Release 2026.2.0

.github/workflows/checks.yaml

@@ -39,3 +39,8 @@ jobs:
 
       - name: Check style
         run: python3 -m ruff check . && ruff format --check .
+
+      - name: Verify schema.json is up to date
+        run: |
+          python scripts/generate_schema.py
+          git diff --exit-code schema.json

.gitignore

@@ -166,3 +166,8 @@ cython_debug/
 # mapping data/output
 notebooks/analysis/analysis_files
 notebooks/analysis/mavedb_files
+
+# debug / ad-hoc mapping output files — prevent accidental commits
+urn:*.json
+tmp:*.json
+*_mapping_*.json

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v1.4.0
+  rev: v6.0.0
   hooks:
   - id: check-added-large-files
   - id: detect-private-key
   - id: trailing-whitespace
   - id: end-of-file-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.2.0
+  rev: v0.15.12
   hooks:
     - id: ruff-format
     - id: ruff

README.md

@@ -17,7 +17,7 @@ This library implements a novel method for mapping [MaveDB scoreset data](https:
 * Universal Transcript Archive (UTA): see [README](https://github.com/biocommons/uta?tab=readme-ov-file#installing-uta-locally) for setup instructions. Users with access to Docker on their local devices can use the available Docker image; otherwise, start a relatively recent (version 14+) PostgreSQL instance and add data from the available database dump.
 * SeqRepo: see [README](https://github.com/biocommons/biocommons.seqrepo?tab=readme-ov-file#requirements) for setup instructions. The SeqRepo data directory must be writeable; see specific instructions [here](https://github.com/biocommons/biocommons.seqrepo/blob/main/docs/store.rst) for more.
 * Gene Normalizer: see [documentation](https://gene-normalizer.readthedocs.io/0.3.0-dev1/install.html) for data setup instructions.
-* blat: Must be available on the local PATH and executable by the user. Otherwise, its location can be set manually with the `BLAT_BIN_PATH` env var. See the [UCSC Genome Browser FAQ](https://genome.ucsc.edu/FAQ/FAQblat.html#blat3) for download instructions. 
+* blat: Must be available on the local PATH and executable by the user. Otherwise, its location can be set manually with the `BLAT_BIN_PATH` env var. See the [UCSC Genome Browser FAQ](https://genome.ucsc.edu/FAQ/FAQblat.html#blat3) for download instructions.
 
 
 ## Installation
@@ -40,6 +40,86 @@ Output is saved in the format `<URN>_mapping_results_<ISO datetime>.json` in the
 
 Use `dcd-map --help` to see other available options.
 
+## Mapping output
+
+Each mapping run produces a single JSON document conforming to [`schema.json`](schema.json) (the JSON Schema serialization of `ScoresetMapping`). Top-level keys:
+
+* `metadata` — the verbatim MaveDB API scoreset response, stored unchanged so no upstream fields are lost.
+* `mapped_date` — ISO 8601 UTC timestamp of when this run completed.
+* `reference_sequences` — per-target reference sequence info per annotation layer.
+* `mapped_scores` — flat list of per-variant `ScoreAnnotation` records (see below).
+* `target_mappings` — per-`(target, alignment_level)` provenance and alignment QC rows. The MaveDB API consumes these as `target_gene_mappings` and uses them to attribute every `mapped_score` back to the alignment that produced it.
+* `error_message` — populated only when the run failed before producing scores.
+
+### `metadata`
+
+The verbatim MaveDB API scoreset response. Stored unchanged so downstream consumers retain access to every upstream field (URN, title, description, target gene definitions, score-column metadata, etc.) without having to query MaveDB again.
+
+### `reference_sequences`
+
+A `dict[target_gene_name, TargetAnnotation]` describing the reference sequences each target was mapped against, organized by annotation layer. Each `TargetAnnotation` carries:
+
+* `gene_info` — `hgnc_symbol` plus the `selection_method` that picked it (transcript-derived, alignment-overlap-derived, variant-overlap-derived, or metadata fallback).
+* `layers` — a `dict[AnnotationLayer, {computed_reference_sequence, mapped_reference_sequence}]` populated only for layers that actually produced mappings. `computed_reference_sequence` is the in-pipeline sequence (e.g. translated protein); `mapped_reference_sequence` lists the canonical accession(s) the variants were ultimately grounded in. Layers with no usable reference are pruned, not emitted as `null`.
+
+This block is the human-readable "what was used as reference" view; programmatic auditing should use `target_mappings` instead.
+
+### `mapped_scores`
+
+A flat list of per-variant `ScoreAnnotation` records. One entry per `(score_record, emitted annotation_layer)` pair. Key fields:
+
+* `mavedb_id`, `score` — identifier and numeric score copied from the MaveDB record.
+* `relation` — fixed at `"SO:is_homologous_to"` while `pre_mapped` is populated.
+* `target_gene_identifier`, `alignment_level` — composite key linking back to a `target_mappings` row (see below).
+* `pre_mapped`, `post_mapped` — VRS variant objects in the target's coordinate frame and in the reference frame, respectively. Either may be `null` for failed mappings.
+* `vrs_version` — VRS schema version used for this record.
+* `error_message` — populated when `post_mapped` is `null` *or* when mapping succeeded with a caveat (e.g. RLE fallback, ambiguous reference allele).
+* `at_mismatched_locus`, `near_gap` — per-variant audit flags, described below.
+
+### `target_mappings`
+
+Per-`(target, alignment_level)` provenance and alignment QC rows. The MaveDB API consumes these as `target_gene_mappings` and uses them to attribute every `mapped_score` back to the alignment that produced it. (See [`schema.json`](schema.json) `TargetMapping` for the wire format.)
+
+### `error_message`
+
+Populated only when the run failed before producing any scores; otherwise omitted. Per-variant errors live on `mapped_scores[].error_message`, not here.
+
+## Audit and provenance details
+
+### `target_mappings` fields
+
+Each row describes the alignment that one set of mapped variants is grounded in:
+
+| Field | Notes |
+|---|---|
+| `target_gene_identifier`, `alignment_level`, `preferred` | Composite key. `(target_gene_identifier, alignment_level)` is unique per run. Exactly one row per target has `preferred=True`. |
+| `tool_name`, `tool_version`, `tool_parameters` | Aligner provenance. `tool_parameters.aligner` is `"blat"` for sequence-based targets and `"cdot_transcript_placement"` for accession-based targets. |
+| `reference_accession`, `reference_sequence_id`, `vrs_version` | Coordinate-frame and run provenance. |
+| `percent_identity`, `alignment_score`, `next_best_alignment_score`, `alignment_length`, `mismatch_count`, `gap_count` | Aggregate QC for the winning HSP. `alignment_score` is the canonical PSL score (`identities − mismatches − qNumInsert − tNumInsert`). |
+| `alignment_string`, `alignment_metadata` | Pairwise visualization plus a small structured payload (CIGAR, `near_gap_window`, `at_mismatched_locus_evaluated`). |
+| `total_variants`, `variants_mapped_cleanly`, `variants_with_mapping_warnings`, `variants_with_alignment_warnings`, `variants_failed` | Per-row variant counts. `variants_with_alignment_warnings` counts variants whose reference position fell on a mismatched base or near a gap. |
+
+### Per-variant audit flags
+
+Each `ScoreAnnotation` is attributable to exactly one `target_mappings` row via the composite key `(target_gene_identifier, alignment_level)`. The pipeline enforces this as a runtime invariant — orphaned scores raise `RuntimeError` rather than silently corrupting downstream joins.
+
+Per-variant locus flags:
+
+* `at_mismatched_locus` — `True` when any base in the variant's reference span mismatches between the target sequence and the reference; `False` when evaluated and no mismatch was found; `None` when per-base sequence content was unavailable for that layer (see `alignment_metadata.at_mismatched_locus_evaluated`), or when the variant is a `ReferenceLengthExpression` allele (large deletions/duplications, always `None`/`None`).
+* `near_gap` — `True` when the variant lies within `alignment_metadata.near_gap_window` reference bases of any alignment gap; `None` for layers without an alignment (e.g. `cdna`).
+
+Completely-failed variants (`pre_mapped is None` and no annotation layer was determined) are attributed to the target's preferred layer so the join invariant holds.
+
+### Regenerating `schema.json`
+
+`schema.json` is checked in and consumed by downstream services (notably the MaveDB API). After any change to `src/dcd_mapping/schemas.py` that alters the public output contract, regenerate it:
+
+```shell
+python scripts/generate_schema.py
+```
+
+Commit the regenerated `schema.json` in the same change.
+
 ## Notebooks
 
 Notebooks for manuscript data analysis and figure generation are provided within `notebooks/analysis`. See [`notebooks/analysis/README.md`](notebooks/analysis/README.md) for more information.

pyproject.toml

@@ -65,7 +65,7 @@ tests = [
     "respx"
 ]
 dev = [
-    "ruff==0.2.0",
+    "ruff~=0.15.0",
     "pre-commit"
 ]
 
@@ -92,7 +92,7 @@ branch = true
 
 [tool.ruff]
 src = ["src"]
-exclude = ["misc/*"]
+exclude = ["misc/*", "notebooks"]
 
 [tool.ruff.lint]
 select = [
@@ -138,7 +138,6 @@ fixable = [
     "SIM",
     "RUF"
 ]
-# ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
@@ -155,7 +154,7 @@ fixable = [
 # S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
-    "ANN101", "ANN003",
+    "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",
@@ -169,4 +168,4 @@ ignore = [
 # ANN102 - missing-type-cls
 # S101 - assert
 # B011 - assert-false
-"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "D103"]
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "D101", "D102", "D103"]