def test_json_for_sample(self):
sample = Sample.objects.first()
json = _get_json_for_sample(sample)
self.assertSetEqual(
set(json.keys()),
{'projectGuid', 'individualGuid', 'sampleGuid', 'createdDate', 'sampleType', 'sampleId', 'sampleStatus',
'datasetFilePath', 'loadedDate', 'datasetType', 'elasticsearchIndex'}
)
def test_json_for_sample(self):
sample = Sample.objects.first()
json = _get_json_for_sample(sample)
self.assertSetEqual(
set(json.keys()),
{'projectGuid', 'individualGuid', 'sampleGuid', 'createdDate', 'sampleType', 'sampleId', 'sampleStatus',
'datasetFilePath', 'loadedDate', 'datasetType', 'elasticsearchIndex'}
)
def _retrieve_samples(cursor, project_guid, individuals_by_guid):
"""Retrieves sample metadata for the given project.
Args:
cursor: connected database cursor that can be used to execute SQL queries.
project_guid (string): project_guid
individuals_by_guid (dict): maps each individual_guid to a dictionary with individual info.
This method adds a "sampleGuids" list to each of these dictionaries.
Returns:
2-tuple with dictionaries: (samples_by_guid, sample_batches_by_guid)
"""
# use raw SQL since the Django ORM doesn't have a good way to express these types of queries.
sample_query = """
SELECT
p.guid AS project_guid,
i.guid AS individual_guid,
s.guid AS sample_guid,
s.created_date AS sample_created_date,
s.sample_type AS sample_sample_type,
s.dataset_type AS sample_dataset_type,
s.sample_id AS sample_sample_id,
s.elasticsearch_index AS sample_elasticsearch_index,
s.dataset_file_path AS sample_dataset_file_path,
s.sample_status AS sample_sample_status,
s.loaded_date AS sample_loaded_date
FROM seqr_sample AS s
JOIN seqr_individual AS i ON s.individual_id=i.id
JOIN seqr_family AS f ON i.family_id=f.id
JOIN seqr_project AS p ON f.project_id=p.id
WHERE p.guid=%s
""".strip()
cursor.execute(sample_query, [project_guid])
columns = [col[0] for col in cursor.description]
samples_by_guid = {}
for row in cursor.fetchall():
record = dict(zip(columns, row))
sample_guid = record['sample_guid']
if sample_guid not in samples_by_guid:
samples_by_guid[sample_guid] = _get_json_for_sample(record)
individual_guid = record['individual_guid']
individuals_by_guid[individual_guid]['sampleGuids'].add(sample_guid)
samples_by_guid[sample_guid]['individualGuid'] = individual_guid
return samples_by_guid