def setUp(self) -> None:
# create 2 phenopackets for 2 individuals; each individual has 1 biosample;
# one of phenopackets has 1 phenotypic feature and 1 disease
self.individual_1 = ph_m.Individual.objects.create(**ph_c.VALID_INDIVIDUAL_1)
self.individual_2 = ph_m.Individual.objects.create(**ph_c.VALID_INDIVIDUAL_2)
self.metadata_1 = ph_m.MetaData.objects.create(**ph_c.VALID_META_DATA_1)
self.metadata_2 = ph_m.MetaData.objects.create(**ph_c.VALID_META_DATA_2)
self.phenopacket_1 = ph_m.Phenopacket.objects.create(
**ph_c.valid_phenopacket(subject=self.individual_1, meta_data=self.metadata_1)
)
self.phenopacket_2 = ph_m.Phenopacket.objects.create(
id='phenopacket:2', subject=self.individual_2, meta_data=self.metadata_2
)
self.disease = ph_m.Disease.objects.create(**ph_c.VALID_DISEASE_1)
self.procedure = ph_m.Procedure.objects.create(**ph_c.VALID_PROCEDURE_1)
self.biosample_1 = ph_m.Biosample.objects.create(**ph_c.valid_biosample_1(self.individual_1, self.procedure))
self.biosample_2 = ph_m.Biosample.objects.create(**ph_c.valid_biosample_2(self.individual_2, self.procedure))
self.phenotypic_feature = ph_m.PhenotypicFeature.objects.create(
**ph_c.valid_phenotypic_feature(self.biosample_1, self.phenopacket_1)
)
self.phenopacket_1.biosamples.set([self.biosample_1])
self.phenopacket_2.biosamples.set([self.biosample_2])
self.phenopacket_1.diseases.set([self.disease])
# experiments
self.instrument = exp_m.Instrument.objects.create(**exp_c.valid_instrument())
self.experiment = exp_m.Experiment.objects.create(**exp_c.valid_experiment(self.biosample_1, self.instrument))
self.experiment_result = exp_m.ExperimentResult.objects.create(**exp_c.valid_experiment_result())
self.experiment.experiment_results.set([self.experiment_result])
def setUp(self) -> None:
self.project = Project.objects.create(**VALID_PROJECT_1)
self.dataset = Dataset.objects.create(**valid_dataset_1(self.project))
to, tr = valid_table_1(self.dataset.identifier, model_compatible=True)
TableOwnership.objects.create(**to)
self.table = Table.objects.create(**tr)
# Set up a dummy phenopacket
self.individual, _ = Individual.objects.get_or_create(
id='patient:1', sex='FEMALE', age={"age": "P25Y3M2D"})
self.procedure = Procedure.objects.create(**VALID_PROCEDURE_1)
self.biosample_1 = Biosample.objects.create(
**valid_biosample_1(self.individual, self.procedure))
self.biosample_2 = Biosample.objects.create(
**valid_biosample_2(None, self.procedure))
self.meta_data = MetaData.objects.create(**VALID_META_DATA_1)
self.phenopacket = Phenopacket.objects.create(id="phenopacket_id:1",
subject=self.individual,
meta_data=self.meta_data,
table=self.table)
self.phenopacket.biosamples.set([self.biosample_1, self.biosample_2])
def setUp(self) -> None:
# individuals (count 8)
individuals = {
f"individual_{i}": ph_m.Individual.objects.create(**ind)
for i, ind in enumerate(VALID_INDIVIDUALS, start=1)
}
# biosamples
self.procedure = ph_m.Procedure.objects.create(
**ph_c.VALID_PROCEDURE_1)
self.biosample_1 = ph_m.Biosample.objects.create(
**ph_c.valid_biosample_1(individuals["individual_1"],
self.procedure))
self.biosample_2 = ph_m.Biosample.objects.create(
**ph_c.valid_biosample_2(individuals["individual_2"],
self.procedure))
# experiments
self.instrument = exp_m.Instrument.objects.create(
**exp_c.valid_instrument())
self.experiment = exp_m.Experiment.objects.create(
**exp_c.valid_experiment(self.biosample_1, self.instrument))
self.experiment_result = exp_m.ExperimentResult.objects.create(
**exp_c.valid_experiment_result())
self.experiment.experiment_results.set([self.experiment_result])
# make a copy and create experiment 2
experiment_2 = deepcopy(
exp_c.valid_experiment(self.biosample_2, self.instrument))
experiment_2["id"] = "experiment:2"
self.experiment = exp_m.Experiment.objects.create(**experiment_2)
def setUp(self):
self.individual_1 = Individual.objects.create(**VALID_INDIVIDUAL_1)
self.individual_2 = Individual.objects.create(**VALID_INDIVIDUAL_2)
self.procedure = Procedure.objects.create(**VALID_PROCEDURE_1)
self.biosample_1 = Biosample.objects.create(
**valid_biosample_1(self.individual_1, self.procedure))
self.biosample_2 = Biosample.objects.create(
**valid_biosample_2(self.individual_2, self.procedure))
self.phenotypic_feature_1 = PhenotypicFeature.objects.create(
**valid_phenotypic_feature(biosample=self.biosample_1))
self.phenotypic_feature_2 = PhenotypicFeature.objects.create(
**valid_phenotypic_feature(biosample=self.biosample_2))
def setUp(self):
self.subject = Individual.objects.create(**VALID_INDIVIDUAL_1)
self.metadata = MetaData.objects.create(**VALID_META_DATA_2)
self.procedure = Procedure.objects.create(**VALID_PROCEDURE_1)
self.biosample_1 = Biosample.objects.create(
**valid_biosample_1(self.subject, self.procedure))
self.biosample_2 = Biosample.objects.create(
**valid_biosample_2(None, self.procedure))
self.phenopacket = Phenopacket.objects.create(
id="phenopacket_id:1",
subject=self.subject,
meta_data=self.metadata,
)
self.phenopacket.biosamples.set([self.biosample_1, self.biosample_2])
def setUp(self) -> None:
self.project = Project.objects.create(**VALID_PROJECT_1)
self.dataset = Dataset.objects.create(**valid_dataset_1(self.project))
to, tr = valid_table_1(self.dataset.identifier, model_compatible=True)
TableOwnership.objects.create(**to)
self.table = Table.objects.create(**tr)
# Set up a dummy phenopacket
self.individual, _ = Individual.objects.get_or_create(
id='patient:1', sex='FEMALE', age={"age": "P25Y3M2D"})
self.procedure = Procedure.objects.create(**VALID_PROCEDURE_1)
self.biosample_1 = Biosample.objects.create(**valid_biosample_1(self.individual, self.procedure))
self.biosample_2 = Biosample.objects.create(**valid_biosample_2(None, self.procedure))
self.meta_data = MetaData.objects.create(**VALID_META_DATA_1)
self.phenopacket = Phenopacket.objects.create(
id="phenopacket_id:1",
subject=self.individual,
meta_data=self.meta_data,
table=self.table
)
self.phenopacket.biosamples.set([self.biosample_1, self.biosample_2])
self.phenotypic_feature = PhenotypicFeature.objects.create(
**valid_phenotypic_feature(phenopacket=self.phenopacket)
)
# table for experiments metadata
to_exp = TableOwnership.objects.create(table_id=uuid.uuid4(), service_id=uuid.uuid4(),
service_artifact="experiments", dataset=self.dataset)
self.t_exp = Table.objects.create(ownership_record=to_exp, name="Table 2", data_type=DATA_TYPE_EXPERIMENT)
# add Experiments metadata and link to self.biosample_1
self.instrument = Instrument.objects.create(**valid_instrument())
self.experiment_result = ExperimentResult.objects.create(**valid_experiment_result())
self.experiment = Experiment.objects.create(**valid_experiment(
biosample=self.biosample_1, instrument=self.instrument, table=self.t_exp))
self.experiment.experiment_results.set([self.experiment_result])
def setUp(self):
i = Individual.objects.create(**VALID_INDIVIDUAL_1)
p = Procedure.objects.create(**VALID_PROCEDURE_1)
self.biosample = Biosample.objects.create(**valid_biosample_1(i, p))
Experiment.objects.create(id='experiment:1',
reference_registry_id='some_id',
qc_flags=['flag 1', 'flag 2'],
experiment_type='Chromatin Accessibility',
experiment_ontology=[{
"id":
"ontology:1",
"label":
"Ontology term 1"
}],
molecule_ontology=[{
"id": "ontology:1",
"label": "Ontology term 1"
}],
molecule='total RNA',
library_strategy='Bisulfite-Seq',
other_fields={"some_field": "value"},
biosample=self.biosample)
def setUp(self):
self.individual = Individual.objects.create(**VALID_INDIVIDUAL_1)
self.procedure = VALID_PROCEDURE_1
self.valid_payload = valid_biosample_1(self.individual.id,
self.procedure)
def setUp(self):
i = Individual.objects.create(**VALID_INDIVIDUAL_1)
p = Procedure.objects.create(**VALID_PROCEDURE_1)
self.biosample = Biosample.objects.create(**valid_biosample_1(i, p))
Experiment.objects.create(**valid_experiment(self.biosample))
