Duplicate implementations in the classification app (two of them dead, drifted code)

[davmlaw]

🤖 Written by Claude

A scan for duplicated implementations (token-normalised clone detection + AST structural similarity across the codebase, then manual verification) turned up several copy-paste pairs in the classification app. Two of them are dead code that has already drifted from its live twin.

1. evidence_key_cleaner is a broken copy of unknown_evidence_key_cleaner

classification/management/commands/evidence_key_cleaner.py and unknown_evidence_key_cleaner.py are identical apart from one line:

parser.add_argument('--key', type='str', required=True)   # evidence_key_cleaner only

--key is never read in handle(), and type='str' (the string, not the builtin) makes argparse raise ValueError: 'str' is not callable inside add_argument — so the command fails on every invocation, including --help. Nothing in the repo references it.

2. Classification.get_allele_info_dict() is dead and has drifted

• classification/models/classification.py:2031 — the method, no callers anywhere (Python, templates or JS)
• classification/models/classification_json.py:21 — the module function actually used, via classification_json.py:179

The live copy has since gained two things the dead one never got:

• the elif g_hgvs := allele_info.imported_g_hgvs_obj: fallback from "Allow g.HGVS classification imports" (Intergenic classifications - missing c.HGVS treated as error #1063)
• SpecialEKeys.VARIANT_COORDINATE in the per-genome-build dict

This is exactly the failure duplication causes — a fix landing in one copy only.

3. Criteria-strength building duplicated

• classification/models/classification_groups.py:375 — criteria_converter nested in acmg_criteria
• classification/models/evidence_mixin_summary_cache.py:209 — criteria_labels

Both walk EvidenceKeyMap.cached().criteria() collecting met criteria, then expand SpecialEKeys.AMP_LEVELS_TO_LEVEL into CriteriaStrength objects with a f"{letter}_{sub_value_label}" custom strength. The two loops are identical; only the output shaping differs (MultiValues vs sorted labels). Both call sites hold a ClassificationModification, which is an EvidenceMixin, so this belongs on the mixin.

4. DiscordanceReportAdminExport._less_more_certain / _up_down_for

classification/admin/classification_admin.py:741 and :764 share an identical seven-line prelude — the cs_to_index lookup, the from_value/to_value ints, and the withdrawn / same / ? guards. Only the final comparison differs (distance from 3 vs. straight >).

Not included

The near-identical context dicts in classification/views/views.py:187 (classifications) and :284 (classification_groupings) are left alone — #1765 proposes deleting the classification_groupings page outright, which removes that duplication properly.

_variant_ids_by_gene and _zipf_weight, byte-identical in classification/fake_reclassifications.py and analysis/fake_variant_tags.py, are tracked separately with the rest of the cross-app duplication rather than here.