Merge pull request #4 from GenomicMedLab/1-implement-testing-and-benc…

…hmarking

1-implement-testing-and-benchmarking

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

pyproject.toml

@@ -28,7 +28,7 @@ dynamic = ["version"]
 
 
 [project.optional-dependencies]
-test = ["pytest", "pytest-cov"]
+test = ["pytest", "pytest-cov","pytest-benchmark"]
 dev = ["pre-commit", "ruff==0.2.0"]
 
 docs = [
@@ -62,13 +62,14 @@ where = ["src"]
 [tool.pytest.ini_options]
 addopts = "--cov=src --cov-report term-missing"
 testpaths = ["tests"]
+pythonpath = ["src"]
 
 [tool.coverage.run]
 branch = true
 
 [tool.ruff]
 src = ["src"]
-exclude = ["docs/source/conf.py"]
+exclude = ["docs/source/conf.py","tests/test_dgidb.py","tests/test_graph_app.py"]
 lint.select = [
     "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
     "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w

tests/test_dgidb.py

@@ -0,0 +1,94 @@
+import pandas as pd
+import pytest
+
+from dgipy.dgidb import get_interactions,get_categories,get_drug
+
+
+def test_get_interactions():
+    """Test that interactions works correctly"""
+    # Search types work correctly
+    query = "braf"
+    with pytest.raises(Exception) as excinfo:
+        results = get_interactions(query, search="fake")
+    assert "Search type must be specified" in str(excinfo.value)
+
+    # Default search type functions correct as 'gene' and not 'drug'
+    query = "imatinib"
+    results = get_interactions(query)
+    assert len(results) == 0
+
+    # Use pandas default is correctly set to 'true'
+    query = "braf"
+    results = get_interactions(query)
+    assert type(results) == type(pd.DataFrame())
+
+    # Use pandas can be toggled to 'false' and returns a dictionary response object
+    query = "braf"
+    results = get_interactions(query, use_pandas=False)
+    assert type(results) != type(pd.DataFrame())
+    assert type(results) == type(dict())
+
+    # Gene search types work correctly
+    query = "braf"
+    results = get_interactions(query, search="genes")
+    assert results.columns[0] == "gene"
+
+    # Gene search is not grabbing drugs
+    query = "imatinib"
+    results = get_interactions(query, search="genes")
+    assert len(results) == 0
+
+    # Drug search types work correctly
+    query = "imatinib"
+    results = get_interactions(query, search="drugs")
+    assert type(results) == type(pd.DataFrame())
+    assert results.columns[0] == "drug"
+
+    # Drug search is not grabbing genes
+    query = "XPO1"
+    results = get_interactions(query, search="drugs")
+    assert len(results) == 0
+
+
+def test_get_categories():
+    """Test that categories works correctly"""
+    # Categories search builds a dataframe (with use_pandas default set to 'true')
+    query = "braf"
+    results = get_categories(query)
+    assert type(results) == type(pd.DataFrame())
+
+    # Categories does not return drugs data
+    query = "imatinib"
+    results = get_categories(query)
+    assert len(results) == 0
+
+    # Use pandas can be toggled to 'false' and returns a dictionary response object
+    query = "imatinib"
+    results = get_categories(query, use_pandas=False)
+    assert type(results) != type(pd.DataFrame())
+    assert type(results) == type(dict())
+
+
+def test_get_drugs():
+    """Test that drug profile works correctly"""
+    # Drug search builds a dataframe (with use_pandas default set to 'true')
+    query = "imatinib"
+    results = get_drug(query)
+    assert type(results) == type(pd.DataFrame())
+
+    # Drug search does not return gene data
+    query = "XPO1"
+    results = get_drug(query)
+    assert (len(results)) == 0
+
+    # Use pandas can be toggled to 'false' and returns dictionary response object
+    query = "imatinib"
+    results = get_drug(query, use_pandas=False)
+    assert type(results) != type(pd.DataFrame())
+    assert type(results) == type(dict())
+
+
+def test_get_interactions_benchmark(benchmark):
+    query = "braf"
+    results = benchmark.pedantic(get_interactions, args=(query,), kwargs={"search": "genes"},rounds=10,warmup_rounds=0,iterations=1)
+    assert results.columns[0] == "gene"

tests/test_graph_app.py

@@ -0,0 +1,9 @@
+import pytest
+
+from dgipy.graph_app import generate_app
+
+
+def test_generate_app():
+    app = generate_app()
+    if __name__ == "__main__":
+        app.run_server()