Merge pull request #29 from TranslatorSRI/trapi_validation

Trapi validation

.github/workflows/dev.yml

@@ -9,24 +9,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout the repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      # Cache docker layers for faster build
-      - uses: satackey/[email protected]
-        # Ignore the failure of a step and avoid terminating the job.
-        continue-on-error: true
+      - uses: actions/setup-python@v5
+        name: Setup python
+        with:
+          python-version: '3.11'
+          cache: 'pip'
 
-      - name: Build
-        run: docker build -t harness-testing -f Dockerfile.test .
+      - name: Install requirements
+        run: pip install -r requirements.txt
+
+      - run: pip install -r requirements-runners.txt
+      - run: pip install -r requirements-test.txt
 
       - name: Run tests and get output
-        run: |
-          echo 'TEST_OUTPUT<<EOF' >> $GITHUB_ENV
-          echo "$(docker run harness-testing)" >> $GITHUB_ENV
-          echo 'EOF' >> $GITHUB_ENV
-
-      - name: Exit if there are any test failures
-        run: '[[ $TEST_OUTPUT != *FAILED* ]]'
+        run: pytest
 
   check-format:
     name: Check that code matches Black formatter

requirements-test.txt

@@ -1,3 +1,4 @@
 pytest==7.4.2
 pytest-asyncio==0.23.3
+pytest-httpx==0.30.0
 pytest-mock==3.11.1

requirements.txt

@@ -1,6 +1,7 @@
 httpx==0.27.0
 pydantic==2.7.1
 # reasoner_pydantic==4.1.6
+setproctitle==1.3.3
 slack_sdk==3.27.2
 tqdm==4.66.4
 translator-testing-model==0.3.2

tests/example_tests.py → tests/helpers/example_tests.py

@@ -34,7 +34,7 @@
                         "tags": [],
                         "input_id": "MONDO:0010794",
                         "input_name": "NARP Syndrome",
-                        "input_category": None,
+                        "input_category": "biolink:Disease",
                         "predicate_id": "biolink:treats",
                         "predicate_name": "treats",
                         "output_id": "DRUGBANK:DB00313",
@@ -48,7 +48,7 @@
                         "in_v1": None,
                         "well_known": False,
                         "test_reference": None,
-                        "runner_settings": ["inferred"],
+                        "test_runner_settings": ["inferred"],
                         "test_metadata": {
                             "id": "1",
                             "name": None,
@@ -67,7 +67,7 @@
                         "tags": [],
                         "input_id": "MONDO:0010794",
                         "input_name": "NARP Syndrome",
-                        "input_category": None,
+                        "input_category": "biolink:Disease",
                         "predicate_id": "biolink:treats",
                         "predicate_name": "treats",
                         "output_id": "MESH:D001463",
@@ -81,7 +81,7 @@
                         "in_v1": None,
                         "well_known": False,
                         "test_reference": None,
-                        "runner_settings": ["inferred"],
+                        "test_runner_settings": ["inferred"],
                         "test_metadata": {
                             "id": "1",
                             "name": None,
@@ -102,7 +102,7 @@
                 "test_case_predicate_name": "treats",
                 "test_case_predicate_id": "biolink:treats",
                 "test_case_input_id": "MONDO:0010794",
-                "test_case_runner_settings": ["inferred"],
+                "test_runner_settings": ["inferred"],
             }
         },
     }

tests/helpers/logger.py

@@ -0,0 +1,61 @@
+"""Logging setup."""
+
+import logging
+
+
+class ColoredFormatter(logging.Formatter):
+    """Colored formatter."""
+
+    prefix = "[%(asctime)s: %(levelname)s/%(name)s]:"
+    default = f"{prefix} %(message)s"
+    error_fmt = f"\x1b[31m{prefix}\x1b[0m %(message)s"
+    warning_fmt = f"\x1b[33m{prefix}\x1b[0m %(message)s"
+    info_fmt = f"\x1b[32m{prefix}\x1b[0m %(message)s"
+    debug_fmt = f"\x1b[34m{prefix}\x1b[0m %(message)s"
+
+    def __init__(self, fmt=default):
+        """Initialize."""
+        logging.Formatter.__init__(self, fmt)
+
+    def format(self, record):
+        """Format record."""
+        format_orig = self._style._fmt
+        if record.levelno == logging.DEBUG:
+            self._style._fmt = ColoredFormatter.debug_fmt
+        elif record.levelno == logging.INFO:
+            self._style._fmt = ColoredFormatter.info_fmt
+        elif record.levelno == logging.WARNING:
+            self._style._fmt = ColoredFormatter.warning_fmt
+        elif record.levelno == logging.ERROR:
+            self._style._fmt = ColoredFormatter.error_fmt
+        result = logging.Formatter.format(self, record)
+        self._style._fmt = format_orig
+        return result
+
+
+def setup_logger():
+    """Set up Test Harness logger."""
+    logger = logging.getLogger("harness")
+    logger.setLevel(logging.DEBUG)
+    handler = logging.StreamHandler()
+    handler.setLevel(logging.DEBUG)
+    handler.setFormatter(ColoredFormatter())
+    logger.addHandler(handler)
+
+    return logger
+
+
+def assert_no_level(logger, allowed_level, exceptions=0):
+    """
+    Check that the logger has no records greater than
+    the allowed level.
+
+    Also has a parameter to specify the number of exceptions
+    to the rule (number of records that will be ignored).
+    """
+    total = 0
+    for record in logger.records:
+        if record.levelno >= allowed_level:
+            total += 1
+        if total > exceptions:
+            raise Exception(f"Invalid Log Record: {record}")

tests/helpers/mock_responses.py

@@ -0,0 +1,80 @@
+"""Mock Test Responses."""
+
+kp_response = {
+    "message": {
+        "query_graph": {
+            "nodes": {
+                "n0": {"ids": ["MESH:D008687"]},
+                "n1": {"categories": ["biolink:Disease"]},
+            },
+            "edges": {
+                "n0n1": {
+                    "subject": "n0",
+                    "object": "n1",
+                    "predicates": ["biolink:treats"],
+                }
+            },
+        },
+        "knowledge_graph": {
+            "nodes": {
+                "MESH:D008687": {
+                    "categories": ["biolink:SmallMolecule"],
+                    "name": "Metformin",
+                    "attributes": [],
+                },
+                "MONDO:0005148": {
+                    "categories": [
+                        "biolink:Disease",
+                    ],
+                    "name": "type 2 diabetes mellitus",
+                    "attributes": [],
+                },
+            },
+            "edges": {
+                "n0n1": {
+                    "subject": "MESH:D008687",
+                    "object": "MONDO:0005148",
+                    "predicate": "biolink:treats",
+                    "sources": [
+                        {
+                            "resource_id": "infores:kp0",
+                            "resource_role": "primary_knowledge_source",
+                        }
+                    ],
+                    "attributes": [],
+                },
+            },
+        },
+        "results": [
+            {
+                "node_bindings": {
+                    "n0": [
+                        {
+                            "id": "MESH:D008687",
+                            "attributes": [],
+                        },
+                    ],
+                    "n1": [
+                        {
+                            "id": "MONDO:0005148",
+                            "attributes": [],
+                        },
+                    ],
+                },
+                "analyses": [
+                    {
+                        "resource_id": "kp0",
+                        "edge_bindings": {
+                            "n0n1": [
+                                {
+                                    "id": "n0n1",
+                                    "attributes": [],
+                                },
+                            ],
+                        },
+                    }
+                ],
+            },
+        ],
+    },
+}

tests/helpers/mocks.py

@@ -0,0 +1,69 @@
+from test_harness.reporter import Reporter
+from test_harness.slacker import Slacker
+from test_harness.runner.query_runner import QueryRunner
+
+
+class MockReporter(Reporter):
+    def __init__(self, base_url=None, refresh_token=None, logger=None):
+        super().__init__()
+        self.base_path = base_url
+        self.test_run_id = 1
+        pass
+
+    async def get_auth(self):
+        pass
+
+    async def create_test_run(self, test_env, suite_name):
+        return 1
+
+    async def create_test(self, test, asset):
+        return 2
+
+    async def upload_labels(self, test_id, labels):
+        pass
+
+    async def upload_logs(self, test_id, logs):
+        pass
+
+    async def upload_artifact_references(self, test_id, artifact_references):
+        pass
+
+    async def upload_screenshots(self, test_id, screenshot):
+        pass
+
+    async def upload_log(self, test_id, message):
+        pass
+
+    async def finish_test(self, test_id, result):
+        return result
+
+    async def finish_test_run(self):
+        pass
+
+
+class MockSlacker(Slacker):
+    def __init__(self):
+        pass
+
+    async def post_notification(self, messages=[]):
+        print(f"posting messages: {messages}")
+        pass
+
+    async def upload_test_results_file(self, filename, extension, results):
+        pass
+
+
+class MockQueryRunner(QueryRunner):
+    async def retrieve_registry(self, trapi_version: str):
+        self.registry = {
+            "staging": {
+                "ars": [
+                    {
+                        "_id": "testing",
+                        "title": "Tester",
+                        "infores": "infores:tester",
+                        "url": "http://tester",
+                    }
+                ],
+            },
+        }

tests/test_main.py

@@ -1,9 +1,9 @@
 import pytest
 
 from test_harness.main import main
-from .example_tests import example_test_cases
 
-from .mocker import (
+from .helpers.example_tests import example_test_cases
+from .helpers.mocks import (
     MockReporter,
     MockSlacker,
 )
@@ -13,17 +13,16 @@
 async def test_main(mocker):
     """Test the main function."""
     # This article is awesome: https://nedbatchelder.com/blog/201908/why_your_mock_doesnt_work.html
-    run_ars_test = mocker.patch("test_harness.run.run_ars_test", return_value="Fail")
     run_tests = mocker.patch("test_harness.main.run_tests", return_value={})
-    mocker.patch("test_harness.slacker.Slacker", return_value=MockSlacker())
+    mocker.patch("test_harness.main.Slacker", return_value=MockSlacker())
     mocker.patch("test_harness.main.Reporter", return_value=MockReporter())
     await main(
         {
             "tests": example_test_cases,
+            "suite": "testing",
             "save_to_dashboard": False,
             "json_output": False,
             "log_level": "ERROR",
         }
     )
-    # run_ui_test.assert_called_once()
     run_tests.assert_called_once()