Indigo tests

Directory with tests: bingo/tests/

Tests with bingo-nosql:

• bigtable
• exact
• markush
• mass
• pseudoatoms
• resonance
• rexact
• rsmarts
• rsub
• sgroups
• similarity
• smarts
• substructure
• tautomers

Tests with bingo-elastic:

• exact
• similarity
• substructure

All tests have PostgreSQL support. System requirements and installation procedure for bingo-postgres are available here.

Tests structure

• tests/
  • data/ - Contains queries, targets data and test cases
  • dbc/ - Contains DB adapters: PostgreSQL, Bingo NOSQL, Bingo Elastic
  • constants.py
  • helpers.py - Set of useful functions
  • logger.py
  • db_config.ini - DB connection parameters
  • requirements.txt - Requirement modules
  • bingo-tests.log - Logs (appears after running tests)
  • conftest.py - Contains pytest fixtures: indigo instance, DB connection
  • ...
  • test_{FUNCTION}/
    • conftest.py - Setup/teardown scripts, molecules/reactions mapping: id - entity
    • test_{FUNCTION}.py
  • ...

Test example

# test_function.py
import pytest

from ..constants import DB_POSTGRES, DB_BINGO, DB_BINGO_ELASTIC
from ..helpers import assert_calculate_query, query_cases

# query_cases - return list of tuples: test cases with expected test result. 
# [(query_id, expected), ]

# assert_calculate_query - Assertion function

db_list = [DB_POSTGRES, DB_BINGO, DB_BINGO_ELASTIC] # List of Databases we run tests in 

@pytest.mark.usefixtures('init_db') # pytest fixture (setup/teardown) defined in coftest.py (near test_function.py)
class TestFunction:
    # Parametrize parameter 'db' in function test_foo with arguments from 'db_list', so the function will run with different 'db' values
    # 'db' is pytest fixture provided in root conftest.py file
    # Parametrize parameters 'query_id' and 'expected' in function test_foo with query_cases, so the function will run with different 'query_id' and 'expected' values
    @pytest.mark.parametrize('db', db_list, indirect=True)
    @pytest.mark.parametrize('query_id, expected', query_cases('function'))
    def test_foo(self, db, entities, query_id, expected):
        # entities - pytest fixture defined in conftest.py (near test_function.py)
        molecule = entities.get(query_id)
        result = db.function(molecule, 'bar-option')
        assert_calculate_query(result, expected)

# Double parametrization does let us run test_foo with different test cases 
# for every database provided in 'db_list'    

Install requirements

pip install -r bingo/tests/requirements.txt

Run docker elastic

docker run -p 9200:9200 --env "discovery.type=single-node" --env "indices.query.bool.max_clause_count=4096" --env "opendistro_security.disabled=true" amazon/opendistro-for-elasticsearch:latest

Running tests

cd bingo/tests
pytest .

Build an image and run docker container with bingo-postgres

docker build --tag epmlsop/bingo-postgres:latest -f bingo/postgres/Dockerfile --build-arg BINGO_PG_VERSION={postgres_version} . 
docker run -d -p 5432:5432 -e "POSTGRES_PASSWORD=password" epmlsop/bingo-postgres:latest

Running tests for bingo-postgres

cd bingo/tests
pytest --db postgres