Remaining duplicate implementations: annotation, snpdb, and cross-app pairs

[davmlaw]

🤖 Written by Claude

Last of the duplication found by the same scan (token-normalised clone detection + AST structural similarity, then manual verification) — everything outside the classification (#1796) and analysis (#1799) apps, plus the cross-app pairs.

1. dump_external_annotation_runs / dump_existing_annotation_runs

annotation/external_annotation.py:155 and :213 share a ~25-line block verbatim: the already-counted too-small rejection, dump(), the dump_count == 0 skip, the too-small revert, the lazily-computed identity, write_dump_metadata, and then the whole write_snakemake_bundle / reverted / logging tail. Only how each acquires its runs differs — one creates them from range locks, the other adopts existing CREATED ones. The comments are copied too, which is the giveaway.

2. Trio and Quad models

snpdb/models/models_cohort.py:773 and :843 — get_permission_class, preview_icon, preview, get_permission_object, _filter_from_permission_object_qs, genome_build, data_archived, get_samples, mother_details and father_details are identical, and __str__ differs only in the class name it prints. sibling_details is a third copy of the same two-line shape.

The fields can't move (related_name differs per model: trio_mother vs quad_mother), but nothing stops the methods sharing.

3. Trio and Quad grids, and the two collection grids

snpdb/grids.py:369 / :400 — QuadsListColumns is TriosListColumns plus two sibling columns; the id/name/user/modified/delete columns and filter_queryset are identical.

snpdb/grids.py:454 / :624 — CustomColumnsCollectionColumns and TagColorsCollectionColumns are identical bar the model: the same five columns and the same filter_for_user queryset.

4. Chromosome density and homozygosity percent graphs

snpdb/graphs/chromosome_density_graph.py:88 and homozygosity_percent_graph.py:113 share an identical ~20-line pcolormesh setup — the dimension juggling, the y_top/y_bottom padding, the masked array and set_clim — including the copied # pcolor says x,y should have dimensions 1 greater than colors comment. Only vmax differs.

5. as_table / as_p template filters

snpdb/templatetags/model_helpers.py:16 and :38 share their whole row-formatting loop; only the HTML each wraps a row in differs. (They also differ in that as_p returns mark_safe, while as_table's callers apply |safe at the template — worth preserving as is.)

6. Fake-data helpers copied between apps

_variant_ids_by_gene and _zipf_weight are byte-identical in classification/fake_reclassifications.py:415,411 and analysis/fake_variant_tags.py:336,348. Both modules are subcommands of manage.py create_fake_data, so they want a shared home at a level both can import. (Moved out of #1798.)

7. Popover hover-stay handler in global.js

variantgrid/static_files/default_static/js/global.js:186 and :211 bind the same mouseenter/mouseleave pair with the same 300ms .popover:hover grace check.

Identified but deliberately left alone

• annotation/tasks/calculate_sample_stats.py has the same ~15-line counter-bump sequence three times (:482 aggregate, :533 per trio mode, :570 comp-het post-processing). It is real duplication and a genuine "add a counter, update three places" hazard, but it is the innermost per-variant accumulation loop of a whole-database stats task, and factoring it into a helper adds a Python call per bucket per variant. Not worth the throughput on a task that walks every variant in the database.
• ClassificationAttachment.get_file_dict / PatientAttachment.get_file_dict (classification/models/variant_models.py:21, patients/models.py:594) are identical bar the URL names, and both models declare the same file/file_type/thumbnail_path fields. Sharing them properly means an abstract attachment model across two apps and the migrations that come with it — a bigger change than the rest of this issue.
• Test fixtures. annotation/tests/ has roughly six copies of the same setUpTestData, and there are repeated blocks within test_annotation_vcf.py. Worth a tidy-up, but sharing fixtures across test classes is a different exercise to deduplicating production code.