Index

_

__init__() (src.mapping.OntologyMapper method) (src.validation.DataValidator method)

B

batch_process() (in module src.batch_processing)

C

CACHE_DIR (src.mapping.OntologyMapper attribute) check_referential_integrity() (src.validation.DataValidator method) child_process_run() (in module src.batch_processing) convert_nans_to_none_for_string_cols() (in module src.batch_processing)

create_missingness_distribution() (in module src.reporting) create_missingness_heatmap() (in module src.reporting) create_numeric_histograms() (in module src.reporting) create_visual_summary() (in module src.reporting)

D

DataValidator (class in src.validation) detect_anomalies() (src.validation.DataValidator method)

detect_conflicts() (src.validation.DataValidator method) detect_missing_data() (in module src.missing_data)

F

fetch_ontology_file_with_cache() (src.mapping.OntologyMapper method)

flag_missing_data_records() (in module src.missing_data)

G

generate_qc_report() (in module src.reporting)

get_file_type() (in module src.batch_processing) get_supported_ontologies() (src.mapping.OntologyMapper method)

I

identify_duplicates() (src.validation.DataValidator method)

impute_missing_data() (in module src.missing_data)

L

load_config() (in module src.configuration) (src.mapping.OntologyMapper method)

load_data() (in module src.input) load_ontologies() (src.mapping.OntologyMapper method) log_activity() (in module src.logging_module)

M

map_term() (src.mapping.OntologyMapper method) map_terms() (src.mapping.OntologyMapper method) module src.batch_processing src.configuration src.input src.logging_module src.mapping src.missing_data src.reporting src.validation

O

OntologyMapper (class in src.mapping)

P

parse_ontology() (src.mapping.OntologyMapper method)

process_file() (in module src.batch_processing)

R

read_csv() (in module src.input) read_json() (in module src.input)

read_tsv() (in module src.input) run_all_validations() (src.validation.DataValidator method)

S

save_config() (in module src.configuration) setup_logging() (in module src.logging_module) src.batch_processing module src.configuration module src.input module src.logging_module module

src.mapping module src.missing_data module src.reporting module src.validation module

U

unique_output_name() (in module src.batch_processing)

V

validate_cells() (src.validation.DataValidator method) validate_format_rowwise() (src.validation.DataValidator method)

validate_row_json_schema() (src.validation.DataValidator method) verify_integrity() (src.validation.DataValidator method)