def test_generate_config_adds_case_paths(
sample_id: str,
mip_dna_analysis_obj: Store.Analysis,
upload_mip_analysis_scout_api: UploadScoutAPI,
):
"""Test that generate config adds case file paths"""
# GIVEN a status db and hk with an analysis
# WHEN generating the scout config for the analysis
result_data: ScoutLoadConfig = upload_mip_analysis_scout_api.generate_config(
mip_dna_analysis_obj)
# THEN the config should contain the multiqc file path
assert result_data.multiqc
def test_generate_balsamic_load_config(
balsamic_analysis_obj: models.Analysis,
upload_balsamic_analysis_scout_api: UploadScoutAPI):
# GIVEN a analysis object that have been run with balsamic
assert balsamic_analysis_obj.pipeline == Pipeline.BALSAMIC
# GIVEN a upload scout api with some balsamic information
# WHEN generating a load config
config = upload_balsamic_analysis_scout_api.generate_config(
analysis_obj=balsamic_analysis_obj)
# THEN assert that the config is a balsamic config
assert isinstance(config, BalsamicLoadConfig)
def test_generate_config_adds_meta_result_key(
result_key: str,
mip_dna_analysis_obj: models.Analysis,
upload_mip_analysis_scout_api: UploadScoutAPI,
):
"""Test that generate config adds the expected result keys"""
# GIVEN a status db and hk with an analysis
assert mip_dna_analysis_obj
# WHEN generating the scout config for the analysis
result_data: ScoutLoadConfig = upload_mip_analysis_scout_api.generate_config(
analysis_obj=mip_dna_analysis_obj)
# THEN the config should contain the rank model version used
assert result_data.dict()[result_key]
def test_generate_config_adds_sample_paths(
sample_id: str,
mip_dna_analysis_obj: models.Analysis,
upload_mip_analysis_scout_api: UploadScoutAPI,
):
"""Test that generate config adds vcf2cytosure file"""
# GIVEN a status db and hk with an analysis
# WHEN generating the scout config for the analysis
result_data: ScoutLoadConfig = upload_mip_analysis_scout_api.generate_config(
mip_dna_analysis_obj)
# THEN the config should contain the sample file path for each sample
sample: ScoutMipIndividual
for sample in result_data.samples:
if sample.sample_id == sample_id:
assert sample.vcf2cytosure