def convert_sample(self, sample_entity: Entity) -> Sample:
sample = Sample(
accession=sample_entity.get_accession('BioSamples'),
name=self.named_attribute(sample_entity, 'sample_title'),
domain=self.named_attribute(sample_entity, 'domain', self.domain),
ncbi_taxon_id=self.named_attribute(sample_entity, 'tax_id'),
species=self.named_attribute(sample_entity, 'scientific_name'))
sample._append_organism_attribute()
for name, value in sample_entity.attributes.items():
if name not in REMOVE_KEYS:
sample.attributes.append(
Attribute(name=name.replace('_', ' '),
value=value,
unit=self.unit_map.get(name, None)))
return sample
def add_alias(self, spec: dict, entity: Entity):
accession = entity.get_accession(f'ENA_{self.ena_type}')
if accession:
spec['@accession'] = ['', fixed_attribute, accession]
else:
spec['@alias'] = ['', fixed_attribute, entity.identifier.index]
def update_links_in_submission(self, submission: Submission, study: Entity) -> dict:
study_accession = study.get_accession('BioStudies')
biostudies_submission = self.get_submission_by_accession(study_accession).json
links_section = self.__get_links_section_from_submission(biostudies_submission)
self.__update_links_section(links_section, study, submission)
return biostudies_submission
def __add_accession(study: Entity, submission_payload: dict):
study_accession: str = study.get_accession('BioStudies')
if study_accession:
submission_payload['accno'] = study_accession
return submission_payload
