Inconsistent hierarchy metrics for flat ontologies

[alexskr]

Background

When an ontology is marked as flat in BioPortal, hierarchy-related metrics are handled inconsistently. The flat flag is a UI/browsing flag set manually for ontologies where tree display wasn't performant — it's not a statement that the ontology has no hierarchy.

Current behavior

For flat ontologies, some hierarchy metrics report real values while others are zeroed out:

Metric	Value	Why
maxDepth	real value (e.g., 7)	Read from metrics.csv generated by owlapi_wrapper, which has no knowledge of the flat flag
classesWithOneChild	0	Skipped by unless is_flat guard in class_metrics
maxChildCount	0	Same
classesWithMoreThan25Children	0	Same
averageChildCount	0	Same

History

Before the owlapi integration (commit 61ee7059), all hierarchy metrics including maxDepth were set to 0 for flat ontologies. The owlapi commit introduced CSV-based maxDepth calculation that bypasses the is_flat check, creating the inconsistency. The test was updated from assert_equal 0 to assert_equal 7 to match.

Options

1. Report real values for all metrics — remove the unless is_flat guard from the groupby_children loop so child metrics also reflect reality. Consistent with maxDepth behavior and with the view that flat is a UI flag.

2. Zero out all hierarchy metrics — add is_flat check to max_depth_fn so maxDepth is also 0. Consistent with pre-owlapi behavior and with the view that flat means "no hierarchy metrics."

Either approach is valid, but the current mixed state should be resolved.

Related

• Clean up metrics: dead code, flat maxDepth fix, remove CSV fallback #277 (metrics cleanup PR — deferred this question per review feedback)