fix(export): In export schema, allow cds name with nuc prefix, as l…

…ong as not equal to `nuc` (#1434)

* fix(export): In export schema, allow cds name with `nuc` prefix, as long as not equal to `nuc`

Fixes #1433

* chore(CHANGES): Add changelog entry

* fix(export): use correct schema for meta.genome_annotations

Co-authored-by: james hadfield <hadfield.james@gmail.com>

---------

Co-authored-by: james hadfield <hadfield.james@gmail.com>

CHANGES.md

@@ -10,9 +10,12 @@
 ### Bug Fixes
 
 * filter: Updated docs with an example of tiered subsampling. [#1425][] (@victorlin)
+* export: Fixes bug [#1433] introduced in v23.1.0, that causes validation to fail when gene names start with `nuc`, e.g. `nucleocapsid`. [#1434][] (@corneliusroemer)
 
 [#1425]: https://github.com/nextstrain/augur/pull/1425
 [#1429]: https://github.com/nextstrain/augur/pull/1429
+[#1433]: https://github.com/nextstrain/augur/issues/1433
+[#1434]: https://github.com/nextstrain/augur/pull/1434
 [#1436]: https://github.com/nextstrain/augur/pull/1436
 
 ## 24.2.3 (23 February 2024)

augur/data/schema-annotations.json

@@ -24,8 +24,9 @@
         }
     },
     "required": ["nuc"],
+    "additionalProperties": false,
     "patternProperties": {
-        "^(?!nuc)[a-zA-Z0-9*_-]+$": {
+        "^(?!nuc$)[a-zA-Z0-9*_-]+$": {
             "$comment": "Each object here defines a single CDS",
             "type": "object",
             "oneOf": [{ "$ref": "#/$defs/startend" }, { "$ref": "#/$defs/segments" }],

augur/data/schema-export-v2.json

@@ -310,7 +310,7 @@
                                 }
                             },
                             "patternProperties": {
-                                "^(?!nuc)[a-zA-Z0-9*_-]+$": {
+                                "^(?!nuc$)[a-zA-Z0-9*_-]+$": {
                                     "description": "Amino acid mutations for this CDS",
                                     "$comment": "properties must exist in the meta.JSON -> annotation object",
                                     "type": "array",