missing object type fix

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
 

framework/json/common/beaconCommonComponents.json

@@ -111,15 +111,19 @@
         },
         "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"
                 }
             ]
         },

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.",

framework/src/common/beaconCommonComponents.yaml

@@ -265,11 +265,13 @@ 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

framework/src/responses/sections/beaconResultsets.yaml

@@ -15,6 +15,7 @@ required:
 additionalProperties: true
 definitions:
   ResultsetInstance:
+    type: object
     properties:
       id:
         description: id of the resultset

models/json/beacon-v2-default-model/common/disease.json

@@ -6,30 +6,22 @@
             "$ref": "./timeElement.json",
             "examples": [
                 {
-                    "ageGroup": {
-                        "id": "NCIT:C49685",
-                        "label": "Adult 18-65 Years Old"
-                    }
+                    "id": "NCIT:C49685",
+                    "label": "Adult 18-65 Years Old"
                 },
                 {
-                    "age": {
-                        "iso8601duration": "P32Y6M1D"
-                    }
+                    "iso8601duration": "P32Y6M1D"
                 },
                 {
-                    "ageRange": {
-                        "end": {
-                            "iso8601duration": "P59Y"
-                        },
-                        "start": {
-                            "iso8601duration": "P18Y"
-                        }
+                    "end": {
+                        "iso8601duration": "P59Y"
+                    },
+                    "start": {
+                        "iso8601duration": "P18Y"
                     }
                 },
                 {
-                    "age": {
-                        "iso8601duration": "P2M4D"
-                    }
+                    "iso8601duration": "P2M4D"
                 }
             ]
         },

models/json/beacon-v2-default-model/genomicVariations/requestParameters.json

@@ -17,14 +17,14 @@
                 "$ref": "./requestParametersComponents.json#/definitions/Assembly"
             },
             "end": {
-                "description": "Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see `start` * for bracket queries, provide 2 values (e.g. [111,222]).\"",
+                "description": "Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see `start` * for bracket queries, provide 2 values (e.g. [111,222]).",
                 "items": {
                     "format": "int64",
                     "minimum": 1,
                     "type": "integer"
                 },
                 "maxItems": 2,
-                "minItems": 0,
+                "minItems": 1,
                 "type": "array"
             },
             "geneId": {
@@ -52,7 +52,7 @@
                 "$ref": "./requestParametersComponents.json#/definitions/RefSeqId"
             },
             "start": {
-                "description": "Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * `start` only:\n  - for single positions, e.g. the start of a specified sequence\n    alteration where the size is given through the specified `alternateBases`\n  - typical use are queries for SNV and small InDels\n  - the use of `start` without an `end` parameter requires the use of\n    `alternateBases`\n* `start` and `end`:\n  - for searching any variant falling fully or partially within the range\n    between `start` and `end` (a.k.a. \"range query\")\n  - additional use of `variantType` OR `alternateBases` can limit the\n    scope of the query\n  - by convention, partial overlaps of variants with the indicated genomic\n    range are accepted; for specific overlap requirements the 4-parameter\n    \"Bracket Queries\" should be employed\n* 2 values in both `start` and `end` for constructing a \"Bracket Query\":\n  - can be used to match any contiguous genomic interval, e.g. for querying\n    imprecise positions\n  - identifies all structural variants starting between `start[0]` and `start[1]`,\n    and ending between `end[0]` <-> `end[1]`\n  - single or double sided precise matches can be achieved by setting\n    `start[1]=start[0]+1` and `end[1]=end[0]+1`",
+                "description": "Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * `start` only:\n  - for single positions, e.g. the start of a specified sequence\nalteration where the size is given through the specified `alternateBases`\n  - typical use are queries for SNV and small InDels\n  - the use of `start` without an `end` parameter requires the use of\n`alternateBases`\n* 1 value each in both `start` and `end`:\n  - for searching any variant falling fully or partially within the range\n    between `start` and `end` (a.k.a. \"range query\")\n  - additional use of `variantType` OR `alternateBases` can limit the\n    scope of the query\n  - by convention, partial overlaps of variants with the indicated genomic\n    range are accepted; for specific overlap requirements the 4-parameter\n    \"Bracket Queries\" should be employed\n* 2 values in both `start` and `end` for constructing a \"Bracket Query\":\n  - can be used to match any contiguous genomic interval, e.g. for querying\n    imprecise positions\n  - identifies all structural variants starting between `start[0]` and `start[1]`,\n    and ending between `end[0]` <-> `end[1]`\n  - single or double sided precise matches can be achieved by setting\n    `start[1]=start[0]+1` and `end[1]=end[0]+1`",
                 "items": {
                     "format": "int64",
                     "minimum": 0,
@@ -87,4 +87,4 @@
         },
         "type": "object"
     }
-}
+}

models/src/beacon-v2-default-model/common/disease.yaml

@@ -20,18 +20,14 @@ properties:
   ageOfOnset:
     $ref: ./timeElement.yaml
     examples:
-      - ageGroup:
-          id: NCIT:C49685
-          label: Adult 18-65 Years Old
-      - age:
-          iso8601duration: P32Y6M1D
-      - ageRange:
-          start:
-            iso8601duration: P18Y
-          end:
-            iso8601duration: P59Y
-      - age:
-          iso8601duration: P2M4D
+      - id: NCIT:C49685
+        label: Adult 18-65 Years Old
+      - iso8601duration: P32Y6M1D
+      - start:
+          iso8601duration: P18Y
+        end:
+          iso8601duration: P59Y
+      - iso8601duration: P2M4D
   stage:
     description: 'Ontology term from Ontology for General Medical Science (OGMS),
       e.g. acute onset (OGMS:0000119). Provenance: GA4GH Phenopackets v2 `Disease.disease_stage`'

models/src/beacon-v2-default-model/genomicVariations/requestParameters.yaml

@@ -16,7 +16,7 @@ g_variant:
           - typical use are queries for SNV and small InDels
           - the use of `start` without an `end` parameter requires the use of
             `alternateBases`
-        * `start` and `end`:
+        * 1 value in both `start` and `end`:
           - for searching any variant falling fully or partially within the range
             between `start` and `end` (a.k.a. "range query")
           - additional use of `variantType` OR `alternateBases` can limit the
@@ -48,7 +48,7 @@ g_variant:
         type: integer
         format: int64
         minimum: 1
-      minItems: 0
+      minItems: 1
       maxItems: 2
     referenceBases:
       $ref: ./requestParametersComponents.yaml#/definitions/ReferenceBases