Variants Batch¶

class genomcore.controllers.variantsBatch.VariantsBatchController(*args, **kwargs)¶

property get_errors¶: This property return a dict with errors inside observations The key of dict is the index in observations.

property total¶: This property return total observations inserted correctly

property status¶: This property return ‘completed’ if all observations was inserted and return ‘failed’ if not

get_status(observationBatchId)¶

Query the status of the one observationBatchId.

Parameters:

observationBatchId – Its a string, this argument is the identifier of transaction

Returns:

Transaction status.

{: ‘id’: ‘67ffd46f709f4a3c230dfe02’, ‘projectId’: 550, ‘observationsTotal’: <Total number of observations in the batch>, ‘observationsCreatedTotal’: <Number of successfully created observations>, ‘observationsValidationFailedTotal’: <Number of observations that failed validation>, ‘observationsValidationFailed’: <List of observations that failed validation with detailed errors>, ‘observationsFailedTotal’: <Number of observations that failed to create>, ‘observationsFailed’: <List of observations that failed with their error messages>, ‘createdAt’: ‘2025-04-16T16:01:51.276Z’, ‘updatedAt’: ‘2025-04-16T16:01:51.344Z’, ‘status’: <string with the status: COMPLETED, FAILED, PENDING>

}

Return type:

dict

wait(sleep=30, log_proccesed=10)¶

This function put a semaphore for waiting all chunks was finished.

Parameters:

sleep – The method sleep 30 seconds by default if find one batch in pending status
log_proccesed – Print log_proccesed lines, by default print 10

create_one_observations_batch(observations: List[dict], retries: int | None = 0) → int¶

Save many genetic variant observations in a queue Kafka without make chunks. Also this method dont wait to kafka finished all insertions

Parameters:

observations (list) – list of observations to save.
retries (int, optional) – number of retries in case of failure. Defaults to 3.

Returns:

Total chunks created.

Return type:

int

create_observations_batch(observations: List[dict], chunksize: int | None = 1000, retries: int | None = 0) → int¶

Save many genetic variant observations in a queue Kafka.

Parameters:

observations (list) – list of observations to save.
chunksize (int, optional) – size of the chunks to send. Defaults to 100000.
retries (int, optional) – number of retries in case of failure. Defaults to 3.

Returns:

Total chunks created.

Return type:

int

__static_attributes__ = ('BatchId', '_errors', '_errors_description', '_ok', '_rel_batchId_groupId')¶