Reports

Reports are the main read interface over Biofilter knowledge and ETL provenance.

For the complete index of all available reports with links to explain guides and notebook tutorials, see the Report Catalog.

Discover and Inspect

List reports:

biofilter report list
biofilter report list --verbose

Explain report:

biofilter report explain --report-name etl_status

Show example input:

biofilter report example-input --report-name entity_relationship_model

Show output columns:

biofilter report available-columns --report-name etl_packages

Run Reports

Basic run:

biofilter report run --report-name etl_status

Export CSV:

biofilter report run --report-name etl_packages --output ./etl_packages.csv

Template-driven params:

biofilter report run --report-name entity_relationship_model --params-template

Dynamic Parameter Injection

Inputs:

biofilter report run --report-name entity_filter --input BRCA1 --input TP53
biofilter report run --report-name entity_filter --input-file ./entities.csv --input-column symbol

Options:

biofilter report run --report-name entity_relationship_model \
  --input TP53 --input BRCA1 \
  --param relationship_scope=input_to_any \
  --param deduplicate_pairs=true

JSON/YAML params:

biofilter report run --report-name entity_relationship_model --params-json '{"relationship_scope":"input_to_any"}'
biofilter report run --report-name entity_relationship_model --params-file ./params.yaml

Load one param from file:

biofilter report run --report-name entity_relationship_model --input TP53 --param relationship_types=@./relationship_types.txt

Explain Guides

report explain prefers markdown guides stored in:

• biofilter/modules/report/reports_explain/report_<module>.md

If a guide file is missing, Biofilter falls back to the report class explain() method.

This model keeps report documentation maintainable:

• update the report module when behavior changes

• update the paired explain markdown for user-facing guidance

Practical Examples

Repository-level example guides:

• docs/reports/snp_snp_model.md