proper filteringTerms definition for models

The previous filteringTerms.yaml/json endpoint definitions were odd: - either defined as empty lists (well, okish) - or having some random values This PR redefines filteringTerms endpoints as containing a list of https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm items. Should be non-breaking.
ga4gh-beacon · Aug 21, 2024 · f37b3df · f37b3df
1 parent 1686220
commit f37b3df
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diff --git a/bin/beaconYamler.py b/bin/beaconYamler.py
@@ -1,4 +1,4 @@
-#!/usr/local/bin/python3
+#!/usr/bin/env python3
 
 import sys, re, json
 import pathlib

diff --git a/framework/json/responses/sections/beaconFilteringTermsResults.json b/framework/json/responses/sections/beaconFilteringTermsResults.json
@@ -21,24 +21,32 @@
                     ],
                     "type": "string"
                 },
+                "scopes": {
+                    "description": "Entry types affected by this filter.",
+                    "examples": [
+                        [
+                            "individual",
+                            "biosample",
+                            "analysis",
+                            "run",
+                            "genomicVariation"
+                        ],
+                        [
+                            "biosample"
+                        ]
+                    ],
+                    "items": {
+                        "type": "string"
+                    },
+                    "type": "array"
+                },
                 "type": {
                     "description": "Either \"custom\", \"alphanumeric\" or ontology/terminology full name. TODO: An ontology ... with a registered prefix does not need a full name so one may better use CURIE to indicate that the resource can be retrieved from the id. This also will allow to provide an enum here.",
                     "examples": [
                         "Human Phenotype Ontology",
                         "alphanumeric"
                     ],
                     "type": "string"
-                },
-                "scopes": {
-                    "description": "Entry types affected by this filter.",
-                    "examples": [
-                        ["individual", "biosample", "analysis", "run", "genomicVariation"], 
-                        ["biosample"]
-                    ],
-                    "type": "array",
-                    "items": {
-                        "type": "string"
-                    }
                 }
             },
             "required": [
@@ -115,4 +123,4 @@
         }
     },
     "type": "object"
-}
+}
diff --git a/framework/src/responses/sections/beaconFilteringTermsResults.yaml b/framework/src/responses/sections/beaconFilteringTermsResults.yaml
@@ -47,7 +47,7 @@ definitions:
           - 'B Lymphoblastic Leukemia/Lymphoma'
           - 'Aplasia/Hypoplasia of the middle ear'
       scopes:
-        description: >- 
+        description: >-
           Entry types affected by this filter.
         examples: 
           - 

diff --git a/models/json/beacon-v2-default-model/analyses/filteringTerms.json b/models/json/beacon-v2-default-model/analyses/filteringTerms.json
@@ -1,4 +1,7 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "filteringTerms": []
+    "items": {
+        "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm"
+    },
+    "type": "array"
 }
diff --git a/models/json/beacon-v2-default-model/biosamples/filteringTerms.json b/models/json/beacon-v2-default-model/biosamples/filteringTerms.json
@@ -1,4 +1,7 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "filteringTerms": []
+    "items": {
+        "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm"
+    },
+    "type": "array"
 }
diff --git a/models/json/beacon-v2-default-model/cohorts/filteringTerms.json b/models/json/beacon-v2-default-model/cohorts/filteringTerms.json
@@ -1,11 +1,7 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "filteringTerms": [
-        {
-            "ftType": "ontologyTerm",
-            "id": "DUO:0000006",
-            "label": "health or medical or biomedical research",
-            "version": "2021-02-23"
-        }
-    ]
+    "items": {
+        "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm"
+    },
+    "type": "array"
 }
diff --git a/models/json/beacon-v2-default-model/common/age.json b/models/json/beacon-v2-default-model/common/age.json
@@ -3,7 +3,7 @@
     "description": "Age value definition. Provenance: GA4GH Phenopackets v2 `Age`",
     "properties": {
         "iso8601duration": {
-            "description": "Represents age as a ISO8601 duration (e.g., 'P40Y10M05D').",
+            "description": "Represents age as a ISO8601 duration (e.g., P40Y10M05D).",
             "example": "P32Y6M1D",
             "type": "string"
         }
@@ -13,4 +13,4 @@
     ],
     "title": "Age",
     "type": "object"
-}
+}
diff --git a/models/json/beacon-v2-default-model/common/ageRange.json b/models/json/beacon-v2-default-model/common/ageRange.json
@@ -12,8 +12,8 @@
         }
     },
     "required": [
-        "end",
-        "start"
+        "start",
+        "end"
     ],
     "title": "AgeRange",
     "type": "object"

diff --git a/models/json/beacon-v2-default-model/common/complexValue.json b/models/json/beacon-v2-default-model/common/complexValue.json
@@ -40,7 +40,9 @@
             "type": "array"
         }
     },
-    "required": [ "typedQuantities" ],
+    "required": [
+        "typedQuantities"
+    ],
     "title": "Complex Value",
     "type": "object"
 }
diff --git a/models/json/beacon-v2-default-model/datasets/filteringTerms.json b/models/json/beacon-v2-default-model/datasets/filteringTerms.json
@@ -1,11 +1,7 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "filteringTerms": [
-        {
-            "ftType": "ontologyTerm",
-            "id": "DUO:0000006",
-            "label": "health or medical or biomedical research",
-            "version": "2021-02-23"
-        }
-    ]
+    "items": {
+        "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm"
+    },
+    "type": "array"
 }
diff --git a/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json b/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json
@@ -1,13 +1,7 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "filteringTerms": [
-        {
-            "ftType": "alphanumeric",
-            "id": "gene"
-        },
-        {
-            "ftType": "alphanumeric",
-            "id": "aminoacidChanges"
-        }
-    ]
+    "items": {
+        "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm"
+    },
+    "type": "array"
 }
diff --git a/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json b/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json
@@ -17,7 +17,7 @@
                 "$ref": "./requestParametersComponents.json#/definitions/Assembly"
             },
             "end": {
-                "description": "Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see `start` * for bracket queries, provide 2 values (e.g. [111,222]).",
+                "description": "Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see `start` * for bracket queries, provide 2 values (e.g. [111,222]).\"",
                 "items": {
                     "format": "int64",
                     "minimum": 1,
@@ -52,7 +52,7 @@
                 "$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\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`",
+                "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* 1 value 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"
     }
-}
+}
diff --git a/models/json/beacon-v2-default-model/individuals/filteringTerms.json b/models/json/beacon-v2-default-model/individuals/filteringTerms.json
@@ -1,4 +1,7 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "filteringTerms": []
+    "items": {
+        "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm"
+    },
+    "type": "array"
 }
diff --git a/models/json/beacon-v2-default-model/runs/filteringTerms.json b/models/json/beacon-v2-default-model/runs/filteringTerms.json
@@ -1,4 +1,7 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "filteringTerms": []
+    "items": {
+        "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm"
+    },
+    "type": "array"
 }
diff --git a/models/src/beacon-v2-default-model/analyses/filteringTerms.yaml b/models/src/beacon-v2-default-model/analyses/filteringTerms.yaml
@@ -1,2 +1,4 @@
 $schema: https://json-schema.org/draft/2020-12/schema
-filteringTerms: []
+type: array
+items:
+  $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm
diff --git a/models/src/beacon-v2-default-model/biosamples/filteringTerms.yaml b/models/src/beacon-v2-default-model/biosamples/filteringTerms.yaml
@@ -1,2 +1,4 @@
 $schema: https://json-schema.org/draft/2020-12/schema
-filteringTerms: []
+type: array
+items:
+  $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm
diff --git a/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml b/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml
@@ -1,6 +1,4 @@
 $schema: https://json-schema.org/draft/2020-12/schema
-filteringTerms:
-  - ftType: ontologyTerm
-    id: DUO:0000006
-    label: health or medical or biomedical research
-    version: '2021-02-23'
+type: array
+items:
+  $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm
diff --git a/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml b/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml
@@ -1,6 +1,4 @@
 $schema: https://json-schema.org/draft/2020-12/schema
-filteringTerms:
-  - ftType: ontologyTerm
-    id: DUO:0000006
-    label: health or medical or biomedical research
-    version: '2021-02-23'
+type: array
+items:
+  $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm
diff --git a/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml b/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml
@@ -1,6 +1,4 @@
 $schema: https://json-schema.org/draft/2020-12/schema
-filteringTerms:
-  - ftType: alphanumeric
-    id: gene
-  - ftType: alphanumeric
-    id: aminoacidChanges
+type: array
+items:
+  $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm
diff --git a/models/src/beacon-v2-default-model/individuals/filteringTerms.yaml b/models/src/beacon-v2-default-model/individuals/filteringTerms.yaml
@@ -1,2 +1,4 @@
 $schema: https://json-schema.org/draft/2020-12/schema
-filteringTerms: []
+type: array
+items:
+  $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm
diff --git a/models/src/beacon-v2-default-model/runs/filteringTerms.yaml b/models/src/beacon-v2-default-model/runs/filteringTerms.yaml
@@ -1,2 +1,4 @@
 $schema: https://json-schema.org/draft/2020-12/schema
-filteringTerms: []
+type: array
+items:
+  $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/definitions/FilteringTerm