def test_build_case_no_case_id(adapter):
# GIVEN a case without case id
case_info = {}
# WHEN case is built
# THEN a PedigreeError should be raised
with pytest.raises(Exception):
build_case(case_info, adapter)
def test_build_minimal_case(institute_database):
# GIVEN a case without case id
case_info = {'case_id': 'test-case', 'owner': 'cust000'}
# WHEN case is built
case_obj = build_case(case_info, institute_database)
# THEN assert that it worked
assert case_obj['_id'] == case_info['case_id']
def test_build_case_no_display_name(institute_database):
# GIVEN a case without case id
case_info = {'case_id': 'test-case', 'owner': 'cust000'}
# WHEN case is built
case_obj = build_case(case_info, institute_database)
# THEN assert that display_name was set to case_id
assert case_obj['display_name'] == case_info['case_id']
def test_build_case_no_owner(institute_database):
# GIVEN a case where owner does not exist in the database
case_info = {'case_id': 'test-case', 'owner': 'cust001'}
# WHEN case is built
# THEN a IntegrityError should be raised since the owner has to exist in the database
with pytest.raises(IntegrityError):
case_obj = build_case(case_info, institute_database)
def test_build_case_no_case_id(adapter):
## GIVEN a case without case id
case_info = {}
## WHEN case is built
## THEN a PedigreeError should be raised
with pytest.raises(PedigreeError):
case_obj = build_case(case_info, adapter)
def case_database(request, panel_database, parsed_case):
"Returns an adapter to a database populated with institute, user and case"
adapter = panel_database
case_obj = build_case(parsed_case, adapter)
adapter._add_case(case_obj)
return adapter
def test_build_case_non_existing_owner(adapter, institute_obj):
adapter.institute_collection.insert_one(institute_obj)
# GIVEN a case without owner
case_info = {"case_id": "test-case"}
# WHEN case is built
with pytest.raises(ConfigError):
# THEN a ConfigError should be raised since a case has to have a owner
case_obj = build_case(case_info, adapter)
def test_build_case_no_owner(adapter, institute_obj):
adapter.institute_collection.insert_one(institute_obj)
# GIVEN a case where owner does not exist in the database
case_info = {"case_id": "test-case", "owner": "cust001"}
# WHEN case is built
# THEN a IntegrityError should be raised since the owner has to exist in the database
with pytest.raises(IntegrityError):
case_obj = build_case(case_info, adapter)
def test_build_case_no_display_name(adapter, institute_obj):
adapter.institute_collection.insert_one(institute_obj)
# GIVEN a case without case id
case_info = {'case_id': 'test-case', 'owner': 'cust000'}
# WHEN case is built
case_obj = build_case(case_info, adapter)
# THEN assert that display_name was set to case_id
assert case_obj['display_name'] == case_info['case_id']
def test_build_minimal_case(adapter, institute_obj):
adapter.institute_collection.insert_one(institute_obj)
# GIVEN a case without case id
case_info = {'case_id': 'test-case', 'owner': 'cust000'}
# WHEN case is built
case_obj = build_case(case_info, adapter)
# THEN assert that it worked
assert case_obj['_id'] == case_info['case_id']
def test_build_case_no_display_name(adapter, institute_obj):
adapter.institute_collection.insert_one(institute_obj)
# GIVEN a case without case id
case_info = {"case_id": "test-case", "owner": "cust000"}
# WHEN case is built
case_obj = build_case(case_info, adapter)
# THEN assert that display_name was set to case_id
assert case_obj["display_name"] == case_info["case_id"]
def test_build_minimal_case(adapter, institute_obj):
adapter.institute_collection.insert_one(institute_obj)
# GIVEN a case without case id
case_info = {"case_id": "test-case", "owner": "cust000"}
# WHEN case is built
case_obj = build_case(case_info, adapter)
# THEN assert that it worked
assert case_obj["_id"] == case_info["case_id"]
def populated_database(request, panel_database, parsed_case):
"Returns an adapter to a database populated with user, institute case, genes, panels"
adapter = panel_database
LOG.info("Adding case to adapter")
case_obj = build_case(parsed_case, adapter)
adapter._add_case(case_obj)
return adapter
def test_build_case_non_existing_owner(institute_database):
# GIVEN a case without owner
# GIVEN a case where owner does not exist in the database
case_info = {
'case_id': 'test-case',
}
# WHEN case is built
# THEN a ConfigError should be raised since a case has to have a owner
with pytest.raises(ConfigError):
case_obj = build_case(case_info, institute_database)
def test_build_case_no_valid_panel(adapter, institute_obj):
"""Test loading a case containing a non-valid gene panel"""
adapter.institute_collection.insert_one(institute_obj)
# GIVEN a case without a valid gene panel
case_info = {"case_id": "test-case", "owner": "cust000", "panel": ["FOO"]}
# WHEN case is built
case_obj = build_case(case_info, adapter)
# THEN assert that case is loaded and panel will not be saved in case document
assert case_obj["panels"] == []
def test_build_case(parsed_case, adapter, institute_obj, dummypanel_obj):
adapter.institute_collection.insert_one(institute_obj)
adapter.panel_collection.insert_one(dummypanel_obj)
# GIVEN a parsed case
# WHEN bulding a case model
case_obj = build_case(parsed_case, adapter)
# THEN make sure it is built in the proper way
assert case_obj['_id'] == parsed_case['case_id']
assert case_obj['display_name'] == parsed_case['display_name']
assert case_obj['owner'] == parsed_case['owner']
assert case_obj['collaborators'] == parsed_case['collaborators']
assert len(case_obj['individuals']) == len(parsed_case['individuals'])
assert case_obj['synopsis'] == ''
assert case_obj['status'] == 'inactive'
assert case_obj['is_research'] == False
assert case_obj['research_requested'] == False
assert case_obj['rerun_requested'] == False
assert case_obj['analysis_date'] == parsed_case['analysis_date']
assert len(case_obj['dynamic_gene_list']) == 0
assert case_obj['genome_build'] == parsed_case['genome_build']
assert case_obj['rank_model_version'] == parsed_case['rank_model_version']
assert case_obj['rank_score_threshold'] == parsed_case[
'rank_score_threshold']
assert case_obj['sv_rank_model_version'] == parsed_case[
'sv_rank_model_version']
assert case_obj['madeline_info'] == parsed_case['madeline_info']
assert case_obj['chromograph_image_files'] == parsed_case[
'chromograph_image_files']
assert case_obj['chromograph_prefixes'] == parsed_case[
'chromograph_prefixes']
assert case_obj['delivery_report'] == parsed_case['delivery_report']
for vcf in case_obj['vcf_files']:
assert vcf in parsed_case['vcf_files']
# assert case_obj['diagnosis_phenotypes'] == []
# assert case_obj['diagnosis_genes'] == []
if (parsed_case['vcf_files'].get('vcf_sv')
or parsed_case['vcf_files'].get('vcf_sv_research')):
assert case_obj['has_svvariants'] == True
else:
assert case_obj['has_svvariants'] == False
def test_build_case(parsed_case, adapter, institute_obj, dummypanel_obj):
adapter.institute_collection.insert_one(institute_obj)
adapter.panel_collection.insert_one(dummypanel_obj)
# GIVEN a parsed case
# WHEN bulding a case model
case_obj = build_case(parsed_case, adapter)
# THEN make sure it is built in the proper way
assert case_obj["_id"] == parsed_case["case_id"]
assert case_obj["display_name"] == parsed_case["display_name"]
assert case_obj["owner"] == parsed_case["owner"]
assert case_obj["collaborators"] == parsed_case["collaborators"]
assert len(case_obj["individuals"]) == len(parsed_case["individuals"])
assert case_obj["synopsis"] == ""
assert case_obj["status"] == "inactive"
assert case_obj["is_research"] == False
assert case_obj["research_requested"] == False
assert case_obj["rerun_requested"] == False
assert case_obj["analysis_date"] == parsed_case["analysis_date"]
assert len(case_obj["dynamic_gene_list"]) == 0
assert case_obj["genome_build"] == parsed_case["genome_build"]
assert case_obj["rank_model_version"] == parsed_case["rank_model_version"]
assert case_obj["rank_score_threshold"] == parsed_case[
"rank_score_threshold"]
assert case_obj["sv_rank_model_version"] == parsed_case[
"sv_rank_model_version"]
assert case_obj["madeline_info"] == parsed_case["madeline_info"]
assert case_obj["chromograph_image_files"] == parsed_case[
"chromograph_image_files"]
assert case_obj["chromograph_prefixes"] == parsed_case[
"chromograph_prefixes"]
assert case_obj["delivery_report"] == parsed_case["delivery_report"]
for vcf in case_obj["vcf_files"]:
assert vcf in parsed_case["vcf_files"]
# assert case_obj['diagnosis_phenotypes'] == []
# assert case_obj['diagnosis_genes'] == []
if parsed_case["vcf_files"].get("vcf_sv") or parsed_case["vcf_files"].get(
"vcf_sv_research"):
assert case_obj["has_svvariants"] == True
else:
assert case_obj["has_svvariants"] == False
def load_scout(adapter, config, ped=None, update=False):
"""Load a new case from a Scout config.
Args:
adapter(MongoAdapter)
config(dict): loading info
ped(Iterable(str)): Pedigree ingformation
update(bool): If existing case should be updated
"""
log.info("Check that the panels exists")
if not check_panels(adapter, config.get('gene_panels', []),
config.get('default_gene_panels')):
raise ConfigError("Some panel(s) does not exist in the database")
log.debug('parse case data from config and ped')
case_data = parse_case(config, ped)
log.debug('build case object from parsed case data')
case_obj = build_case(case_data, adapter)
log.info("Delete variants for case %s", case_obj['case_id'])
delete_variants(adapter=adapter, case_obj=case_obj)
log.info("Load clinical SNV variants for case %s", case_obj['case_id'])
adapter.load_variants(case_obj=case_obj,
variant_type='clinical',
category='snv',
rank_threshold=case_data['rank_score_threshold'])
if config.get('vcf_sv'):
log.info("Load SV variants for case %s", case_obj['case_id'])
adapter.load_variants(case_obj=case_obj,
variant_type='clinical',
category='sv',
rank_threshold=case_data['rank_score_threshold'])
log.debug('load case object into database')
load_case(
adapter=adapter,
case_obj=case_obj,
update=update,
)
def case_obj(request, parsed_case, panel_database):
adapter = panel_database
logger.info("Create a case obj")
case = build_case(parsed_case, adapter)
return case
def test_build_case(parsed_case, adapter, institute_obj, testpanel_obj):
"""Test function that build a case object when a case is loaded"""
# GIVEN a database containing an institute
adapter.institute_collection.insert_one(institute_obj)
# A gene panel
adapter.panel_collection.insert_one(testpanel_obj)
# And a phenotype term
adapter.hpo_term_collection.insert_one({
"_id": "HP:0001250",
"hpo_id": "HP:0001250",
"description": "Seizures"
})
# GIVEN a parsed case
# WHEN bulding a case model
case_obj = build_case(parsed_case, adapter)
# THEN make sure it is built in the proper way
assert case_obj["_id"] == parsed_case["case_id"]
assert case_obj["display_name"] == parsed_case["display_name"]
assert case_obj["owner"] == parsed_case["owner"]
assert case_obj["collaborators"] == parsed_case["collaborators"]
assert len(case_obj["individuals"]) == len(parsed_case["individuals"])
assert case_obj["synopsis"] != ""
assert case_obj["phenotype_terms"]
assert case_obj["cohorts"]
# Since case object contains cohorts, also its institute should be updated with the same cohorts
assert "cohorts" not in institute_obj
updated_institute = adapter.institute_collection.find_one()
assert "cohorts" in updated_institute
assert case_obj["status"] == "inactive"
assert case_obj["is_research"] is False
assert case_obj["research_requested"] is False
assert case_obj["rerun_requested"] is False
assert case_obj["analysis_date"] == parsed_case["analysis_date"]
assert len(case_obj["dynamic_gene_list"]) == 0
assert case_obj["genome_build"] == parsed_case["genome_build"]
assert case_obj["rank_model_version"] == parsed_case["rank_model_version"]
assert case_obj["rank_score_threshold"] == parsed_case[
"rank_score_threshold"]
assert case_obj["sv_rank_model_version"] == parsed_case[
"sv_rank_model_version"]
assert case_obj["madeline_info"] == parsed_case["madeline_info"]
assert case_obj["delivery_report"] == parsed_case["delivery_report"]
for vcf in case_obj["vcf_files"]:
assert vcf in parsed_case["vcf_files"]
# assert case_obj['diagnosis_phenotypes'] == []
# assert case_obj['diagnosis_genes'] == []
if parsed_case["vcf_files"].get("vcf_sv") or parsed_case["vcf_files"].get(
"vcf_sv_research"):
assert case_obj["has_svvariants"] is True
else:
assert case_obj["has_svvariants"] is False
