Merge pull request #96 from genomic-medicine-sweden/dev-update-tests

Update test suite

pyproject.toml

@@ -32,6 +32,10 @@ inputs = ["NGPIris"]
 pythonpath = [
   "."
 ]
+testpaths = [
+  "tests"
+]
+addopts = "--strict-markers"  # Adds command-line options
 filterwarnings = "ignore::urllib3.connectionpool.InsecureRequestWarning"
 
 [project.scripts]

tests/conftest.py

@@ -0,0 +1,67 @@
+
+from pytest import Config, fixture, UsageError
+from configparser import ConfigParser
+from typing import Any, Generator
+from shutil import rmtree
+
+from NGPIris.hcp import HCPHandler
+
+class CustomConfig:
+    """A typed wrapper around pytest.Config for dynamic attributes."""
+    def __init__(self, pytest_config : Config):
+        self._config = pytest_config
+
+    @property
+    def hcp_h(self) -> HCPHandler:
+        """Access the HCPHandler instance."""
+        return getattr(self._config, "hcp_h")
+
+    def __getattr__(self, name : str) -> Any:
+        """Dynamically get attributes set during pytest configuration."""
+        return getattr(self._config, name)
+
+def set_section(config : Config, parser : ConfigParser, section : str) -> None:
+    parse_dict = dict(parser.items(section))
+    for k, v in parse_dict.items():
+        setattr(config, k, v)  # Adds attributes dynamically to pytest.Config
+
+def pytest_addoption(parser) -> None:
+    parser.addoption(
+        "--config",
+        action="store",
+        default=None,
+        help="Path to the configuration file (e.g., path/to/config.ini)",
+    )
+
+def pytest_configure(config : Config) -> None:
+    config_path = config.getoption("--config")
+    if not config_path:
+        raise UsageError("--config argument is required.")
+    else:
+        parser = ConfigParser()
+        parser.read(str(config_path))
+
+        # Add the INI parser to config
+        setattr(config, "parser", parser)
+
+        # Dynamically add an HCPHandler instance to config
+        setattr(config, "hcp_h", HCPHandler(parser.get("General", "credentials_path")))
+
+        # Dynamically add all key-value pairs from "HCP_tests" section
+        set_section(config, parser, "HCP_tests")
+
+@fixture(scope = "session")
+def hcp_result_path(pytestconfig : Config) -> str:
+    return pytestconfig.parser.get("HCP_tests", "result_path") # type: ignore
+
+@fixture(scope = "session", autouse = True)
+def clean_up_after_tests(hcp_result_path : str) -> Generator[None, Any, None]:
+    # Setup code can go here if needed
+    yield
+    # Teardown code
+    rmtree(hcp_result_path)
+
+@fixture
+def custom_config(pytestconfig : Config) -> CustomConfig:
+    """Provide the typed wrapper for pytest.Config."""
+    return CustomConfig(pytestconfig)

tests/test_conf_template.ini

@@ -1,3 +1,7 @@
-[hcp_tests]
-bucket = 
-data_test_file = 80MB_test_file
+[General]
+credentials_path = 
+
+[HCP_tests]
+test_bucket = 
+test_file_path = tests/data/80MB_test_file
+result_path = tests/data/results/

tests/test_hci.py

@@ -1,10 +1,14 @@
 
+from configparser import ConfigParser
 from NGPIris.hci import HCIHandler
 from random import randint
 from json import dump
 from os import remove
 
-hci_h = HCIHandler("credentials/testCredentials.json")
+ini_config = ConfigParser()
+ini_config.read("tests/test_conf.ini")
+
+hci_h = HCIHandler(ini_config.get("General", "credentials_path"))
 hci_h.request_token()
 
 def test_list_index_names_type() -> None: