<gh_stars>10-100
import tempfile
import warnings
from pathlib import Path

import pytest

warnings.filterwarnings("ignore", category=DeprecationWarning)

import genomics_data_index.api as gdi

from genomics_data_index.test.integration import reference_file, sample_dirs, basic_mlst_file
from genomics_data_index.configuration.connector.DataIndexConnection import DataIndexConnection
from genomics_data_index.storage.model.QueryFeatureMutationSPDI import QueryFeatureMutationSPDI
from genomics_data_index.storage.model.QueryFeatureMLST import QueryFeatureMLST
from genomics_data_index.storage.io.mutation.NucleotideSampleDataPackage import NucleotideSampleDataPackage
from genomics_data_index.storage.io.mlst.MLSTSampleDataPackage import MLSTSampleDataPackage
from genomics_data_index.storage.io.mlst.MLSTTSeemannFeaturesReader import MLSTTSeemannFeaturesReader
from genomics_data_index.storage.io.processor.SerialSampleFilesProcessor import SerialSampleFilesProcessor
from genomics_data_index.storage.model.db import Sample


@pytest.fixture
def loaded_genomics_index() -> gdi.GenomicsDataIndex:
    tmp_dir = Path(tempfile.mkdtemp())
    database_connection = DataIndexConnection.connect(database_connection='sqlite:///:memory:',
                                                      database_dir=tmp_dir)

    # Load Nucleotide variation
    database_connection.reference_service.add_reference_genome(reference_file)
    snippy_tmp_dir = Path(tempfile.mkdtemp())
    data_package = NucleotideSampleDataPackage.create_from_snippy(sample_dirs,
                                                                  SerialSampleFilesProcessor(snippy_tmp_dir))
    database_connection.variation_service.insert(data_package, feature_scope_name='genome')

    # Load MLST
    mlst_package = MLSTSampleDataPackage(MLSTTSeemannFeaturesReader(mlst_file=basic_mlst_file))
    database_connection.mlst_service.insert(mlst_package)

    return gdi.GenomicsDataIndex(connection=database_connection)


def test_query_single_mutation(loaded_genomics_index: gdi.GenomicsDataIndex):
    gi = loaded_genomics_index
    db = gi.connection.database
    sampleB = db.get_session().query(Sample).filter(Sample.name == 'SampleB').one()
    sample1 = db.get_session().query(Sample).filter(Sample.name == 'CFSAN002349').one()
    sample2 = db.get_session().query(Sample).filter(Sample.name == 'CFSAN023463').one()

    query_result = gi.samples_query().hasa(QueryFeatureMutationSPDI('reference:5061:G:A'))
    assert 1 == len(query_result)
    assert {sampleB.id} == set(query_result.sample_set)
    assert 9 == len(query_result.universe_set)

    query_result = gi.samples_query().hasa(QueryFeatureMutationSPDI('reference:5061:G:A'))
    assert 1 == len(query_result)
    assert {sampleB.id} == set(query_result.sample_set)
    assert 9 == len(query_result.universe_set)

    query_result = gi.samples_query().hasa(QueryFeatureMLST('mlst:lmonocytogenes:abcZ:1'))
    assert 2 == len(query_result)
    assert {sample1.id, sample2.id} == set(query_result.sample_set)
    assert 9 == len(query_result.universe_set)

    assert {'CFSAN002349', 'CFSAN023463'} == set(query_result.tolist())
    assert {sample1.id, sample2.id} == set(query_result.tolist(names=False))

import tempfile
import warnings
from pathlib import Path

import pytest

warnings.filterwarnings("ignore", category=DeprecationWarning)

import genomics_data_index.api as gdi

from genomics_data_index.test.integration import reference_file, sample_dirs, basic_mlst_file
from genomics_data_index.configuration.connector.DataIndexConnection import DataIndexConnection
from genomics_data_index.storage.model.QueryFeatureMutationSPDI import QueryFeatureMutationSPDI
from genomics_data_index.storage.model.QueryFeatureMLST import QueryFeatureMLST
from genomics_data_index.storage.io.mutation.NucleotideSampleDataPackage import NucleotideSampleDataPackage
from genomics_data_index.storage.io.mlst.MLSTSampleDataPackage import MLSTSampleDataPackage
from genomics_data_index.storage.io.mlst.MLSTTSeemannFeaturesReader import MLSTTSeemannFeaturesReader
from genomics_data_index.storage.io.processor.SerialSampleFilesProcessor import SerialSampleFilesProcessor
from genomics_data_index.storage.model.db import Sample


@pytest.fixture
def loaded_genomics_index() -> gdi.GenomicsDataIndex:
    tmp_dir = Path(tempfile.mkdtemp())
    database_connection = DataIndexConnection.connect(database_connection='sqlite:///:memory:',
                                                      database_dir=tmp_dir)

    # Load Nucleotide variation
    database_connection.reference_service.add_reference_genome(reference_file)
    snippy_tmp_dir = Path(tempfile.mkdtemp())
    data_package = NucleotideSampleDataPackage.create_from_snippy(sample_dirs,
                                                                  SerialSampleFilesProcessor(snippy_tmp_dir))
    database_connection.variation_service.insert(data_package, feature_scope_name='genome')

    # Load MLST
    mlst_package = MLSTSampleDataPackage(MLSTTSeemannFeaturesReader(mlst_file=basic_mlst_file))
    database_connection.mlst_service.insert(mlst_package)

    return gdi.GenomicsDataIndex(connection=database_connection)


def test_query_single_mutation(loaded_genomics_index: gdi.GenomicsDataIndex):
    gi = loaded_genomics_index
    db = gi.connection.database
    sampleB = db.get_session().query(Sample).filter(Sample.name == 'SampleB').one()
    sample1 = db.get_session().query(Sample).filter(Sample.name == 'CFSAN002349').one()
    sample2 = db.get_session().query(Sample).filter(Sample.name == 'CFSAN023463').one()

    query_result = gi.samples_query().hasa(QueryFeatureMutationSPDI('reference:5061:G:A'))
    assert 1 == len(query_result)
    assert {sampleB.id} == set(query_result.sample_set)
    assert 9 == len(query_result.universe_set)

    query_result = gi.samples_query().hasa(QueryFeatureMutationSPDI('reference:5061:G:A'))
    assert 1 == len(query_result)
    assert {sampleB.id} == set(query_result.sample_set)
    assert 9 == len(query_result.universe_set)

    query_result = gi.samples_query().hasa(QueryFeatureMLST('mlst:lmonocytogenes:abcZ:1'))
    assert 2 == len(query_result)
    assert {sample1.id, sample2.id} == set(query_result.sample_set)
    assert 9 == len(query_result.universe_set)

    assert {'CFSAN002349', 'CFSAN023463'} == set(query_result.tolist())
    assert {sample1.id, sample2.id} == set(query_result.tolist(names=False))
# Load Nucleotide variation # Load MLST