do not structure schema

(postpone for another commit)
ga4gh-beacon · Jul 31, 2023 · 753d12f · 753d12f
1 parent bad1f13
commit 753d12f
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diff --git a/framework/json/common/filteringTerms.json b/framework/json/common/filteringTerms.json
@@ -1,39 +1,15 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "additionalProperties": true,
     "definitions": {
-        "FilteringTerm": {
-            "title": "Filtering Term Element",
-            "type": "object",
+        "AlphanumericFilter": {
+            "description": "Filter results based on operators and values applied to alphanumeric fields.",
             "properties": {
                 "id": {
-                    "description": "Custom filter terms should contain a unique identifier.",
-                    "examples": [ "demographic.ethnicity:asian" ],
-                    "type": "string"
-                },
-                "scope": {
-                    "description": "The entry type to which the filter applies",
-                    "examples": [ "biosamples" ],
+                    "description": "Field identfier to be queried.",
+                    "example": "ageOfOnset",
                     "type": "string"
-                }
-            },
-            "anyOf": [
-                {
-                    "$ref": "#/definitions/OntologyFilter"
                 },
-                {
-                    "$ref": "#/definitions/AlphanumericFilter"
-                },
-                {
-                    "$ref": "#/definitions/CustomFilter"
-                }
-            ],
-            "required": [
-                "id"
-            ]
-        },
-        "AlphanumericFilter": {
-            "description": "Filter results based on operators and values applied to alphanumeric fields.",
-            "properties": {
                 "operator": {
                     "default": "=",
                     "description": "Defines how the value relates to the field `id`.",
@@ -48,30 +24,74 @@
                     "examples": [ ">" ],
                     "type": "string"
                 },
+                "scope": {
+                    "description": "The entry type to which the filter applies",
+                    "example": "individuals",
+                    "type": "string"
+                },
                 "value": {
                     "description": "Alphanumeric search term to be used within the query which can contain wildcard characters (%) to denote any number of unknown characters.  Values can be assocatied with units if applicable.",
                     "examples": [ "P70Y" ],
                     "type": "string"
                 }
             },
             "required": [
+                "id",
                 "operator",
                 "value"
             ],
             "type": "object"
         },
         "CustomFilter": {
             "description": "Filter results to include records that contain a custom term defined by this Beacon.",
+            "properties": {
+                "id": {
+                    "description": "Custom filter terms should contain a unique identifier.",
+                    "example": "demographic.ethnicity:asian",
+                    "type": "string"
+                },
+                "scope": {
+                    "description": "The entry type to which the filter applies",
+                    "example": "individuals",
+                    "type": "string"
+                }
+            },
+            "required": [
+                "id"
+            ],
             "type": "object"
         },
+        "FilteringTerm": {
+            "anyOf": [
+                {
+                    "$ref": "#/definitions/OntologyFilter"
+                },
+                {
+                    "$ref": "#/definitions/AlphanumericFilter"
+                },
+                {
+                    "$ref": "#/definitions/CustomFilter"
+                }
+            ]
+        },
         "OntologyFilter": {
             "description": "Filter results to include records that contain a specific ontology term.",
             "properties": {
+                "id": {
+                    "description": "Term ID to be queried, using CURIE syntax where possible.",
+                    "example": "HP:0002664",
+                    "type": "string"
+                },
                 "includeDescendantTerms": {
                     "default": true,
                     "description": "Define if the Beacon should implement the ontology hierarchy, thus query the descendant terms of `id`.",
                     "type": "boolean"
                 },
+                "scope": {
+                    "description": "The entry type to which the filter applies",
+                    "examples": [ "biosamples" ],
+                    "type": "string"
+                },
                 "similarity": {
                     "default": "exact",
                     "description": "Allow the Beacon to return results which do not match the filter exactly, but do match to a certain degree of similarity. The Beacon defines the semantic similarity model implemented and how to apply the thresholds of 'high', 'medium' and 'low' similarity.",
@@ -84,13 +104,16 @@
                     "type": "string"
                 }
             },
+            "required": [
+                "id"
+            ],
             "type": "object"
         }
     },
     "description": "Filtering terms are the main means to select subsets of records from a Beacon response. While the name implies the application to a generated response, in practice implementations may apply them at the query stage. Note: In the processing of Beacon v2.0 requests multiple filters are assumed to be chained by the logical AND operator.",
-    "title": "Filtering Term Element",
-    "type": "array",
     "items": {
         "$ref": "#/definitions/FilteringTerm"
-    }
+    },
+    "title": "Filtering Terms Array",
+    "type": "array"
 }
diff --git a/framework/src/common/filteringTerms.yaml b/framework/src/common/filteringTerms.yaml
@@ -11,28 +11,22 @@ items:
   $ref: '#/definitions/FilteringTerm'
 definitions:
   FilteringTerm:
-    properties:
-      id:
-        type: string
-        description: Term ID to be queried, using CURIE syntax where possible.
-        examples: 
-          - HP:0002664
-      scope:
-        type: string
-        description: The entry type to which the filter applies
-        examples:
-          - biosamples
     anyOf:
       - $ref: '#/definitions/OntologyFilter'
       - $ref: '#/definitions/AlphanumericFilter'
       - $ref: '#/definitions/CustomFilter'  
-    required:
-      - id
   OntologyFilter:
     type: object
     description: Filter results to include records that contain a specific ontology
       term.
+    required:
+      - id
     properties:
+      id:
+        type: string
+        description: Term ID to be queried, using CURIE syntax where possible.
+        examples:
+          - HP:0002664
       includeDescendantTerms:
         type: boolean
         default: true
@@ -50,14 +44,25 @@ definitions:
           exactly, but do match to a certain degree of similarity. The Beacon defines
           the semantic similarity model implemented and how to apply the thresholds
           of 'high', 'medium' and 'low' similarity.
+      scope:
+        type: string
+        description: The entry type to which the filter applies
+        examples:
+          - biosamples
   AlphanumericFilter:
     description: Filter results based on operators and values applied to alphanumeric
       fields.
     type: object
     required:
+      - id
       - operator
       - value
     properties:
+      id:
+        type: string
+        description: Field identfier to be queried.
+        examples:
+          - ageOfOnset
       operator:
         type: string
         enum:
@@ -69,14 +74,34 @@ definitions:
           - <=
         description: Defines how the value relates to the field `id`.
         default: '='
-        example: '>'
+        examples:
+          - '>'
       value:
         type: string
-        description: Alphanumeric search term to be used within the query which can
+        description: >-
+          Alphanumeric search term to be used within the query which can
           contain wildcard characters (%) to denote any number of unknown characters.  Values
           can be assocatied with units if applicable.
         example: P70Y
+      scope:
+        type: string
+        description: The entry type to which the filter applies
+        examples:
+          - individuals
   CustomFilter:
     type: object
     description: Filter results to include records that contain a custom term defined
-      by this Beacon.
+      by this Beacon.
+    required:
+      - id
+    properties:
+      id:
+        type: string
+        description: Custom filter terms should contain a unique identifier.
+        example: demographic.ethnicity:asian
+      scope:
+        type: string
+        description: The entry type to which the filter applies
+        examples:
+          - individuals
+additionalProperties: true