chore(schemas): regenerate JSON schema files

Author: ivan-aksamentov

packages/nextclade-schemas/input-pathogen-json.schema.json

@@ -1,88 +1,149 @@
 $schema: http://json-schema.org/draft-07/schema#
 title: DatasetCollection
+description: A named group of datasets from a single maintainer (e.g. "nextstrain", "community").
 type: object
 required:
 - datasets
 - meta
 properties:
   meta:
-    $ref: '#/definitions/DatasetCollectionMeta'
+    description: 'Collection metadata: identifier, display name, maintainer contact information'
+    allOf:
+    - $ref: '#/definitions/DatasetCollectionMeta'
   datasets:
+    description: Datasets belonging to this collection
     type: array
     items:
       $ref: '#/definitions/Dataset'
 definitions:
   DatasetCollectionMeta:
+    description: 'Metadata describing a dataset collection: identity, branding, and maintainer information.'
     type: object
     required:
     - id
     properties:
       id:
+        description: Unique identifier for this collection (e.g. "nextstrain")
         type: string
       title:
+        description: Human-readable display name (e.g. "Nextstrain")
         type:
         - string
         - 'null'
       description:
+        description: Short description of the collection and its maintainer
         type:
         - string
         - 'null'
       color:
+        description: Brand color for UI display (CSS hex, e.g. "#9067b5")
         type:
         - string
         - 'null'
       icon:
+        description: Path to the collection icon image
         type:
         - string
         - 'null'
       maintainers:
+        description: People or organizations maintaining this collection
         type: array
         items:
           $ref: '#/definitions/DatasetCollectionUrl'
       urls:
+        description: 'Related URLs: source repository, contact page, documentation'
         type: array
         items:
           $ref: '#/definitions/DatasetCollectionUrl'
   DatasetCollectionUrl:
+    description: A named URL entry used for maintainer contacts and related links.
     type: object
     required:
     - name
     - url
     properties:
       name:
+        description: Label describing this URL (e.g. "source", "contact")
         type: string
       url:
+        description: The URL
         type: string
   Dataset:
+    description: A single Nextclade dataset providing reference data and configuration for one pathogen.
+    examples:
+    - $schema: https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/internal-dataset-json.schema.json
+      path: nextstrain/rsv/a/EPI_ISL_412866
+      shortcuts:
+      - rsv_a
+      - nextstrain/rsv/a
+      attributes:
+        name: RSV-A
+        reference name: hRSV/A/England/397/2017
+        reference accession: EPI_ISL_412866
+      files:
+        reference: reference.fasta
+        pathogenJson: pathogen.json
+        genomeAnnotation: genome_annotation.gff3
+        treeJson: tree.json
+        examples: sequences.fasta
+        readme: README.md
+        changelog: CHANGELOG.md
+      versions:
+      - tag: 2026-01-06--14-59-32Z
+        updatedAt: 2026-01-06T14:59:32Z
+        compatibility:
+          cli: 3.0.0
+          web: 3.0.0
+      version:
+        tag: 2026-01-06--14-59-32Z
+        updatedAt: 2026-01-06T14:59:32Z
+        compatibility:
+          cli: 3.0.0
+          web: 3.0.0
     type: object
     required:
     - path
     properties:
       path:
+        description: Unique path-like identifier (e.g. "nextstrain/sars-cov-2/wuhan-hu-1/orfs")
         type: string
       shortcuts:
+        description: Short alias names for this dataset (e.g. "sars-cov-2", "rsv_a")
         type: array
         items:
           type: string
       attributes:
-        $ref: '#/definitions/DatasetAttributes'
+        description: 'Dataset attributes: name, reference info, status flags'
+        allOf:
+        - $ref: '#/definitions/DatasetAttributes'
       meta:
-        $ref: '#/definitions/DatasetMeta'
+        description: 'Dataset-level metadata: source code URL, bug tracker, authors'
+        allOf:
+        - $ref: '#/definitions/DatasetMeta'
       files:
-        $ref: '#/definitions/DatasetFiles'
+        description: Filenames of dataset components (reference, annotation, tree, etc.)
+        allOf:
+        - $ref: '#/definitions/DatasetFiles'
       capabilities:
-        $ref: '#/definitions/DatasetCapabilities'
+        description: 'Advertised analysis capabilities: clade counts, QC rules, primer support'
+        allOf:
+        - $ref: '#/definitions/DatasetCapabilities'
       versions:
+        description: All available tagged releases, ordered newest-first
         type: array
         items:
           $ref: '#/definitions/DatasetVersion'
       version:
-        $ref: '#/definitions/DatasetVersion'
+        description: The latest (default) version of this dataset
+        allOf:
+        - $ref: '#/definitions/DatasetVersion'
       type:
+        description: Whether the dataset is a directory-based dataset or an Auspice JSON
         anyOf:
         - $ref: '#/definitions/DatasetType'
         - type: 'null'
       maintenance:
+        description: Maintainer and support information for this dataset
         anyOf:
         - $ref: '#/definitions/DatasetMaintenance'
         - type: 'null'
@@ -117,131 +178,185 @@ definitions:
         - 'null'
     additionalProperties: true
   DatasetMeta:
+    description: 'Dataset-level metadata: authorship and project links.'
     type: object
     properties:
       source code:
+        description: URL to the dataset source code repository
         type:
         - string
         - 'null'
       bugs:
+        description: URL to the bug tracker or issue page
         type:
         - string
         - 'null'
       authors:
+        description: List of dataset authors or maintainers
         type: array
         items:
           type: string
   DatasetFiles:
+    description: Filenames of dataset components, relative to the dataset version directory.
+    examples:
+    - reference: reference.fasta
+      pathogenJson: pathogen.json
+      genomeAnnotation: genome_annotation.gff3
+      treeJson: tree.json
+      examples: sequences.fasta
+      readme: README.md
+      changelog: CHANGELOG.md
     type: object
     properties:
       reference:
+        description: Reference sequence FASTA file (e.g. "reference.fasta")
         type:
         - string
         - 'null'
       pathogenJson:
+        description: Pathogen configuration file (e.g. "pathogen.json")
         type:
         - string
         - 'null'
       genomeAnnotation:
+        description: Genome annotation in GFF3 format (e.g. "genome_annotation.gff3")
         type:
         - string
         - 'null'
       treeJson:
+        description: Reference phylogenetic tree in Auspice JSON format (e.g. "tree.json")
         type:
         - string
         - 'null'
       examples:
+        description: Example query sequences for testing (e.g. "sequences.fasta")
         type:
         - string
         - 'null'
       readme:
+        description: Dataset README documentation file
         type:
         - string
         - 'null'
       changelog:
+        description: Dataset changelog file
         type:
         - string
         - 'null'
   DatasetCapabilities:
+    description: Analysis features supported by a dataset, used for UI display and filtering.
     type: object
     properties:
       clades:
+        description: Number of distinct clade values defined in the reference tree
         type:
         - integer
         - 'null'
         format: uint
         minimum: 0.0
       customClades:
+        description: 'Additional clade classification systems and their value counts (e.g. "Nextclade_pango": 4731)'
         type: object
         additionalProperties:
           type: integer
           format: uint
           minimum: 0.0
       qc:
+        description: QC rule names enabled for this dataset (e.g. "missingData", "privateMutations")
         type: array
         items:
           type: string
       primers:
+        description: Whether PCR primer mutation detection is available
         type:
         - boolean
         - 'null'
       other:
+        description: Other capabilities not covered above (e.g. "phenotypeData", "mutLabels")
         type: array
         items:
           type: string
   DatasetVersion:
+    description: A tagged release of a dataset, identified by a timestamp tag.
+    examples:
+    - tag: 2026-01-06--14-59-32Z
+      updatedAt: 2026-01-06T14:59:32Z
+      compatibility:
+        cli: 3.0.0
+        web: 3.0.0
     type: object
     required:
     - tag
     properties:
       tag:
+        description: Version identifier in timestamp format (e.g. "2026-01-06--14-59-32Z")
         type: string
       updatedAt:
+        description: ISO 8601 timestamp of when this version was published
         type:
         - string
         - 'null'
       compatibility:
+        description: Minimum CLI/web versions required to use this dataset version
         anyOf:
         - $ref: '#/definitions/DatasetCompatibility'
         - type: 'null'
   DatasetCompatibility:
+    description: Minimum application versions required to use a dataset version.
     type: object
     properties:
       cli:
+        description: Minimum Nextclade CLI semver version (e.g. "3.0.0-alpha.0")
         type: string
       web:
+        description: Minimum Nextclade Web semver version (e.g. "3.0.0-alpha.0")
         type: string
   DatasetType:
-    type: string
-    enum:
-    - directory
-    - auspiceJson
-    - other
+    description: How dataset content is structured.
+    oneOf:
+    - description: Standard dataset with individual files in a directory
+      type: string
+      enum:
+      - directory
+    - description: Single Auspice JSON file used as both tree and dataset
+      type: string
+      enum:
+      - auspiceJson
+    - description: Other dataset format
+      type: string
+      enum:
+      - other
   DatasetMaintenance:
     description: Contact and documentation URLs for dataset maintenance
     type: object
     properties:
       website:
+        description: URLs for the project or organization website.
         type: array
         items:
           type: string
       documentation:
+        description: URLs for dataset documentation and usage guides.
         type: array
         items:
           type: string
       source code:
+        description: URLs for the source code repositories used to build the dataset.
         type: array
         items:
           type: string
       issues:
+        description: URLs for reporting bugs and requesting features related to the dataset.
         type: array
         items:
           type: string
       organizations:
+        description: Names of organizations responsible for maintaining the dataset.
         type: array
         items:
           type: string
       authors:
+        description: Names and contact information of dataset authors.
         type: array
         items:
           type: string