Bases: BaseAnnotationCombiner

Collapses sample-level annotations to the series-level and adds study-forward annotations.

Example:

>>> combiner = StudyCombiner()
>>> combiner.combine(SAMPLE_COMBINED_BSON).clean().save(SERIES_COMBINED_BSON)

deleted_studies property

Load and return deleted studies. Stored in the DELETED_STUDIES file.

combine(sample_combined_bson=SAMPLE_COMBINED_BSON, db_path=OMICIDX_DB)

Load sample annotations, collapse them, and combine with study-forward annotations.

Parameters:
  • sample_combined_bson (Path, default: SAMPLE_COMBINED_BSON ) –

    Path to the combined sample annotations BSON file generated from the SampleCombiner module.
Returns:
  • StudyCombiner –

    self, for chaining.

add_existing_source_annotation(source_anno, study_anno) staticmethod

Append an annotation to a source that already exists for a partucular study attribute annotation.