongoDB server.
+- **`db_name`** *(string, required)*: Name of the database located on the MongoDB server.
 
 
   Examples: