def test_run_component_create(self):
run = Run(value=self.json_entries_runs[0])
component = Component(value=self.json_entries_components[0])
test_run_component = RunComponent(
run_reference=run.to_reference(),
component_reference=component.to_reference())
test_run_component.save()
assert "_id" in test_run_component.json
def test_sample_component_create(self):
sample = Sample(value=self.json_entries_samples[0])
component = Component(value=self.json_entries_components[0])
test_sample_component = SampleComponent(
sample_reference=sample.to_reference(),
component_reference=component.to_reference())
test_sample_component.save()
assert "_id" in test_sample_component.json
def test_component_create_from_ref(self):
_id = "000000000000000000000001"
name = "test_component"
component = Component.load(
reference=ComponentReference(_id=_id, name=name))
assert component.delete() == True
test_component = Component(value=self.json_entries[0])
test_component.save()
json = component.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
def datadump(samplecomponent_ref_json: Dict):
samplecomponent_ref = SampleComponentReference(value=samplecomponent_ref_json)
samplecomponent = SampleComponent.load(samplecomponent_ref)
sample = Sample.load(samplecomponent.sample)
component = Component.load(samplecomponent.component)
serotype = sample.get_category("serotype")
if serotype is None:
serotype = Category(value={
"name": "serotype",
"component": samplecomponent.component,
"summary": {
"serotype": "",
"antigenic profile": "",
"status": "",
},
"report": {}
})
extract_serotype_results(serotype, samplecomponent["results"], samplecomponent["component"]["name"])
samplecomponent.set_category(serotype)
sample.set_category(serotype)
samplecomponent.save_files()
common.set_status_and_save(sample, samplecomponent, "Success")
with open(os.path.join(samplecomponent["component"]["name"], "datadump_complete"), "w+") as fh:
fh.write("done")
def initialize():
with open(os.path.join(os.path.dirname(__file__), 'config.yaml')) as fh:
config: Dict = yaml.load(fh, Loader=yaml.FullLoader)
if not(datahandling.has_a_database_connection()):
raise ConnectionError("BIFROST_DB_KEY is not set or other connection error")
global COMPONENT
try:
component_ref = ComponentReference(name=config["name"])
COMPONENT = Component.load(component_ref)
if COMPONENT is not None and '_id' in COMPONENT.json:
return
else:
COMPONENT = Component(value=config)
install_component()
except Exception as e:
print(traceback.format_exc(), file=sys.stderr)
return
def test_component_create(self):
test_component = Component(name="test_component")
print(test_component)
test_component.save()
assert "_id" in test_component.json
def test_component_delete(self):
_id = "000000000000000000000001"
name = "test_component"
component = Component.load(ComponentReference(_id=_id, name=name))
assert component.delete() == True