Implementing GitHub CI

.github/workflows/python-app.yml

@@ -0,0 +1,55 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+  pull_request:
+    branches: [ "master", "develop" ]
+
+permissions:
+  contents: read
+
+jobs:
+  test-runner:
+
+    runs-on: ubuntu-latest
+    services:
+      redis-stack:
+        image: redis/redis-stack-server
+        options: >-
+          --health-cmd "redis-cli ping"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports: 
+          - 6379:6379
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.9"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r test-requirements.txt
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Lint with black
+        run: |
+          black --check --verbose -- . 
+      - name: Test with pytest
+        run: |
+          pytest
+        env:
+          REDIS_URL: localhost
+          REDIS_PORT: 6379
+          FAIR_COMBINE_ENV: test

.gitignore

@@ -2,3 +2,4 @@
 /redis_data/.testfile
 /redis_data/dump.rdb
 /app/test_main.http
+/.coverage

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+# See https://pre-commit.com for more information
+    # See https://pre-commit.com/hooks.html for more hooks
+    repos:
+      - repo: https://github.com/ambv/black
+        rev: 22.3.0
+        hooks:
+          - id: black
+            language_version: python3
+      - repo: https://github.com/pre-commit/pre-commit-hooks
+        rev: v2.0.0
+        hooks:
+          - id: flake8

README.md

@@ -33,3 +33,14 @@ Endpoints are accessible at `http://localhost:8000`.
 
 If you have redis-cli or RedisInsight installed, the redis endpoint can be accessed at `http://localhost:6379` 
 
+# Testing
+
+First install test requirements.
+```shell
+pip install -r test-requirements.txt
+```
+
+Then, you can simply run all tests using pytest.
+```shell
+pytest
+```

app/dependencies/settings.py

@@ -3,8 +3,12 @@
 from pydantic import BaseSettings
 from typing import List
 
+
 class Config(BaseSettings):
     app_name: str = "FAIR Combine API"
+    redis_db_number: int = 0
+    indicators_path = "app/metrics/metrics.csv"
+
     allowed_origins: List[str] = []
     # List of indicators that applied to archive (if no archive, their statuses will be set to 'failed')
     archive_indicators: List[str] = [
@@ -81,7 +85,10 @@ class Config(BaseSettings):
     # Mapping of indicators with their direct parent. Until parent status is 'success', children cannot be set.
     # Not happy with this, as it means that the Config is dynamically set
     assessment_dependencies: dict[str, dict] = {
-        "CA-RDA-I3-02Archive": {"condition": "or", "indicators": ["CA-RDA-I3-01Archive"]},
+        "CA-RDA-I3-02Archive": {
+            "condition": "or",
+            "indicators": ["CA-RDA-I3-01Archive"],
+        },
         "CA-RDA-I3-02Model": {"condition": "or", "indicators": ["CA-RDA-I3-01Model"]},
         "CA-RDA-I3-03MA": {"condition": "or", "indicators": ["CA-RDA-I3-01MA"]},
         "CA-RDA-I3-03MM": {"condition": "or", "indicators": ["CA-RDA-I3-01MM"]},
@@ -101,8 +108,12 @@ class ProdConfig(Config):
     pass
 
 
+class TestConfig(Config):
+    redis_db_number = 15
+
+
 @lru_cache()
 def get_settings():
     env = os.environ.get("FAIR_COMBINE_ENV", "dev")
-    config = {"dev": DevConfig, "prod": ProdConfig}.get(env)()
+    config = {"dev": DevConfig, "prod": ProdConfig, "test": TestConfig}.get(env)()
     return config

app/main.py

@@ -10,20 +10,22 @@
 tags_metadata = [
     {
         "name": "Indicators",
-        "description": "FAIR Combine assessments. Endpoints to retrieve the descriptions of the assessments done by the application "
-                       "to evaluate how FAIR a resource is/"
+        "description": "FAIR Combine assessments. Endpoints to retrieve the descriptions of the assessments done by "
+        "the application "
+        "to evaluate how FAIR a resource is/",
     },
     {
         "name": "Tasks",
-        "description": "FAIR Combine tasks. Endpoints allow to retrieve the details of a specific assessment associated with a session, "
-                       "to update an assessment status or to retrieve the documentation of FAIR Combine assessments."
+        "description": "FAIR Combine tasks. Endpoints allow to retrieve the details of a specific assessment "
+        "associated with a session, "
+        "to update an assessment status or to retrieve the documentation of FAIR Combine assessments.",
     },
     {
         "name": "Sessions",
-        "description": "FAIR Combine assessment session. Endpoints to create a new session, to load a previously exported session, "
-                       "or to display the details of an existing session."
+        "description": "FAIR Combine assessment session. Endpoints to create a new session, to load a previously "
+        "exported session, "
+        "or to display the details of an existing session.",
     },
-
 ]
 
 description = """

app/metrics/assessments_lifespan.py

@@ -4,6 +4,7 @@
 from fastapi import FastAPI
 from csv import DictReader
 
+from app.dependencies.settings import get_settings
 import app.models as models
 
 fair_indicators = {}
@@ -18,7 +19,8 @@ async def get_tasks_definitions(app: FastAPI):
     :param app: The FastAPI application that will use the content of `metrics.csv`
     :return: None
     """
-    regex = re.compile("^CA\-RDA\-([FAIR][1-9](\.[0-9])?)\-")
+    regex = re.compile(r"^CA-RDA-([FAIR][1-9](\.[0-9])?)-")
+    config = get_settings()
 
     def parse_line(line):
         sub_group = regex.search(line["TaskName"]).groups()[0]
@@ -31,12 +33,12 @@ def parse_line(line):
                 priority=line["TaskPriority"].lower(),
                 question=line["TaskQuestion"],
                 short=line["TaskShortDescription"],
-                description=line["TaskDetails"]
+                description=line["TaskDetails"],
             )
         }
 
     # Get the list of tasks and their definitions from internal file
-    with open("app/metrics/metrics.csv", "r") as file_handler:
+    with open(config.indicators_path, "r") as file_handler:
         csv_reader = DictReader(file_handler, dialect="unix")
         [fair_indicators.update(parse_line(line)) for line in csv_reader]
 

app/metrics/base_example.py

@@ -1,5 +1,6 @@
 from fair_test import FairTest, FairTestEvaluation
 
+
 class MetricTest(FairTest):
     metric_path = "fair-test-example"
     metric_version = "0.1.0"
@@ -14,7 +15,7 @@ def execute_metric(self, object):
 
     def evaluate(self, eval: FairTestEvaluation):
         eval.info(
-            f"Running FairCombine example. This test will pass",
+            "Running FairCombine example. This test will pass",
         )
 
         # Retrieving subject of the evaluation (a model or an archive)
@@ -31,4 +32,4 @@ class ManualMetricTest(FairTest):
 
 
 class AutomaticMetricTest(FairTest):
-    pass
+    pass

app/models/__init__.py

@@ -1,4 +1,10 @@
-from .session import Session, SessionStatus, SessionHandler, SessionSubjectIn, SubjectType
+from .session import (
+    Session,
+    SessionStatus,
+    SessionHandler,
+    SessionSubjectIn,
+    SubjectType,
+)
 from .tasks import Task, TaskStatus, Indicator, TaskPriority, IndicatorDependency
 
 __all__ = [
@@ -12,4 +18,4 @@
     SessionSubjectIn,
     SubjectType,
     IndicatorDependency,
-]
+]