diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4612940bc..23e896033 100644
--- 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/README.md b/README.md
index e54f57934..0868929e1 100644
--- a/README.md
+++ b/README.md
@@ -28,7 +28,40 @@ As with other schema projects, here we separate between the schema source files
There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, after editing `...yaml` schema files somewhere in the `/src` tree, a (local) run of `bin/yamlerRunner.sh` - which re-generates the `....json` files in the `/json` tree) has to be performed before pushing changes.
-### Changes
+### Changelog
+
+## 2.1.1
+
+*Released, October, 8, 2024*
+[Beacon-v2.1.1](https://github.com/ga4gh-beacon/beacon-v2/tree/5ea17fbd0d2ba533aa1e85f7271f9a2cc9be6794)
+
+* Changed uri for uri-template in Endpoint.singleEntryUrl
+
+
+## 2.1.0
+
+*Released, July, 19, 2024*
+[Beacon-v2.1.0](https://github.com/ga4gh-beacon/beacon-v2/tree/16862205c79294fae5473f7fa330bf5929b3b120)
+
+* Relocated TypedQuantity required to proper level of the schema for complexValue
+* Added end and start entities for ageRange and iso8601duration for age
+* Filtering terms scopes changed from string to array of strings
+
+## 2.0.1
+
+*Released July, 16, 2024*
+[Beacon-v2.0.1](https://github.com/ga4gh-beacon/beacon-v2/tree/f6f85c445922831bd398552384593206c86287de)
+
+* Replaced ENSGLOSSARY for SO ontology family in documentation examples
+* Moved CURIE to beaconCommonComponents
+* Created filtering terms entity
+* Removed validation directories
+* Several fixes to entity types, typos and other non-breaking changes
+
+## 2.0.0
+
+*Released June, 21, 2022*
+[Beacon-v2.0.0](https://github.com/ga4gh-beacon/beacon-v2/tree/d07ef1626321f7428374a4f68d864dfa5e98370f)
* change notes with respect to the repository & documentation are now in [docs.genomebeacons.org](https://docs.genomebeacons.org/changes-todo/)
* NOTE: on 2022-06-20 the previous development repositories have been archived:
diff --git a/bin/beaconYamler.py b/bin/beaconYamler.py
index 022ea5fc2..e0d05d78e 100755
--- 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/bin/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl
index 96e59c17f..1285de4de 100755
--- a/bin/beacon_yaml2md.pl
+++ b/bin/beacon_yaml2md.pl
@@ -729,9 +729,9 @@ sub add_properties_vrs {
my ( $property, $data ) = @_;
my %url = (
'SequenceExpression' =>
-'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/',
+'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/',
'CopyNumber' =>
-'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/'
+'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/'
);
if ( exists $url{$property} ) {
$data->{properties} =
diff --git a/bin/deref_schemas/biosamples/defaultSchema.yaml b/bin/deref_schemas/biosamples/defaultSchema.yaml
index 79c3e36de..02f5b5571 100644
--- a/bin/deref_schemas/biosamples/defaultSchema.yaml
+++ b/bin/deref_schemas/biosamples/defaultSchema.yaml
@@ -260,7 +260,7 @@ properties:
title: Value
type: object
- $schema: https://json-schema.org/draft/2020-12/schema
- definitions:
+ $defs:
TypedQuantity:
properties:
quantity:
@@ -1064,7 +1064,7 @@ properties:
description: List of phenotypic abnormalities of the sample. RECOMMENDED.
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or biosample.
properties:
evidence:
diff --git a/bin/deref_schemas/cohorts/defaultSchema.yaml b/bin/deref_schemas/cohorts/defaultSchema.yaml
index 9290fc70a..6baeed72a 100644
--- a/bin/deref_schemas/cohorts/defaultSchema.yaml
+++ b/bin/deref_schemas/cohorts/defaultSchema.yaml
@@ -2,7 +2,7 @@
$comment: 'version: ga4gh-beacon-cohort-v2.0.0'
$schema: https://json-schema.org/draft/2020-12/schema
additionalProperties: &1 !!perl/scalar:JSON::PP::Boolean 1
-definitions:
+$defs:
CohortCriteria:
description: Criteria used for defining the cohort. It is assumed that all cohort participants will match or NOT match such criteria.
properties:
@@ -366,7 +366,7 @@ definitions:
description: Phenotypic condition(s) in cohort inclusion criteria
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or biosample.
properties:
evidence:
@@ -1660,7 +1660,7 @@ properties:
description: Phenotypic condition(s) in cohort inclusion criteria
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or biosample.
properties:
evidence:
@@ -2406,7 +2406,7 @@ properties:
description: Phenotypic condition(s) in cohort inclusion criteria
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or biosample.
properties:
evidence:
diff --git a/bin/deref_schemas/datasets/defaultSchema.yaml b/bin/deref_schemas/datasets/defaultSchema.yaml
index 434a04245..237fb9e92 100644
--- a/bin/deref_schemas/datasets/defaultSchema.yaml
+++ b/bin/deref_schemas/datasets/defaultSchema.yaml
@@ -13,7 +13,7 @@ properties:
dataUseConditions:
$schema: https://json-schema.org/draft/2020-12/schema
additionalProperties: 1
- definitions:
+ $defs:
DUODataUse:
allOf:
- description: 'Data Use Ontology codes and additional information associated with a data object (e.g. sample, dataset).'
diff --git a/bin/deref_schemas/genomicVariations/defaultSchema.yaml b/bin/deref_schemas/genomicVariations/defaultSchema.yaml
index 2894f3ca3..4705bbe43 100644
--- a/bin/deref_schemas/genomicVariations/defaultSchema.yaml
+++ b/bin/deref_schemas/genomicVariations/defaultSchema.yaml
@@ -2,7 +2,7 @@
$comment: 'version: ga4gh-beacon-variant-v2.0.0'
$schema: https://json-schema.org/draft/2020-12/schema
additionalProperties: &1 !!perl/scalar:JSON::PP::Boolean 1
-definitions:
+$defs:
CaseLevelVariant:
description: ''
properties:
diff --git a/bin/deref_schemas/individuals/defaultSchema.yaml b/bin/deref_schemas/individuals/defaultSchema.yaml
index 3a9eaa481..6eaa3028a 100644
--- a/bin/deref_schemas/individuals/defaultSchema.yaml
+++ b/bin/deref_schemas/individuals/defaultSchema.yaml
@@ -739,7 +739,7 @@ properties:
title: Value
type: object
- $schema: https://json-schema.org/draft/2020-12/schema
- definitions:
+ $defs:
TypedQuantity:
properties:
quantity:
@@ -1299,7 +1299,7 @@ properties:
items:
$schema: https://json-schema.org/draft/2020-12/schema
additionalProperties: 1
- definitions:
+ $defs:
pedigreeMember:
examples:
- membersInProband:
@@ -1696,7 +1696,7 @@ properties:
phenotypicFeatures:
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or biosample.
properties:
evidence:
diff --git a/bin/deref_schemas/obj/Complex Value.yaml b/bin/deref_schemas/obj/Complex Value.yaml
index de5657e33..98d47cc3a 100644
--- a/bin/deref_schemas/obj/Complex Value.yaml
+++ b/bin/deref_schemas/obj/Complex Value.yaml
@@ -1,7 +1,7 @@
---
Complex Value:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions:
+ $defs:
TypedQuantity:
properties:
quantity:
diff --git a/bin/deref_schemas/obj/CopyNumber.yaml b/bin/deref_schemas/obj/CopyNumber.yaml
index 0ac7b7d77..ec96fa12b 100644
--- a/bin/deref_schemas/obj/CopyNumber.yaml
+++ b/bin/deref_schemas/obj/CopyNumber.yaml
@@ -1,4 +1,4 @@
---
CopyNumber:
- properties: '[VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber)'
+ properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber)'
type: allOf
diff --git a/bin/deref_schemas/obj/dataUseConditions.yaml b/bin/deref_schemas/obj/dataUseConditions.yaml
index 111618b4c..90a3154d8 100644
--- a/bin/deref_schemas/obj/dataUseConditions.yaml
+++ b/bin/deref_schemas/obj/dataUseConditions.yaml
@@ -2,7 +2,7 @@
dataUseConditions:
$schema: https://json-schema.org/draft/2020-12/schema
additionalProperties: 1
- definitions:
+ $defs:
DUODataUse:
allOf:
- description: Data Use Ontology codes and additional information associated
diff --git a/bin/deref_schemas/obj/exclusionCriteria.yaml b/bin/deref_schemas/obj/exclusionCriteria.yaml
index 15cfa272c..36cd4cf00 100644
--- a/bin/deref_schemas/obj/exclusionCriteria.yaml
+++ b/bin/deref_schemas/obj/exclusionCriteria.yaml
@@ -413,7 +413,7 @@ exclusionCriteria:
description: Phenotypic condition(s) in cohort inclusion criteria
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or
biosample.
properties:
diff --git a/bin/deref_schemas/obj/inclusionCriteria.yaml b/bin/deref_schemas/obj/inclusionCriteria.yaml
index 25521d4c3..65c5db613 100644
--- a/bin/deref_schemas/obj/inclusionCriteria.yaml
+++ b/bin/deref_schemas/obj/inclusionCriteria.yaml
@@ -413,7 +413,7 @@ inclusionCriteria:
description: Phenotypic condition(s) in cohort inclusion criteria
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or
biosample.
properties:
diff --git a/bin/deref_schemas/obj/measurementValue.yaml b/bin/deref_schemas/obj/measurementValue.yaml
index 97cc689fe..98cc0ed0e 100644
--- a/bin/deref_schemas/obj/measurementValue.yaml
+++ b/bin/deref_schemas/obj/measurementValue.yaml
@@ -3,7 +3,7 @@ measurementValue:
properties:
Complex Value:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions:
+ $defs:
TypedQuantity:
properties:
quantity:
diff --git a/bin/deref_schemas/obj/measurements.yaml b/bin/deref_schemas/obj/measurements.yaml
index eafeb9ca9..e2d027a48 100644
--- a/bin/deref_schemas/obj/measurements.yaml
+++ b/bin/deref_schemas/obj/measurements.yaml
@@ -168,7 +168,7 @@ measurements:
title: Value
type: object
- $schema: https://json-schema.org/draft/2020-12/schema
- definitions:
+ $defs:
TypedQuantity:
properties:
quantity:
diff --git a/bin/deref_schemas/obj/measures.yaml b/bin/deref_schemas/obj/measures.yaml
index 907476373..13657c498 100644
--- a/bin/deref_schemas/obj/measures.yaml
+++ b/bin/deref_schemas/obj/measures.yaml
@@ -166,7 +166,7 @@ measures:
title: Value
type: object
- $schema: https://json-schema.org/draft/2020-12/schema
- definitions:
+ $defs:
TypedQuantity:
properties:
quantity:
diff --git a/bin/deref_schemas/obj/pedigrees.yaml b/bin/deref_schemas/obj/pedigrees.yaml
index a6212e677..959351274 100644
--- a/bin/deref_schemas/obj/pedigrees.yaml
+++ b/bin/deref_schemas/obj/pedigrees.yaml
@@ -3,7 +3,7 @@ pedigrees:
items:
$schema: https://json-schema.org/draft/2020-12/schema
additionalProperties: 1
- definitions:
+ $defs:
pedigreeMember:
examples:
- membersInProband:
diff --git a/bin/deref_schemas/obj/phenotypicConditions.yaml b/bin/deref_schemas/obj/phenotypicConditions.yaml
index 235f70bd7..609b02201 100644
--- a/bin/deref_schemas/obj/phenotypicConditions.yaml
+++ b/bin/deref_schemas/obj/phenotypicConditions.yaml
@@ -3,7 +3,7 @@ phenotypicConditions:
description: Phenotypic condition(s) in cohort inclusion criteria
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or biosample.
properties:
evidence:
diff --git a/bin/deref_schemas/obj/phenotypicFeatures.yaml b/bin/deref_schemas/obj/phenotypicFeatures.yaml
index 4a8323a07..d41141008 100644
--- a/bin/deref_schemas/obj/phenotypicFeatures.yaml
+++ b/bin/deref_schemas/obj/phenotypicFeatures.yaml
@@ -2,7 +2,7 @@
phenotypicFeatures:
items:
$schema: https://json-schema.org/draft/2020-12/schema
- definitions: {}
+ $defs: {}
description: Used to describe a phenotype that characterizes the subject or biosample.
properties:
evidence:
diff --git a/bin/yamlerRunner.sh b/bin/yamlerRunner.sh
index a7821edfa..f6c16395b 100755
--- a/bin/yamlerRunner.sh
+++ b/bin/yamlerRunner.sh
@@ -1,28 +1,13 @@
BASEDIR=$(dirname $0)
UNITYPATH=$BASEDIR/..
-
-# initial conversion from separate schemas
-# DEPRECATED
-# BEACONMODELPATH=$BASEDIR/../../beacon-v2-Models/BEACON-V2-Model
-# BEACONFRAMEWORKPATH=$BASEDIR/../../beacon-framework-v2
-
BEACONMODELNAME=beacon-v2-default-model
-# for UPSTREAM in $BEACONMODELPATH $BEACONFRAMEWORKPATH
-# do
-# echo "pulling $UPSTREAM"
-# git -C $UPSTREAM pull
-# done
-
for KIND in src json
do
mkdir -p $UNITYPATH/models/$KIND/$BEACONMODELNAME
mkdir -p $UNITYPATH/framework/$KIND
done
-# $BASEDIR/beaconYamler.py -i $BEACONMODELPATH -t json -x yaml -o $UNITYPATH/models/src/$BEACONMODELNAME
-# $BASEDIR/beaconYamler.py -i $BEACONFRAMEWORKPATH -t json -x yaml -o $UNITYPATH/framework/src
-
# recurring conversion from the source files to the exported versions
$BASEDIR/beaconYamler.py -i $UNITYPATH/models/src/$BEACONMODELNAME -t yaml -x json -o $UNITYPATH/models/json/$BEACONMODELNAME
$BASEDIR/beaconYamler.py -i $UNITYPATH/framework/src -t yaml -x json -o $UNITYPATH/framework/json
diff --git a/docs/schemas-md/obj/CopyNumber.md b/docs/schemas-md/obj/CopyNumber.md
index f4738d0fb..e55d7cca3 100644
--- a/docs/schemas-md/obj/CopyNumber.md
+++ b/docs/schemas-md/obj/CopyNumber.md
@@ -1,3 +1,3 @@
|Term | Description | Type | Properties | Example | Enum|
| ---| ---| ---| ---| ---| --- |
-| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber) | NA | NA|
+| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber) | NA | NA|
diff --git a/docs/variant-queries.md b/docs/variant-queries.md
index 698ccc016..9ffc7e393 100644
--- a/docs/variant-queries.md
+++ b/docs/variant-queries.md
@@ -374,18 +374,19 @@ values to underlying genomic variations had not been precisely defined.
This table is maintained in parallel with the [hCNV community documentation](https://cnvar.org/resources/CNV-annotation-standards/#cnv-term-use-comparison-in-computational-fileschema-formats).
-| [EFO](https://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO | GA4GH [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) ⇒
[VRS proposal](https://github.com/ga4gh/vrs/issues/404)[^1] | Notes |
+| [EFO](http://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO | GA4GH [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html#copynumberchange)[^1] | Notes |
| ------------------------------------------- | ------------------------------------------------------------------------------ | -------------------------------------------- | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | ----- |
-| [`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070) copy number gain | `DUP`[^2] or
[`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070) | `DUP`
`SVCLAIM=D`[^3] | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`low-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) (implicit) ⇒ [`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070) copy number gain | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
-| [`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or
[`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071) | `DUP`
`SVCLAIM=D`[^3] | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`low-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) ⇒ [`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain | |
-| [`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or
[`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072) | `DUP`
`SVCLAIM=D`[^3] | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`high-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) ⇒ [`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
-| [`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | `DUP`[^2] or
[`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073) | `DUP`
`SVCLAIM=D`[^3] | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`high-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) ⇒ [`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
-| [`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | `DEL`[^2] or
[`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) (implicit) ⇒ [`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
-| [`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or
[`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) ⇒ [`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | |
-| [`EFO:0020073`](https://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or
[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) ⇒ [`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941) high-level copy number loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
-| [`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or
[`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`complete loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) ⇒ [`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |
-
-##### Last updated 2023-03-22 by @mbaudis (EFO:0020073)
+| [`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070) copy number gain | `DUP`[^2] or
[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070) | `DUP`
`SVCLAIM=D`[^3] | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070) gain | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
+| [`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or
[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071) | `DUP`
`SVCLAIM=D`[^3] | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071) low-level gain | |
+| [`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or
[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072) | `DUP`
`SVCLAIM=D`[^3] | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072) high-level gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
+| [`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | `DUP`[^2] or
[`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073) | `DUP`
`SVCLAIM=D`[^3] | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072) high-level gain[^4] | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
+| [`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | `DEL`[^2] or
[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067) loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
+| [`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or
[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level loss | |
+| [`EFO:0020073`](http://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or
[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941) high-level loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
+| [`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or
[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) | `DEL`
`SVCLAIM=D`[^3] | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) complete genomic loss | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |
+
+
+##### Last updated 2023-07-13 to align with 2023-03-22 hCNV documentation (VRS 1.3 adjustment) by @mbaudis
##### updated 2023-03-20 by @mbaudis (VRS proposal)
## Query Parameter Change Log
@@ -417,17 +418,17 @@ recommended for query forms
and `alternateBases`
-[^1]: The VRS annotations refer to the status at v1.2 (2022). The GA4GH VRS team
-is currently (Spring 2023) preparing an updated specification which will introduce
-the new class `CopyNumberChange` ([discussion...](https://github.com/ga4gh/vrs/issues/404#issuecomment-1472599849)) with the use of the EFO terms (including a new term
-for `high level deletion (EFO:0020073)` in the April 2023 EFO release).
+[^1]: The VRS annotations refer to the status from v1.3 (2022) when
+the new class `CopyNumberChange` ([discussion...](https://github.com/ga4gh/vrs/issues/404#issuecomment-1472599849))
+with the use of the EFO terms.
[^2]: While the use of VCF derived (`DUP`, `DEL`) values had been introduced with
beacon v1, usage of these terms has always been a _recommendation_ rather than an integral part
of the API. We now encourage the support of more specific terms (particularly EFO)
-by Beacon developers. As example, the Progentix Beacon API [uses EFO terms](https://progenetix.org/search/) but
+by Beacon developers. As example, the Progentix Beacon API [uses EFO terms](http://progenetix.org/search/) but
provides an internal term expansion for legacy `DUP`, `DEL` support.
[^3]: VCFv4.4 introduces an `SVCLAIM` field to disambiguate between _in situ_ events (such as
tandem duplications; known _adjacency_/ _break junction_: `SVCLAIM=J`) and events where e.g. only the
change in _abundance_ / _read depth_ (`SVCLAIM=D`) has been determined. Both **J** and **D** flags can be combined.
+[^4]: VRS did not adopt the "amplification" term due to possible inconsistencies
diff --git a/framework/json/common/beaconCommonComponents.json b/framework/json/common/beaconCommonComponents.json
index 728c35267..8c73c1074 100644
--- a/framework/json/common/beaconCommonComponents.json
+++ b/framework/json/common/beaconCommonComponents.json
@@ -1,6 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "definitions": {
+ "$defs": {
"$schema": {
"$comment": "TO REVIEW: adding a `format` or `regex` attribute that validates correctly against a file path (relative).",
"description": "Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.",
@@ -76,11 +75,10 @@
},
"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"
@@ -89,7 +87,7 @@
"description": "A handover is a typed link for attaching actionable links to results, non purely informational, requests. The goal of the handovers is to list the different actions available, e.g.:\n* a link to a request access page * linking to a file for download, e.g. a VCF file\nAnother common scenario is to provide a fast summary response (e.g. BeconCountResponse) and to provide access to different endpoints for the entities matched by the query using temporary access tokens in the handover URLs.",
"properties": {
"handoverType": {
- "$ref": "#/definitions/HandoverType"
+ "$ref": "#/$defs/HandoverType"
},
"note": {
"description": "An optional text including considerations on the handover link provided.",
@@ -111,15 +109,19 @@
},
"HandoverType": {
"$ref": "./ontologyTerm.json",
- "description": "Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use `CUSTOM` for the `id` when no ontology is available.",
+ "description": "Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use \"CUSTOM:123455\" CURIE-style `id` when no ontology is available.",
"examples": [
{
- "id": "EFO:0004157",
- "label": "BAM format"
+ "id": "EDAM:2572",
+ "label": "BAM"
+ },
+ {
+ "id": "EDAM:3016",
+ "label": "VCF"
},
{
- "id": "CUSTOM",
- "label": "download genomic variants in .pgxseg file format"
+ "id": "CUSTOM:pgxseg",
+ "label": "genomic variants in .pgxseg file format"
}
]
},
@@ -140,10 +142,6 @@
],
"type": "string"
},
- "Info": {
- "description": "Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.",
- "type": "object"
- },
"Limit": {
"default": 10,
"description": "Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.",
@@ -154,7 +152,7 @@
"ListOfHandovers": {
"description": "Set of handovers to be added in one section the response.",
"items": {
- "$ref": "#/definitions/Handover",
+ "$ref": "#/$defs/Handover",
"description": "Requested schema to be used for individuals in the response."
},
"type": "array"
@@ -162,7 +160,7 @@
"ListOfSchemas": {
"description": "Set of schemas to be used in the response to a request.",
"items": {
- "$ref": "#/definitions/SchemasPerEntity"
+ "$ref": "#/$defs/SchemasPerEntity"
},
"type": "array"
},
@@ -188,22 +186,22 @@
"description": "Pagination to apply or that has been applied on the results.",
"properties": {
"currentPage": {
- "$ref": "#/definitions/PageToken",
+ "$ref": "#/$defs/PageToken",
"description": "Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested."
},
"limit": {
- "$ref": "#/definitions/Limit"
+ "$ref": "#/$defs/Limit"
},
"nextPage": {
- "$ref": "#/definitions/PageToken",
+ "$ref": "#/$defs/PageToken",
"description": "Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available"
},
"previousPage": {
- "$ref": "#/definitions/PageToken",
+ "$ref": "#/$defs/PageToken",
"description": "Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one."
},
"skip": {
- "$ref": "#/definitions/Skip"
+ "$ref": "#/$defs/Skip"
}
},
"type": "object"
@@ -240,6 +238,7 @@
"type": "boolean"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Definition of relatively simple components used in different points of the Beacon specification, both in requests and responses, therefore not associated exclusively with one or the other. Separate schema documents are provided for complex components.",
"title": "Beacon Common Components",
"type": "object"
diff --git a/framework/json/common/info.json b/framework/json/common/info.json
new file mode 100644
index 000000000..69826f5ed
--- /dev/null
+++ b/framework/json/common/info.json
@@ -0,0 +1,6 @@
+{
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "description": "Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.",
+ "title": "Info",
+ "type": "object"
+}
\ No newline at end of file
diff --git a/framework/json/common/ontologyTerm.json b/framework/json/common/ontologyTerm.json
index 6d092cf08..0a351caa0 100644
--- a/framework/json/common/ontologyTerm.json
+++ b/framework/json/common/ontologyTerm.json
@@ -4,7 +4,7 @@
"description": "Definition of an ontology term.",
"properties": {
"id": {
- "$ref": "./beaconCommonComponents.json#/definitions/CURIE"
+ "$ref": "./beaconCommonComponents.json#/$defs/CURIE"
},
"label": {
"description": "The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.",
diff --git a/framework/json/common/validation/beaconCommonComponents.json b/framework/json/common/validation/beaconCommonComponents.json
deleted file mode 100644
index 99bb55603..000000000
--- a/framework/json/common/validation/beaconCommonComponents.json
+++ /dev/null
@@ -1,54 +0,0 @@
-{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": false,
- "properties": {
- "$schema": {
- "description": "Added here to allow the example to comply with the 'additionalProperties:true' restriction.",
- "type": "string"
- },
- "apiVersion": {
- "$ref": "../beaconCommonComponents.json#/definitions/ApiVersion"
- },
- "beaconError": {
- "$ref": "../beaconCommonComponents.json#/definitions/BeaconError"
- },
- "beaconId": {
- "$ref": "../beaconCommonComponents.json#/definitions/BeaconId"
- },
- "exists": {
- "$ref": "../beaconCommonComponents.json#/definitions/Exists"
- },
- "filters": {
- "$ref": "../beaconCommonComponents.json#/definitions/Filters"
- },
- "handover": {
- "$ref": "../beaconCommonComponents.json#/definitions/Handover"
- },
- "handoverType": {
- "$ref": "../beaconCommonComponents.json#/definitions/HandoverType"
- },
- "includeResultsetResponses": {
- "$ref": "../beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
- },
- "info": {
- "$ref": "../beaconCommonComponents.json#/definitions/Info"
- },
- "listOfHandovers": {
- "$ref": "../beaconCommonComponents.json#/definitions/ListOfHandovers"
- },
- "listOfSchemas": {
- "$ref": "../beaconCommonComponents.json#/definitions/ListOfSchemas"
- },
- "numTotalResults": {
- "$ref": "../beaconCommonComponents.json#/definitions/NumTotalResults"
- },
- "pagination": {
- "$ref": "../beaconCommonComponents.json#/definitions/Pagination"
- },
- "schemasPerEntity": {
- "$ref": "../beaconCommonComponents.json#/definitions/SchemasPerEntity"
- }
- },
- "title": "Schema for validating Beacon Common Components examples",
- "type": "object"
-}
\ No newline at end of file
diff --git a/framework/json/configuration/beaconConfigurationSchema.json b/framework/json/configuration/beaconConfigurationSchema.json
index 02d54a3a0..20c2e0556 100644
--- a/framework/json/configuration/beaconConfigurationSchema.json
+++ b/framework/json/configuration/beaconConfigurationSchema.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"EntryTypes": {
"additionalProperties": {
"$ref": "./entryTypeDefinition.json",
@@ -12,19 +10,21 @@
"type": "object"
}
},
- "description": "Files complaint with this schema are the configuration ones. The details returned in `service-info` are mirroring the ones in this configuration file.",
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
+ "description": "The Beacon configuration reports several attributes of the beacon instance related to security, maturity and available entry types. Where appropriate the details returned in `service-info` should mirror the ones in this configuration.",
"properties": {
"$schema": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
+ "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
},
"entryTypes": {
- "$ref": "#/definitions/EntryTypes"
+ "$ref": "#/$defs/EntryTypes"
},
"maturityAttributes": {
"description": "Declares the level of maturity of the Beacon instance.",
"properties": {
"productionStatus": {
- "description": "`DEV`= 'Service potentially unstable, not real data', which availability and data should not be used in production setups. `TEST`= 'Service stable, not real data'. 'PROD'= 'Service stable, actual data'.",
+ "description": "* `DEV`: Service potentially unstable, _i.e._ potentially not real data,\n inconsistent availability; data should not be used in production setups \n* `TEST`: Service is stable but data should be considered synthetic * `PROD`: Service stable with real world data ",
"enum": [
"DEV",
"TEST",
@@ -39,7 +39,7 @@
"description": "Configuration of the security aspects of the Beacon. By default, a Beacon that does not declare the configuration settings would return `boolean` (true/false) responses, and only if the user is authenticated and explicitly authorized to access the Beacon resources. Although this is the safest set of settings, it is not recommended unless the Beacon shares very sensitive information. Non sensitive Beacons should preferably opt for a `record` and `PUBLIC` combination.",
"properties": {
"defaultGranularity": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/Granularity",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/Granularity",
"description": "Default granularity. Some responses could return higher detail, but this would be the granularity by default."
},
"securityLevels": {
diff --git a/framework/json/configuration/beaconMapSchema.json b/framework/json/configuration/beaconMapSchema.json
index b5335e28b..d4d97ab2e 100644
--- a/framework/json/configuration/beaconMapSchema.json
+++ b/framework/json/configuration/beaconMapSchema.json
@@ -1,12 +1,10 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"Endpoint": {
"properties": {
"endpoints": {
"additionalProperties": {
- "$ref": "#/definitions/RelatedEndpoint"
+ "$ref": "#/$defs/RelatedEndpoint"
},
"description": "Optional. A list describing additional endpoints implemented by this Beacon instance for that entry type. Additional details on the endpoint parameters, supported HTTP verbs, etc. could be obtained by parsing the OpenAPI definition referenced in the `openAPIEndpointsDefinition` attribute.",
"minProperties": 0,
@@ -18,7 +16,7 @@
},
"filteringTermsUrl": {
"description": "Optional. Returns the list of filtering terms that could be applied to this entry type. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that endpoint. Also, in very simple Beacons, that endpoint could be the one of the few implemented, together with \u00b4rootUrl` and \u00b4singleEntryUrl`, in which case the whole map of endpoints is found in the current Map.",
- "format": "uri",
+ "format": "uri-template",
"type": "string"
},
"openAPIEndpointsDefinition": {
@@ -32,7 +30,7 @@
},
"singleEntryUrl": {
"description": "Optional, but recommended. Returns only one instance of this entry, identified by an `id`. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that base endpoint. Also, in very simple Beacons, that endpoint could be the only one implemented, together with \u00b4rootUrl`, in which case the whole map of endpoints is found in the current Map.",
- "format": "uri",
+ "format": "uri-template",
"type": "string"
}
},
@@ -50,7 +48,7 @@
},
"url": {
"description": "Endpoint URL",
- "format": "uri",
+ "format": "uri-template",
"type": "string"
}
},
@@ -61,14 +59,16 @@
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Map of a Beacon, its entry types and endpoints. It isconceptually similar to a website sitemap.",
"properties": {
"$schema": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
+ "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
},
"endpointSets": {
"additionalProperties": {
- "$ref": "#/definitions/Endpoint"
+ "$ref": "#/$defs/Endpoint"
},
"description": "List of enpoints included in this Beacon instance. This is list is meant to inform Beacon clients, e.g. a Beacon Network, about the available endpoints, it is not used to generate any automatic list, but could be used for Beacon validation purposes.",
"minProperties": 1,
diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json
index af25f70b1..03579a683 100644
--- a/framework/json/configuration/entryTypeDefinition.json
+++ b/framework/json/configuration/entryTypeDefinition.json
@@ -1,11 +1,10 @@
{
- "$comment": "TO DO: The tagged parts should reference to `common/ontologizedElement.json`. But that configuration fails to validate. Further investigation is required, but should not affect the resulting schema.",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "Definition of an element or entry type including the Beacon v2 required and suggested attributes. This schema purpose is to describe each type of entities included in a Beacon, hence Beacon clients could have some metadata about such entities.\n\nThe `id` attribute is the key that should be used in other parts of the Beacon Model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that fully describe an entry type.",
+ "description": "Definition of an element or scope of the element, to describe each type of entry type included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filtering terms, request parameters, etc.) that are relvant for an entry type.",
"properties": {
"$schema": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
+ "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
},
"aCollectionOf": {
"description": "If the entry type is a collection of other entry types, (e.g. a Dataset is a collection of Records), then this attribute must list the entry types that could be included. One collection type could be defined as included more than one entry type (e.g. a Dataset could include Individuals or Genomic Variants), in such cases the entries are alternative, meaning that a given instance of this entry type could be of only one of the types (e.g. a given Dataset contains Individuals, while another Dataset could contain Genomic Variants, but not both at once).",
@@ -30,13 +29,17 @@
"type": "string"
},
"filteringTerms": {
- "$comment": "TO DO: Double-check the proper way of referencing a path or relative path. 'format: uri' is throwing validation errors for relative file paths",
- "description": "Reference to the file with the list of filtering terms that could be used to filter this concept in this instance of Beacon. The referenced file could be used to populate the `filteringTerms`endpoint. Having it independently should allow for updating the list of accepted filtering terms when it is necessary.",
+ "$comment": "TO DO: Evaluate switch this to `url` or a more specific way for allowing URLs and local file paths (is this necessary?).",
+ "description": "Reference to the list of filtering terms that could be used to filter records of this entry type in this beacon.",
"type": "string"
},
"id": {
- "$comments": "++++++ THIS IS THE START OF THE ontologized element ++++++",
- "description": "A (unique) identifier of the element.",
+ "description": "A unique identifier of the element.",
+ "examples": [
+ "biosample",
+ "individual",
+ "dataset"
+ ],
"type": "string"
},
"name": {
@@ -44,11 +47,20 @@
"type": "string"
},
"nonFilteredQueriesAllowed": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/NonFilteredQueriesAllowed"
+ "$ref": "../common/beaconCommonComponents.json#/$defs/NonFilteredQueriesAllowed"
},
"ontologyTermForThisType": {
- "$comments": "++++++ THIS IS THE END OF THE ontologized element ++++++",
- "$ref": "../common/ontologyTerm.json"
+ "$ref": "../common/ontologyTerm.json",
+ "examples": [
+ {
+ "id": "EFO:0000542",
+ "label": "individual"
+ },
+ {
+ "id": "OBI:0000747",
+ "label": "material sample"
+ }
+ ]
},
"partOfSpecification": {
"description": "This is label to group together entry types that are part of the same specification.",
@@ -59,7 +71,6 @@
"required": [
"id",
"name",
- "ontologyTermForThisType",
"partOfSpecification",
"defaultSchema"
],
diff --git a/framework/json/configuration/entryTypesSchema.json b/framework/json/configuration/entryTypesSchema.json
index 7e6c47285..1b75804f6 100644
--- a/framework/json/configuration/entryTypesSchema.json
+++ b/framework/json/configuration/entryTypesSchema.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"EntryTypes": {
"additionalProperties": {
"$ref": "./entryTypeDefinition.json",
@@ -11,10 +9,12 @@
"minProperties": 1
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Schema for the Enrty Types list.",
"properties": {
"entryTypes": {
- "$ref": "#/definitions/EntryTypes",
+ "$ref": "#/$defs/EntryTypes",
"description": "List of entry types."
}
},
diff --git a/framework/json/configuration/filteringTermsSchema.json b/framework/json/configuration/filteringTermsSchema.json
index 462e04b2f..ba7d19d9c 100644
--- a/framework/json/configuration/filteringTermsSchema.json
+++ b/framework/json/configuration/filteringTermsSchema.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"FilterTerm": {
"properties": {
"ftType": {
@@ -47,12 +45,14 @@
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Schema for the Filtering Terms list related to the hosting entry type. It is kept separated to allow updating it independently.",
"properties": {
"filteringTerms": {
"description": "List of filtering terms that could be used to filter this concept in this instance of Beacon.",
"items": {
- "$ref": "#/definitions/FilterTerm"
+ "$ref": "#/$defs/FilterTerm"
},
"minItems": 0,
"type": "array"
diff --git a/framework/json/endpoints.json b/framework/json/endpoints.json
index e394ad28f..5f7fe9da4 100644
--- a/framework/json/endpoints.json
+++ b/framework/json/endpoints.json
@@ -5,7 +5,7 @@
"in": "query",
"name": "limit",
"schema": {
- "$ref": "./common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "./common/beaconCommonComponents.json#/$defs/Limit"
}
},
"requestedSchema": {
@@ -22,7 +22,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "./common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "./common/beaconCommonComponents.json#/$defs/Skip"
}
}
},
diff --git a/framework/json/requests/beaconRequestBody.json b/framework/json/requests/beaconRequestBody.json
index 8b6116bf7..3d6088cff 100644
--- a/framework/json/requests/beaconRequestBody.json
+++ b/framework/json/requests/beaconRequestBody.json
@@ -1,6 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "definitions": {
+ "$defs": {
"BeaconQuery": {
"description": "Parameters to limit the list of returned results.",
"properties": {
@@ -9,10 +8,10 @@
"description": "Ontology based filters. Using CURIE syntax is encouraged."
},
"includeResultsetResponses": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
+ "$ref": "../common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses"
},
"pagination": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/Pagination",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/Pagination",
"description": "Pagination parameters applied to response documents, in case of record level granularity."
},
"requestParameters": {
@@ -20,28 +19,29 @@
"description": "Parameters used for the entry type specific query elements."
},
"requestedGranularity": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/Granularity",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/Granularity",
"description": "Requested granularity for the response. Beacons do not have to respond with the requested granularity, e.g. may respond with count results although record level granularity had been requested but indicate the granularity of the response in the response's metadata."
},
"testMode": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/TestMode",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/TestMode",
"description": "Used for indicating that a request or response is done in a test context."
}
},
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Schema for the Beacon request. It is named `RequestBody` to keep the same nomenclature used by OpenAPI v3, but it actually contains the definition of the whole HTTP POST request payload.",
"properties": {
"$schema": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
+ "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
},
"meta": {
"$ref": "./beaconRequestMeta.json",
"description": "Information relevant for building the response."
},
"query": {
- "$ref": "#/definitions/BeaconQuery"
+ "$ref": "#/$defs/BeaconQuery"
}
},
"required": [
diff --git a/framework/json/requests/beaconRequestMeta.json b/framework/json/requests/beaconRequestMeta.json
index 79b6a6e87..36e0d46fc 100644
--- a/framework/json/requests/beaconRequestMeta.json
+++ b/framework/json/requests/beaconRequestMeta.json
@@ -3,14 +3,14 @@
"description": "Meta section of the Beacon request. It includes request context details relevant for the Beacon server when processing the request.",
"properties": {
"$schema": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
+ "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
},
"apiVersion": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/ApiVersion",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/ApiVersion",
"description": "API version expected by the client to be supported by the server and used in the response format."
},
"requestedSchemas": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/ListOfSchemas",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfSchemas",
"description": "Set of schemas to be used in the response."
}
},
diff --git a/framework/json/requests/filteringTerms.json b/framework/json/requests/filteringTerms.json
index 3c0550f7f..732b49c56 100644
--- a/framework/json/requests/filteringTerms.json
+++ b/framework/json/requests/filteringTerms.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"AlphanumericFilter": {
"description": "Filter results based on operators and values applied to alphanumeric fields.",
"properties": {
@@ -64,13 +62,13 @@
"FilteringTerm": {
"anyOf": [
{
- "$ref": "#/definitions/OntologyFilter"
+ "$ref": "#/$defs/OntologyFilter"
},
{
- "$ref": "#/definitions/AlphanumericFilter"
+ "$ref": "#/$defs/AlphanumericFilter"
},
{
- "$ref": "#/definitions/CustomFilter"
+ "$ref": "#/$defs/CustomFilter"
}
]
},
@@ -110,9 +108,11 @@
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Filtering terms are the main means to select subsets of records from a Beacon response. While the name implies the application to a generated response, in practice implementations may apply them at the query stage. Note: In the processing of Beacon v2.0 requests multiple filters are assumed to be chained by the logical AND operator.",
"items": {
- "$ref": "#/definitions/FilteringTerm"
+ "$ref": "#/$defs/FilteringTerm"
},
"title": "Filtering Term Element",
"type": "array"
diff --git a/framework/json/requests/validation/filteringTerms.json b/framework/json/requests/validation/filteringTerms.json
deleted file mode 100644
index e4d51516e..000000000
--- a/framework/json/requests/validation/filteringTerms.json
+++ /dev/null
@@ -1,109 +0,0 @@
-{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": false,
- "definitions": {
- "AlphanumericFilter": {
- "description": "Filter results based on operators and values applied to alphanumeric fields.",
- "properties": {
- "id": {
- "description": "Field identfier to be queried.",
- "example": "age",
- "type": "string"
- },
- "operator": {
- "default": "=",
- "description": "Defines how the value relates to the field `id`.",
- "enum": [
- "=",
- "<",
- ">",
- "!",
- ">=",
- "<="
- ],
- "example": ">",
- "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.",
- "example": "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"
- }
- },
- "required": [
- "id"
- ],
- "type": "object"
- },
- "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"
- },
- "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.",
- "enum": [
- "exact",
- "high",
- "medium",
- "low"
- ],
- "type": "string"
- }
- },
- "required": [
- "id"
- ],
- "type": "object"
- }
- },
- "description": "Rules for selecting records based upon the field values those records contain. Filters are seperated by the logical AND operator.",
- "properties": {
- "$schema": {
- "description": "Added here to allow the example to comply with the 'additionalProperties:true' restriction.",
- "type": "string"
- },
- "filters": {
- "items": {
- "anyOf": [
- {
- "$ref": "#/definitions/OntologyFilter"
- },
- {
- "$ref": "#/definitions/AlphanumericFilter"
- },
- {
- "$ref": "#/definitions/CustomFilter"
- }
- ]
- },
- "type": "array"
- }
- },
- "title": "Filtering Term Element"
-}
\ No newline at end of file
diff --git a/framework/json/responses/beaconBooleanResponse.json b/framework/json/responses/beaconBooleanResponse.json
index 7aae7ffe6..6bc1b9124 100644
--- a/framework/json/responses/beaconBooleanResponse.json
+++ b/framework/json/responses/beaconBooleanResponse.json
@@ -1,13 +1,13 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
- "description": "Complete definition for a minimal response that provides *only* a `Boolean` exists true|false answer.",
+ "description": "Complete definition for a minimal response that provides *only* an aggregate Boolean `\"exists\": true` or `\"exists\": false` answer to the query. \nAdditional information - which should not consist of record-level information - can be provided through `beaconHandovers`. ",
"properties": {
"beaconHandovers": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/ListOfHandovers",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfHandovers",
"description": "List of handovers that apply to the whole response, not to any resultset or result in particular."
},
"info": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/Info",
+ "$ref": "../common/info.json",
"description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification."
},
"meta": {
diff --git a/framework/json/responses/beaconCollectionsResponse.json b/framework/json/responses/beaconCollectionsResponse.json
index 61f294744..6f819dc0a 100644
--- a/framework/json/responses/beaconCollectionsResponse.json
+++ b/framework/json/responses/beaconCollectionsResponse.json
@@ -1,14 +1,14 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "Beacon response that includes details about the collections in this Beacon.",
+ "description": "A type of Beacon response that includes details about the **collections** in a beacon. The types of collections are defined in each beacon's configuration; if using the Beacon v2+ default model usually the types `dataset` and `cohort` are supported.",
"properties": {
"beaconHandovers": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/ListOfHandovers",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfHandovers",
"description": "List of handovers that apply to the whole response, not to any resultset or result in particular."
},
"info": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/Info",
+ "$ref": "../common/info.json",
"description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification."
},
"meta": {
diff --git a/framework/json/responses/beaconConfigurationResponse.json b/framework/json/responses/beaconConfigurationResponse.json
index ccd15687e..3551db860 100644
--- a/framework/json/responses/beaconConfigurationResponse.json
+++ b/framework/json/responses/beaconConfigurationResponse.json
@@ -1,7 +1,7 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "Information about the Beacon. Aimed to Beacon clients like web pages or Beacon networks.",
+ "description": "The `beaconConfigurationResponse` returns information about configuration parameters of a given beacon instance such as maturity or security attributes or supported entry types. It is directed towards Beacon clients like web pages or network aggregators.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
diff --git a/framework/json/responses/beaconCountResponse.json b/framework/json/responses/beaconCountResponse.json
index 7c5b1ad46..b3b72f69b 100644
--- a/framework/json/responses/beaconCountResponse.json
+++ b/framework/json/responses/beaconCountResponse.json
@@ -1,13 +1,13 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
- "description": "Complete definition for a response that does not include record level details but provides `Boolean` and `count` information.",
+ "description": "Complete definition for a minimal response that provides an aggregate Boolean `\"exists\": true` or `\"exists\": false` answer to the query as well as the count of the matched records.\nAdditional information - which should not consist of record-level information - can be provided through `beaconHandovers`. ",
"properties": {
"beaconHandovers": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/ListOfHandovers",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfHandovers",
"description": "List of handovers that apply to the whole response, not to any resultset or result in particular."
},
"info": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/Info",
+ "$ref": "../common/info.json",
"description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification."
},
"meta": {
diff --git a/framework/json/responses/beaconEntryTypesResponse.json b/framework/json/responses/beaconEntryTypesResponse.json
index 2c2cc5514..d18fa8137 100644
--- a/framework/json/responses/beaconEntryTypesResponse.json
+++ b/framework/json/responses/beaconEntryTypesResponse.json
@@ -1,7 +1,7 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "Response including a list of Entry types definitions.",
+ "description": "The `beaconEntryTypesResponse` provides information about the entry types served through a beacon, including their definitions and pointers to their schemas.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
diff --git a/framework/json/responses/beaconErrorResponse.json b/framework/json/responses/beaconErrorResponse.json
index 07da8d70c..3f01c1a16 100644
--- a/framework/json/responses/beaconErrorResponse.json
+++ b/framework/json/responses/beaconErrorResponse.json
@@ -1,10 +1,10 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "An unsuccessful operation.",
+ "description": "A `beaconErrorResponse` denotes an unsuccessful operation, e.g. due to a missing parameter or an invalid query. The response contains an error object.",
"properties": {
"error": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/BeaconError"
+ "$ref": "../common/beaconCommonComponents.json#/$defs/BeaconError"
},
"meta": {
"$ref": "./sections/beaconResponseMeta.json"
diff --git a/framework/json/responses/beaconInfoResponse.json b/framework/json/responses/beaconInfoResponse.json
index a221e746c..5ed2651fe 100644
--- a/framework/json/responses/beaconInfoResponse.json
+++ b/framework/json/responses/beaconInfoResponse.json
@@ -1,7 +1,7 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "Information about the Beacon. Aimed at Beacon clients like web pages or Beacon networks.",
+ "description": "The `beaconInfoResponse` provides metadata describing a Beacon instance, such as its name, the organization responsible for the Beacon, contact information, site logo and alternative URLs and importantly the beacon's API version. It is based on the GA4GH `service-info` standard.\nThe content of the `beaconInfoResponse` can be used by clients such as web front ends or beacon aggregators to evaluate potential access patterns and to display information about the beacon.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
diff --git a/framework/json/responses/beaconMapResponse.json b/framework/json/responses/beaconMapResponse.json
index d915b4a29..f2c059151 100644
--- a/framework/json/responses/beaconMapResponse.json
+++ b/framework/json/responses/beaconMapResponse.json
@@ -1,7 +1,7 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "Information about the Beacon. Aimed to Beacon clients like web pages or Beacon networks.",
+ "description": "A `beaconMapResponse` provides information about the beacon instance such as the different endpoints supported by this implementation of the Beacon API. This response is aimed to allow Beacon clients such as web front ends and Beacon network aggregators to evaluate which access patterns can be implemented against individual beacons.",
"properties": {
"meta": {
"$ref": "./sections/beaconInformationalResponseMeta.json",
diff --git a/framework/json/responses/beaconResultsetsResponse.json b/framework/json/responses/beaconResultsetsResponse.json
index 159fadaab..4a2943248 100644
--- a/framework/json/responses/beaconResultsetsResponse.json
+++ b/framework/json/responses/beaconResultsetsResponse.json
@@ -1,14 +1,14 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "Beacon response that includes record level details, grouped in Resultsets.",
+ "description": "A `beaconResultsetsResponse` returns the results of a query against a beacon or beacon aggregator. Beyond the `responseSummary` for overall matches the response contains details about the matches in individual **collections** in the beacon or beacon network. This type of response is required when serving a request with a \"record\" level `responseGranularity`, and `beaconResultsets` typically contain a list of records matched by the query.\nThe types of `beaconResultsets` objects are defined in the beacon's configuration; e.g. if using the Beacon v2+ default model the types `dataset` and `cohort` are supported as result sets. ",
"properties": {
"beaconHandovers": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/ListOfHandovers",
+ "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfHandovers",
"description": "List of handovers that apply to the whole response, not to any resultset or result in particular."
},
"info": {
- "$ref": "../common/beaconCommonComponents.json#/definitions/Info",
+ "$ref": "../common/info.json",
"description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification."
},
"meta": {
diff --git a/framework/json/responses/examples-sections/beaconResultsets-MAX-example.json b/framework/json/responses/examples-sections/beaconResultsets-MAX-example.json
index 1406dc8f6..8ec48fb86 100644
--- a/framework/json/responses/examples-sections/beaconResultsets-MAX-example.json
+++ b/framework/json/responses/examples-sections/beaconResultsets-MAX-example.json
@@ -30,7 +30,7 @@
"url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0"
}
],
- "type": "dataset"
+ "setType": "dataset"
}
]
}
\ No newline at end of file
diff --git a/framework/json/responses/ga4gh-service-info-1-0-0-schema.json b/framework/json/responses/ga4gh-service-info-1-0-0-schema.json
index 326fd13ea..61811fe83 100644
--- a/framework/json/responses/ga4gh-service-info-1-0-0-schema.json
+++ b/framework/json/responses/ga4gh-service-info-1-0-0-schema.json
@@ -1,6 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "definitions": {
+ "$defs": {
"ServiceType": {
"description": "Type of a GA4GH service",
"properties": {
@@ -28,6 +27,7 @@
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "A way for a service to describe basic metadata concerning a service alongside a set of capabilities and/or limitations of the service. More information on [GitHub](https://github.com/ga4gh-discovery/ga4gh-service-info/).",
"properties": {
"contactUrl": {
@@ -90,7 +90,7 @@
"type": "object"
},
"type": {
- "$ref": "#/definitions/ServiceType"
+ "$ref": "#/$defs/ServiceType"
},
"updatedAt": {
"description": "Timestamp describing when the service was last updated (RFC 3339 format)",
diff --git a/framework/json/responses/sections/beaconBooleanResponseSection.json b/framework/json/responses/sections/beaconBooleanResponseSection.json
index 80c8d0cb0..12b5a01af 100644
--- a/framework/json/responses/sections/beaconBooleanResponseSection.json
+++ b/framework/json/responses/sections/beaconBooleanResponseSection.json
@@ -3,7 +3,7 @@
"description": "Boolean (true/false) response section.",
"properties": {
"exists": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Exists"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/Exists"
}
},
"required": [
diff --git a/framework/json/responses/sections/beaconCountResponseSection.json b/framework/json/responses/sections/beaconCountResponseSection.json
index 6a9e95e86..a23871775 100644
--- a/framework/json/responses/sections/beaconCountResponseSection.json
+++ b/framework/json/responses/sections/beaconCountResponseSection.json
@@ -3,10 +3,10 @@
"description": "Payload definition for the \"count\" response.",
"properties": {
"exists": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Exists"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/Exists"
},
"numTotalResults": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/NumTotalResults",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/NumTotalResults",
"description": "Total number of results."
}
},
diff --git a/framework/json/responses/sections/beaconFilteringTermsResults.json b/framework/json/responses/sections/beaconFilteringTermsResults.json
index 1755fb582..75a582dd4 100644
--- a/framework/json/responses/sections/beaconFilteringTermsResults.json
+++ b/framework/json/responses/sections/beaconFilteringTermsResults.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"FilteringTerm": {
"description": "Entities can be filtered using this term.",
"properties": {
@@ -21,6 +19,25 @@
],
"type": "string"
},
+ "scopes": {
+ "description": "Entry types affected by this filter.",
+ "examples": [
+ [
+ "individual",
+ "biosample",
+ "analysis",
+ "run",
+ "genomicVariation"
+ ],
+ [
+ "biosample"
+ ]
+ ],
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
"type": {
"description": "Either \"custom\", \"alphanumeric\" or ontology/terminology full name. TODO: An ontology ... with a registered prefix does not need a full name so one may better use CURIE to indicate that the resource can be retrieved from the id. This also will allow to provide an enum here.",
"examples": [
@@ -28,17 +45,6 @@
"alphanumeric"
],
"type": "string"
- },
- "scopes": {
- "description": "Entry types affected by this filter.",
- "examples": [
- ["individual", "biosample", "analysis", "run", "genomicVariation"],
- ["biosample"]
- ],
- "type": "array",
- "items": {
- "type": "string"
- }
}
},
"required": [
@@ -99,20 +105,22 @@
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Filtering terms and ontology resources utilised in this Beacon.",
"properties": {
"filteringTerms": {
"items": {
- "$ref": "#/definitions/FilteringTerm"
+ "$ref": "#/$defs/FilteringTerm"
},
"type": "array"
},
"resources": {
"items": {
- "$ref": "#/definitions/Resource"
+ "$ref": "#/$defs/Resource"
},
"type": "array"
}
},
"type": "object"
-}
+}
\ No newline at end of file
diff --git a/framework/json/responses/sections/beaconInfoResults.json b/framework/json/responses/sections/beaconInfoResults.json
index 9b431df0b..0773b1dba 100644
--- a/framework/json/responses/sections/beaconInfoResults.json
+++ b/framework/json/responses/sections/beaconInfoResults.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"BeaconOrganization": {
"description": "Organization owning the Beacon.",
"properties": {
@@ -22,7 +20,7 @@
"type": "string"
},
"info": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Info",
+ "$ref": "../../common/info.json",
"description": "Additional unspecified metadata about the host Organization."
},
"logoUrl": {
@@ -45,6 +43,8 @@
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Metadata describing a Beacon instance.",
"properties": {
"alternativeUrl": {
@@ -55,7 +55,7 @@
"type": "string"
},
"apiVersion": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ApiVersion"
},
"createDateTime": {
"description": "The date/time the Beacon was created (ISO 8601 format).",
@@ -83,10 +83,10 @@
"type": "string"
},
"id": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/BeaconId"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/BeaconId"
},
"info": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Info",
+ "$ref": "../../common/info.json",
"description": "Additional unspecified metadata about the Beacon service."
},
"name": {
@@ -94,7 +94,7 @@
"type": "string"
},
"organization": {
- "$ref": "#/definitions/BeaconOrganization"
+ "$ref": "#/$defs/BeaconOrganization"
},
"updateDateTime": {
"description": "The time the Beacon was updated in (ISO 8601 format).",
@@ -105,7 +105,7 @@
"type": "string"
},
"version": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ApiVersion",
"description": "TODO: This is a legacy use / duplication?"
},
"welcomeUrl": {
diff --git a/framework/json/responses/sections/beaconInformationalResponseMeta.json b/framework/json/responses/sections/beaconInformationalResponseMeta.json
index 5031198c8..c3fd53353 100644
--- a/framework/json/responses/sections/beaconInformationalResponseMeta.json
+++ b/framework/json/responses/sections/beaconInformationalResponseMeta.json
@@ -5,13 +5,13 @@
"description": "Meta information about the response.",
"properties": {
"apiVersion": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ApiVersion"
},
"beaconId": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/BeaconId"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/BeaconId"
},
"returnedSchemas": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfSchemas"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ListOfSchemas"
}
},
"required": [
diff --git a/framework/json/responses/sections/beaconReceivedRequestSummary.json b/framework/json/responses/sections/beaconReceivedRequestSummary.json
index 56ad90674..c0abbad4d 100644
--- a/framework/json/responses/sections/beaconReceivedRequestSummary.json
+++ b/framework/json/responses/sections/beaconReceivedRequestSummary.json
@@ -3,18 +3,18 @@
"description": "Section of the response that summarize the request received as it has been interpreted by the Beacon server. This summary can help to identify differences between the incoming request and its interpretation or processing, e.g. in the response granularity or pagination. The required properties include those that should be part of every request.",
"properties": {
"apiVersion": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ApiVersion",
"description": "API version expected by the client to be supported by the server and used in the response format."
},
"filters": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Filters",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/Filters",
"description": "Filters as submitted in the request."
},
"includeResultsetResponses": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses"
},
"pagination": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Pagination",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/Pagination",
"description": "Pagination as requested for the results."
},
"requestParameters": {
@@ -22,17 +22,17 @@
"description": "Dictionary of request parameters received in the `RequestBody` or as part of a GET request."
},
"requestedGranularity": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Granularity",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/Granularity",
"description": "Requested granularity for the response which may differe from the response's actual granularity."
},
"requestedSchemas": {
"$comment": "TODO: Add the format attribute as a uri.",
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfSchemas",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ListOfSchemas",
"description": "Set of schemas to be used in the response to a request. `minItems: 0` is used to confirm that an empty array is acceptable here.",
"minItems": 0
},
"testMode": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/TestMode",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/TestMode",
"description": "Used for indicating that a request was received in a test context."
}
},
diff --git a/framework/json/responses/sections/beaconResponseMeta.json b/framework/json/responses/sections/beaconResponseMeta.json
index b2206fe2e..85eff8f95 100644
--- a/framework/json/responses/sections/beaconResponseMeta.json
+++ b/framework/json/responses/sections/beaconResponseMeta.json
@@ -3,24 +3,24 @@
"description": "Information about the response that could be relevant for the Beacon client in order to interpret the results.",
"properties": {
"apiVersion": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ApiVersion"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ApiVersion"
},
"beaconId": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/BeaconId"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/BeaconId"
},
"receivedRequestSummary": {
"$ref": "./beaconReceivedRequestSummary.json"
},
"returnedGranularity": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Granularity",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/Granularity",
"description": "Granularity of the Beacon response which may differ from the requested one. For details see the prototype definition."
},
"returnedSchemas": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfSchemas",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ListOfSchemas",
"description": "The `returnedSchemas` parameter indicates that the request has been interpreted for the indicated entity. This helps to disambiguate between negative responses due to e.g. no hit on a well understood request and failures to interpret or answer the request due to a missing entity. "
},
"testMode": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/TestMode"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/TestMode"
}
},
"required": [
diff --git a/framework/json/responses/sections/beaconResultsets.json b/framework/json/responses/sections/beaconResultsets.json
index 6ddeb3a88..0d56cd50f 100644
--- a/framework/json/responses/sections/beaconResultsets.json
+++ b/framework/json/responses/sections/beaconResultsets.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"ResultsetInstance": {
"additionalProperties": true,
"properties": {
@@ -29,7 +27,7 @@
"type": "integer"
},
"resultsHandovers": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfHandovers",
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/ListOfHandovers",
"description": "List of handovers that apply to this resultset, not to the whole Beacon or to a result in particular."
},
"setType": {
@@ -44,17 +42,20 @@
"exists",
"resultsCount",
"results"
- ]
+ ],
+ "type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Sets of results to be returned as query response.",
"properties": {
"$schema": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/$schema"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/$schema"
},
"resultSets": {
"items": {
- "$ref": "#/definitions/ResultsetInstance"
+ "$ref": "#/$defs/ResultsetInstance"
},
"minItems": 0,
"type": "array"
diff --git a/framework/json/responses/sections/beaconSummaryResponseSection.json b/framework/json/responses/sections/beaconSummaryResponseSection.json
index cc64e55d8..9e19e647c 100644
--- a/framework/json/responses/sections/beaconSummaryResponseSection.json
+++ b/framework/json/responses/sections/beaconSummaryResponseSection.json
@@ -3,10 +3,10 @@
"description": "Beacon results summary section.",
"properties": {
"exists": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/Exists"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/Exists"
},
"numTotalResults": {
- "$ref": "../../common/beaconCommonComponents.json#/definitions/NumTotalResults"
+ "$ref": "../../common/beaconCommonComponents.json#/$defs/NumTotalResults"
}
},
"required": [
diff --git a/framework/src/common/beaconCommonComponents.yaml b/framework/src/common/beaconCommonComponents.yaml
index c0044ed5c..8af76d1a9 100644
--- a/framework/src/common/beaconCommonComponents.yaml
+++ b/framework/src/common/beaconCommonComponents.yaml
@@ -6,7 +6,7 @@ description: >-
exclusively with one or the other.
Separate schema documents are provided for complex components.
type: object
-definitions:
+$defs:
$schema:
type: string
$comment: 'TO REVIEW: adding a `format` or `regex` attribute that validates correctly
@@ -67,7 +67,7 @@ definitions:
Set of schemas to be used in the response to a request.
type: array
items:
- $ref: '#/definitions/SchemasPerEntity'
+ $ref: '#/$defs/SchemasPerEntity'
SchemasPerEntity:
description: >-
Schema to be used for the requested entry type in the response.
@@ -91,24 +91,24 @@ definitions:
type: object
properties:
skip:
- $ref: '#/definitions/Skip'
+ $ref: '#/$defs/Skip'
limit:
- $ref: '#/definitions/Limit'
+ $ref: '#/$defs/Limit'
currentPage:
description: >-
Token of the returned page. To be used only in the response to allow
the client to check if the returned page is the one requested.
- $ref: '#/definitions/PageToken'
+ $ref: '#/$defs/PageToken'
nextPage:
description: >-
Token of the next page. Used to navigate forward. If empty, it is
assumed that no more pages are available
- $ref: '#/definitions/PageToken'
+ $ref: '#/$defs/PageToken'
previousPage:
description: >-
Token of the previous page. Used to navigate backwards. If empty, it
is assumed that the current page is the first one.
- $ref: '#/definitions/PageToken'
+ $ref: '#/$defs/PageToken'
Skip:
description: >-
* In the request: number of pages to skip
@@ -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:
@@ -214,22 +212,12 @@ definitions:
minimum: 0
examples:
- 123
- Info:
- description: >-
- Placeholder to allow the Beacon to return any additional information that
- is necessary or could be of interest in relation to the query or the entry
- returned.
- It is recommended to encapsulate additional informations in this attribute
- instead of directly adding attributes at the same level than the others in
- order to avoid collision in the names of attributes in future versions of
- the specification.
- type: object
ListOfHandovers:
description: Set of handovers to be added in one section the response.
type: array
items:
description: Requested schema to be used for individuals in the response.
- $ref: '#/definitions/Handover'
+ $ref: '#/$defs/Handover'
Handover:
type: object
description: >-
@@ -249,7 +237,7 @@ definitions:
- url
properties:
handoverType:
- $ref: '#/definitions/HandoverType'
+ $ref: '#/$defs/HandoverType'
note:
type: string
description: >-
@@ -265,11 +253,13 @@ 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.
$ref: ./ontologyTerm.yaml
examples:
- - id: EFO:0004157
- label: BAM format
- - id: CUSTOM
- label: download genomic variants in .pgxseg file format
+ - id: EDAM:2572
+ label: BAM
+ - id: EDAM:3016
+ label: VCF
+ - id: CUSTOM:pgxseg
+ label: genomic variants in .pgxseg file format
diff --git a/framework/src/common/info.yaml b/framework/src/common/info.yaml
new file mode 100644
index 000000000..2b29ef3fd
--- /dev/null
+++ b/framework/src/common/info.yaml
@@ -0,0 +1,11 @@
+$schema: https://json-schema.org/draft/2020-12/schema
+title: Info
+description: >-
+ Placeholder to allow the Beacon to return any additional information that
+ is necessary or could be of interest in relation to the query or the entry
+ returned.
+ It is recommended to encapsulate additional informations in this attribute
+ instead of directly adding attributes at the same level than the others in
+ order to avoid collision in the names of attributes in future versions of
+ the specification.
+type: object
diff --git a/framework/src/common/ontologyTerm.yaml b/framework/src/common/ontologyTerm.yaml
index bc1ad7bc5..1978ff0b8 100644
--- a/framework/src/common/ontologyTerm.yaml
+++ b/framework/src/common/ontologyTerm.yaml
@@ -4,7 +4,7 @@ description: Definition of an ontology term.
type: object
properties:
id:
- $ref: './beaconCommonComponents.yaml#/definitions/CURIE'
+ $ref: './beaconCommonComponents.yaml#/$defs/CURIE'
label:
type: string
description: The text that describes the term. By default it could be the preferred
diff --git a/framework/src/common/validation/beaconCommonComponents.yaml b/framework/src/common/validation/beaconCommonComponents.yaml
deleted file mode 100644
index ac0b6d9f3..000000000
--- a/framework/src/common/validation/beaconCommonComponents.yaml
+++ /dev/null
@@ -1,37 +0,0 @@
-$schema: https://json-schema.org/draft/2020-12/schema
-title: Schema for validating Beacon Common Components examples
-type: object
-properties:
- $schema:
- type: string
- description: Added here to allow the example to comply with the 'additionalProperties:true'
- restriction.
- beaconId:
- $ref: ../beaconCommonComponents.yaml#/definitions/BeaconId
- apiVersion:
- $ref: ../beaconCommonComponents.yaml#/definitions/ApiVersion
- beaconError:
- $ref: ../beaconCommonComponents.yaml#/definitions/BeaconError
- listOfSchemas:
- $ref: ../beaconCommonComponents.yaml#/definitions/ListOfSchemas
- schemasPerEntity:
- $ref: ../beaconCommonComponents.yaml#/definitions/SchemasPerEntity
- pagination:
- $ref: ../beaconCommonComponents.yaml#/definitions/Pagination
- includeResultsetResponses:
- $ref: ../beaconCommonComponents.yaml#/definitions/IncludeResultsetResponses
- filters:
- $ref: ../beaconCommonComponents.yaml#/definitions/Filters
- exists:
- $ref: ../beaconCommonComponents.yaml#/definitions/Exists
- numTotalResults:
- $ref: ../beaconCommonComponents.yaml#/definitions/NumTotalResults
- info:
- $ref: ../beaconCommonComponents.yaml#/definitions/Info
- handover:
- $ref: ../beaconCommonComponents.yaml#/definitions/Handover
- handoverType:
- $ref: ../beaconCommonComponents.yaml#/definitions/HandoverType
- listOfHandovers:
- $ref: ../beaconCommonComponents.yaml#/definitions/ListOfHandovers
-additionalProperties: false
diff --git a/framework/src/configuration/beaconConfigurationSchema.yaml b/framework/src/configuration/beaconConfigurationSchema.yaml
index f6f013d92..6eaef9f28 100644
--- a/framework/src/configuration/beaconConfigurationSchema.yaml
+++ b/framework/src/configuration/beaconConfigurationSchema.yaml
@@ -1,26 +1,31 @@
$schema: https://json-schema.org/draft/2020-12/schema
title: Beacon Configuration
-description: Files complaint with this schema are the configuration ones. The details
- returned in `service-info` are mirroring the ones in this configuration file.
+description: >-
+ The Beacon configuration reports several attributes of the beacon instance related
+ to security, maturity and available entry types.
+ Where appropriate the details returned in `service-info` should mirror the ones in this configuration.
type: object
properties:
$schema:
- $ref: ../common/beaconCommonComponents.yaml#/definitions/$schema
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/$schema
maturityAttributes:
description: Declares the level of maturity of the Beacon instance.
type: object
properties:
productionStatus:
- description: "`DEV`= 'Service potentially unstable, not real data', which\
- \ availability and data should not be used in production setups. `TEST`=\
- \ 'Service stable, not real data'. 'PROD'= 'Service stable, actual data'."
+ description: >-
+ * `DEV`: Service potentially unstable, _i.e._ potentially not real data,
+ inconsistent availability; data should not be used in production setups
+ * `TEST`: Service is stable but data should be considered synthetic
+ * `PROD`: Service stable with real world data
type: string
enum:
- DEV
- TEST
- PROD
securityAttributes:
- description: Configuration of the security aspects of the Beacon. By default,
+ description: >-
+ Configuration of the security aspects of the Beacon. By default,
a Beacon that does not declare the configuration settings would return `boolean`
(true/false) responses, and only if the user is authenticated and explicitly
authorized to access the Beacon resources. Although this is the safest set of
@@ -31,7 +36,7 @@ properties:
defaultGranularity:
description: Default granularity. Some responses could return higher detail,
but this would be the granularity by default.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/Granularity
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/Granularity
securityLevels:
description: All access levels supported by the Beacon. Any combination is
valid, as every option would apply to different parts of the Beacon.
@@ -44,8 +49,8 @@ properties:
default:
- CONTROLLED
entryTypes:
- $ref: '#/definitions/EntryTypes'
-definitions:
+ $ref: '#/$defs/EntryTypes'
+$defs:
EntryTypes:
description: This is a dictionary of the entry types implemented in this Beacon
instance.
diff --git a/framework/src/configuration/beaconMapSchema.yaml b/framework/src/configuration/beaconMapSchema.yaml
index ce1cff2c2..500d2087e 100644
--- a/framework/src/configuration/beaconMapSchema.yaml
+++ b/framework/src/configuration/beaconMapSchema.yaml
@@ -5,7 +5,7 @@ description: Map of a Beacon, its entry types and endpoints. It isconceptually s
type: object
properties:
$schema:
- $ref: ../common/beaconCommonComponents.yaml#/definitions/$schema
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/$schema
endpointSets:
description: List of enpoints included in this Beacon instance. This is list is
meant to inform Beacon clients, e.g. a Beacon Network, about the available endpoints,
@@ -13,9 +13,9 @@ properties:
validation purposes.
type: object
additionalProperties:
- $ref: '#/definitions/Endpoint'
+ $ref: '#/$defs/Endpoint'
minProperties: 1
-definitions:
+$defs:
Endpoint:
type: object
properties:
@@ -46,7 +46,7 @@ definitions:
be the only one implemented, together with ´rootUrl`, in which case the
whole map of endpoints is found in the current Map.
type: string
- format: uri
+ format: uri-template
filteringTermsUrl:
description: Optional. Returns the list of filtering terms that could be applied
to this entry type. It is added here for convenience of the Beacon clients,
@@ -55,7 +55,7 @@ definitions:
the few implemented, together with ´rootUrl` and ´singleEntryUrl`, in which
case the whole map of endpoints is found in the current Map.
type: string
- format: uri
+ format: uri-template
endpoints:
description: Optional. A list describing additional endpoints implemented
by this Beacon instance for that entry type. Additional details on the endpoint
@@ -63,7 +63,7 @@ definitions:
OpenAPI definition referenced in the `openAPIEndpointsDefinition` attribute.
type: object
additionalProperties:
- $ref: '#/definitions/RelatedEndpoint'
+ $ref: '#/$defs/RelatedEndpoint'
minProperties: 0
required:
- entryType
@@ -74,7 +74,7 @@ definitions:
url:
description: Endpoint URL
type: string
- format: uri
+ format: uri-template
returnedEntryType:
description: Which entry type is returned by querying this endpoint. It MUST
match one of the entry types defined in the Beacon configuration file (`beaconConfiguration.json`).
diff --git a/framework/src/configuration/entryTypeDefinition.yaml b/framework/src/configuration/entryTypeDefinition.yaml
index f9d47608b..2a57b8c2a 100644
--- a/framework/src/configuration/entryTypeDefinition.yaml
+++ b/framework/src/configuration/entryTypeDefinition.yaml
@@ -1,23 +1,22 @@
$schema: https://json-schema.org/draft/2020-12/schema
title: ''
-description: "Definition of an element or entry type including the Beacon v2 required\
- \ and suggested attributes. This schema purpose is to describe each type of entities\
- \ included in a Beacon, hence Beacon clients could have some metadata about such\
- \ entities.\n\nThe `id` attribute is the key that should be used in other parts\
- \ of the Beacon Model to allow Beacon clients to identify the different parts (e.g.\
- \ endpoints, filteringTerms, request parameters, etc.) that fully describe an entry\
- \ type."
+description: >-
+ Definition of an element or scope of the element, to describe each type of entry type included
+ in a beacon.
+ The `id` attribute is the key that should be used in other parts of the data model
+ to allow Beacon clients to identify the different parts (e.g. endpoints, filtering
+ terms, request parameters, etc.) that are relvant for an entry type.
type: object
-$comment: 'TO DO: The tagged parts should reference to `common/ontologizedElement.json`.
- But that configuration fails to validate. Further investigation is required, but
- should not affect the resulting schema.'
properties:
$schema:
- $ref: ../common/beaconCommonComponents.yaml#/definitions/$schema
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/$schema
id:
- $comments: ++++++ THIS IS THE START OF THE ontologized element ++++++
type: string
- description: A (unique) identifier of the element.
+ description: A unique identifier of the element.
+ examples:
+ - biosample
+ - individual
+ - dataset
name:
type: string
description: A distinctive name for the element.
@@ -26,7 +25,11 @@ properties:
description: A textual description for the element.
ontologyTermForThisType:
$ref: ../common/ontologyTerm.yaml
- $comments: ++++++ THIS IS THE END OF THE ontologized element ++++++
+ examples:
+ - id: EFO:0000542
+ label: individual
+ - id: OBI:0000747
+ label: material sample
partOfSpecification:
description: This is label to group together entry types that are part of the
same specification.
@@ -54,19 +57,18 @@ properties:
items:
$ref: ../common/basicElement.yaml
filteringTerms:
- description: Reference to the file with the list of filtering terms that could
- be used to filter this concept in this instance of Beacon. The referenced file
- could be used to populate the `filteringTerms`endpoint. Having it independently
- should allow for updating the list of accepted filtering terms when it is necessary.
+ description: >-
+ Reference to the list of filtering terms that could be used to filter records
+ of this entry type in this beacon.
type: string
- $comment: "TO DO: Double-check the proper way of referencing a path or relative\
- \ path. 'format: uri' is throwing validation errors for relative file paths"
+ $comment: >-
+ TO DO: Evaluate switch this to `url` or a more specific way for allowing
+ URLs and local file paths (is this necessary?).
nonFilteredQueriesAllowed:
- $ref: ../common/beaconCommonComponents.yaml#/definitions/NonFilteredQueriesAllowed
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/NonFilteredQueriesAllowed
required:
- id
- name
- - ontologyTermForThisType
- partOfSpecification
- defaultSchema
additionalProperties: true
diff --git a/framework/src/configuration/entryTypesSchema.yaml b/framework/src/configuration/entryTypesSchema.yaml
index 5f69a408f..8b88438e0 100644
--- a/framework/src/configuration/entryTypesSchema.yaml
+++ b/framework/src/configuration/entryTypesSchema.yaml
@@ -5,8 +5,8 @@ type: object
properties:
entryTypes:
description: List of entry types.
- $ref: '#/definitions/EntryTypes'
-definitions:
+ $ref: '#/$defs/EntryTypes'
+$defs:
EntryTypes:
description: This is a dictionary of the entry types implemented in this Beacon
instance.
diff --git a/framework/src/configuration/filteringTermsSchema.yaml b/framework/src/configuration/filteringTermsSchema.yaml
index c20f5bd42..8fa414db8 100644
--- a/framework/src/configuration/filteringTermsSchema.yaml
+++ b/framework/src/configuration/filteringTermsSchema.yaml
@@ -9,9 +9,9 @@ properties:
in this instance of Beacon.
type: array
items:
- $ref: '#/definitions/FilterTerm'
+ $ref: '#/$defs/FilterTerm'
minItems: 0
-definitions:
+$defs:
FilterTerm:
type: object
properties:
diff --git a/framework/src/endpoints.yaml b/framework/src/endpoints.yaml
index 9e26e10ec..b1af44b9f 100644
--- a/framework/src/endpoints.yaml
+++ b/framework/src/endpoints.yaml
@@ -143,9 +143,9 @@ components:
name: skip
in: query
schema:
- $ref: ./common/beaconCommonComponents.yaml#/definitions/Skip
+ $ref: ./common/beaconCommonComponents.yaml#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: ./common/beaconCommonComponents.yaml#/definitions/Limit
+ $ref: ./common/beaconCommonComponents.yaml#/$defs/Limit
diff --git a/framework/src/requests/beaconRequestBody.yaml b/framework/src/requests/beaconRequestBody.yaml
index 18fc1586b..3649f7c87 100644
--- a/framework/src/requests/beaconRequestBody.yaml
+++ b/framework/src/requests/beaconRequestBody.yaml
@@ -6,14 +6,14 @@ description: >-
type: object
properties:
$schema:
- $ref: ../common/beaconCommonComponents.yaml#/definitions/$schema
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/$schema
meta:
description: >-
Information relevant for building the response.
$ref: ./beaconRequestMeta.yaml
query:
- $ref: '#/definitions/BeaconQuery'
-definitions:
+ $ref: '#/$defs/BeaconQuery'
+$defs:
BeaconQuery:
description: >-
Parameters to limit the list of returned results.
@@ -28,23 +28,23 @@ definitions:
Ontology based filters. Using CURIE syntax is encouraged.
$ref: ./filteringTerms.yaml
includeResultsetResponses:
- $ref: ../common/beaconCommonComponents.yaml#/definitions/IncludeResultsetResponses
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/IncludeResultsetResponses
pagination:
description: >-
Pagination parameters applied to response documents, in case of record
level granularity.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/Pagination
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/Pagination
requestedGranularity:
description: >-
Requested granularity for the response. Beacons do not have to respond
with the requested granularity, e.g. may respond with count results
although record level granularity had been requested but indicate the
granularity of the response in the response's metadata.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/Granularity
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/Granularity
testMode:
description: >-
Used for indicating that a request or response is done in a test
context.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/TestMode
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/TestMode
required:
- meta
diff --git a/framework/src/requests/beaconRequestMeta.yaml b/framework/src/requests/beaconRequestMeta.yaml
index c7da2f44d..4b3f934b8 100644
--- a/framework/src/requests/beaconRequestMeta.yaml
+++ b/framework/src/requests/beaconRequestMeta.yaml
@@ -4,13 +4,13 @@ description: Meta section of the Beacon request. It includes request context det
type: object
properties:
$schema:
- $ref: ../common/beaconCommonComponents.yaml#/definitions/$schema
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/$schema
apiVersion:
description: API version expected by the client to be supported by the server
and used in the response format.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/ApiVersion
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/ApiVersion
requestedSchemas:
description: Set of schemas to be used in the response.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/ListOfSchemas
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/ListOfSchemas
required:
- apiVersion
diff --git a/framework/src/requests/filteringTerms.yaml b/framework/src/requests/filteringTerms.yaml
index 23b7cddd0..2b1a8fbbc 100644
--- a/framework/src/requests/filteringTerms.yaml
+++ b/framework/src/requests/filteringTerms.yaml
@@ -8,13 +8,13 @@ description: >-
to be chained by the logical AND operator.
type: array
items:
- $ref: '#/definitions/FilteringTerm'
-definitions:
+ $ref: '#/$defs/FilteringTerm'
+$defs:
FilteringTerm:
anyOf:
- - $ref: '#/definitions/OntologyFilter'
- - $ref: '#/definitions/AlphanumericFilter'
- - $ref: '#/definitions/CustomFilter'
+ - $ref: '#/$defs/OntologyFilter'
+ - $ref: '#/$defs/AlphanumericFilter'
+ - $ref: '#/$defs/CustomFilter'
OntologyFilter:
type: object
description: Filter results to include records that contain a specific ontology
diff --git a/framework/src/requests/validation/filteringTerms.yaml b/framework/src/requests/validation/filteringTerms.yaml
deleted file mode 100644
index 6fa00be82..000000000
--- a/framework/src/requests/validation/filteringTerms.yaml
+++ /dev/null
@@ -1,88 +0,0 @@
-$schema: https://json-schema.org/draft/2020-12/schema
-title: Filtering Term Element
-description: Rules for selecting records based upon the field values those records
- contain. Filters are seperated by the logical AND operator.
-properties:
- $schema:
- type: string
- description: Added here to allow the example to comply with the 'additionalProperties:true'
- restriction.
- filters:
- type: array
- items:
- anyOf:
- - $ref: '#/definitions/OntologyFilter'
- - $ref: '#/definitions/AlphanumericFilter'
- - $ref: '#/definitions/CustomFilter'
-definitions:
- 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.
- example: HP:0002664
- includeDescendantTerms:
- type: boolean
- default: true
- description: Define if the Beacon should implement the ontology hierarchy,
- thus query the descendant terms of `id`.
- similarity:
- type: string
- enum:
- - exact
- - high
- - medium
- - low
- 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.
- 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.
- example: age
- operator:
- type: string
- enum:
- - '='
- - <
- - '>'
- - '!'
- - '>='
- - <=
- description: Defines how the value relates to the field `id`.
- default: '='
- example: '>'
- value:
- type: string
- 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
- CustomFilter:
- type: object
- description: Filter results to include records that contain a custom term defined
- by this Beacon.
- required:
- - id
- properties:
- id:
- type: string
- description: Custom filter terms should contain a unique identifier.
- example: demographic.ethnicity:asian
-additionalProperties: false
diff --git a/framework/src/responses/beaconBooleanResponse.yaml b/framework/src/responses/beaconBooleanResponse.yaml
index 976a03628..51226547c 100644
--- a/framework/src/responses/beaconBooleanResponse.yaml
+++ b/framework/src/responses/beaconBooleanResponse.yaml
@@ -1,7 +1,10 @@
$schema: https://json-schema.org/draft/2020-12/schema
description: >-
- Complete definition for a minimal response that provides *only* a `Boolean`
- exists true|false answer.
+ Complete definition for a minimal response that provides *only* an aggregate
+ Boolean `"exists": true` or `"exists": false` answer to the query.
+
+ Additional information - which should not consist of record-level information -
+ can be provided through `beaconHandovers`.
type: object
properties:
meta:
@@ -17,13 +20,13 @@ properties:
description: >-
Additional details that could be of interest. Provided to clearly
enclose any attribute that is not part of the Beacon specification.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/Info
+ $ref: ../common/info.yaml
beaconHandovers:
description: >-
List of handovers that apply to the whole response, not to any resultset
or result in particular.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/ListOfHandovers
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/ListOfHandovers
required:
- meta
- responseSummary
diff --git a/framework/src/responses/beaconCollectionsResponse.yaml b/framework/src/responses/beaconCollectionsResponse.yaml
index ed30f724b..d6e55766d 100644
--- a/framework/src/responses/beaconCollectionsResponse.yaml
+++ b/framework/src/responses/beaconCollectionsResponse.yaml
@@ -1,5 +1,9 @@
$schema: https://json-schema.org/draft/2020-12/schema
-description: Beacon response that includes details about the collections in this Beacon.
+description: >-
+ A type of Beacon response that includes details about the **collections** in a
+ beacon. The types of collections are defined in each beacon's configuration;
+ if using the Beacon v2+ default model usually the types `dataset` and `cohort`
+ are supported.
type: object
properties:
meta:
@@ -27,11 +31,11 @@ properties:
description: >-
Additional details that could be of interest. Provided to clearly
enclose any attribute that is not part of the Beacon specification.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/Info
+ $ref: ../common/info.yaml
beaconHandovers:
description: List of handovers that apply to the whole response, not to any resultset
or result in particular.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/ListOfHandovers
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/ListOfHandovers
required:
- meta
- responseSummary
diff --git a/framework/src/responses/beaconConfigurationResponse.yaml b/framework/src/responses/beaconConfigurationResponse.yaml
index 28d38626d..f4ee49954 100644
--- a/framework/src/responses/beaconConfigurationResponse.yaml
+++ b/framework/src/responses/beaconConfigurationResponse.yaml
@@ -1,8 +1,10 @@
$schema: https://json-schema.org/draft/2020-12/schema
type: object
description: >-
- Information about the Beacon. Aimed to Beacon clients like web pages
- or Beacon networks.
+ The `beaconConfigurationResponse` returns information about configuration
+ parameters of a given beacon instance such as maturity or security attributes
+ or supported entry types. It is directed towards Beacon clients like web pages
+ or network aggregators.
properties:
meta:
description: >-
diff --git a/framework/src/responses/beaconCountResponse.yaml b/framework/src/responses/beaconCountResponse.yaml
index 7b9d11570..1f03c9a6b 100644
--- a/framework/src/responses/beaconCountResponse.yaml
+++ b/framework/src/responses/beaconCountResponse.yaml
@@ -1,7 +1,11 @@
$schema: https://json-schema.org/draft/2020-12/schema
description: >-
- Complete definition for a response that does not include record level
- details but provides `Boolean` and `count` information.
+ Complete definition for a minimal response that provides an aggregate Boolean
+ `"exists": true` or `"exists": false` answer to the query as well as the count
+ of the matched records.
+
+ Additional information - which should not consist of record-level information -
+ can be provided through `beaconHandovers`.
type: object
properties:
meta:
@@ -17,12 +21,12 @@ properties:
description: >-
Additional details that could be of interest. Provided to clearly
enclose any attribute that is not part of the Beacon specification.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/Info
+ $ref: ../common/info.yaml
beaconHandovers:
description: >-
List of handovers that apply to the whole response, not to any resultset
or result in particular.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/ListOfHandovers
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/ListOfHandovers
required:
- meta
- responseSummary
diff --git a/framework/src/responses/beaconEntryTypesResponse.yaml b/framework/src/responses/beaconEntryTypesResponse.yaml
index 16e5aef37..2919bf009 100644
--- a/framework/src/responses/beaconEntryTypesResponse.yaml
+++ b/framework/src/responses/beaconEntryTypesResponse.yaml
@@ -1,7 +1,9 @@
$schema: https://json-schema.org/draft/2020-12/schema
type: object
description: >-
- Response including a list of Entry types definitions.
+ The `beaconEntryTypesResponse` provides information about the entry types
+ served through a beacon, including their definitions and pointers to their
+ schemas.
properties:
meta:
description: >-
diff --git a/framework/src/responses/beaconErrorResponse.yaml b/framework/src/responses/beaconErrorResponse.yaml
index beaf8afa8..eb1669d3a 100644
--- a/framework/src/responses/beaconErrorResponse.yaml
+++ b/framework/src/responses/beaconErrorResponse.yaml
@@ -1,12 +1,13 @@
$schema: https://json-schema.org/draft/2020-12/schema
type: object
description: >-
- An unsuccessful operation.
+ A `beaconErrorResponse` denotes an unsuccessful operation, e.g. due to a missing
+ parameter or an invalid query. The response contains an error object.
properties:
meta:
$ref: ./sections/beaconResponseMeta.yaml
error:
- $ref: ../common/beaconCommonComponents.yaml#/definitions/BeaconError
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/BeaconError
required:
- meta
- error
diff --git a/framework/src/responses/beaconInfoResponse.yaml b/framework/src/responses/beaconInfoResponse.yaml
index 720015f8f..011610860 100644
--- a/framework/src/responses/beaconInfoResponse.yaml
+++ b/framework/src/responses/beaconInfoResponse.yaml
@@ -1,8 +1,14 @@
$schema: https://json-schema.org/draft/2020-12/schema
type: object
description: >-
- Information about the Beacon. Aimed at Beacon clients like web pages
- or Beacon networks.
+ The `beaconInfoResponse` provides metadata describing a Beacon instance, such
+ as its name, the organization responsible for the Beacon, contact information,
+ site logo and alternative URLs and importantly the beacon's API version. It is
+ based on the GA4GH `service-info` standard.
+
+ The content of the `beaconInfoResponse` can be used by clients such as web front
+ ends or beacon aggregators to evaluate potential access patterns and to display
+ information about the beacon.
properties:
meta:
description: >-
diff --git a/framework/src/responses/beaconMapResponse.yaml b/framework/src/responses/beaconMapResponse.yaml
index 08a70e0ad..c230024bb 100644
--- a/framework/src/responses/beaconMapResponse.yaml
+++ b/framework/src/responses/beaconMapResponse.yaml
@@ -1,8 +1,10 @@
$schema: https://json-schema.org/draft/2020-12/schema
type: object
description: >-
- Information about the Beacon. Aimed to Beacon clients like web pages
- or Beacon networks.
+ A `beaconMapResponse` provides information about the beacon instance such as the
+ different endpoints supported by this implementation of the Beacon API. This response
+ is aimed to allow Beacon clients such as web front ends and Beacon network aggregators
+ to evaluate which access patterns can be implemented against individual beacons.
properties:
meta:
description: >-
diff --git a/framework/src/responses/beaconResultsetsResponse.yaml b/framework/src/responses/beaconResultsetsResponse.yaml
index bbb8a0e18..ff230fe81 100644
--- a/framework/src/responses/beaconResultsetsResponse.yaml
+++ b/framework/src/responses/beaconResultsetsResponse.yaml
@@ -1,5 +1,15 @@
$schema: https://json-schema.org/draft/2020-12/schema
-description: Beacon response that includes record level details, grouped in Resultsets.
+description: >-
+ A `beaconResultsetsResponse` returns the results of a query against a beacon
+ or beacon aggregator. Beyond the `responseSummary` for overall matches the
+ response contains details about the matches in individual **collections** in
+ the beacon or beacon network. This type of response is required when serving
+ a request with a "record" level `responseGranularity`, and `beaconResultsets`
+ typically contain a list of records matched by the query.
+
+ The types of `beaconResultsets` objects are defined in the beacon's configuration;
+ e.g. if using the Beacon v2+ default model the types `dataset` and `cohort` are
+ supported as result sets.
type: object
properties:
meta:
@@ -15,12 +25,12 @@ properties:
description: >-
Additional details that could be of interest. Provided to clearly
enclose any attribute that is not part of the Beacon specification.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/Info
+ $ref: ../common/info.yaml
beaconHandovers:
description: >-
List of handovers that apply to the whole response, not to any resultset
or result in particular.
- $ref: ../common/beaconCommonComponents.yaml#/definitions/ListOfHandovers
+ $ref: ../common/beaconCommonComponents.yaml#/$defs/ListOfHandovers
response:
description: >-
Response for queries that recovers any result.
diff --git a/framework/src/responses/examples-sections/beaconResultsets-MAX-example.yaml b/framework/src/responses/examples-sections/beaconResultsets-MAX-example.yaml
index f2ae4015b..d7f5a0c80 100644
--- a/framework/src/responses/examples-sections/beaconResultsets-MAX-example.yaml
+++ b/framework/src/responses/examples-sections/beaconResultsets-MAX-example.yaml
@@ -4,7 +4,7 @@ resultSets:
type: dataset
exists: false
- id: datasetB
- type: dataset
+ setType: dataset
exists: true
resultsCount: 2
resultsHandovers:
diff --git a/framework/src/responses/ga4gh-service-info-1-0-0-schema.yaml b/framework/src/responses/ga4gh-service-info-1-0-0-schema.yaml
index a00ce4b3d..97842018e 100644
--- a/framework/src/responses/ga4gh-service-info-1-0-0-schema.yaml
+++ b/framework/src/responses/ga4gh-service-info-1-0-0-schema.yaml
@@ -25,7 +25,7 @@ properties:
Name of this service. Should be human readable.
example: My project
type:
- $ref: '#/definitions/ServiceType'
+ $ref: '#/$defs/ServiceType'
description:
type: string
description: >-
@@ -91,7 +91,7 @@ properties:
but other identifiers, such as dates or commit hashes, are also allowed. The
version should be changed whenever the service is updated.
example: 1.0.0
-definitions:
+$defs:
ServiceType:
description: Type of a GA4GH service
type: object
diff --git a/framework/src/responses/sections/beaconBooleanResponseSection.yaml b/framework/src/responses/sections/beaconBooleanResponseSection.yaml
index 928331fad..bd4052ecf 100644
--- a/framework/src/responses/sections/beaconBooleanResponseSection.yaml
+++ b/framework/src/responses/sections/beaconBooleanResponseSection.yaml
@@ -5,4 +5,4 @@ required:
- exists
properties:
exists:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Exists
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/Exists
diff --git a/framework/src/responses/sections/beaconCountResponseSection.yaml b/framework/src/responses/sections/beaconCountResponseSection.yaml
index 6ee9924c4..14c1994d3 100644
--- a/framework/src/responses/sections/beaconCountResponseSection.yaml
+++ b/framework/src/responses/sections/beaconCountResponseSection.yaml
@@ -4,10 +4,10 @@ description: >-
type: object
properties:
exists:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Exists
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/Exists
numTotalResults:
description: Total number of results.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/NumTotalResults
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/NumTotalResults
required:
- exists
- numTotalResults
diff --git a/framework/src/responses/sections/beaconFilteringTermsResults.yaml b/framework/src/responses/sections/beaconFilteringTermsResults.yaml
index 05748d8cc..f0a654b46 100644
--- a/framework/src/responses/sections/beaconFilteringTermsResults.yaml
+++ b/framework/src/responses/sections/beaconFilteringTermsResults.yaml
@@ -6,12 +6,12 @@ properties:
resources:
type: array
items:
- $ref: '#/definitions/Resource'
+ $ref: '#/$defs/Resource'
filteringTerms:
type: array
items:
- $ref: '#/definitions/FilteringTerm'
-definitions:
+ $ref: '#/$defs/FilteringTerm'
+$defs:
FilteringTerm:
type: object
description: >-
diff --git a/framework/src/responses/sections/beaconInfoResults.yaml b/framework/src/responses/sections/beaconInfoResults.yaml
index db432fe09..3c5cbaebc 100644
--- a/framework/src/responses/sections/beaconInfoResults.yaml
+++ b/framework/src/responses/sections/beaconInfoResults.yaml
@@ -10,13 +10,13 @@ required:
- organization
properties:
id:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/BeaconId
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/BeaconId
name:
type: string
description: >-
Name of the Beacon.
apiVersion:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ApiVersion
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ApiVersion
environment:
type: string
description: "Environment the service is running in. Use this to distinguish\n\
@@ -29,7 +29,7 @@ properties:
examples:
- dev
organization:
- $ref: '#/definitions/BeaconOrganization'
+ $ref: '#/$defs/BeaconOrganization'
description:
type: string
description: >-
@@ -37,7 +37,7 @@ properties:
version:
description: >-
TODO: This is a legacy use / duplication?
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ApiVersion
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ApiVersion
welcomeUrl:
type: string
description: >-
@@ -67,8 +67,8 @@ properties:
info:
description: >-
Additional unspecified metadata about the Beacon service.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Info
-definitions:
+ $ref: ../../common/info.yaml
+$defs:
BeaconOrganization:
description: >-
Organization owning the Beacon.
@@ -109,5 +109,5 @@ definitions:
3986 format).
info:
description: Additional unspecified metadata about the host Organization.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Info
+ $ref: ../../common/info.yaml
additionalProperties: true
diff --git a/framework/src/responses/sections/beaconInformationalResponseMeta.yaml b/framework/src/responses/sections/beaconInformationalResponseMeta.yaml
index c1255cd4c..6bcc2beb4 100644
--- a/framework/src/responses/sections/beaconInformationalResponseMeta.yaml
+++ b/framework/src/responses/sections/beaconInformationalResponseMeta.yaml
@@ -4,11 +4,11 @@ description: >-
type: object
properties:
beaconId:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/BeaconId
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/BeaconId
apiVersion:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ApiVersion
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ApiVersion
returnedSchemas:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ListOfSchemas
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ListOfSchemas
$comment: 'TO REVIEW: the required properties below results in a warning in the example.'
required:
- beaconId
diff --git a/framework/src/responses/sections/beaconReceivedRequestSummary.yaml b/framework/src/responses/sections/beaconReceivedRequestSummary.yaml
index c15df32dc..6c6774507 100644
--- a/framework/src/responses/sections/beaconReceivedRequestSummary.yaml
+++ b/framework/src/responses/sections/beaconReceivedRequestSummary.yaml
@@ -11,39 +11,39 @@ properties:
description: >-
API version expected by the client to be supported by the server
and used in the response format.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ApiVersion
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ApiVersion
requestedSchemas:
description: >-
Set of schemas to be used in the response to a request.
`minItems: 0` is used to confirm that an empty array is acceptable here.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ListOfSchemas
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ListOfSchemas
minItems: 0
$comment: >-
TODO: Add the format attribute as a uri.
filters:
description: >-
Filters as submitted in the request.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Filters
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/Filters
requestParameters:
description: >-
Dictionary of request parameters received in the `RequestBody` or as part
of a GET request.
$ref: ../../requests/requestParameters.yaml
includeResultsetResponses:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/IncludeResultsetResponses
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/IncludeResultsetResponses
pagination:
description: >-
Pagination as requested for the results.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Pagination
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/Pagination
requestedGranularity:
description: >-
Requested granularity for the response which may differe from the
response's actual granularity.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Granularity
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/Granularity
testMode:
description: >-
Used for indicating that a request was received in a test context.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/TestMode
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/TestMode
required:
- apiVersion
- requestedSchemas
diff --git a/framework/src/responses/sections/beaconResponseMeta.yaml b/framework/src/responses/sections/beaconResponseMeta.yaml
index 84239c672..6155d035f 100644
--- a/framework/src/responses/sections/beaconResponseMeta.yaml
+++ b/framework/src/responses/sections/beaconResponseMeta.yaml
@@ -5,23 +5,23 @@ description: >-
type: object
properties:
beaconId:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/BeaconId
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/BeaconId
apiVersion:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ApiVersion
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ApiVersion
returnedSchemas:
description: >-
The `returnedSchemas` parameter indicates that the request has been interpreted
for the indicated entity. This helps to disambiguate between negative responses
due to e.g. no hit on a well understood request and failures to interpret or
answer the request due to a missing entity.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ListOfSchemas
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ListOfSchemas
returnedGranularity:
description: >-
Granularity of the Beacon response which may differ from the requested one.
For details see the prototype definition.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Granularity
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/Granularity
testMode:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/TestMode
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/TestMode
receivedRequestSummary:
$ref: ./beaconReceivedRequestSummary.yaml
required:
diff --git a/framework/src/responses/sections/beaconResultsets.yaml b/framework/src/responses/sections/beaconResultsets.yaml
index 246ef8277..4f257ca90 100644
--- a/framework/src/responses/sections/beaconResultsets.yaml
+++ b/framework/src/responses/sections/beaconResultsets.yaml
@@ -4,17 +4,18 @@ description: Sets of results to be returned as query response.
type: object
properties:
$schema:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/$schema
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/$schema
resultSets:
type: array
items:
- $ref: '#/definitions/ResultsetInstance'
+ $ref: '#/$defs/ResultsetInstance'
minItems: 0
required:
- resultSets
additionalProperties: true
-definitions:
+$defs:
ResultsetInstance:
+ type: object
properties:
id:
description: id of the resultset
@@ -33,7 +34,7 @@ definitions:
resultsHandovers:
description: List of handovers that apply to this resultset, not to the whole
Beacon or to a result in particular.
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/ListOfHandovers
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/ListOfHandovers
info:
description: Additional details that could be of interest about the Resultset.
Provided to clearly enclose any attribute that is not part of the Beacon
diff --git a/framework/src/responses/sections/beaconSummaryResponseSection.yaml b/framework/src/responses/sections/beaconSummaryResponseSection.yaml
index 7fb855a15..2f9dfa433 100644
--- a/framework/src/responses/sections/beaconSummaryResponseSection.yaml
+++ b/framework/src/responses/sections/beaconSummaryResponseSection.yaml
@@ -3,8 +3,8 @@ description: Beacon results summary section.
type: object
properties:
exists:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/Exists
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/Exists
numTotalResults:
- $ref: ../../common/beaconCommonComponents.yaml#/definitions/NumTotalResults
+ $ref: ../../common/beaconCommonComponents.yaml#/$defs/NumTotalResults
required:
- exists
diff --git a/models/json/beacon-v2-default-model/analyses/defaultSchema.json b/models/json/beacon-v2-default-model/analyses/defaultSchema.json
index e2fd84089..b3ed73ee1 100644
--- a/models/json/beacon-v2-default-model/analyses/defaultSchema.json
+++ b/models/json/beacon-v2-default-model/analyses/defaultSchema.json
@@ -2,17 +2,17 @@
"$comment": "version: ga4gh-beacon-analysis-v2.0.0",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
- "description": "Schema for a sequencing bioinformatics analysis.",
+ "description": "The `analysis` schema represents a information about the data analysis steps leading to (a set of) genomic variation call(s).",
"properties": {
"aligner": {
- "description": "Reference to mapping/alignment software",
+ "description": "Name or identifier of the mapping/alignment software/pipeline",
"examples": [
"bwa-0.7.8"
],
"type": "string"
},
"analysisDate": {
- "description": "Date at which analysis was performed.",
+ "description": "Date at which analysis was performed.\n",
"examples": [
"2021-10-17"
],
@@ -20,51 +20,55 @@
"type": "string"
},
"biosampleId": {
- "description": "Reference to the `id` of the biosample this analysis is reporting on.",
+ "description": "Local reference to the `id` of the biosample this analysis is reporting on.",
"examples": [
- "S0001"
+ "S0001",
+ "onekgbs-NA07346"
],
"type": "string"
},
"id": {
- "description": "Analysis reference ID (external accession or internal ID)",
+ "description": "Analysis id for internal referencing; unique in the dataset.",
"type": "string"
},
"individualId": {
- "description": "Reference to the `id` of the individual this analysis is reporting on.",
+ "description": "Local reference to the `id` of the individual this analysis is reporting on.",
"examples": [
- "P0001"
+ "P0001",
+ "onekgind-NA07346"
],
"type": "string"
},
"info": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info"
+ "$ref": "../common/info.json"
},
"pipelineName": {
- "description": "Analysis pipeline and version if a standardized pipeline was used",
+ "description": "Analysis pipeline and version.",
"examples": [
"Pipeline-panel-0001-v1"
],
"type": "string"
},
"pipelineRef": {
- "description": "Link to Analysis pipeline resource",
+ "description": "Link to information about or repository of the analysis pipeline.",
"examples": [
- "https://doi.org/10.48511/workflowhub.workflow.111.1"
+ "https://doi.org/10.48511/workflowhub.workflow.111.1",
+ "https://doi.org/10.1093/bib/bbad541"
],
"type": "string"
},
"runId": {
- "description": "Run identifier (external accession or internal ID).",
+ "description": "Local reference to the associated experimental run.",
"examples": [
"SRR10903401"
],
"type": "string"
},
"variantCaller": {
- "description": "Reference to variant calling software / pipeline",
+ "description": "Name or identifier of the variant calling software/pipeline",
"examples": [
- "GATK4.0"
+ "GATK4.0",
+ "labelSeg"
],
"type": "string"
}
@@ -74,6 +78,6 @@
"analysisDate",
"pipelineName"
],
- "title": "Sequencing bioinformatics analysis",
+ "title": "Bioinformatics analysis",
"type": "object"
}
\ No newline at end of file
diff --git a/models/json/beacon-v2-default-model/analyses/endpoints.json b/models/json/beacon-v2-default-model/analyses/endpoints.json
index 570d7201d..ec8fe9d85 100644
--- a/models/json/beacon-v2-default-model/analyses/endpoints.json
+++ b/models/json/beacon-v2-default-model/analyses/endpoints.json
@@ -25,13 +25,13 @@
}
},
"includeResultsetResponses": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses"
},
"limit": {
"in": "query",
"name": "limit",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit"
}
},
"requestedSchema": {
@@ -48,7 +48,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip"
}
}
},
@@ -91,7 +91,7 @@
"paths": {
"/analyses": {
"get": {
- "description": "Get a list of bioinformatics analysis",
+ "description": "Get a Beacon response for bioinformatics analyses",
"operationId": "getAnalyses",
"parameters": [
{
@@ -123,7 +123,7 @@
]
},
"post": {
- "description": "Get a list of bioinformatics analysis",
+ "description": "Get a Beacon response for bioinformatics analyses",
"operationId": "postAnalysesRequest",
"requestBody": {
"content": {
@@ -207,8 +207,8 @@
},
"/analyses/{id}/g_variants": {
"get": {
- "description": "Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id'",
- "operationId": "getOneAnalysisVariants",
+ "description": "Get a *genomic variations* response for one bioinformatics analysis, identified by its (unique) 'id'",
+ "operationId": "getOneAnalysisVariationsRequest",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
@@ -239,8 +239,8 @@
}
],
"post": {
- "description": "Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id'",
- "operationId": "postOneAnalysisVariantsRequest",
+ "description": "Get a *genomic variations* response for one bioinformatics analysis, identified by its (unique) 'id'",
+ "operationId": "postOneAnalysisVariationsRequest",
"requestBody": {
"content": {
"application/json": {
diff --git a/models/json/beacon-v2-default-model/beaconMap.json b/models/json/beacon-v2-default-model/beaconMap.json
index 4c9a12a78..a7681a24f 100644
--- a/models/json/beacon-v2-default-model/beaconMap.json
+++ b/models/json/beacon-v2-default-model/beaconMap.json
@@ -1,9 +1,9 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"endpointSets": {
- "analysis": {
+ "analysisEndpoints": {
"endpoints": {
- "genomicVariant": {
+ "genomicVariantLookup": {
"returnedEntryType": "genomicVariant",
"url": "https://exampleBeacons.org/analyses/{id}/g_variants"
}
@@ -13,17 +13,17 @@
"rootUrl": "https://exampleBeacons.org/analyses",
"singleEntryUrl": "https://exampleBeacons.org/analyses/{id}"
},
- "biosample": {
+ "biosampleEndpoints": {
"endpoints": {
- "analysis": {
+ "analysisLookup": {
"returnedEntryType": "analysis",
"url": "https://exampleBeacons.org/biosamples/{id}/analyses"
},
- "genomicVariant": {
+ "genomicVariantLookup": {
"returnedEntryType": "genomicVariant",
"url": "https://exampleBeacons.org/biosamples/{id}/g_variants"
},
- "run": {
+ "runLookup": {
"returnedEntryType": "run",
"url": "https://exampleBeacons.org/biosamples/{id}/runs"
}
@@ -33,25 +33,25 @@
"rootUrl": "https://exampleBeacons.org/biosamples",
"singleEntryUrl": "https://exampleBeacons.org/biosamples/{id}"
},
- "cohort": {
+ "cohortEndpoints": {
"endpoints": {
- "analyses": {
+ "analysisLookup": {
"returnedEntryType": "analysis",
"url": "https://exampleBeacons.org/cohorts/{id}/analyses"
},
- "biosample": {
+ "biosampleLookup": {
"returnedEntryType": "biosample",
"url": "https://exampleBeacons.org/cohorts/{id}/biosamples"
},
- "genomicVariant": {
+ "genomicVariantLookup": {
"returnedEntryType": "genomicVariant",
"url": "https://exampleBeacons.org/cohorts/{id}/g_variants"
},
- "individual": {
+ "individualLookup": {
"returnedEntryType": "individual",
"url": "https://exampleBeacons.org/cohorts/{id}/individuals"
},
- "runs": {
+ "runLookup": {
"returnedEntryType": "run",
"url": "https://exampleBeacons.org/cohorts/{id}/runs"
}
@@ -62,25 +62,25 @@
"rootUrl": "https://exampleBeacons.org/cohorts",
"singleEntryUrl": "https://exampleBeacons.org/cohorts/{id}"
},
- "dataset": {
+ "datasetEndpoints": {
"endpoints": {
- "analyses": {
+ "analysisLookup": {
"returnedEntryType": "analysis",
"url": "https://exampleBeacons.org/datasets/{id}/analyses"
},
- "biosample": {
+ "biosampleLookup": {
"returnedEntryType": "biosample",
"url": "https://exampleBeacons.org/datasets/{id}/biosamples"
},
- "genomicVariant": {
+ "genomicVariantLookup": {
"returnedEntryType": "genomicVariant",
"url": "https://exampleBeacons.org/datasets/{id}/g_variants"
},
- "individual": {
+ "individualLookup": {
"returnedEntryType": "individual",
"url": "https://exampleBeacons.org/datasets/{id}/individuals"
},
- "runs": {
+ "runLookup": {
"returnedEntryType": "run",
"url": "https://exampleBeacons.org/datasets/{id}/runs"
}
@@ -91,21 +91,21 @@
"rootUrl": "https://exampleBeacons.org/datasets",
"singleEntryUrl": "https://exampleBeacons.org/datasets/{id}"
},
- "genomicVariant": {
+ "genomicVariantEndpoints": {
"endpoints": {
- "analyses": {
+ "analysisLookup": {
"returnedEntryType": "analysis",
"url": "https://exampleBeacons.org/g_variants/{id}/analyses"
},
- "biosample": {
+ "biosampleLookup": {
"returnedEntryType": "biosample",
"url": "https://exampleBeacons.org/g_variants/{id}/biosamples"
},
- "individual": {
+ "individualLookup": {
"returnedEntryType": "individual",
"url": "https://exampleBeacons.org/g_variants/{id}/individuals"
},
- "runs": {
+ "runLookup": {
"returnedEntryType": "run",
"url": "https://exampleBeacons.org/g_variants/{id}/runs"
}
@@ -115,21 +115,21 @@
"rootUrl": "https://exampleBeacons.org/g_variants",
"singleEntryUrl": "https://exampleBeacons.org/g_variants/{id}"
},
- "individual": {
+ "individualEndpoints": {
"endpoints": {
- "analyses": {
+ "analysisLookup": {
"returnedEntryType": "analysis",
"url": "https://exampleBeacons.org/individuals/{id}/analyses"
},
- "biosample": {
+ "biosampleLookup": {
"returnedEntryType": "biosample",
"url": "https://exampleBeacons.org/individuals/{id}/biosamples"
},
- "genomicVariant": {
+ "genomicVariantLookup": {
"returnedEntryType": "genomicVariant",
"url": "https://exampleBeacons.org/individuals/{id}/g_variants"
},
- "runs": {
+ "runLookup": {
"returnedEntryType": "run",
"url": "https://exampleBeacons.org/individuals/{id}/runs"
}
@@ -140,13 +140,13 @@
"rootUrl": "https://exampleBeacons.org/individuals",
"singleEntryUrl": "https://exampleBeacons.org/individuals/{id}"
},
- "run": {
+ "runEndpoints": {
"endpoints": {
- "analysis": {
+ "analysisLookup": {
"returnedEntryType": "analysis",
"url": "https://exampleBeacons.org/runs/{id}/analyses"
},
- "genomicVariant": {
+ "genomicVariantLookup": {
"returnedEntryType": "genomicVariant",
"url": "https://exampleBeacons.org/runs/{id}/g_variants"
}
diff --git a/models/json/beacon-v2-default-model/biosamples/defaultSchema.json b/models/json/beacon-v2-default-model/biosamples/defaultSchema.json
index c1a2d65da..e6eca7082 100644
--- a/models/json/beacon-v2-default-model/biosamples/defaultSchema.json
+++ b/models/json/beacon-v2-default-model/biosamples/defaultSchema.json
@@ -82,7 +82,7 @@
"type": "string"
},
"info": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info"
+ "$ref": "../common/info.json"
},
"measurements": {
"description": "List of measurements of the sample.",
diff --git a/models/json/beacon-v2-default-model/biosamples/endpoints.json b/models/json/beacon-v2-default-model/biosamples/endpoints.json
index 533d5ceda..56968b137 100644
--- a/models/json/beacon-v2-default-model/biosamples/endpoints.json
+++ b/models/json/beacon-v2-default-model/biosamples/endpoints.json
@@ -29,13 +29,13 @@
}
},
"includeResultsetResponses": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses"
},
"limit": {
"in": "query",
"name": "limit",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit"
}
},
"requestedSchema": {
@@ -52,7 +52,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip"
}
}
},
@@ -95,7 +95,7 @@
"paths": {
"/biosamples": {
"get": {
- "description": "Get a list of biosamples",
+ "description": "Get a Beacon response for biosamples",
"operationId": "getBiosamples",
"parameters": [
{
@@ -127,7 +127,7 @@
]
},
"post": {
- "description": "Get a list of biosamples",
+ "description": "Get a Beacon response for biosamples",
"operationId": "postBiosamplesRequest",
"requestBody": {
"content": {
@@ -204,8 +204,8 @@
},
"/biosamples/{id}/analyses": {
"get": {
- "description": "Get the analysis list from one biosample, identified by its (unique) 'id'",
- "operationId": "getOneBiosampleAnalysis",
+ "description": "Get an *analyses* response from one biosample, identified by its (unique) 'id'",
+ "operationId": "getOneBiosampleAnalyses",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
@@ -236,8 +236,8 @@
}
],
"post": {
- "description": "Get the analysis list from one biosample, identified by its (unique) 'id'",
- "operationId": "postOneBiosampleAnalysis",
+ "description": "Get an *analyses* response from one biosample, identified by its (unique) 'id'",
+ "operationId": "postOneBiosampleAnalyses",
"requestBody": {
"content": {
"application/json": {
@@ -264,8 +264,8 @@
},
"/biosamples/{id}/g_variants": {
"get": {
- "description": "Get the genomic variants list from one biosample, identified by its (unique) 'id'",
- "operationId": "getOneBiosampleGenomicVariants",
+ "description": "Get a *genomic variations* response from one biosample, identified by its (unique) 'id'",
+ "operationId": "getOneBiosampleGenomicVariations",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
@@ -296,8 +296,8 @@
}
],
"post": {
- "description": "Get the genomic variants list from one biosample, identified by its (unique) 'id'",
- "operationId": "postOneBiosampleGenomicVariants",
+ "description": "Get a *genomic variations* response from one biosample, identified by its (unique) 'id'",
+ "operationId": "postOneBiosampleGenomicVariations",
"requestBody": {
"content": {
"application/json": {
@@ -324,7 +324,7 @@
},
"/biosamples/{id}/runs": {
"get": {
- "description": "Get the runs list from one biosample, identified by its (unique) 'id'",
+ "description": "Get a *runs* response from one biosample, identified by its (unique) 'id'",
"operationId": "getOneBiosampleRuns",
"parameters": [
{
@@ -363,7 +363,7 @@
}
],
"post": {
- "description": "Get the runs list from one biosample, identified by its (unique) 'id'",
+ "description": "Get a *runs* response from one biosample, identified by its (unique) 'id'",
"operationId": "postOneBiosampleRuns",
"requestBody": {
"content": {
diff --git a/models/json/beacon-v2-default-model/cohorts/defaultSchema.json b/models/json/beacon-v2-default-model/cohorts/defaultSchema.json
index 95541595a..72449f3a4 100644
--- a/models/json/beacon-v2-default-model/cohorts/defaultSchema.json
+++ b/models/json/beacon-v2-default-model/cohorts/defaultSchema.json
@@ -1,8 +1,6 @@
{
"$comment": "version: ga4gh-beacon-cohort-v2.0.0",
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"CohortCriteria": {
"description": "Criteria used for defining the cohort. It is assumed that all cohort participants will match or NOT match such criteria.",
"properties": {
@@ -20,21 +18,21 @@
"ethnicities": {
"description": "Ethnias in cohort inclusion criteria",
"items": {
- "$ref": "../common/commonDefinitions.json#/definitions/Ethnicity"
+ "$ref": "../common/commonDefinitions.json#/$defs/Ethnicity"
},
"type": "array"
},
"genders": {
"description": "Gender(s) in cohort inclusion criteria",
"items": {
- "$ref": "../common/commonDefinitions.json#/definitions/Sex"
+ "$ref": "../common/commonDefinitions.json#/$defs/Sex"
},
"type": "array"
},
"locations": {
"description": "Geographic location(s) in cohort inclusion criteria",
"items": {
- "$ref": "../common/commonDefinitions.json#/definitions/GeographicLocation"
+ "$ref": "../common/commonDefinitions.json#/$defs/GeographicLocation"
},
"type": "array"
},
@@ -52,7 +50,7 @@
"description": "TBD",
"properties": {
"eventAgeRange": {
- "$ref": "#/definitions/DataAvailabilityAndDistribution",
+ "$ref": "#/$defs/DataAvailabilityAndDistribution",
"description": "Individual age range, obtained from individual level info of the cohort members"
},
"eventCases": {
@@ -72,7 +70,7 @@
"type": "integer"
},
"eventDataTypes": {
- "$ref": "#/definitions/DataAvailabilityAndDistribution",
+ "$ref": "#/$defs/DataAvailabilityAndDistribution",
"description": "Aggregated data type information available for each cohort data type as declared in `cohortDataTypes`, and obtained from individual level info of the cohort members",
"type": "object"
},
@@ -87,19 +85,19 @@
"type": "string"
},
"eventDiseases": {
- "$ref": "#/definitions/DataAvailabilityAndDistribution",
+ "$ref": "#/$defs/DataAvailabilityAndDistribution",
"description": "Aggregated information of disease/condition(s) obtained from individual level info of the cohort members"
},
"eventEthnicities": {
- "$ref": "#/definitions/DataAvailabilityAndDistribution",
+ "$ref": "#/$defs/DataAvailabilityAndDistribution",
"description": "Aggregated information of ethnicity obtained from individual level info of the cohort members"
},
"eventGenders": {
- "$ref": "#/definitions/DataAvailabilityAndDistribution",
+ "$ref": "#/$defs/DataAvailabilityAndDistribution",
"description": "Aggregated information of gender(s) obtained from individual level info of the cohort members"
},
"eventLocations": {
- "$ref": "#/definitions/DataAvailabilityAndDistribution",
+ "$ref": "#/$defs/DataAvailabilityAndDistribution",
"description": "Aggregated information of geographic location obtained from individual level info of the cohort members"
},
"eventNum": {
@@ -113,7 +111,7 @@
"type": "integer"
},
"eventPhenotypes": {
- "$ref": "#/definitions/DataAvailabilityAndDistribution",
+ "$ref": "#/$defs/DataAvailabilityAndDistribution",
"description": "Aggregated information of phenotype(s) obtained from individual level info of the cohort members"
},
"eventSize": {
@@ -208,10 +206,12 @@
"type": "array"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "A cohort available in the beacon.",
"properties": {
"cohortDataTypes": {
- "$ref": "#/definitions/DataTypesArray"
+ "$ref": "#/$defs/DataTypesArray"
},
"cohortDesign": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
@@ -252,12 +252,12 @@
"collectionEvents": {
"description": "TBD",
"items": {
- "$ref": "#/definitions/CollectionEvent"
+ "$ref": "#/$defs/CollectionEvent"
},
"type": "array"
},
"exclusionCriteria": {
- "$ref": "#/definitions/CohortCriteria",
+ "$ref": "#/$defs/CohortCriteria",
"description": "Exclusion criteria used for defining the cohort. It is assumed that NONE of the cohort participants will match such criteria.",
"type": "object"
},
@@ -269,7 +269,7 @@
"type": "string"
},
"inclusionCriteria": {
- "$ref": "#/definitions/CohortCriteria",
+ "$ref": "#/$defs/CohortCriteria",
"description": "Inclusion criteria used for defining the cohort. It is assumed that all cohort participants will match such criteria.",
"type": "object"
},
diff --git a/models/json/beacon-v2-default-model/cohorts/endpoints.json b/models/json/beacon-v2-default-model/cohorts/endpoints.json
index 1e36b7462..7908ea741 100644
--- a/models/json/beacon-v2-default-model/cohorts/endpoints.json
+++ b/models/json/beacon-v2-default-model/cohorts/endpoints.json
@@ -28,7 +28,7 @@
"in": "query",
"name": "limit",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit"
}
},
"requestedSchema": {
@@ -45,7 +45,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip"
}
}
},
@@ -108,7 +108,7 @@
"paths": {
"/cohorts": {
"get": {
- "description": "Get a list of cohorts",
+ "description": "Get a Beacon *cohorts* response",
"operationId": "getCohorts",
"parameters": [
{
@@ -137,7 +137,7 @@
]
},
"post": {
- "description": "Get a list of cohorts",
+ "description": "Get a Beacon *cohorts* response",
"operationId": "postCohortsRequest",
"requestBody": {
"content": {
@@ -219,7 +219,7 @@
},
"/cohorts/{id}/filtering_terms": {
"get": {
- "description": "Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'",
+ "description": "Get a response about the *filtering terms* that could be used with a given cohort, identified by its (unique) 'id'",
"operationId": "getOneCohortFilteringTerms",
"parameters": [
{
@@ -255,7 +255,7 @@
}
],
"post": {
- "description": "Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'",
+ "description": "Get a response about the *filtering terms* that could be used with a given cohort, identified by its (unique) 'id'",
"operationId": "postOneCohortFilteringTerms",
"requestBody": {
"content": {
@@ -290,7 +290,7 @@
},
"/cohorts/{id}/individuals": {
"get": {
- "description": "Get the individuals from one cohort, identified by its (unique) 'id'",
+ "description": "Get an *individuals* response for one cohort, identified by its (unique) 'id'",
"operationId": "getOneCohortIndividuals",
"parameters": [
{
@@ -322,7 +322,7 @@
}
],
"post": {
- "description": "Get the individuals from one cohort, identified by its (unique) 'id'",
+ "description": "Get an *individuals* response for one cohort, identified by its (unique) 'id'",
"operationId": "postOneCohortEntries",
"requestBody": {
"content": {
diff --git a/models/json/beacon-v2-default-model/cohorts/filteringTerms.json b/models/json/beacon-v2-default-model/cohorts/filteringTerms.json
index d53359eb0..9cd753def 100644
--- a/models/json/beacon-v2-default-model/cohorts/filteringTerms.json
+++ b/models/json/beacon-v2-default-model/cohorts/filteringTerms.json
@@ -1,11 +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"
- }
- ]
+ "filteringTerms": []
}
\ No newline at end of file
diff --git a/models/json/beacon-v2-default-model/common/age.json b/models/json/beacon-v2-default-model/common/age.json
index e7f4a6c66..f6b941fde 100644
--- 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"
-}
+}
\ No newline at end of file
diff --git a/models/json/beacon-v2-default-model/common/ageRange.json b/models/json/beacon-v2-default-model/common/ageRange.json
index 31fb79c76..1bb6ff693 100644
--- 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/commonDefinitions.json b/models/json/beacon-v2-default-model/common/commonDefinitions.json
index 197e950ad..73d8c3f61 100644
--- a/models/json/beacon-v2-default-model/common/commonDefinitions.json
+++ b/models/json/beacon-v2-default-model/common/commonDefinitions.json
@@ -1,6 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "definitions": {
+ "$defs": {
"Ethnicity": {
"$ref": "../../../../framework/json/common/ontologyTerm.json",
"description": "Ethnic background of the individual. Recommended is the use of a value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ]",
@@ -148,6 +147,7 @@
]
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Definitions for concepts used in several entry types, but that having only one property are not complex enough to require a full independent schema document.",
"title": "Common Definitions"
}
\ No newline at end of file
diff --git a/models/json/beacon-v2-default-model/common/complexValue.json b/models/json/beacon-v2-default-model/common/complexValue.json
index fd9993392..3dd34192d 100644
--- a/models/json/beacon-v2-default-model/common/complexValue.json
+++ b/models/json/beacon-v2-default-model/common/complexValue.json
@@ -1,6 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "definitions": {
+ "$defs": {
"TypedQuantity": {
"properties": {
"quantity": {
@@ -30,17 +29,20 @@
]
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Definition of a complex value class. Provenance: GA4GH Phenopackets v2 `TypedQuantity`",
"properties": {
"typedQuantities": {
"description": "List of quantities required to fully describe the complex value",
"items": {
- "$ref": "#/definitions/TypedQuantity"
+ "$ref": "#/$defs/TypedQuantity"
},
"type": "array"
}
},
- "required": [ "typedQuantities" ],
+ "required": [
+ "typedQuantities"
+ ],
"title": "Complex Value",
"type": "object"
}
\ No newline at end of file
diff --git a/models/json/beacon-v2-default-model/common/dataUseConditions.json b/models/json/beacon-v2-default-model/common/dataUseConditions.json
index 4c4548a9b..df4aec7fe 100644
--- a/models/json/beacon-v2-default-model/common/dataUseConditions.json
+++ b/models/json/beacon-v2-default-model/common/dataUseConditions.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"DUODataUse": {
"allOf": [
{
@@ -60,11 +58,13 @@
]
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Data use conditions",
"properties": {
"duoDataUse": {
"items": {
- "$ref": "#/definitions/DUODataUse"
+ "$ref": "#/$defs/DUODataUse"
},
"minItems": 1,
"type": "array"
diff --git a/models/json/beacon-v2-default-model/common/disease.json b/models/json/beacon-v2-default-model/common/disease.json
index 5da7a797d..c3b0041cd 100644
--- a/models/json/beacon-v2-default-model/common/disease.json
+++ b/models/json/beacon-v2-default-model/common/disease.json
@@ -6,30 +6,22 @@
"$ref": "./timeElement.json",
"examples": [
{
- "ageGroup": {
- "id": "NCIT:C49685",
- "label": "Adult 18-65 Years Old"
- }
+ "id": "NCIT:C49685",
+ "label": "Adult 18-65 Years Old"
},
{
- "age": {
- "iso8601duration": "P32Y6M1D"
- }
+ "iso8601duration": "P32Y6M1D"
},
{
- "ageRange": {
- "end": {
- "iso8601duration": "P59Y"
- },
- "start": {
- "iso8601duration": "P18Y"
- }
+ "end": {
+ "iso8601duration": "P59Y"
+ },
+ "start": {
+ "iso8601duration": "P18Y"
}
},
{
- "age": {
- "iso8601duration": "P2M4D"
- }
+ "iso8601duration": "P2M4D"
}
]
},
@@ -66,7 +58,7 @@
"type": "string"
},
"severity": {
- "$ref": "./commonDefinitions.json#/definitions/SeverityLevel",
+ "$ref": "./commonDefinitions.json#/$defs/SeverityLevel",
"examples": [
{
"id": "HP:0012828",
diff --git a/models/json/beacon-v2-default-model/common/exposure.json b/models/json/beacon-v2-default-model/common/exposure.json
index 6fd27fd63..9e139e0ca 100644
--- a/models/json/beacon-v2-default-model/common/exposure.json
+++ b/models/json/beacon-v2-default-model/common/exposure.json
@@ -33,7 +33,7 @@
]
},
"unit": {
- "$ref": "../common/commonDefinitions.json#/definitions/Unit",
+ "$ref": "../common/commonDefinitions.json#/$defs/Unit",
"description": "Unit of the exposure. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants."
},
"value": {
diff --git a/models/json/beacon-v2-default-model/common/pedigree.json b/models/json/beacon-v2-default-model/common/pedigree.json
index 2b769f09e..1516d075b 100644
--- a/models/json/beacon-v2-default-model/common/pedigree.json
+++ b/models/json/beacon-v2-default-model/common/pedigree.json
@@ -1,7 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$defs": {
"pedigreeMember": {
"examples": [
{
@@ -97,6 +95,8 @@
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Pedigree studies in which the individual is part of.",
"properties": {
"disease": {
@@ -110,7 +110,7 @@
"members": {
"description": "List of members of the pedigree. If the current pedigree definition is attached to the proband, it contains the whole list of pedigree members, including the proband. If the definition is attached to an individual different than the proband, it only contains two entries: one that describes that member, e.g. the proband mother or father, and one that points to the proband.",
"items": {
- "$ref": "#/definitions/pedigreeMember"
+ "$ref": "#/$defs/pedigreeMember"
},
"minItems": 1,
"type": "array"
diff --git a/models/json/beacon-v2-default-model/common/phenotypicFeature.json b/models/json/beacon-v2-default-model/common/phenotypicFeature.json
index edcf1581f..695e3a1d3 100644
--- a/models/json/beacon-v2-default-model/common/phenotypicFeature.json
+++ b/models/json/beacon-v2-default-model/common/phenotypicFeature.json
@@ -1,6 +1,6 @@
{
+ "$defs": {},
"$schema": "https://json-schema.org/draft/2020-12/schema",
- "definitions": {},
"description": "Used to describe a phenotype that characterizes the subject or biosample.",
"properties": {
"evidence": {
@@ -61,7 +61,7 @@
"description": "Age or time at which the feature resolved or abated."
},
"severity": {
- "$ref": "./commonDefinitions.json#/definitions/SeverityLevel",
+ "$ref": "./commonDefinitions.json#/$defs/SeverityLevel",
"examples": [
{
"id": "HP:0012828",
diff --git a/models/json/beacon-v2-default-model/common/quantity.json b/models/json/beacon-v2-default-model/common/quantity.json
index 1a9969704..c3af5dc07 100644
--- a/models/json/beacon-v2-default-model/common/quantity.json
+++ b/models/json/beacon-v2-default-model/common/quantity.json
@@ -9,7 +9,7 @@
"example": {}
},
"unit": {
- "$ref": "./commonDefinitions.json#/definitions/Unit"
+ "$ref": "./commonDefinitions.json#/$defs/Unit"
},
"value": {
"description": "The value of the quantity in the units",
diff --git a/models/json/beacon-v2-default-model/common/referenceRange.json b/models/json/beacon-v2-default-model/common/referenceRange.json
index 2f538934c..70b45e102 100644
--- a/models/json/beacon-v2-default-model/common/referenceRange.json
+++ b/models/json/beacon-v2-default-model/common/referenceRange.json
@@ -18,7 +18,7 @@
"type": "number"
},
"unit": {
- "$ref": "./commonDefinitions.json#/definitions/Unit",
+ "$ref": "./commonDefinitions.json#/$defs/Unit",
"description": "The kind of unit.",
"examples": [
{
diff --git a/models/json/beacon-v2-default-model/common/timeElement.json b/models/json/beacon-v2-default-model/common/timeElement.json
index a6c00035c..22b26e3f4 100644
--- a/models/json/beacon-v2-default-model/common/timeElement.json
+++ b/models/json/beacon-v2-default-model/common/timeElement.json
@@ -13,7 +13,7 @@
"$ref": "./gestationalAge.json"
},
{
- "$ref": "./commonDefinitions.json#/definitions/Timestamp"
+ "$ref": "./commonDefinitions.json#/$defs/Timestamp"
},
{
"$ref": "./timeInterval.json"
diff --git a/models/json/beacon-v2-default-model/common/timeInterval.json b/models/json/beacon-v2-default-model/common/timeInterval.json
index 1d4a2a475..94f8b9862 100644
--- a/models/json/beacon-v2-default-model/common/timeInterval.json
+++ b/models/json/beacon-v2-default-model/common/timeInterval.json
@@ -5,13 +5,13 @@
"description": "Time interval with start and end defined as ISO8601 time stamps.",
"properties": {
"end": {
- "$ref": "./commonDefinitions.json#/definitions/Timestamp",
+ "$ref": "./commonDefinitions.json#/$defs/Timestamp",
"examples": [
"2022-03-10T15:25:07Z"
]
},
"start": {
- "$ref": "./commonDefinitions.json#/definitions/Timestamp",
+ "$ref": "./commonDefinitions.json#/$defs/Timestamp",
"examples": [
"1999-08-05T17:21:00+01:00",
"2002-09-21T02:37:00-08:00"
diff --git a/models/json/beacon-v2-default-model/datasets/defaultSchema.json b/models/json/beacon-v2-default-model/datasets/defaultSchema.json
index 41acb023d..51e28141c 100644
--- a/models/json/beacon-v2-default-model/datasets/defaultSchema.json
+++ b/models/json/beacon-v2-default-model/datasets/defaultSchema.json
@@ -5,7 +5,7 @@
"description": "A dataset available in the beacon",
"properties": {
"createDateTime": {
- "$ref": "../common/commonDefinitions.json#/definitions/Timestamp",
+ "$ref": "../common/commonDefinitions.json#/$defs/Timestamp",
"description": "The time the dataset was created (ISO 8601 format)",
"examples": [
"2017-01-17T20:33:40Z"
@@ -37,7 +37,7 @@
"type": "string"
},
"info": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info"
+ "$ref": "../common/info.json"
},
"name": {
"description": "Name of the dataset",
@@ -47,7 +47,7 @@
"type": "string"
},
"updateDateTime": {
- "$ref": "../common/commonDefinitions.json#/definitions/Timestamp",
+ "$ref": "../common/commonDefinitions.json#/$defs/Timestamp",
"description": "The time the dataset was updated in (ISO 8601 format)",
"examples": [
"2017-01-17T20:33:40Z"
diff --git a/models/json/beacon-v2-default-model/datasets/endpoints.json b/models/json/beacon-v2-default-model/datasets/endpoints.json
index 3fdc832a4..29994ad6d 100644
--- a/models/json/beacon-v2-default-model/datasets/endpoints.json
+++ b/models/json/beacon-v2-default-model/datasets/endpoints.json
@@ -26,7 +26,7 @@
"in": "query",
"name": "limit",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit"
}
},
"requestedSchema": {
@@ -43,7 +43,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip"
}
}
},
@@ -135,7 +135,7 @@
]
},
"post": {
- "description": "Get a list of datasets",
+ "description": "Get a Beacon *datasets* response",
"operationId": "postDatasetsRequest",
"requestBody": {
"content": {
@@ -217,7 +217,7 @@
},
"/datasets/{id}/biosamples": {
"get": {
- "description": "Get the biosamples list from one dataset, identified by its (unique) 'id'",
+ "description": "Get a *biosamples* response for one dataset, identified by its (unique) 'id'",
"operationId": "getOneDatasetBiosamples",
"parameters": [
{
@@ -249,7 +249,7 @@
}
],
"post": {
- "description": "Get the biosamples list from one dataset, identified by its (unique) 'id'",
+ "description": "Get a *biosamples* response for one dataset, identified by its (unique) 'id'",
"operationId": "postOneDatasetBiosamples",
"requestBody": {
"content": {
@@ -277,7 +277,7 @@
},
"/datasets/{id}/filtering_terms": {
"get": {
- "description": "Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id'",
+ "description": "Get a response about the *filtering terms* that could be used with a given dataset, identified by its (unique) 'id'",
"operationId": "getOneDatasetFilteringTerms",
"parameters": [
{
@@ -313,7 +313,7 @@
}
],
"post": {
- "description": "Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id'",
+ "description": "Get a response about the *filtering terms* that could be used with a given dataset, identified by its (unique) 'id'",
"operationId": "postOneDatasetFilteringTerms",
"requestBody": {
"content": {
@@ -348,7 +348,7 @@
},
"/datasets/{id}/g_variants": {
"get": {
- "description": "Get the genomic variants list from one dataset, identified by its (unique) 'id'",
+ "description": "Get a *genomic variations* response for one dataset, identified by its (unique) 'id'",
"operationId": "getOneDatasetEntries",
"parameters": [
{
@@ -380,7 +380,7 @@
}
],
"post": {
- "description": "Get the genomic variants list from one dataset, identified by its (unique) 'id'",
+ "description": "Get a *genomic variations* response for one dataset, identified by its (unique) 'id'",
"operationId": "postOneDatasetEntries",
"requestBody": {
"content": {
@@ -408,7 +408,7 @@
},
"/datasets/{id}/individuals": {
"get": {
- "description": "Get the individuals list from one dataset, identified by its (unique) 'id'",
+ "description": "Get an *individuals* response for one dataset, identified by its (unique) 'id'",
"operationId": "getOneDatasetIndividuals",
"parameters": [
{
@@ -440,7 +440,7 @@
}
],
"post": {
- "description": "Get the biosamples list from one dataset, identified by its (unique) 'id'",
+ "description": "Get an *individuals* response for one dataset, identified by its (unique) 'id'",
"operationId": "postOneDatasetIndividuals",
"requestBody": {
"content": {
diff --git a/models/json/beacon-v2-default-model/datasets/filteringTerms.json b/models/json/beacon-v2-default-model/datasets/filteringTerms.json
index d53359eb0..9cd753def 100644
--- a/models/json/beacon-v2-default-model/datasets/filteringTerms.json
+++ b/models/json/beacon-v2-default-model/datasets/filteringTerms.json
@@ -1,11 +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"
- }
- ]
+ "filteringTerms": []
}
\ No newline at end of file
diff --git a/models/json/beacon-v2-default-model/endpoints.json b/models/json/beacon-v2-default-model/endpoints.json
index 9c72ad0ef..0116f2fdf 100644
--- a/models/json/beacon-v2-default-model/endpoints.json
+++ b/models/json/beacon-v2-default-model/endpoints.json
@@ -5,7 +5,7 @@
"in": "query",
"name": "limit",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit"
}
},
"requestedSchema": {
@@ -22,7 +22,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip"
}
}
},
diff --git a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
index fc3b7f047..19d42db14 100644
--- a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
+++ b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
@@ -1,8 +1,6 @@
{
- "$comment": "version: ga4gh-beacon-variant-v2.0.0",
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "additionalProperties": true,
- "definitions": {
+ "$comment": "version: ga4gh-beacon-variant-v2.1.0",
+ "$defs": {
"CaseLevelVariant": {
"description": "",
"properties": {
@@ -56,7 +54,7 @@
},
"clinicalInterpretations": {
"items": {
- "$ref": "#/definitions/PhenoClinicEffect"
+ "$ref": "#/$defs/PhenoClinicEffect"
},
"type": "array"
},
@@ -76,7 +74,7 @@
},
"phenotypicEffects": {
"items": {
- "$ref": "#/definitions/PhenoClinicEffect"
+ "$ref": "#/$defs/PhenoClinicEffect"
},
"type": "array"
},
@@ -115,7 +113,7 @@
"properties": {
"frequencies": {
"items": {
- "$ref": "#/definitions/PopulationFrequency"
+ "$ref": "#/$defs/PopulationFrequency"
},
"minItems": 1,
"type": "array"
@@ -274,7 +272,7 @@
"type": "string"
},
"location": {
- "$ref": "https://raw.githubusercontent.com/ga4gh/vrs/main/schema/vrs.json#/definitions/Location"
+ "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location"
},
"referenceBases": {
"description": "Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`.",
@@ -340,7 +338,7 @@
"genomicFeatures": {
"description": "List of Genomic feature(s) affected by the variant.",
"items": {
- "$ref": "#/definitions/GenomicFeature"
+ "$ref": "#/$defs/GenomicFeature"
},
"type": "array"
},
@@ -368,7 +366,7 @@
"description": "List of annotated effects on disease or phenotypes.",
"properties": {
"annotatedWith": {
- "$ref": "#/definitions/SoftwareTool"
+ "$ref": "#/$defs/SoftwareTool"
},
"category": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
@@ -508,13 +506,13 @@
"properties": {
"clinicalInterpretations": {
"items": {
- "$ref": "#/definitions/PhenoClinicEffect"
+ "$ref": "#/$defs/PhenoClinicEffect"
},
"type": "array"
},
"phenotypicEffects": {
"items": {
- "$ref": "#/definitions/PhenoClinicEffect"
+ "$ref": "#/$defs/PhenoClinicEffect"
},
"type": "array"
}
@@ -522,26 +520,28 @@
"type": "object"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "additionalProperties": true,
"description": "Schema for a genomic variant entry.",
"properties": {
"caseLevelData": {
"description": "caseLevelData reports about the variation instances observed in individual analyses.",
"items": {
- "$ref": "#/definitions/CaseLevelVariant"
+ "$ref": "#/$defs/CaseLevelVariant"
},
"type": "array"
},
"frequencyInPopulations": {
"items": {
- "$ref": "#/definitions/FrequencyInPopulations"
+ "$ref": "#/$defs/FrequencyInPopulations"
},
"type": "array"
},
"identifiers": {
- "$ref": "#/definitions/Identifiers"
+ "$ref": "#/$defs/Identifiers"
},
"molecularAttributes": {
- "$ref": "#/definitions/MolecularAttributes"
+ "$ref": "#/$defs/MolecularAttributes"
},
"variantInternalId": {
"description": "Reference to the **internal** variant ID. This represents the primary key/identifier of that variant **inside** a given Beacon instance. Different Beacon instances may use identical id values, referring to unrelated variants. Public identifiers such as the GA4GH Variant Representation Id (VRSid) MUST be returned in the `identifiers` section. A Beacon instance can, of course, use the VRSid as their own internal id but still MUST represent this then in the `identifiers` section.",
@@ -552,18 +552,18 @@
"type": "string"
},
"variantLevelData": {
- "$ref": "#/definitions/VariantLevelData"
+ "$ref": "#/$defs/VariantLevelData"
},
"variation": {
"oneOf": [
{
- "$ref": "https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/MolecularVariation"
+ "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation"
},
{
- "$ref": "https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/SystemicVariation"
+ "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation"
},
{
- "$ref": "#/definitions/LegacyVariation"
+ "$ref": "#/$defs/LegacyVariation"
}
]
}
diff --git a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json
index e9101f04f..362d4a44c 100644
--- a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json
+++ b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json
@@ -81,13 +81,13 @@
}
},
"includeResultsetResponses": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses"
},
"limit": {
"in": "query",
"name": "limit",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit"
}
},
"referenceBases": {
@@ -118,7 +118,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip"
}
},
"start": {
@@ -193,8 +193,8 @@
"paths": {
"/g_variants": {
"get": {
- "description": "Get a list of example entries",
- "operationId": "getExampleEntries",
+ "description": "Get a Beacon response for genomic variations",
+ "operationId": "getGenomicVariations",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
@@ -258,8 +258,8 @@
]
},
"post": {
- "description": "Get a list of example entries",
- "operationId": "postExampleEntriesRequest",
+ "description": "Get a Beacon response for genomic variations",
+ "operationId": "postGenomicVariationsRequest",
"requestBody": {
"content": {
"application/json": {
@@ -335,8 +335,8 @@
},
"/g_variants/{id}/biosamples": {
"get": {
- "description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'",
- "operationId": "getOneGenomicVariantBiosamples",
+ "description": "Get a *biosamples* response from one genomic variant, identified by its (unique) 'id'",
+ "operationId": "getOneGenomicVariationBiosamples",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
@@ -367,8 +367,8 @@
}
],
"post": {
- "description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'",
- "operationId": "postOneGenomicVariantBiosamples",
+ "description": "Get a *biosamples* response from one genomic variant, identified by its (unique) 'id'",
+ "operationId": "postOneGenomicVariationBiosamples",
"requestBody": {
"content": {
"application/json": {
@@ -395,8 +395,8 @@
},
"/g_variants/{id}/individuals": {
"get": {
- "description": "Get the individuals list from one genomic variant, identified by its (unique) 'id'",
- "operationId": "getOneGenomicVariantIndividuals",
+ "description": "Get an *individuals* response from one genomic variant, identified by its (unique) 'id'",
+ "operationId": "getOneGenomicVariationIndividuals",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
@@ -427,8 +427,8 @@
}
],
"post": {
- "description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'",
- "operationId": "postOneGenomicVariantIndividuals",
+ "description": "Get an *individuals* response from one genomic variant, identified by its (unique) 'id'",
+ "operationId": "postOneGenomicVariationIndividuals",
"requestBody": {
"content": {
"application/json": {
diff --git a/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json b/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json
index 3241f2272..9cd753def 100644
--- a/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json
+++ b/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json
@@ -1,13 +1,4 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
- "filteringTerms": [
- {
- "ftType": "alphanumeric",
- "id": "gene"
- },
- {
- "ftType": "alphanumeric",
- "id": "aminoacidChanges"
- }
- ]
+ "filteringTerms": []
}
\ No newline at end of file
diff --git a/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json b/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json
index 48381aaf7..0651ccf29 100644
--- a/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json
+++ b/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json
@@ -3,7 +3,7 @@
"g_variant": {
"properties": {
"alternateBases": {
- "$ref": "./requestParametersComponents.json#/definitions/AlternateBases"
+ "$ref": "./requestParametersComponents.json#/$defs/AlternateBases"
},
"aminoacidChange": {
"description": "Aminoacid alteration of interest. Format 1 letter",
@@ -14,7 +14,7 @@
"type": "string"
},
"assemblyId": {
- "$ref": "./requestParametersComponents.json#/definitions/Assembly"
+ "$ref": "./requestParametersComponents.json#/$defs/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]).\"",
@@ -24,7 +24,7 @@
"type": "integer"
},
"maxItems": 2,
- "minItems": 0,
+ "minItems": 1,
"type": "array"
},
"geneId": {
@@ -43,16 +43,16 @@
"type": "string"
},
"mateName": {
- "$ref": "./requestParametersComponents.json#/definitions/RefSeqId"
+ "$ref": "./requestParametersComponents.json#/$defs/RefSeqId"
},
"referenceBases": {
- "$ref": "./requestParametersComponents.json#/definitions/ReferenceBases"
+ "$ref": "./requestParametersComponents.json#/$defs/ReferenceBases"
},
"referenceName": {
- "$ref": "./requestParametersComponents.json#/definitions/RefSeqId"
+ "$ref": "./requestParametersComponents.json#/$defs/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\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,
diff --git a/models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json b/models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json
index 60ff1da6e..fbe5026cb 100644
--- a/models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json
+++ b/models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json
@@ -1,6 +1,5 @@
{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "definitions": {
+ "$defs": {
"AlternateBases": {
"description": "Alternate bases for this variant (starting from `start`). * Accepted values: `[ACGTN]*` * The current specification supports allelic variants, **not** genotype queries\n (i.e. multiple co-occurring alleles).\n* N is a wildcard, that denotes the position of any base,\n and can be used as a standalone base of any type or within a partially known\n sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT]\n and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.\n* an *empty value* is used in the case of deletions with the maximally trimmed,\n deleted sequence being indicated in `ReferenceBases`\n* Categorical variant queries, e.g. such *not* being represented through\n sequence & position, make use of the `variantType` parameter.",
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
@@ -30,5 +29,6 @@
"type": "string"
}
},
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
"description": "Component definitions used in `requestParameters`."
}
\ No newline at end of file
diff --git a/models/json/beacon-v2-default-model/individuals/defaultSchema.json b/models/json/beacon-v2-default-model/individuals/defaultSchema.json
index 69f989a65..c916b09bd 100644
--- a/models/json/beacon-v2-default-model/individuals/defaultSchema.json
+++ b/models/json/beacon-v2-default-model/individuals/defaultSchema.json
@@ -12,7 +12,7 @@
"type": "array"
},
"ethnicity": {
- "$ref": "../common/commonDefinitions.json#/definitions/Ethnicity",
+ "$ref": "../common/commonDefinitions.json#/$defs/Ethnicity",
"description": "Ethnic background of the individual. Value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ] "
},
"exposures": {
@@ -22,7 +22,7 @@
"type": "array"
},
"geographicOrigin": {
- "$ref": "../common/commonDefinitions.json#/definitions/GeographicLocation",
+ "$ref": "../common/commonDefinitions.json#/$defs/GeographicLocation",
"description": "Individual's country or region of origin (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America)."
},
"id": {
@@ -31,7 +31,7 @@
"type": "string"
},
"info": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info"
+ "$ref": "../common/info.json"
},
"interventionsOrProcedures": {
"items": {
@@ -40,7 +40,7 @@
"type": "array"
},
"karyotypicSex": {
- "$ref": "../common/commonDefinitions.json#/definitions/KaryotypicSex",
+ "$ref": "../common/commonDefinitions.json#/$defs/KaryotypicSex",
"description": "The chromosomal sex of an individual represented from a selection of options."
},
"measures": {
@@ -62,8 +62,8 @@
"type": "array"
},
"sex": {
- "$ref": "../common/commonDefinitions.json#/definitions/Sex",
- "description": "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197)."
+ "$ref": "../common/commonDefinitions.json#/$defs/Sex",
+ "description": "Sex of the individual. Value from NCIT General Qualifier `NCIT:C27993`: * `unknown`: not assessed or not availablel `NCIT:C17998` * `female`: `NCIT:C16576` * `male`: `NCIT:C20197`"
},
"treatments": {
"items": {
diff --git a/models/json/beacon-v2-default-model/individuals/endpoints.json b/models/json/beacon-v2-default-model/individuals/endpoints.json
index 32898cb17..cd7d307c1 100644
--- a/models/json/beacon-v2-default-model/individuals/endpoints.json
+++ b/models/json/beacon-v2-default-model/individuals/endpoints.json
@@ -25,13 +25,13 @@
}
},
"includeResultsetResponses": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses"
},
"limit": {
"in": "query",
"name": "limit",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit"
}
},
"requestedSchema": {
@@ -48,7 +48,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip"
}
}
},
@@ -123,7 +123,7 @@
]
},
"post": {
- "description": "Get a list of example entries",
+ "description": "Get a Beacon response for individuals",
"operationId": "postIndividualsRequest",
"requestBody": {
"content": {
@@ -238,7 +238,7 @@
}
],
"post": {
- "description": "Get details about one Individual, identified by its (unique) 'id'",
+ "description": "Get details about one individual, identified by its (unique) 'id'",
"operationId": "postOneIndividual",
"requestBody": {
"content": {
@@ -266,7 +266,7 @@
},
"/individuals/{id}/biosamples": {
"get": {
- "description": "Get the biosamples list from one individual, identified by its (unique) 'id'",
+ "description": "Get a *biosamples* response for one individual, identified by its (unique) 'id'",
"operationId": "getOneIndividualBiosamples",
"parameters": [
{
@@ -298,7 +298,7 @@
}
],
"post": {
- "description": "Get the biosamples list from one individual, identified by its (unique) 'id'",
+ "description": "Get a *biosamples* response for one individual, identified by its (unique) 'id'",
"operationId": "postOneIndividualBiosamples",
"requestBody": {
"content": {
@@ -326,7 +326,7 @@
},
"/individuals/{id}/g_variants": {
"get": {
- "description": "Get the genomic variants list from one individual, identified by its (unique) 'id'",
+ "description": "Get a *genomic variations* response for one individual, identified by its (unique) 'id'",
"operationId": "getOneIndividualGenomicVariants",
"parameters": [
{
@@ -358,7 +358,7 @@
}
],
"post": {
- "description": "Get the genomic variants list from one individual, identified by its (unique) 'id'",
+ "description": "Get a *genomic variations* response for one individual, identified by its (unique) 'id'",
"operationId": "potOneIndividualGenomicVariants",
"requestBody": {
"content": {
diff --git a/models/json/beacon-v2-default-model/runs/defaultSchema.json b/models/json/beacon-v2-default-model/runs/defaultSchema.json
index 6e49d8dfb..e3f4040d9 100644
--- a/models/json/beacon-v2-default-model/runs/defaultSchema.json
+++ b/models/json/beacon-v2-default-model/runs/defaultSchema.json
@@ -26,7 +26,7 @@
"type": "string"
},
"info": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info"
+ "$ref": "../common/info.json"
},
"libraryLayout": {
"description": "Ontology value for the library layout e.g \"PAIRED\", \"SINGLE\" #todo add Ontology name?",
diff --git a/models/json/beacon-v2-default-model/runs/endpoints.json b/models/json/beacon-v2-default-model/runs/endpoints.json
index b5084bba7..70ade3bce 100644
--- a/models/json/beacon-v2-default-model/runs/endpoints.json
+++ b/models/json/beacon-v2-default-model/runs/endpoints.json
@@ -33,7 +33,7 @@
}
},
"includeResultsetResponses": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses"
},
"individualId": {
"in": "path",
@@ -47,7 +47,7 @@
"in": "query",
"name": "limit",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit"
}
},
"requestedSchema": {
@@ -64,7 +64,7 @@
"in": "query",
"name": "skip",
"schema": {
- "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip"
+ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip"
}
}
},
@@ -107,7 +107,7 @@
"paths": {
"/runs": {
"get": {
- "description": "Get a list of sequencing runs",
+ "description": "Get a Beacon response for experimental runs",
"operationId": "getRuns",
"parameters": [
{
@@ -139,7 +139,7 @@
]
},
"post": {
- "description": "Get a list of sequencing runs",
+ "description": "Get a Beacon response for experimental runs",
"operationId": "postRunsRequest",
"requestBody": {
"content": {
@@ -167,7 +167,7 @@
},
"/runs/{id}": {
"get": {
- "description": "Get details about one sequencing run, identified by its (unique) 'id'",
+ "description": "Get details about one experimental run, identified by its (unique) 'id'",
"operationId": "getOneRun",
"responses": {
"200": {
@@ -188,7 +188,7 @@
}
],
"post": {
- "description": "Get details about one Run, identified by its (unique) 'id'",
+ "description": "Get details about one experimental run, identified by its (unique) 'id'",
"operationId": "postOneRun",
"requestBody": {
"content": {
@@ -216,7 +216,7 @@
},
"/runs/{id}/analyses": {
"get": {
- "description": "Get the analysis list from one sequencing run, identified by its (unique) 'id'",
+ "description": "Get a *analyses* response for one experimental run, identified by its (unique) 'id'",
"operationId": "getOneRunAnalysis",
"parameters": [
{
@@ -248,7 +248,7 @@
}
],
"post": {
- "description": "Get the analysis list from one sequencing run, identified by its (unique) 'id'",
+ "description": "Get a *analyses* response for one experimental run, identified by its (unique) 'id'",
"operationId": "postOneRunAnalysis",
"requestBody": {
"content": {
@@ -276,8 +276,8 @@
},
"/runs/{id}/g_variants": {
"get": {
- "description": "Get the genomic variants list from one run, identified by its (unique) 'id'",
- "operationId": "getOneRunGenomicVariants",
+ "description": "Get a *genomic variations* response for one experimental run, identified by its (unique) 'id'",
+ "operationId": "getOneRunGenomicVariations",
"parameters": [
{
"$ref": "#/components/parameters/requestedSchema"
@@ -308,8 +308,8 @@
}
],
"post": {
- "description": "Get the genomic variants list from one run, identified by its (unique) 'id'",
- "operationId": "potOneRunGenomicVariants",
+ "description": "Get a *genomic variations* response for one experimental run, identified by its (unique) 'id'",
+ "operationId": "potOneRunGenomicVariations",
"requestBody": {
"content": {
"application/json": {
diff --git a/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml b/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml
index 8eb87b5be..7622118fc 100644
--- a/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml
+++ b/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml
@@ -1,57 +1,70 @@
$schema: https://json-schema.org/draft/2020-12/schema
-title: Sequencing bioinformatics analysis
+title: Bioinformatics analysis
$comment: 'version: ga4gh-beacon-analysis-v2.0.0'
-description: Schema for a sequencing bioinformatics analysis.
+description: >-
+ The `analysis` schema represents a information about the data analysis steps
+ leading to (a set of) genomic variation call(s).
type: object
properties:
id:
- description: Analysis reference ID (external accession or internal ID)
+ description: >-
+ Analysis id for internal referencing; unique in the dataset.
type: string
runId:
- description: Run identifier (external accession or internal ID).
+ description: >-
+ Local reference to the associated experimental run.
type: string
examples:
- SRR10903401
biosampleId:
- description: Reference to the `id` of the biosample this analysis is reporting
- on.
+ description: >-
+ Local reference to the `id` of the biosample this analysis is reporting on.
type: string
examples:
- S0001
+ - onekgbs-NA07346
individualId:
- description: Reference to the `id` of the individual this analysis is reporting
- on.
+ description: >-
+ Local reference to the `id` of the individual this analysis is reporting on.
type: string
examples:
- P0001
+ - onekgind-NA07346
analysisDate:
- description: Date at which analysis was performed.
+ description: >
+ Date at which analysis was performed.
type: string
format: date
examples:
- '2021-10-17'
pipelineName:
- description: Analysis pipeline and version if a standardized pipeline was used
+ description: >-
+ Analysis pipeline and version.
type: string
examples:
- Pipeline-panel-0001-v1
pipelineRef:
- description: Link to Analysis pipeline resource
+ description: >-
+ Link to information about or repository of the analysis pipeline.
type: string
examples:
- https://doi.org/10.48511/workflowhub.workflow.111.1
+ - https://doi.org/10.1093/bib/bbad541
aligner:
- description: Reference to mapping/alignment software
+ description: >-
+ Name or identifier of the mapping/alignment software/pipeline
type: string
examples:
- bwa-0.7.8
variantCaller:
- description: Reference to variant calling software / pipeline
+ description: >-
+ Name or identifier of the variant calling software/pipeline
type: string
examples:
- GATK4.0
+ - labelSeg
info:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info
+ $ref: ../common/info.yaml
required:
- id
- analysisDate
diff --git a/models/src/beacon-v2-default-model/analyses/endpoints.yaml b/models/src/beacon-v2-default-model/analyses/endpoints.yaml
index 8f5d5457a..fed2b1661 100644
--- a/models/src/beacon-v2-default-model/analyses/endpoints.yaml
+++ b/models/src/beacon-v2-default-model/analyses/endpoints.yaml
@@ -18,7 +18,7 @@ paths:
- $ref: '#/components/parameters/limit'
- $ref: '#/components/parameters/includeResultsetResponses'
- $ref: '#/components/parameters/filters'
- description: Get a list of bioinformatics analysis
+ description: Get a Beacon response for bioinformatics analyses
operationId: getAnalyses
tags:
- GET Endpoints
@@ -28,7 +28,7 @@ paths:
default:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get a list of bioinformatics analysis
+ description: Get a Beacon response for bioinformatics analyses
operationId: postAnalysesRequest
tags:
- POST Endpoints
@@ -52,7 +52,8 @@ paths:
parameters:
- $ref: '#/components/parameters/entryId'
get:
- description: Get details about one bioinformatics analysis, identified by its
+ description: >-
+ Get details about one bioinformatics analysis, identified by its
(unique) 'id'
operationId: getOneAnalysis
tags:
@@ -64,7 +65,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get details about one bioinformatics analysis, identified by its
+ description: >-
+ Get details about one bioinformatics analysis, identified by its
(unique) 'id'
operationId: postOneAnalysisRequest
tags:
@@ -89,9 +91,10 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the list of variants instances for one bioinformatics analysis,
+ description: >-
+ Get a *genomic variations* response for one bioinformatics analysis,
identified by its (unique) 'id'
- operationId: getOneAnalysisVariants
+ operationId: getOneAnalysisVariationsRequest
tags:
- GET Endpoints
responses:
@@ -101,9 +104,10 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the list of variants instances for one bioinformatics analysis,
+ description: >-
+ Get a *genomic variations* response for one bioinformatics analysis,
identified by its (unique) 'id'
- operationId: postOneAnalysisVariantsRequest
+ operationId: postOneAnalysisVariationsRequest
tags:
- POST Endpoints
requestBody:
@@ -143,14 +147,14 @@ components:
name: skip
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit
includeResultsetResponses:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses
entryId:
name: id
in: path
diff --git a/models/src/beacon-v2-default-model/beaconMap.yaml b/models/src/beacon-v2-default-model/beaconMap.yaml
index 3da0cd2a4..823d60f74 100644
--- a/models/src/beacon-v2-default-model/beaconMap.yaml
+++ b/models/src/beacon-v2-default-model/beaconMap.yaml
@@ -1,119 +1,119 @@
$schema: https://json-schema.org/draft/2020-12/schema
endpointSets:
- dataset:
+ datasetEndpoints:
entryType: dataset
openAPIEndpointsDefinition: https://exampleBeacons.org/datasets/endpoints.json
rootUrl: https://exampleBeacons.org/datasets
singleEntryUrl: https://exampleBeacons.org/datasets/{id}
filteringTermsUrl: https://exampleBeacons.org/datasets/{id}/filtering_terms
endpoints:
- genomicVariant:
+ genomicVariantLookup:
returnedEntryType: genomicVariant
url: https://exampleBeacons.org/datasets/{id}/g_variants
- biosample:
+ biosampleLookup:
returnedEntryType: biosample
url: https://exampleBeacons.org/datasets/{id}/biosamples
- individual:
+ individualLookup:
returnedEntryType: individual
url: https://exampleBeacons.org/datasets/{id}/individuals
- runs:
+ runLookup:
returnedEntryType: run
url: https://exampleBeacons.org/datasets/{id}/runs
- analyses:
+ analysisLookup:
returnedEntryType: analysis
url: https://exampleBeacons.org/datasets/{id}/analyses
- cohort:
+ cohortEndpoints:
entryType: cohort
openAPIEndpointsDefinition: https://exampleBeacons.org/cohorts/endpoints.json
rootUrl: https://exampleBeacons.org/cohorts
singleEntryUrl: https://exampleBeacons.org/cohorts/{id}
filteringTermsUrl: https://exampleBeacons.org/cohorts/{id}/filtering_terms
endpoints:
- individual:
+ individualLookup:
returnedEntryType: individual
url: https://exampleBeacons.org/cohorts/{id}/individuals
- genomicVariant:
+ genomicVariantLookup:
returnedEntryType: genomicVariant
url: https://exampleBeacons.org/cohorts/{id}/g_variants
- biosample:
+ biosampleLookup:
returnedEntryType: biosample
url: https://exampleBeacons.org/cohorts/{id}/biosamples
- runs:
+ runLookup:
returnedEntryType: run
url: https://exampleBeacons.org/cohorts/{id}/runs
- analyses:
+ analysisLookup:
returnedEntryType: analysis
url: https://exampleBeacons.org/cohorts/{id}/analyses
- genomicVariant:
+ genomicVariantEndpoints:
entryType: genomicVariant
openAPIEndpointsDefinition: https://exampleBeacons.org/genomicVariations/endpoints.json
rootUrl: https://exampleBeacons.org/g_variants
singleEntryUrl: https://exampleBeacons.org/g_variants/{id}
endpoints:
- biosample:
+ biosampleLookup:
returnedEntryType: biosample
url: https://exampleBeacons.org/g_variants/{id}/biosamples
- individual:
+ individualLookup:
returnedEntryType: individual
url: https://exampleBeacons.org/g_variants/{id}/individuals
- runs:
+ runLookup:
returnedEntryType: run
url: https://exampleBeacons.org/g_variants/{id}/runs
- analyses:
+ analysisLookup:
returnedEntryType: analysis
url: https://exampleBeacons.org/g_variants/{id}/analyses
- individual:
+ individualEndpoints:
entryType: individual
openAPIEndpointsDefinition: https://exampleBeacons.org/individuals/endpoints.json
rootUrl: https://exampleBeacons.org/individuals
singleEntryUrl: https://exampleBeacons.org/individuals/{id}
filteringTermsUrl: https://exampleBeacons.org/individuals/{id}/filtering_terms
endpoints:
- genomicVariant:
+ genomicVariantLookup:
returnedEntryType: genomicVariant
url: https://exampleBeacons.org/individuals/{id}/g_variants
- biosample:
+ biosampleLookup:
returnedEntryType: biosample
url: https://exampleBeacons.org/individuals/{id}/biosamples
- runs:
+ runLookup:
returnedEntryType: run
url: https://exampleBeacons.org/individuals/{id}/runs
- analyses:
+ analysisLookup:
returnedEntryType: analysis
url: https://exampleBeacons.org/individuals/{id}/analyses
- biosample:
+ biosampleEndpoints:
entryType: biosample
openAPIEndpointsDefinition: https://exampleBeacons.org/biosamples/endpoints.json
rootUrl: https://exampleBeacons.org/biosamples
singleEntryUrl: https://exampleBeacons.org/biosamples/{id}
endpoints:
- run:
+ runLookup:
returnedEntryType: run
url: https://exampleBeacons.org/biosamples/{id}/runs
- analysis:
+ analysisLookup:
returnedEntryType: analysis
url: https://exampleBeacons.org/biosamples/{id}/analyses
- genomicVariant:
+ genomicVariantLookup:
returnedEntryType: genomicVariant
url: https://exampleBeacons.org/biosamples/{id}/g_variants
- run:
+ runEndpoints:
entryType: run
openAPIEndpointsDefinition: https://exampleBeacons.org/runs/endpoints.json
rootUrl: https://exampleBeacons.org/runs
singleEntryUrl: https://exampleBeacons.org/runs/{id}
endpoints:
- analysis:
+ analysisLookup:
returnedEntryType: analysis
url: https://exampleBeacons.org/runs/{id}/analyses
- genomicVariant:
+ genomicVariantLookup:
returnedEntryType: genomicVariant
url: https://exampleBeacons.org/runs/{id}/g_variants
- analysis:
+ analysisEndpoints:
entryType: analysis
openAPIEndpointsDefinition: https://exampleBeacons.org/analyses/endpoints.json
rootUrl: https://exampleBeacons.org/analyses
singleEntryUrl: https://exampleBeacons.org/analyses/{id}
endpoints:
- genomicVariant:
+ genomicVariantLookup:
returnedEntryType: genomicVariant
url: https://exampleBeacons.org/analyses/{id}/g_variants
diff --git a/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml b/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml
index 8a9b7eae7..c90eda4d0 100644
--- a/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml
+++ b/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml
@@ -160,7 +160,7 @@ properties:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json
example: {}
info:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info
+ $ref: ../common/info.yaml
required:
- id
- biosampleStatus
diff --git a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml
index 50b80d8bb..8595c1732 100644
--- a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml
+++ b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml
@@ -18,7 +18,7 @@ paths:
- $ref: '#/components/parameters/limit'
- $ref: '#/components/parameters/includeResultsetResponses'
- $ref: '#/components/parameters/filters'
- description: Get a list of biosamples
+ description: Get a Beacon response for biosamples
operationId: getBiosamples
tags:
- GET Endpoints
@@ -28,7 +28,7 @@ paths:
default:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get a list of biosamples
+ description: Get a Beacon response for biosamples
operationId: postBiosamplesRequest
tags:
- POST Endpoints
@@ -48,7 +48,8 @@ paths:
parameters:
- $ref: '#/components/parameters/entryId'
get:
- description: Get details about one biosample, identified by its (unique) 'id'
+ description: >-
+ Get details about one biosample, identified by its (unique) 'id'
operationId: getOneBiosample
tags:
- GET Endpoints
@@ -59,7 +60,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get details about one Biosample, identified by its (unique) 'id'
+ description: >-
+ Get details about one Biosample, identified by its (unique) 'id'
operationId: postOneBiosample
tags:
- POST Endpoints
@@ -83,9 +85,10 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the genomic variants list from one biosample, identified by
+ description: >-
+ Get a *genomic variations* response from one biosample, identified by
its (unique) 'id'
- operationId: getOneBiosampleGenomicVariants
+ operationId: getOneBiosampleGenomicVariations
tags:
- GET Endpoints
responses:
@@ -95,9 +98,10 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the genomic variants list from one biosample, identified by
+ description: >-
+ Get a *genomic variations* response from one biosample, identified by
its (unique) 'id'
- operationId: postOneBiosampleGenomicVariants
+ operationId: postOneBiosampleGenomicVariations
tags:
- POST Endpoints
requestBody:
@@ -120,9 +124,10 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the analysis list from one biosample, identified by its (unique)
- 'id'
- operationId: getOneBiosampleAnalysis
+ description: >-
+ Get an *analyses* response from one biosample, identified by its
+ (unique) 'id'
+ operationId: getOneBiosampleAnalyses
tags:
- GET Endpoints
responses:
@@ -132,9 +137,10 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the analysis list from one biosample, identified by its (unique)
- 'id'
- operationId: postOneBiosampleAnalysis
+ description: >-
+ Get an *analyses* response from one biosample, identified by its
+ (unique) 'id'
+ operationId: postOneBiosampleAnalyses
tags:
- POST Endpoints
requestBody:
@@ -157,8 +163,8 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the runs list from one biosample, identified by its (unique)
- 'id'
+ description: >-
+ Get a *runs* response from one biosample, identified by its (unique) 'id'
operationId: getOneBiosampleRuns
tags:
- GET Endpoints
@@ -173,8 +179,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the runs list from one biosample, identified by its (unique)
- 'id'
+ description: >-
+ Get a *runs* response from one biosample, identified by its (unique) 'id'
operationId: postOneBiosampleRuns
tags:
- POST Endpoints
@@ -219,14 +225,14 @@ components:
name: skip
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit
includeResultsetResponses:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses
entryId:
name: id
in: path
diff --git a/models/src/beacon-v2-default-model/cohorts/defaultSchema.yaml b/models/src/beacon-v2-default-model/cohorts/defaultSchema.yaml
index 755184103..314679448 100644
--- a/models/src/beacon-v2-default-model/cohorts/defaultSchema.yaml
+++ b/models/src/beacon-v2-default-model/cohorts/defaultSchema.yaml
@@ -52,13 +52,13 @@ properties:
Inclusion criteria used for defining the cohort. It is assumed that
all cohort participants will match such criteria.
type: object
- $ref: '#/definitions/CohortCriteria'
+ $ref: '#/$defs/CohortCriteria'
exclusionCriteria:
description: >-
Exclusion criteria used for defining the cohort. It is assumed that
NONE of the cohort participants will match such criteria.
type: object
- $ref: '#/definitions/CohortCriteria'
+ $ref: '#/$defs/CohortCriteria'
cohortSize:
description: >-
Count of unique Individuals in cohort (individuals meeting criteria
@@ -69,13 +69,13 @@ properties:
- 14765
- 20000
cohortDataTypes:
- $ref: '#/definitions/DataTypesArray'
+ $ref: '#/$defs/DataTypesArray'
collectionEvents:
description: TBD
type: array
items:
- $ref: '#/definitions/CollectionEvent'
-definitions:
+ $ref: '#/$defs/CollectionEvent'
+$defs:
CollectionEvent:
description: TBD
type: object
@@ -145,39 +145,39 @@ definitions:
description: >-
Aggregated information of geographic location obtained from individual
level info of the cohort members
- $ref: '#/definitions/DataAvailabilityAndDistribution'
+ $ref: '#/$defs/DataAvailabilityAndDistribution'
eventGenders:
description: >-
Aggregated information of gender(s) obtained from individual
level info of the cohort members
- $ref: '#/definitions/DataAvailabilityAndDistribution'
+ $ref: '#/$defs/DataAvailabilityAndDistribution'
eventEthnicities:
description: >-
Aggregated information of ethnicity obtained from individual
level info of the cohort members
- $ref: '#/definitions/DataAvailabilityAndDistribution'
+ $ref: '#/$defs/DataAvailabilityAndDistribution'
eventAgeRange:
description: >-
Individual age range, obtained from individual level info of the
cohort members
- $ref: '#/definitions/DataAvailabilityAndDistribution'
+ $ref: '#/$defs/DataAvailabilityAndDistribution'
eventDiseases:
description: >-
Aggregated information of disease/condition(s) obtained from
individual level info of the cohort members
- $ref: '#/definitions/DataAvailabilityAndDistribution'
+ $ref: '#/$defs/DataAvailabilityAndDistribution'
eventPhenotypes:
description: >-
Aggregated information of phenotype(s) obtained from individual
level info of the cohort members
- $ref: '#/definitions/DataAvailabilityAndDistribution'
+ $ref: '#/$defs/DataAvailabilityAndDistribution'
eventDataTypes:
description: >-
Aggregated data type information available for each cohort data
type as declared in `cohortDataTypes`, and obtained from individual
level info of the cohort members
type: object
- $ref: '#/definitions/DataAvailabilityAndDistribution'
+ $ref: '#/$defs/DataAvailabilityAndDistribution'
CohortCriteria:
description: >-
Criteria used for defining the cohort. It is assumed that all cohort
@@ -189,19 +189,19 @@ definitions:
Geographic location(s) in cohort inclusion criteria
type: array
items:
- $ref: ../common/commonDefinitions.yaml#/definitions/GeographicLocation
+ $ref: ../common/commonDefinitions.yaml#/$defs/GeographicLocation
genders:
description: >-
Gender(s) in cohort inclusion criteria
type: array
items:
- $ref: ../common/commonDefinitions.yaml#/definitions/Sex
+ $ref: ../common/commonDefinitions.yaml#/$defs/Sex
ethnicities:
description: >-
Ethnias in cohort inclusion criteria
type: array
items:
- $ref: ../common/commonDefinitions.yaml#/definitions/Ethnicity
+ $ref: ../common/commonDefinitions.yaml#/$defs/Ethnicity
diseaseConditions:
description: >-
Diseases in cohort inclusion criteria
diff --git a/models/src/beacon-v2-default-model/cohorts/endpoints.yaml b/models/src/beacon-v2-default-model/cohorts/endpoints.yaml
index 9fd0e999a..b9585b700 100644
--- a/models/src/beacon-v2-default-model/cohorts/endpoints.yaml
+++ b/models/src/beacon-v2-default-model/cohorts/endpoints.yaml
@@ -22,7 +22,7 @@ paths:
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- $ref: '#/components/parameters/filters'
- description: Get a list of cohorts
+ description: Get a Beacon *cohorts* response
operationId: getCohorts
tags:
- GET Endpoints
@@ -32,7 +32,7 @@ paths:
default:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get a list of cohorts
+ description: Get a Beacon *cohorts* response
operationId: postCohortsRequest
tags:
- POST Endpoints
@@ -89,7 +89,8 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the individuals from one cohort, identified by its (unique)
+ description: >-
+ Get an *individuals* response for one cohort, identified by its (unique)
'id'
operationId: getOneCohortIndividuals
tags:
@@ -101,7 +102,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the individuals from one cohort, identified by its (unique)
+ description: >-
+ Get an *individuals* response for one cohort, identified by its (unique)
'id'
operationId: postOneCohortEntries
tags:
@@ -125,8 +127,9 @@ paths:
parameters:
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the list of filtering terms that could be used with a given
- cohort, identified by its (unique) 'id'
+ description: >-
+ Get a response about the *filtering terms* that could be used with a
+ given cohort, identified by its (unique) 'id'
operationId: getOneCohortFilteringTerms
tags:
- GET Endpoints
@@ -141,8 +144,9 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the list of filtering terms that could be used with a given
- cohort, identified by its (unique) 'id'
+ description: >-
+ Get a response about the *filtering terms* that could be used with a
+ given cohort, identified by its (unique) 'id'
operationId: postOneCohortFilteringTerms
tags:
- POST Endpoints
@@ -196,12 +200,12 @@ components:
name: skip
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit
entryId:
name: id
in: path
diff --git a/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml b/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml
index 92b6ef659..42a7c53bb 100644
--- a/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml
+++ b/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml
@@ -1,6 +1,2 @@
$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'
+filteringTerms: []
\ No newline at end of file
diff --git a/models/src/beacon-v2-default-model/common/commonDefinitions.yaml b/models/src/beacon-v2-default-model/common/commonDefinitions.yaml
index 08a7b1756..75d2129f8 100644
--- a/models/src/beacon-v2-default-model/common/commonDefinitions.yaml
+++ b/models/src/beacon-v2-default-model/common/commonDefinitions.yaml
@@ -2,7 +2,7 @@ $schema: https://json-schema.org/draft/2020-12/schema
title: Common Definitions
description: Definitions for concepts used in several entry types, but that having
only one property are not complex enough to require a full independent schema document.
-definitions:
+$defs:
Sex:
description: 'Sex of the individual. Recommended values from NCIT General Qualifier
(NCIT:C27993): "unknown" (not assessed or not available) - NCIT:C17998; "female"
diff --git a/models/src/beacon-v2-default-model/common/complexValue.yaml b/models/src/beacon-v2-default-model/common/complexValue.yaml
index 058a91b9f..c32435cbf 100644
--- a/models/src/beacon-v2-default-model/common/complexValue.yaml
+++ b/models/src/beacon-v2-default-model/common/complexValue.yaml
@@ -8,11 +8,11 @@ properties:
description: List of quantities required to fully describe the complex value
type: array
items:
- $ref: '#/definitions/TypedQuantity'
+ $ref: '#/$defs/TypedQuantity'
required:
- typedQuantities
-definitions:
+$defs:
TypedQuantity:
properties:
quantityType:
diff --git a/models/src/beacon-v2-default-model/common/dataUseConditions.yaml b/models/src/beacon-v2-default-model/common/dataUseConditions.yaml
index ebb110d79..40bd7d1d2 100644
--- a/models/src/beacon-v2-default-model/common/dataUseConditions.yaml
+++ b/models/src/beacon-v2-default-model/common/dataUseConditions.yaml
@@ -6,9 +6,9 @@ properties:
duoDataUse:
type: array
items:
- $ref: '#/definitions/DUODataUse'
+ $ref: '#/$defs/DUODataUse'
minItems: 1
-definitions:
+$defs:
DUODataUse:
allOf:
- description: Data Use Ontology codes and additional information associated
diff --git a/models/src/beacon-v2-default-model/common/disease.yaml b/models/src/beacon-v2-default-model/common/disease.yaml
index a4f5f5719..dac18f852 100644
--- a/models/src/beacon-v2-default-model/common/disease.yaml
+++ b/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`'
@@ -44,7 +40,7 @@ properties:
- id: OGMS:0000106
label: remission
severity:
- $ref: ./commonDefinitions.yaml#/definitions/SeverityLevel
+ $ref: ./commonDefinitions.yaml#/$defs/SeverityLevel
examples:
- id: HP:0012828
label: Severe
diff --git a/models/src/beacon-v2-default-model/common/exposure.yaml b/models/src/beacon-v2-default-model/common/exposure.yaml
index 70fa94cfb..635c87491 100644
--- a/models/src/beacon-v2-default-model/common/exposure.yaml
+++ b/models/src/beacon-v2-default-model/common/exposure.yaml
@@ -22,7 +22,7 @@ properties:
description: >-
Unit of the exposure. Recommended from NCIT Unit of Category ontology
term (NCIT:C42568) descendants.
- $ref: ../common/commonDefinitions.yaml#/definitions/Unit
+ $ref: ../common/commonDefinitions.yaml#/$defs/Unit
duration:
description: >-
Exposure duration in ISO8601 format
diff --git a/models/src/beacon-v2-default-model/common/pedigree.yaml b/models/src/beacon-v2-default-model/common/pedigree.yaml
index b4cb0d7d4..67b542a76 100644
--- a/models/src/beacon-v2-default-model/common/pedigree.yaml
+++ b/models/src/beacon-v2-default-model/common/pedigree.yaml
@@ -21,9 +21,9 @@ properties:
than the proband, it only contains two entries: one that describes that member,
e.g. the proband mother or father, and one that points to the proband.'
items:
- $ref: '#/definitions/pedigreeMember'
+ $ref: '#/$defs/pedigreeMember'
minItems: 1
-definitions:
+$defs:
pedigreeMember:
type: object
properties:
diff --git a/models/src/beacon-v2-default-model/common/phenotypicFeature.yaml b/models/src/beacon-v2-default-model/common/phenotypicFeature.yaml
index e73b22f9e..8f28393c4 100644
--- a/models/src/beacon-v2-default-model/common/phenotypicFeature.yaml
+++ b/models/src/beacon-v2-default-model/common/phenotypicFeature.yaml
@@ -50,7 +50,7 @@ properties:
description: The evidence for an assertion of the observation of a type. RECOMMENDED.
$ref: ./evidence.yaml
severity:
- $ref: ./commonDefinitions.yaml#/definitions/SeverityLevel
+ $ref: ./commonDefinitions.yaml#/$defs/SeverityLevel
examples:
- id: HP:0012828
label: Severe
@@ -61,6 +61,6 @@ properties:
feature.
type: string
example: Some free text
-definitions: {}
+$defs: {}
required:
- featureType
diff --git a/models/src/beacon-v2-default-model/common/quantity.yaml b/models/src/beacon-v2-default-model/common/quantity.yaml
index 5cf191123..56a409f0e 100644
--- a/models/src/beacon-v2-default-model/common/quantity.yaml
+++ b/models/src/beacon-v2-default-model/common/quantity.yaml
@@ -4,7 +4,7 @@ description: 'Definition of a quantity class. Provenance: GA4GH Phenopackets v2
type: object
properties:
unit:
- $ref: ./commonDefinitions.yaml#/definitions/Unit
+ $ref: ./commonDefinitions.yaml#/$defs/Unit
value:
description: The value of the quantity in the units
type: number
diff --git a/models/src/beacon-v2-default-model/common/referenceRange.yaml b/models/src/beacon-v2-default-model/common/referenceRange.yaml
index a6316d379..8e882e44f 100644
--- a/models/src/beacon-v2-default-model/common/referenceRange.yaml
+++ b/models/src/beacon-v2-default-model/common/referenceRange.yaml
@@ -5,7 +5,7 @@ type: object
properties:
unit:
description: The kind of unit.
- $ref: ./commonDefinitions.yaml#/definitions/Unit
+ $ref: ./commonDefinitions.yaml#/$defs/Unit
examples:
- id: NCIT:C49670
label: Millimeter of Mercury
diff --git a/models/src/beacon-v2-default-model/common/timeElement.yaml b/models/src/beacon-v2-default-model/common/timeElement.yaml
index 2c09a3468..febb4fd38 100644
--- a/models/src/beacon-v2-default-model/common/timeElement.yaml
+++ b/models/src/beacon-v2-default-model/common/timeElement.yaml
@@ -9,6 +9,6 @@ oneOf:
- $ref: ./age.yaml
- $ref: ./ageRange.yaml
- $ref: ./gestationalAge.yaml
- - $ref: ./commonDefinitions.yaml#/definitions/Timestamp
+ - $ref: ./commonDefinitions.yaml#/$defs/Timestamp
- $ref: ./timeInterval.yaml
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json
diff --git a/models/src/beacon-v2-default-model/common/timeInterval.yaml b/models/src/beacon-v2-default-model/common/timeInterval.yaml
index 023953e46..1c9ac2ed6 100644
--- a/models/src/beacon-v2-default-model/common/timeInterval.yaml
+++ b/models/src/beacon-v2-default-model/common/timeInterval.yaml
@@ -5,12 +5,12 @@ type: object
$comments: From https://github.com/phenopackets/phenopacket-schema/blob/v2/docs/time-interval.rst
properties:
start:
- $ref: ./commonDefinitions.yaml#/definitions/Timestamp
+ $ref: ./commonDefinitions.yaml#/$defs/Timestamp
examples:
- '1999-08-05T17:21:00+01:00'
- '2002-09-21T02:37:00-08:00'
end:
- $ref: ./commonDefinitions.yaml#/definitions/Timestamp
+ $ref: ./commonDefinitions.yaml#/$defs/Timestamp
examples:
- '2022-03-10T15:25:07Z'
required:
diff --git a/models/src/beacon-v2-default-model/datasets/defaultSchema.yaml b/models/src/beacon-v2-default-model/datasets/defaultSchema.yaml
index d9f8cbe30..1747613c6 100644
--- a/models/src/beacon-v2-default-model/datasets/defaultSchema.yaml
+++ b/models/src/beacon-v2-default-model/datasets/defaultSchema.yaml
@@ -19,12 +19,12 @@ properties:
examples:
- This dataset provides examples of the actual data in this Beacon instance.
createDateTime:
- $ref: ../common/commonDefinitions.yaml#/definitions/Timestamp
+ $ref: ../common/commonDefinitions.yaml#/$defs/Timestamp
description: The time the dataset was created (ISO 8601 format)
examples:
- '2017-01-17T20:33:40Z'
updateDateTime:
- $ref: ../common/commonDefinitions.yaml#/definitions/Timestamp
+ $ref: ../common/commonDefinitions.yaml#/$defs/Timestamp
description: The time the dataset was updated in (ISO 8601 format)
examples:
- '2017-01-17T20:33:40Z'
@@ -40,7 +40,7 @@ properties:
examples:
- https://example.org/wiki/Main_Page
info:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info
+ $ref: ../common/info.yaml
dataUseConditions:
description: Data use conditions applying to this dataset.
$ref: ../common/dataUseConditions.yaml
diff --git a/models/src/beacon-v2-default-model/datasets/endpoints.yaml b/models/src/beacon-v2-default-model/datasets/endpoints.yaml
index dc2c34d31..320f0cd66 100644
--- a/models/src/beacon-v2-default-model/datasets/endpoints.yaml
+++ b/models/src/beacon-v2-default-model/datasets/endpoints.yaml
@@ -32,7 +32,7 @@ paths:
default:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get a list of datasets
+ description: Get a Beacon *datasets* response
operationId: postDatasetsRequest
tags:
- POST Endpoints
@@ -89,7 +89,8 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the genomic variants list from one dataset, identified by its
+ description: >-
+ Get a *genomic variations* response for one dataset, identified by its
(unique) 'id'
operationId: getOneDatasetEntries
tags:
@@ -101,7 +102,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the genomic variants list from one dataset, identified by its
+ description: >-
+ Get a *genomic variations* response for one dataset, identified by its
(unique) 'id'
operationId: postOneDatasetEntries
tags:
@@ -126,7 +128,8 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the biosamples list from one dataset, identified by its (unique)
+ description: >-
+ Get a *biosamples* response for one dataset, identified by its (unique)
'id'
operationId: getOneDatasetBiosamples
tags:
@@ -138,7 +141,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the biosamples list from one dataset, identified by its (unique)
+ description: >-
+ Get a *biosamples* response for one dataset, identified by its (unique)
'id'
operationId: postOneDatasetBiosamples
tags:
@@ -163,7 +167,8 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the individuals list from one dataset, identified by its (unique)
+ description: >-
+ Get an *individuals* response for one dataset, identified by its (unique)
'id'
operationId: getOneDatasetIndividuals
tags:
@@ -175,7 +180,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the biosamples list from one dataset, identified by its (unique)
+ description: >-
+ Get an *individuals* response for one dataset, identified by its (unique)
'id'
operationId: postOneDatasetIndividuals
tags:
@@ -199,8 +205,9 @@ paths:
parameters:
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the list of filtering terms that could be used with a given
- dataset, identified by its (unique) 'id'
+ description: >-
+ Get a response about the *filtering terms* that could be used with a
+ given dataset, identified by its (unique) 'id'
operationId: getOneDatasetFilteringTerms
tags:
- GET Endpoints
@@ -215,8 +222,9 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the list of filtering terms that could be used with a given
- dataset, identified by its (unique) 'id'
+ description: >-
+ Get a response about the *filtering terms* that could be used with a
+ given dataset, identified by its (unique) 'id'
operationId: postOneDatasetFilteringTerms
tags:
- POST Endpoints
@@ -270,12 +278,12 @@ components:
name: skip
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit
entryId:
name: id
in: path
diff --git a/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml b/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml
index 92b6ef659..42a7c53bb 100644
--- a/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml
+++ b/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml
@@ -1,6 +1,2 @@
$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'
+filteringTerms: []
\ No newline at end of file
diff --git a/models/src/beacon-v2-default-model/endpoints.yaml b/models/src/beacon-v2-default-model/endpoints.yaml
index a8b5716f0..3b744b30e 100644
--- a/models/src/beacon-v2-default-model/endpoints.yaml
+++ b/models/src/beacon-v2-default-model/endpoints.yaml
@@ -143,9 +143,9 @@ components:
name: skip
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit
diff --git a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
index 7011dd6a7..df68f4d7d 100644
--- a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
+++ b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
@@ -1,6 +1,6 @@
$schema: https://json-schema.org/draft/2020-12/schema
title: Genomic Variation
-$comment: 'version: ga4gh-beacon-variant-v2.0.0'
+$comment: 'version: ga4gh-beacon-variant-v2.1.0'
description: >-
Schema for a genomic variant entry.
type: object
@@ -10,9 +10,9 @@ required:
properties:
variation:
oneOf:
- - $ref: https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/MolecularVariation
- - $ref: https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/SystemicVariation
- - $ref: '#/definitions/LegacyVariation'
+ - $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation
+ - $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation
+ - $ref: '#/$defs/LegacyVariation'
variantInternalId:
description: >-
Reference to the **internal** variant ID. This represents the primary
@@ -27,22 +27,22 @@ properties:
- var00001
- v110112
identifiers:
- $ref: '#/definitions/Identifiers'
+ $ref: '#/$defs/Identifiers'
molecularAttributes:
- $ref: '#/definitions/MolecularAttributes'
+ $ref: '#/$defs/MolecularAttributes'
caseLevelData:
type: array
description: caseLevelData reports about the variation instances observed in individual
analyses.
items:
- $ref: '#/definitions/CaseLevelVariant'
+ $ref: '#/$defs/CaseLevelVariant'
variantLevelData:
- $ref: '#/definitions/VariantLevelData'
+ $ref: '#/$defs/VariantLevelData'
frequencyInPopulations:
type: array
items:
- $ref: '#/definitions/FrequencyInPopulations'
-definitions:
+ $ref: '#/$defs/FrequencyInPopulations'
+$defs:
LegacyVariation:
type: object
required:
@@ -51,7 +51,7 @@ definitions:
- location
properties:
location:
- $ref: https://raw.githubusercontent.com/ga4gh/vrs/main/schema/vrs.json#/definitions/Location
+ $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location
variantType:
description: >-
The `variantType` declares the nature of the variation in relation
@@ -168,7 +168,7 @@ definitions:
description: List of Genomic feature(s) affected by the variant.
type: array
items:
- $ref: '#/definitions/GenomicFeature'
+ $ref: '#/$defs/GenomicFeature'
molecularEffects:
description: >-
Ontology term that includes describes the class of molecular
@@ -270,7 +270,7 @@ definitions:
- id: ECO:0000006
label: experimental evidence
annotatedWith:
- $ref: '#/definitions/SoftwareTool'
+ $ref: '#/$defs/SoftwareTool'
required:
- conditionId
- effect
@@ -297,7 +297,7 @@ definitions:
frequencies:
type: array
items:
- $ref: '#/definitions/PopulationFrequency'
+ $ref: '#/$defs/PopulationFrequency'
minItems: 1
required:
- source
@@ -394,11 +394,11 @@ definitions:
clinicalInterpretations:
type: array
items:
- $ref: '#/definitions/PhenoClinicEffect'
+ $ref: '#/$defs/PhenoClinicEffect'
phenotypicEffects:
type: array
items:
- $ref: '#/definitions/PhenoClinicEffect'
+ $ref: '#/$defs/PhenoClinicEffect'
required:
- biosampleId
VariantLevelData:
@@ -407,11 +407,11 @@ definitions:
clinicalInterpretations:
type: array
items:
- $ref: '#/definitions/PhenoClinicEffect'
+ $ref: '#/$defs/PhenoClinicEffect'
phenotypicEffects:
type: array
items:
- $ref: '#/definitions/PhenoClinicEffect'
+ $ref: '#/$defs/PhenoClinicEffect'
SoftwareTool:
type: object
properties:
diff --git a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml
index 44b59a736..3f4397d34 100644
--- a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml
+++ b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml
@@ -29,8 +29,8 @@ paths:
- $ref: '#/components/parameters/geneId'
- $ref: '#/components/parameters/aminoacidChange'
- $ref: '#/components/parameters/filters'
- description: Get a list of example entries
- operationId: getExampleEntries
+ description: Get a Beacon response for genomic variations
+ operationId: getGenomicVariations
tags:
- GET Endpoints
responses:
@@ -39,8 +39,8 @@ paths:
default:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get a list of example entries
- operationId: postExampleEntriesRequest
+ description: Get a Beacon response for genomic variations
+ operationId: postGenomicVariationsRequest
tags:
- POST Endpoints
requestBody:
@@ -59,8 +59,8 @@ paths:
parameters:
- $ref: '#/components/parameters/entryId'
get:
- description: Get details about one genomic variation, identified by its (unique)
- 'id'
+ description: >-
+ Get details about one genomic variation, identified by its (unique) 'id'
operationId: getOneGenomicVariation
tags:
- GET Endpoints
@@ -71,8 +71,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get details about one genomic variation, identified by its (unique)
- 'id'
+ description: >-
+ Get details about one genomic variation, identified by its (unique) 'id'
operationId: postOneGenomicVariation
tags:
- POST Endpoints
@@ -96,9 +96,10 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the biosamples list from one genomic variant, identified by
- its (unique) 'id'
- operationId: getOneGenomicVariantBiosamples
+ description: >-
+ Get a *biosamples* response from one genomic variant, identified by its
+ (unique) 'id'
+ operationId: getOneGenomicVariationBiosamples
tags:
- GET Endpoints
responses:
@@ -108,9 +109,10 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the biosamples list from one genomic variant, identified by
- its (unique) 'id'
- operationId: postOneGenomicVariantBiosamples
+ description: >-
+ Get a *biosamples* response from one genomic variant, identified by its
+ (unique) 'id'
+ operationId: postOneGenomicVariationBiosamples
tags:
- POST Endpoints
requestBody:
@@ -133,9 +135,10 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the individuals list from one genomic variant, identified by
+ description: >-
+ Get an *individuals* response from one genomic variant, identified by
its (unique) 'id'
- operationId: getOneGenomicVariantIndividuals
+ operationId: getOneGenomicVariationIndividuals
tags:
- GET Endpoints
responses:
@@ -145,9 +148,10 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the biosamples list from one genomic variant, identified by
+ description: >-
+ Get an *individuals* response from one genomic variant, identified by
its (unique) 'id'
- operationId: postOneGenomicVariantIndividuals
+ operationId: postOneGenomicVariationIndividuals
tags:
- POST Endpoints
requestBody:
@@ -187,14 +191,14 @@ components:
name: skip
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit
includeResultsetResponses:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses
entryId:
name: id
in: path
diff --git a/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml b/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml
index ca25a1cd9..42a7c53bb 100644
--- a/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml
+++ b/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml
@@ -1,6 +1,2 @@
$schema: https://json-schema.org/draft/2020-12/schema
-filteringTerms:
- - ftType: alphanumeric
- id: gene
- - ftType: alphanumeric
- id: aminoacidChanges
+filteringTerms: []
\ No newline at end of file
diff --git a/models/src/beacon-v2-default-model/genomicVariations/requestParameters.yaml b/models/src/beacon-v2-default-model/genomicVariations/requestParameters.yaml
index 37c5b9e48..166bccf12 100644
--- a/models/src/beacon-v2-default-model/genomicVariations/requestParameters.yaml
+++ b/models/src/beacon-v2-default-model/genomicVariations/requestParameters.yaml
@@ -3,9 +3,9 @@ g_variant:
type: object
properties:
assemblyId:
- $ref: ./requestParametersComponents.yaml#/definitions/Assembly
+ $ref: ./requestParametersComponents.yaml#/$defs/Assembly
referenceName:
- $ref: ./requestParametersComponents.yaml#/definitions/RefSeqId
+ $ref: ./requestParametersComponents.yaml#/$defs/RefSeqId
start:
description: >-
Precise or fuzzy start coordinate position(s), allele locus
@@ -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
@@ -48,12 +48,12 @@ g_variant:
type: integer
format: int64
minimum: 1
- minItems: 0
+ minItems: 1
maxItems: 2
referenceBases:
- $ref: ./requestParametersComponents.yaml#/definitions/ReferenceBases
+ $ref: ./requestParametersComponents.yaml#/$defs/ReferenceBases
alternateBases:
- $ref: ./requestParametersComponents.yaml#/definitions/AlternateBases
+ $ref: ./requestParametersComponents.yaml#/$defs/AlternateBases
variantType:
description: >-
The `variantType` is used to query variants which are not defined through
@@ -98,7 +98,7 @@ g_variant:
format: int64
minimum: 1
mateName:
- $ref: ./requestParametersComponents.yaml#/definitions/RefSeqId
+ $ref: ./requestParametersComponents.yaml#/$defs/RefSeqId
geneId:
description: >-
* A gene identifier
diff --git a/models/src/beacon-v2-default-model/genomicVariations/requestParametersComponents.yaml b/models/src/beacon-v2-default-model/genomicVariations/requestParametersComponents.yaml
index 82f13b863..af503ad40 100644
--- a/models/src/beacon-v2-default-model/genomicVariations/requestParametersComponents.yaml
+++ b/models/src/beacon-v2-default-model/genomicVariations/requestParametersComponents.yaml
@@ -1,7 +1,7 @@
$schema: https://json-schema.org/draft/2020-12/schema
description: >-
Component definitions used in `requestParameters`.
-definitions:
+$defs:
Assembly:
description: >-
Genomic assembly accession and version as RefSqeq assembly accession
diff --git a/models/src/beacon-v2-default-model/individuals/defaultSchema.yaml b/models/src/beacon-v2-default-model/individuals/defaultSchema.yaml
index 50dcd46e2..ede6165f2 100644
--- a/models/src/beacon-v2-default-model/individuals/defaultSchema.yaml
+++ b/models/src/beacon-v2-default-model/individuals/defaultSchema.yaml
@@ -9,26 +9,28 @@ properties:
type: string
example: P0001
sex:
- description: "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993):\
- \ 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576),\
- \ or 'male', (NCIT:C20197)."
- $ref: ../common/commonDefinitions.yaml#/definitions/Sex
+ description: >-
+ Sex of the individual. Value from NCIT General Qualifier `NCIT:C27993`:
+ * `unknown`: not assessed or not availablel `NCIT:C17998`
+ * `female`: `NCIT:C16576`
+ * `male`: `NCIT:C20197`
+ $ref: ../common/commonDefinitions.yaml#/$defs/Sex
karyotypicSex:
description: The chromosomal sex of an individual represented from a selection
of options.
- $ref: ../common/commonDefinitions.yaml#/definitions/KaryotypicSex
+ $ref: ../common/commonDefinitions.yaml#/$defs/KaryotypicSex
ethnicity:
description: 'Ethnic background of the individual. Value from NCIT Race (NCIT:C17049)
ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic
ancestral origin category that is assigned to a population group based mainly
on physical characteristics that are thought to be distinct and inherent. [
NCI ] '
- $ref: ../common/commonDefinitions.yaml#/definitions/Ethnicity
+ $ref: ../common/commonDefinitions.yaml#/$defs/Ethnicity
geographicOrigin:
description: Individual's country or region of origin (birthplace or residence
place regardless of ethnic origin). Value from GAZ Geographic Location ontology
(GAZ:00000448), e.g. GAZ:00002459 (United States of America).
- $ref: ../common/commonDefinitions.yaml#/definitions/GeographicLocation
+ $ref: ../common/commonDefinitions.yaml#/$defs/GeographicLocation
diseases:
description: List of disease(s) been diagnosed to the individual, defined by disease
ontology ID(s), age of onset, stage and the presence of family history.
@@ -60,7 +62,7 @@ properties:
items:
$ref: ../common/exposure.yaml
info:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info
+ $ref: ../common/info.yaml
required:
- id
- sex
diff --git a/models/src/beacon-v2-default-model/individuals/endpoints.yaml b/models/src/beacon-v2-default-model/individuals/endpoints.yaml
index 7ed5a46fe..8adfaa779 100644
--- a/models/src/beacon-v2-default-model/individuals/endpoints.yaml
+++ b/models/src/beacon-v2-default-model/individuals/endpoints.yaml
@@ -28,7 +28,7 @@ paths:
default:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get a list of example entries
+ description: Get a Beacon response for individuals
operationId: postIndividualsRequest
tags:
- POST Endpoints
@@ -48,7 +48,8 @@ paths:
parameters:
- $ref: '#/components/parameters/entryId'
get:
- description: Get details about one individual, identified by its (unique) 'id'
+ description: >-
+ Get details about one individual, identified by its (unique) 'id'
operationId: getOneIndividual
tags:
- GET Endpoints
@@ -59,7 +60,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get details about one Individual, identified by its (unique) 'id'
+ description: >-
+ Get details about one individual, identified by its (unique) 'id'
operationId: postOneIndividual
tags:
- POST Endpoints
@@ -83,7 +85,8 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the genomic variants list from one individual, identified by
+ description: >-
+ Get a *genomic variations* response for one individual, identified by
its (unique) 'id'
operationId: getOneIndividualGenomicVariants
tags:
@@ -95,7 +98,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the genomic variants list from one individual, identified by
+ description: >-
+ Get a *genomic variations* response for one individual, identified by
its (unique) 'id'
operationId: potOneIndividualGenomicVariants
tags:
@@ -120,7 +124,8 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the biosamples list from one individual, identified by its
+ description: >-
+ Get a *biosamples* response for one individual, identified by its
(unique) 'id'
operationId: getOneIndividualBiosamples
tags:
@@ -132,7 +137,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the biosamples list from one individual, identified by its
+ description: >-
+ Get a *biosamples* response for one individual, identified by its
(unique) 'id'
operationId: postOneIndividualBiosamples
tags:
@@ -214,14 +220,14 @@ components:
name: skip
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit
includeResultsetResponses:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses
entryId:
name: id
in: path
diff --git a/models/src/beacon-v2-default-model/runs/defaultSchema.yaml b/models/src/beacon-v2-default-model/runs/defaultSchema.yaml
index ac04dda4b..fc7efff95 100644
--- a/models/src/beacon-v2-default-model/runs/defaultSchema.yaml
+++ b/models/src/beacon-v2-default-model/runs/defaultSchema.yaml
@@ -74,7 +74,7 @@ properties:
- id: EFO:0010938
label: large-insert clone DNA microarray
info:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info
+ $ref: ../common/info.yaml
required:
- id
- biosampleId
diff --git a/models/src/beacon-v2-default-model/runs/endpoints.yaml b/models/src/beacon-v2-default-model/runs/endpoints.yaml
index 473bea53c..773f7bddb 100644
--- a/models/src/beacon-v2-default-model/runs/endpoints.yaml
+++ b/models/src/beacon-v2-default-model/runs/endpoints.yaml
@@ -18,7 +18,7 @@ paths:
- $ref: '#/components/parameters/limit'
- $ref: '#/components/parameters/includeResultsetResponses'
- $ref: '#/components/parameters/filters'
- description: Get a list of sequencing runs
+ description: Get a Beacon response for experimental runs
operationId: getRuns
tags:
- GET Endpoints
@@ -28,7 +28,7 @@ paths:
default:
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get a list of sequencing runs
+ description: Get a Beacon response for experimental runs
operationId: postRunsRequest
tags:
- POST Endpoints
@@ -48,8 +48,8 @@ paths:
parameters:
- $ref: '#/components/parameters/entryId'
get:
- description: Get details about one sequencing run, identified by its (unique)
- 'id'
+ description: >-
+ Get details about one experimental run, identified by its (unique) 'id'
operationId: getOneRun
tags:
- GET Endpoints
@@ -60,7 +60,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get details about one Run, identified by its (unique) 'id'
+ description: >-
+ Get details about one experimental run, identified by its (unique) 'id'
operationId: postOneRun
tags:
- POST Endpoints
@@ -84,9 +85,10 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the genomic variants list from one run, identified by its (unique)
- 'id'
- operationId: getOneRunGenomicVariants
+ description: >-
+ Get a *genomic variations* response for one experimental run, identified
+ by its (unique) 'id'
+ operationId: getOneRunGenomicVariations
tags:
- GET Endpoints
responses:
@@ -96,9 +98,10 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the genomic variants list from one run, identified by its (unique)
- 'id'
- operationId: potOneRunGenomicVariants
+ description: >-
+ Get a *genomic variations* response for one experimental run, identified
+ by its (unique) 'id'
+ operationId: potOneRunGenomicVariations
tags:
- POST Endpoints
requestBody:
@@ -121,7 +124,8 @@ paths:
- $ref: '#/components/parameters/requestedSchema'
- $ref: '#/components/parameters/skip'
- $ref: '#/components/parameters/limit'
- description: Get the analysis list from one sequencing run, identified by its
+ description: >-
+ Get a *analyses* response for one experimental run, identified by its
(unique) 'id'
operationId: getOneRunAnalysis
tags:
@@ -133,7 +137,8 @@ paths:
description: An unsuccessful operation
$ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json
post:
- description: Get the analysis list from one sequencing run, identified by its
+ description: >-
+ Get a *analyses* response for one experimental run, identified by its
(unique) 'id'
operationId: postOneRunAnalysis
tags:
@@ -175,14 +180,14 @@ components:
name: skip
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip
limit:
name: limit
in: query
schema:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit
includeResultsetResponses:
- $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses
+ $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses
entryId:
name: id
in: path