def test_include_mip_case_files(mip_config_builder: MipConfigBuilder):
# GIVEN a housekeeper version bundle with some mip analysis files
# GIVEN a case load object
# GIVEN a mip file handler
# WHEN including the case level files
mip_config_builder.build_load_config()
# THEN assert that the mandatory snv vcf was added
assert mip_config_builder.load_config.vcf_snv
def test_include_phenotype_terms(mip_config_builder: MipConfigBuilder):
# GIVEN a config builder with some data
# GIVEN a config without a phenotype terms
assert mip_config_builder.load_config.phenotype_terms is None
# WHEN including the phenotype terms
mip_config_builder.include_phenotype_terms()
# THEN assert that the phenotype terms were added
assert mip_config_builder.load_config.phenotype_terms is not None
def test_include_synopsis(mip_config_builder: MipConfigBuilder):
# GIVEN a config builder with some data
# GIVEN a config without synopsis
assert mip_config_builder.load_config.synopsis is None
# WHEN including the synopsis
mip_config_builder.build_load_config()
# THEN assert that the synopsis was added
assert mip_config_builder.load_config.synopsis
def test_include_delivery_report_mip(mip_config_builder: MipConfigBuilder):
# GIVEN a config builder with some data
# GIVEN a config without a delivery report
assert mip_config_builder.load_config.delivery_report is None
# WHEN including the delivery report
mip_config_builder.include_delivery_report()
# THEN assert that the delivery report was added
assert mip_config_builder.load_config.delivery_report is not None
def test_add_mandatory_info_to_mip_config(
analysis_obj: models.Analysis, mip_config_builder: MipConfigBuilder):
# GIVEN an cg analysis object
# GIVEN a mip load config object
assert mip_config_builder.load_config.owner is None
# GIVEN a file handler with some housekeeper version data
# WHEN adding the mandatory information
mip_config_builder.add_common_info_to_load_config()
# THEN assert mandatory field owner was set
assert mip_config_builder.load_config.owner
def test_include_alignment_file_individual(mip_config_builder: MipConfigBuilder, sample_id: str):
# GIVEN a mip config builder with some information
# WHEN building the scout load config
mip_config_builder.build_load_config()
# THEN assert that the alignment file was added to sample id
file_found = False
for sample in mip_config_builder.load_config.samples:
if sample.sample_id == sample_id:
assert sample.alignment_path is not None
file_found = True
assert file_found
def test_include_mip_sample_subject_id(
mip_config_builder: MipConfigBuilder, sample_id: str, caplog
):
# GIVEN subject_id on the sample
caplog.set_level(level=logging.DEBUG)
# WHEN building the config
mip_config_builder.build_load_config()
# THEN the subject_id was added to the scout sample
subject_id_found = False
for sample in mip_config_builder.load_config.samples:
if sample.sample_id == sample_id:
subject_id_found = True
assert sample.subject_id is not None
assert subject_id_found
def test_include_mip_sample_files(mip_config_builder: MipConfigBuilder, sample_id: str):
# GIVEN a housekeeper version bundle with some mip analysis files
# GIVEN a case load object
# GIVEN that there are no sample level mt_bam
# GIVEN a mip file handler
# WHEN including the case level files
mip_config_builder.build_load_config()
# THEN assert that the mandatory snv vcf was added
file_found = False
for sample in mip_config_builder.load_config.samples:
if sample.sample_id == sample_id:
assert sample.mt_bam is not None
file_found = True
assert file_found
def test_extract_generic_filepath(mip_config_builder: MipConfigBuilder):
"""Test that parsing of file path"""
# GIVEN files paths ending with
file_path1 = "/some/path/gatkcomb_rhocall_vt_af_chromograph_sites_X.png"
file_path2 = "/some/path/gatkcomb_rhocall_vt_af_chromograph_sites_12.png"
# THEN calling extracting the generic path will remove numeric id and fuffix
generic_path = "/some/path/gatkcomb_rhocall_vt_af_chromograph_sites_"
# THEN
assert mip_config_builder.extract_generic_filepath(file_path1) == generic_path
assert mip_config_builder.extract_generic_filepath(file_path2) == generic_path
def fixture_mip_config_builder(
mip_dna_analysis_hk_version: hk_models.Version,
mip_dna_analysis_obj: models.Analysis,
lims_api: MockLimsAPI,
mip_analysis_api: MockMipAnalysis,
madeline_api: MockMadelineAPI,
) -> MipConfigBuilder:
return MipConfigBuilder(
hk_version_obj=mip_dna_analysis_hk_version,
analysis_obj=mip_dna_analysis_obj,
lims_api=lims_api,
mip_analysis_api=mip_analysis_api,
madeline_api=madeline_api,
)
def test_mip_config_builder(
hk_version_obj: hk_models.Version,
mip_dna_analysis_obj: models.Analysis,
lims_api: MockLimsAPI,
mip_analysis_api: MockMipAnalysis,
madeline_api: MockMadelineAPI,
):
# GIVEN a mip file handler
# WHEN instantiating
config_builder = MipConfigBuilder(
hk_version_obj=hk_version_obj,
analysis_obj=mip_dna_analysis_obj,
lims_api=lims_api,
mip_analysis_api=mip_analysis_api,
madeline_api=madeline_api,
)
# THEN assert that the correct case tags was used
assert isinstance(config_builder.case_tags, CaseTags)
def fixture_mip_file_handler(mip_dna_analysis_hk_version: hk_models.Version) -> MipConfigBuilder:
return MipConfigBuilder(hk_version_obj=mip_dna_analysis_hk_version)