Initial commit

tests/conftest.py

@@ -0,0 +1,47 @@
+import logging
+from pathlib import Path
+
+import pytest
+
+from pcdigitizer import enable_logging
+
+TEST_DIR: Path = Path(__file__).resolve().parent
+TMP_DIR: Path = TEST_DIR / "tmp"
+
+
+@pytest.fixture(scope="session", autouse=True)
+def turn_on_logging() -> None:
+    """Enable loguru logging at DEBUG level for the entire test session."""
+    enable_logging(logging.DEBUG)
+
+
+@pytest.fixture
+def test_dir() -> Path:
+    """Return the absolute path to the tests/ directory."""
+    return TEST_DIR
+
+
+@pytest.fixture
+def tmp_dir() -> Path:
+    """Return the path to the shared temporary output directory."""
+    TMP_DIR.mkdir(parents=True, exist_ok=True)
+    return TMP_DIR
+
+
+@pytest.fixture
+def mock_session(test_dir):
+    """A fake requests.Session that returns saved fixture files."""
+
+    class FakeResponse:
+        def __init__(self, content: bytes, status_code: int = 200):
+            self.content = content
+            self.status_code = status_code
+
+    class FakeSession:
+        def get(self, url):
+            if "heading/Dissociation" in url:
+                fixture = test_dir / "files" / "dissociation-constants-1.json"
+                return FakeResponse(fixture.read_bytes())
+            return FakeResponse(b'{"Fault": "not found"}', status_code=404)
+
+    return FakeSession()

tests/test_dissociation_constant_processing.py

@@ -0,0 +1,33 @@
+import polars as pl
+
+from pcdigitizer import Annotation, GetAnnotationPage
+
+
+def test_process_dissociation_data(test_dir, mock_session):
+    """Makes request for the first page of the `"Dissociation Constants"` and
+    processes the data into a polars DataFrame.
+
+    Makes the following request:
+    [pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading/Dissociation%20Constants/JSON?page=1](https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading/Dissociation%20Constants/JSON?page=1).
+    """
+    task = GetAnnotationPage()
+    df = task.do(
+        item=1, annotation=Annotation.DISSOCIATION_CONSTANTS, session=mock_session
+    )
+
+    # TODO: Need to implement actual tests
+    assert not df.is_empty()
+    assert df.columns == [
+        "cid",
+        "sid",
+        "pclid",
+        "pka_label",
+        "pka_value",
+        "temperature_C",
+        "comment",
+    ]
+    assert df.schema["pka_value"] == pl.Float64
+    assert df.schema["cid"] == pl.Int64
+
+    csv_path = test_dir / "tmp" / "test_process_dissociation_data.csv"
+    df.write_csv(csv_path)

tests/test_pc_api.py

@@ -0,0 +1,48 @@
+import polars as pl
+
+from pcdigitizer import Annotation, PubChemAPI
+
+
+def test_source_df():
+    df = PubChemAPI.get_sources()
+
+    columns = df.columns
+    assert len(columns) == 23
+    assert columns[0] == "Source Name"
+    assert columns[-3] == "License URL"
+
+    source_name = "Hazardous Substances Data Bank"
+    source_count = df.select(
+        (pl.col("Source Name").str.contains(source_name)).sum()
+    ).item()
+    assert source_count == 1
+
+
+def test_source_annotations():
+    annotations = PubChemAPI.get_source_annotations(
+        "Hazardous Substances Data Bank (HSDB)"
+    )
+    assert len(annotations["Compound"]) == 246
+
+
+def test_annotations():
+    annotations = PubChemAPI.get_annotations()
+    annotation_types = sorted(annotations.keys())
+    assert annotation_types == [
+        "Assay",
+        "Cell",
+        "Compound",
+        "Element",
+        "Gene",
+        "Pathway",
+        "Protein",
+        "Taxonomy",
+    ]
+    assert "Dissociation Constants" in annotations["Compound"]
+
+
+def test_get_data(mock_session):
+    data = PubChemAPI.get_data(
+        Annotation.DISSOCIATION_CONSTANTS, 1, session=mock_session
+    )
+    assert len(data) == 1000

tests/tmp/.gitignore

@@ -0,0 +1,2 @@
+*
+!.gitignore