Data Source factory upgrade

.github/workflows/ci_tests.yml

@@ -30,3 +30,38 @@ jobs:
 
       # Documentation
       run_build_docs: false
+
+  pytest:
+    name: pytest
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        # Supported Python versions (according to pyproject.toml)
+        python-version: ['3.9', '3.10']
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install -U pip
+        pip install -U setuptools wheel flit
+        pip install -e .[dev]
+
+    - name: Run pytest
+      run: pytest -v -rs --cov=s7 --cov-report=xml --cov-report=term-missing
+
+    - name: Upload code coverage report
+      if: github.repository == 'SINTEF/soft7' && matrix.python-version == '3.9'
+      uses: codecov/codecov-action@v3
+      with:
+        fail_ci_if_error: true
+        flags: pytest
+        token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -25,19 +25,27 @@ repos:
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]
 
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.292
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
     hooks:
-      - id: ruff
-        args:
-        - "--fix"
-        - "--exit-non-zero-on-fix"
+    - id: pyupgrade
+      args: ["--py39-plus", "--keep-runtime-typing"]
 
   - repo: https://github.com/ambv/black
-    rev: 23.9.1
+    rev: 23.11.0
     hooks:
     - id: black
 
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.5
+    hooks:
+    - id: ruff
+      args:
+      - "--fix"
+      - "--exit-non-zero-on-fix"
+      - "--show-fixes"
+      - "--no-unsafe-fixes"
+
   - repo: https://github.com/PyCQA/bandit
     rev: 1.7.5
     hooks:
@@ -46,9 +54,10 @@ repos:
       files: ^s7/.*$
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.0
+    rev: v1.7.0
     hooks:
     - id: mypy
+      exclude: ^tests/.*$
       additional_dependencies:
       - pydantic>=2,<3
       - types-PyYAML

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 SINTEF
+Copyright (c) 2023 SINTEF
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1 +1,73 @@
 # SOFT7
+
+## OTEAPI plugin
+
+The `soft7` packages comes with an [OTEAPI](https://github.com/EMMC-ASBL/oteapi-core) plugin that allows one to convert any core parser data to a SOFT7 Entity instance.
+
+To use the plugin, call the `'soft7'` `functionType` function strategy.
+
+### Test the plugin
+
+At the root of the repository is a [Docker Compose](https://docs.docker.com/compose/) file, which, when run, will start an [OTEAPI Service](https://github.com/EMMC-ASBL/oteapi-services#readme) that includes the `soft7` OTEAPI plugin.
+
+To start the service, run:
+
+```bash
+docker compose pull
+docker compose up -d
+```
+
+To follow along with the installation of the `soft7` package and startup of the OTEAPI Service, run:
+
+```bash
+docker logs -f soft7-oteapi-1
+```
+
+Press Ctrl+C to stop following the logs.
+
+To eventually stop the services, run:
+
+```bash
+docker compose down
+```
+
+But first, let's test the plugin.
+
+Open a Python shell, an [IPython shell](https://ipython.org/), or a [Jupyter Notebook](https://jupyter.org/), and run:
+
+```python
+from s7.factories import create_datasource
+
+# Let us use an OPTIMADE structure from the Materials Project as our "raw" data source.
+# The chosen structure is mp-1228448 (Al2O3):
+# https://materialsproject.org/materials/mp-1228448/
+# For more information about OPTIMADE, see https://www.optimade.org/
+# For more information about the Materials Project, see https://materialsproject.org/
+dataresource_config = {
+    "downloadUrl": (
+        "https://optimade.materialsproject.org/v1/structures/mp-1228448?"
+        "response_format=json"
+    ),
+    "mediaType": "application/json",
+}
+
+# We need to setup a mapping configuration to tell the plugin how to map the OPTIMADE
+# structure to a SOFT7 Entity instance.
+# This requires knowledge of the OPTIMADE structure and the SOFT7 Entity.
+# In our case the OPTIMADE structure specification is available at
+# https://github.com/Materials-Consortia/OPTIMADE/blob/v1.1.0/optimade.rst#structures-entries
+# and the SOFT7 Entity of choice is the `OPTIMADEStructure` Entity, which can be found
+# at http://onto-ns.com/meta/1.0/OPTIMADEStructure
+mapping_config = {
+    "mappingType": "triples",
+    "prefixes": {
+        "optimade": "https://optimade.materialsproject.org/v1/structures/mp-1228448#",
+        "soft7": "http://onto-ns.com/meta/1.0/OPTIMADEStructure#",
+    },
+    "triples": {
+        ("optimade:data.id", "", "soft7:properties.id"),
+        ("optimade:data.type", "", "soft7:properties.type"),
+        ("optimade:data.attributes", "", "soft7:properties."),
+    }
+}
+```

agraph.cfg

@@ -0,0 +1,17 @@
+# AllegroGraph configuration file
+RunAs agraph
+SessionPorts 10000-10034
+Port 10035
+SettingsDirectory /agraph/data/settings
+LogDir /agraph/data
+PidFile /agraph/data/agraph.pid
+InstanceTimeout 604800
+SuperUser dbuser:test123
+<RootCatalog>
+ Main /agraph/data/rootcatalog
+</RootCatalog>
+
+<SystemCatalog>
+ Main /agraph/data/systemcatalog
+ InstanceTimeout 10
+</SystemCatalog>

docker-compose.yml

@@ -0,0 +1,48 @@
+version: "3"
+
+services:
+  oteapi:
+    image: ghcr.io/emmc-asbl/oteapi:${DOCKER_OTEAPI_VERSION:-latest}
+    ports:
+      - "${PORT:-8080}:8080"
+    environment:
+      OTEAPI_REDIS_TYPE: redis
+      OTEAPI_REDIS_HOST: redis
+      OTEAPI_REDIS_PORT: 6379
+      OTEAPI_prefix: "${OTEAPI_prefix:-/api/v1}"
+      OTEAPI_INCLUDE_REDISADMIN: "${OTEAPI_INCLUDE_REDISADMIN:-False}"
+      OTEAPI_EXPOSE_SECRETS: "${OTEAPI_EXPOSE_SECRETS:-True}"
+      OTEAPI_AUTHENTICAION_DEPENDENCIES:
+      OTEAPI_PLUGIN_PACKAGES: "-v -e /soft7"
+    depends_on:
+      - redis
+    networks:
+      - otenet
+    volumes:
+      - "${PWD}:/soft7"
+
+  redis:
+    image: redis:latest
+    volumes:
+      - redis-persist:/data
+    networks:
+      - otenet
+
+  agraph:
+    image: franzinc/agraph:v7.2.0
+    volumes:
+      - agraph-data:/agraph/data
+      - ./agraph.cfg:/agraph/etc/agraph.cfg
+    ports:
+      - "10000-10035:10000-10035"
+    restart: on-failure
+    shm_size: 4g
+    networks:
+      - otenet
+
+volumes:
+  redis-persist:
+  agraph-data:
+
+networks:
+  otenet: