"""Comprehensive tests for drug CLI commands."""
import json
from unittest.mock import patch
import pytest
from typer.testing import CliRunner
from biomcp.cli.main import app
runner = CliRunner()
@pytest.fixture
def mock_drug_info_imatinib():
"""Create a mock drug info response for imatinib."""
return """## Drug: Imatinib
- **Formula**: C29H31N7O
- **DrugBank ID**: DB00619
- **ChEMBL ID**: CHEMBL941
- **PubChem CID**: 5291
- **ChEBI ID**: CHEBI:45783
- **InChIKey**: KTUFNOKKBVMGRW-UHFFFAOYSA-N
- **Trade Names**: Gleevec, Glivec
### Description
Imatinib is a tyrosine kinase inhibitor used in the treatment of multiple cancers...
### Indication
Treatment of chronic myeloid leukemia, acute lymphoblastic leukemia, and gastrointestinal stromal tumors...
### Mechanism of Action
Inhibits BCR-ABL tyrosine kinase, the constitutive abnormal gene product of the Philadelphia chromosome...
### External Links
- [DrugBank](https://www.drugbank.ca/drugs/DB00619)
- [ChEMBL](https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL941/)
- [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/5291)
- [ChEBI](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:45783)"""
@pytest.fixture
def mock_drug_info_aspirin():
"""Create a mock drug info response for aspirin."""
return """## Drug: Aspirin
- **Formula**: C9H8O4
- **DrugBank ID**: DB00945
- **ChEMBL ID**: CHEMBL25
- **PubChem CID**: 2244
- **InChIKey**: BSYNRYMUTXBXSQ-UHFFFAOYSA-N
- **Trade Names**: Bayer Aspirin, Ecotrin, Bufferin
### Description
Aspirin is a salicylate used to treat pain, fever, inflammation, and migraines...
### External Links
- [DrugBank](https://www.drugbank.ca/drugs/DB00945)
- [ChEMBL](https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL25/)
- [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/2244)"""
@pytest.fixture
def mock_drug_info_multiword():
"""Create a mock drug info response for multi-word drug name."""
return """## Drug: Idecabtagene Vicleucel
- **DrugBank ID**: DB15769
- **Trade Names**: Abecma
### Description
Idecabtagene vicleucel is a B-cell maturation antigen (BCMA)-directed CAR T-cell immunotherapy...
### Indication
Treatment of adult patients with relapsed or refractory multiple myeloma...
### External Links
- [DrugBank](https://www.drugbank.ca/drugs/DB15769)"""
@pytest.fixture
def mock_drug_info_pembrolizumab():
"""Create a mock drug info response for pembrolizumab."""
return """## Drug: Pembrolizumab
- **DrugBank ID**: DB09037
- **Trade Names**: Keytruda
### Description
Pembrolizumab is a humanized monoclonal antibody used in cancer immunotherapy...
### Indication
Treatment of melanoma, non-small cell lung cancer, and other cancers...
### Mechanism of Action
Binds to PD-1 receptor to block interaction with PD-L1 and PD-L2...
### External Links
- [DrugBank](https://www.drugbank.ca/drugs/DB09037)"""
class TestDrugGetCommand:
"""Test the 'drug get' command."""
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_by_name_imatinib(
self, mock_get_drug, mock_drug_info_imatinib
):
"""Test getting drug info by name (imatinib)."""
mock_get_drug.return_value = mock_drug_info_imatinib
result = runner.invoke(app, ["drug", "get", "imatinib"])
assert result.exit_code == 0
assert "Imatinib" in result.stdout
assert "DrugBank ID**: DB00619" in result.stdout
assert "ChEMBL ID**: CHEMBL941" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_by_name_aspirin(
self, mock_get_drug, mock_drug_info_aspirin
):
"""Test getting drug info by name (aspirin)."""
mock_get_drug.return_value = mock_drug_info_aspirin
result = runner.invoke(app, ["drug", "get", "aspirin"])
assert result.exit_code == 0
assert "Aspirin" in result.stdout
assert "DrugBank ID**: DB00945" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_multiword_name_quoted(
self, mock_get_drug, mock_drug_info_multiword
):
"""Test getting drug with multi-word name (quoted) - CRITICAL for URL encoding fix."""
mock_get_drug.return_value = mock_drug_info_multiword
result = runner.invoke(app, ["drug", "get", "idecabtagene vicleucel"])
assert result.exit_code == 0
assert "Idecabtagene Vicleucel" in result.stdout
assert "Abecma" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_multiword_name_pembrolizumab(
self, mock_get_drug, mock_drug_info_pembrolizumab
):
"""Test getting drug with multi-word name (pembrolizumab) - validates URL encoding."""
mock_get_drug.return_value = mock_drug_info_pembrolizumab
result = runner.invoke(app, ["drug", "get", "pembrolizumab"])
assert result.exit_code == 0
assert "Pembrolizumab" in result.stdout
assert "Keytruda" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_multiword_name_with_spaces(
self, mock_get_drug, mock_drug_info_multiword
):
"""Test getting drug with multiple spaces in name - ensures proper URL encoding."""
mock_get_drug.return_value = mock_drug_info_multiword
# Test with the actual multi-word drug name as it would be typed
result = runner.invoke(app, ["drug", "get", "idecabtagene vicleucel"])
assert result.exit_code == 0
assert "Idecabtagene Vicleucel" in result.stdout
# Verify the mock was called with the correct argument
mock_get_drug.assert_called_once()
# Get the actual call arguments
# The first argument should be the coroutine from get_drug()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_by_drugbank_id(
self, mock_get_drug, mock_drug_info_imatinib
):
"""Test getting drug info by DrugBank ID."""
mock_get_drug.return_value = mock_drug_info_imatinib
result = runner.invoke(app, ["drug", "get", "DB00619"])
assert result.exit_code == 0
assert "Imatinib" in result.stdout
assert "DB00619" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_by_chembl_id(
self, mock_get_drug, mock_drug_info_aspirin
):
"""Test getting drug info by ChEMBL ID."""
mock_get_drug.return_value = mock_drug_info_aspirin
result = runner.invoke(app, ["drug", "get", "CHEMBL25"])
assert result.exit_code == 0
assert "Aspirin" in result.stdout or "CHEMBL25" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_not_found(self, mock_get_drug):
"""Test handling of non-existent drug."""
error_msg = "Drug 'INVALID_DRUG_XYZ' not found in MyChem.info"
mock_get_drug.return_value = error_msg
result = runner.invoke(app, ["drug", "get", "INVALID_DRUG_XYZ"])
assert result.exit_code == 0
assert "not found" in result.stdout
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_with_json_flag(self, mock_get_drug):
"""Test getting drug info with --json flag."""
json_output = json.dumps(
{
"drug_id": "CHEMBL941",
"name": "Imatinib",
"drugbank_id": "DB00619",
"chembl_id": "CHEMBL941",
"formula": "C29H31N7O",
"_links": {
"DrugBank": "https://www.drugbank.ca/drugs/DB00619",
"ChEMBL": "https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL941/",
},
},
indent=2,
)
mock_get_drug.return_value = json_output
result = runner.invoke(app, ["drug", "get", "imatinib", "--json"])
assert result.exit_code == 0
assert "CHEMBL941" in result.stdout
assert "Imatinib" in result.stdout
assert "DB00619" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_with_json_short_flag(self, mock_get_drug):
"""Test getting drug info with -j short flag."""
json_output = json.dumps(
{"drug_id": "CHEMBL941", "name": "Imatinib"}, indent=2
)
mock_get_drug.return_value = json_output
result = runner.invoke(app, ["drug", "get", "imatinib", "-j"])
assert result.exit_code == 0
assert "Imatinib" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_multiword_with_json(self, mock_get_drug):
"""Test getting multi-word drug name with JSON output."""
json_output = json.dumps(
{
"drug_id": "DB15769",
"name": "Idecabtagene Vicleucel",
"drugbank_id": "DB15769",
"tradename": ["Abecma"],
},
indent=2,
)
mock_get_drug.return_value = json_output
result = runner.invoke(
app, ["drug", "get", "idecabtagene vicleucel", "--json"]
)
assert result.exit_code == 0
assert "Idecabtagene Vicleucel" in result.stdout
assert "DB15769" in result.stdout
mock_get_drug.assert_called_once()
class TestDrugSearchCommand:
"""Test the 'drug search' command."""
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_basic(self, mock_get_drug, mock_drug_info_imatinib):
"""Test basic drug search."""
mock_get_drug.return_value = mock_drug_info_imatinib
result = runner.invoke(app, ["drug", "search", "imatinib"])
assert result.exit_code == 0
assert "Imatinib" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_multiword_query(
self, mock_get_drug, mock_drug_info_multiword
):
"""Test drug search with multi-word query - validates URL encoding fix."""
mock_get_drug.return_value = mock_drug_info_multiword
result = runner.invoke(app, ["drug", "search", "kinase inhibitor"])
assert result.exit_code == 0
# Should contain either the search term or drug information
assert "Drug:" in result.stdout or "kinase" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_with_page(
self, mock_get_drug, mock_drug_info_aspirin
):
"""Test drug search with page parameter."""
mock_get_drug.return_value = mock_drug_info_aspirin
result = runner.invoke(
app, ["drug", "search", "aspirin", "--page", "2"]
)
assert result.exit_code == 0
# Should show development note when pagination is used
assert "development" in result.stdout.lower()
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_with_page_short_flag(
self, mock_get_drug, mock_drug_info_aspirin
):
"""Test drug search with -p short flag for page."""
mock_get_drug.return_value = mock_drug_info_aspirin
result = runner.invoke(app, ["drug", "search", "aspirin", "-p", "2"])
assert result.exit_code == 0
assert "development" in result.stdout.lower()
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_with_page_size(
self, mock_get_drug, mock_drug_info_imatinib
):
"""Test drug search with page_size parameter."""
mock_get_drug.return_value = mock_drug_info_imatinib
result = runner.invoke(
app, ["drug", "search", "imatinib", "--page-size", "20"]
)
assert result.exit_code == 0
assert "development" in result.stdout.lower()
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_with_pagination(
self, mock_get_drug, mock_drug_info_aspirin
):
"""Test drug search with full pagination parameters."""
mock_get_drug.return_value = mock_drug_info_aspirin
result = runner.invoke(
app,
["drug", "search", "aspirin", "--page", "2", "--page-size", "20"],
)
assert result.exit_code == 0
assert "development" in result.stdout.lower()
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_with_json_output(self, mock_get_drug):
"""Test drug search with JSON output."""
json_output = json.dumps(
{
"drug_id": "CHEMBL941",
"name": "Imatinib",
"drugbank_id": "DB00619",
},
indent=2,
)
mock_get_drug.return_value = json_output
result = runner.invoke(app, ["drug", "search", "imatinib", "--json"])
assert result.exit_code == 0
assert "Imatinib" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_with_json_short_flag(self, mock_get_drug):
"""Test drug search with -j short flag."""
json_output = json.dumps(
{"drug_id": "CHEMBL941", "name": "Imatinib"}, indent=2
)
mock_get_drug.return_value = json_output
result = runner.invoke(app, ["drug", "search", "imatinib", "-j"])
assert result.exit_code == 0
assert "Imatinib" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_multiword_with_json(self, mock_get_drug):
"""Test drug search with multi-word query and JSON output."""
json_output = json.dumps(
{"name": "Idecabtagene Vicleucel", "tradename": ["Abecma"]},
indent=2,
)
mock_get_drug.return_value = json_output
result = runner.invoke(app, ["drug", "search", "CAR T cell", "--json"])
assert result.exit_code == 0
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_not_found(self, mock_get_drug):
"""Test drug search with no results."""
error_msg = "Drug 'INVALID_QUERY_XYZ' not found in MyChem.info"
mock_get_drug.return_value = error_msg
result = runner.invoke(app, ["drug", "search", "INVALID_QUERY_XYZ"])
assert result.exit_code == 0
assert "not found" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_search_drugs_with_all_options(self, mock_get_drug):
"""Test drug search with all available options."""
json_output = json.dumps({"name": "Imatinib"}, indent=2)
mock_get_drug.return_value = json_output
result = runner.invoke(
app,
[
"drug",
"search",
"imatinib",
"--page",
"2",
"--page-size",
"20",
"--json",
],
)
assert result.exit_code == 0
assert "Imatinib" in result.stdout
assert "development" in result.stdout.lower()
mock_get_drug.assert_called_once()
class TestDrugCliIntegration:
"""Integration-style tests for drug CLI (still using mocks)."""
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_full_flow(self, mock_get_drug, mock_drug_info_imatinib):
"""Test full drug get flow with mocked output."""
mock_get_drug.return_value = mock_drug_info_imatinib
result = runner.invoke(app, ["drug", "get", "imatinib"])
assert result.exit_code == 0
assert "Imatinib" in result.stdout
assert "Formula**: C29H31N7O" in result.stdout
assert "DrugBank ID**: DB00619" in result.stdout
assert "External Links" in result.stdout
@patch("biomcp.cli.drugs.get_drug")
def test_get_drug_with_trade_names(
self, mock_get_drug, mock_drug_info_aspirin
):
"""Test drug with trade names."""
mock_get_drug.return_value = mock_drug_info_aspirin
result = runner.invoke(app, ["drug", "get", "aspirin"])
assert result.exit_code == 0
assert "Aspirin" in result.stdout
assert "Trade Names" in result.stdout
@patch("biomcp.cli.drugs.get_drug")
def test_drug_command_error_handling(self, mock_get_drug):
"""Test error handling in drug commands."""
error_msg = "Error retrieving drug information: API connection error"
mock_get_drug.return_value = error_msg
result = runner.invoke(app, ["drug", "get", "imatinib"])
# Should exit successfully but show error message
assert result.exit_code == 0
assert "Error" in result.stdout
def test_drug_help_command(self):
"""Test drug command help text."""
result = runner.invoke(app, ["drug", "--help"])
assert result.exit_code == 0
assert "drug" in result.stdout.lower()
assert "get" in result.stdout.lower()
assert "search" in result.stdout.lower()
def test_drug_get_help_command(self):
"""Test drug get command help text."""
result = runner.invoke(app, ["drug", "get", "--help"])
assert result.exit_code == 0
assert "imatinib" in result.stdout.lower()
assert "idecabtagene vicleucel" in result.stdout.lower()
assert "json" in result.stdout.lower()
def test_drug_search_help_command(self):
"""Test drug search command help text."""
result = runner.invoke(app, ["drug", "search", "--help"])
assert result.exit_code == 0
assert "search" in result.stdout.lower()
assert "page" in result.stdout.lower()
assert "json" in result.stdout.lower()
class TestDrugMultiWordUrlEncoding:
"""Specific tests for multi-word drug name URL encoding fix."""
@patch("biomcp.cli.drugs.get_drug")
def test_multiword_drug_idecabtagene_vicleucel(
self, mock_get_drug, mock_drug_info_multiword
):
"""Test idecabtagene vicleucel (the bug report case)."""
mock_get_drug.return_value = mock_drug_info_multiword
result = runner.invoke(app, ["drug", "get", "idecabtagene vicleucel"])
assert result.exit_code == 0
assert "Idecabtagene Vicleucel" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_multiword_drug_with_three_words(self, mock_get_drug):
"""Test drug name with three words."""
mock_response = """## Drug: Test Drug Name
- **DrugBank ID**: DB99999"""
mock_get_drug.return_value = mock_response
result = runner.invoke(app, ["drug", "get", "test drug name"])
assert result.exit_code == 0
assert "Drug:" in result.stdout
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_multiword_search_query(
self, mock_get_drug, mock_drug_info_imatinib
):
"""Test search with multi-word query."""
mock_get_drug.return_value = mock_drug_info_imatinib
result = runner.invoke(
app, ["drug", "search", "tyrosine kinase inhibitor"]
)
assert result.exit_code == 0
mock_get_drug.assert_called_once()
@patch("biomcp.cli.drugs.get_drug")
def test_multiword_with_special_characters(self, mock_get_drug):
"""Test drug name with special characters (hyphens, etc)."""
mock_response = """## Drug: Test-Drug-Name
- **DrugBank ID**: DB88888"""
mock_get_drug.return_value = mock_response
result = runner.invoke(app, ["drug", "get", "test-drug-name"])
assert result.exit_code == 0
mock_get_drug.assert_called_once()
