Madhava/validator

docs/examples/abcg2-rs2231142-pgx.yaml

@@ -1,6 +1,11 @@
 schema: "bioscript:variant"
 version: "1.0"
 variant_id: "ABCG2_rs2231142"
+tags:
+  - "gene:abcg2"
+  - "domain:pgx"
+  - "input:vcf"
+  - "input:cram"
 label: "ABCG2 rs2231142"
 gene: "ABCG2"
 summary: "ABCG2 SNV locus with pharmacogenomic interpretation"
@@ -26,16 +31,6 @@ alleles:
     - "T"
   canonical_alt: "A"
 
-research:
-  tasks:
-    - "Verify canonical dbSNP, ClinVar, and Ensembl annotations"
-    - "Collect PharmGKB and disease-association references for ABCG2"
-  tags:
-    - "abcg2"
-    - "pgx"
-    - "snv"
-    - "rs2231142"
-
 clinical:
   pgx:
     gene: "ABCG2"

docs/panel-schema.md

@@ -0,0 +1,109 @@
+# Panel Schema
+
+Use a panel when you want one manifest that points to a curated set of runnable variant records.
+
+Right now the Rust runner supports variant members directly. Keep the shape simple.
+
+## Schema Identity
+
+```yaml
+schema: "bioscript:panel:1.0"
+version: "1.0"
+```
+
+## Minimal Shape
+
+```yaml
+schema: "bioscript:panel:1.0"
+version: "1.0"
+name: "traits-common"
+label: "Common Traits"
+tags:
+  - "type:trait"
+
+members:
+  - kind: "variant"
+    path: "variants/rs671.yaml"
+    version: "1.0"
+  - kind: "variant"
+    path: "variants/rs713598.yaml"
+    version: "1.0"
+```
+
+## Purpose
+
+A panel is:
+
+- a selection manifest
+- a stable name for a bundle of variants
+- something the Rust `bioscript` command can run directly
+
+It is not:
+
+- a full remote package manager
+- a replacement for richer assay manifests
+
+## Members
+
+Each member must currently be:
+
+```yaml
+- kind: "variant"
+  path: "variants/rs671.yaml"
+  version: "1.0"
+```
+
+Rules:
+
+- `kind` is required
+- exactly one of `path` or `download` is required
+- current runner support is `variant` members only
+- `version` is recommended for local members
+- `sha256` is optional for local members
+
+## Permissions And Downloads
+
+Panels may declare remote downloads up front even if the current runner only executes local members.
+
+```yaml
+permissions:
+  domains:
+    - "https://example.org"
+
+downloads:
+  - id: "remote-rs671"
+    url: "https://example.org/variants/rs671.yaml"
+    sha256: "0123456789abcdef0123456789abcdef0123456789abcdef0123456789abcdef"
+    version: "1.0"
+```
+
+Validation rules:
+
+- `permissions.domains` entries must be origins only
+- every `downloads[*].url` origin must also appear in `permissions.domains`
+- `downloads[*].sha256` must be a 64-character lowercase hex digest
+
+This keeps host approval focused on which remote origins may be contacted.
+
+## Running Panels
+
+Examples:
+
+```bash
+bioscript panel.yaml --input-file sample.txt --output-file output.tsv
+bioscript panel.yaml --input-file sample.txt --filter tag=type:trait
+bioscript panel.yaml --input-file sample.txt --filter name=rs671
+```
+
+Current filter keys:
+
+- `kind`
+- `name`
+- `path`
+- `tag`
+
+## Future Relationship To Catalogues And Assays
+
+- `panel` is the small runnable collection manifest
+- `catalogue` can later become a larger published index over many panels and items
+- `assay` can later become the richer multi-file runnable bundle with declared assets and overrides

docs/panel-schema.yaml

@@ -0,0 +1,14 @@
+schema: "bioscript:panel:1.0"
+version: "1.0"
+name: "traits-common"
+label: "Common Traits"
+tags:
+  - "type:trait"
+
+members:
+  - kind: "variant"
+    path: "variants/rs671.yaml"
+    version: "1.0"
+  - kind: "variant"
+    path: "variants/rs713598.yaml"
+    version: "1.0"