Merge pull request #82 from ga4gh-beacon/schema-urgent-fixes

missing object type fix
ga4gh-beacon · Jul 16, 2024 · de014e8 · de014e8
2 parents ae4214a + 731de0e
commit de014e8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,7 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
  * Fixed `POST`queries for `g_variant` (w/ examples)
- * Removed 'json' references inside the yaml version (PR [#43] (https://github.com/ga4gh-beacon/beacon-v2/pull/43))
+ * Removed 'json' references inside the yaml version (PR [#43](https://github.com/ga4gh-beacon/beacon-v2/pull/43))
+ * added missing `type: object` to `ResultsetInstance` (PR [#82](https://github.com/ga4gh-beacon/beacon-v2/pull/82))
 
 ### Deprecated
 

diff --git a/framework/json/common/beaconCommonComponents.json b/framework/json/common/beaconCommonComponents.json
@@ -76,11 +76,10 @@
         },
         "Granularity": {
             "default": "boolean",
-            "description": "Level of detail of the response:\n* `boolean`: returns true/false' responses * `count`: adds the total number of positive results found * `aggregated`: returns summary, aggregated or distribution like responses * `record`: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:\n    - keeping non-mandatory attributes empty\n    - Beacon to provide a minimal record definition",
+            "description": "Level of detail of the response:\n* `boolean`: returns true/false' responses * `count`: adds the total number of positive results found * `record`: returns details for every row. In cases where a Beacon prefers to return records with fewer than allattributes, different strategies have to be considered w/o adding them to the current design, e.g.:\n    - keeping non-mandatory attributes empty\n    - Beacon to provide a minimal record definition",
             "enum": [
                 "boolean",
                 "count",
-                "aggregated",
                 "record"
             ],
             "type": "string"
@@ -111,15 +110,19 @@
         },
         "HandoverType": {
             "$ref": "./ontologyTerm.json",
-            "description": "Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use `CUSTOM` for the `id` when no ontology is available.",
+            "description": "Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use \"CUSTOM:123455\" CURIE-style `id` when no ontology is available.",
             "examples": [
                 {
-                    "id": "EFO:0004157",
-                    "label": "BAM format"
+                    "id": "EDAM:2572",
+                    "label": "BAM"
                 },
                 {
-                    "id": "CUSTOM",
-                    "label": "download genomic variants in .pgxseg file format"
+                    "id": "EDAM:3016",
+                    "label": "VCF"
+                },
+                {
+                    "id": "CUSTOM:pgxseg",
+                    "label": "genomic variants in .pgxseg file format"
                 }
             ]
         },

diff --git a/framework/json/common/validation/beaconCommonComponents.json b/framework/json/common/validation/beaconCommonComponents.json
diff --git a/framework/json/requests/validation/filteringTerms.json b/framework/json/requests/validation/filteringTerms.json
diff --git a/framework/json/responses/sections/beaconResultsets.json b/framework/json/responses/sections/beaconResultsets.json
@@ -44,7 +44,8 @@
                 "exists",
                 "resultsCount",
                 "results"
-            ]
+            ],
+            "type": "object"
         }
     },
     "description": "Sets of results to be returned as query response.",

diff --git a/framework/src/common/beaconCommonComponents.yaml b/framework/src/common/beaconCommonComponents.yaml
@@ -137,7 +137,6 @@ definitions:
 
       * `boolean`: returns true/false' responses
       * `count`: adds the total number of positive results found
-      * `aggregated`: returns summary, aggregated or distribution like responses
       * `record`: returns details for every row. In cases where a Beacon prefers
       to return records with fewer than allattributes, different strategies have
       to be considered w/o adding them to the current design, e.g.:
@@ -147,7 +146,6 @@ definitions:
     enum:
       - boolean
       - count
-      - aggregated
       - record
     default: boolean
   TestMode:
@@ -265,11 +263,13 @@ definitions:
         example: https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/
   HandoverType:
     description: >-
-      Handover type, as an Ontology_term object with CURIE syntax for the `id` value.
-      Use `CUSTOM` for the `id` when no ontology is available.
+      Handover type, as an Ontology_term object with CURIE syntax for the `id`
+      value. Use "CUSTOM:123455" CURIE-style `id` when no ontology is available.
     $ref: ./ontologyTerm.yaml
     examples:
-      - id: EFO:0004157
-        label: BAM format
-      - id: CUSTOM
-        label: download genomic variants in .pgxseg file format
+      - id: EDAM:2572
+        label: BAM
+      - id: EDAM:3016
+        label: VCF
+      - id: CUSTOM:pgxseg
+        label: genomic variants in .pgxseg file format
diff --git a/framework/src/common/validation/beaconCommonComponents.yaml b/framework/src/common/validation/beaconCommonComponents.yaml
diff --git a/framework/src/requests/validation/filteringTerms.yaml b/framework/src/requests/validation/filteringTerms.yaml
diff --git a/framework/src/responses/sections/beaconResultsets.yaml b/framework/src/responses/sections/beaconResultsets.yaml
@@ -15,6 +15,7 @@ required:
 additionalProperties: true
 definitions:
   ResultsetInstance:
+    type: object
     properties:
       id:
         description: id of the resultset