[validate] allow local $refs

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nextstrain · Aug 16, 2023 · ea250de · ea250de
1 parent d6246ca
commit ea250de
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Showing 2 changed files with 23 additions and 40 deletions.
diff --git a/augur/data/schema-export-v2.json b/augur/data/schema-export-v2.json
@@ -51,44 +51,7 @@
                     }
                 },
                 "genome_annotations": {
-                    "description": "Genome annotations (e.g. genes), relative to the reference genome",
-                    "$comment": "Required for the entropy panel",
-                    "type": "object",
-                    "required": ["nuc"],
-                    "additionalProperties": false,
-                    "properties": {
-                        "nuc": {
-                            "type": "object",
-                            "properties": {
-                                "seqid":{
-                                    "description": "Sequence on which the coordinates below are valid. Could be viral segment, bacterial contig, etc",
-                                    "$comment": "currently unused by Auspice",
-                                    "type": "string"
-                                },
-                                "type": {
-                                    "description": "Type of the feature. could be mRNA, CDS, or similar",
-                                    "$comment": "currently unused by Auspice",
-                                    "type": "string"
-                                },
-                                "start": {
-                                    "description": "Gene start position (one-based, following GFF format)",
-                                    "type": "number"
-                                },
-                                "end": {
-                                    "description": "Gene end position (one-based closed, last position of feature, following GFF format)",
-                                    "type": "number"
-                                },
-                                "strand": {
-                                    "description": "Positive or negative strand",
-                                    "type": "string",
-                                    "enum": ["-","+"]
-                                }
-                            }
-                        }
-                    },
-                    "patternProperties": {
-                        "^[a-zA-Z0-9*_-]+$": {"$ref": "#/properties/meta/properties/genome_annotations/properties/nuc"}
-                    }
+                    "$ref": "genome_annotations#"
                 },
                 "filters": {
                     "description": "These appear as filters in the footer of Auspice (which populates the displayed values based upon the tree)",

diff --git a/augur/validate.py b/augur/validate.py
@@ -25,7 +25,7 @@ class ValidateError(Exception):
     pass
 
 
-def load_json_schema(path):
+def load_json_schema(path, refs=None):
     '''
     Load a JSON schema from the augur included set of schemas
     (located in augur/data)
@@ -40,6 +40,12 @@ def load_json_schema(path):
         Validator.check_schema(schema)
     except jsonschema.exceptions.SchemaError as err:
         raise ValidateError(f"Schema {path} is not a valid JSON Schema ({Validator.META_SCHEMA['$schema']}). Error: {err}")
+
+    if refs:
+        # Make the validator aware of additional schemas
+        schema_store = {k: json.loads(resource_string(__package__, os.path.join("data", v))) for k,v in refs.items()}
+        resolver = jsonschema.RefResolver.from_schema(schema,store=schema_store)
+        return Validator(schema, resolver=resolver)
     return Validator(schema)
 
 def load_json(path):
@@ -163,7 +169,21 @@ def auspice_config_v2(config_json, **kwargs):
     validate(config, schema, config_json)
 
 def export_v2(main_json, **kwargs):
-    main_schema = load_json_schema("schema-export-v2.json")
+    # The main_schema uses references to other (local) JSONs so we need to
+    # define the mapping to use here. Because the main_schema uses the $id
+    # "https://nextstrain.org/schemas/dataset/v2" this is combined with the
+    # value we use for $ref to create a URI, and it is this URI we need to
+    # specify here so that the local file is used. If we don't provide this
+    # mapping then we'll attempt to fetch this URI, and nextstrain.org will
+    # return 404 with a JSON response "{'error': 'Not Found'}"... and jsonschema
+    # will treat that as a valid schema and proceed. For development purposes I
+    # suggest you remove the $id from the main schema to avoid remote schema
+    # requests. Perhaps one day we'll parse this straight from the schema
+    # itself.                                               james August 2023
+    refs = {
+        'https://nextstrain.org/schemas/dataset/genome_annotations': "schema-annotations.json"
+    }
+    main_schema = load_json_schema("schema-export-v2.json", refs)
 
     if main_json.endswith("frequencies.json") or main_json.endswith("entropy.json") or main_json.endswith("sequences.json"):
         raise ValidateError("This validation subfunction is for the main `augur export v2` JSON only.")