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Merged
BrapiCoordinatorSelby merged 5 commits into from
Jun 8, 2026
Merged

670 merge v21 changes into v2.2 update the json to be consistent and validated #672

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ca68c96
merged up changed from V2.1 that affect the generation of OpenAPI. Re…
Jun 6, 2026
22276d3
removed redundant options. TOOD review override options
Jun 6, 2026
f262606
make options files consistent and commented.
Jun 6, 2026
6e172fe
removed info block so that files are generated correctly.
Jun 6, 2026
5ca1510
remove compareAll
Jun 6, 2026
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3 changes: 0 additions & 3 deletions .github/workflows/generate-schema.yml
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Expand Up @@ -87,9 +87,6 @@ jobs:
- name: Generate OpenAPI, GraphQL and OWL
working-directory: ./generator
run: ./gradlew generateAll
- name: Compare OpenAPI
working-directory: ./generator
run: ./gradlew compareAll
- name: Commit generated files
if: needs.check.outputs.skip_commit == 'false'
uses: stefanzweifel/git-auto-commit-action@v5
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5 changes: 4 additions & 1 deletion Specification/BrAPI-Schema/BrAPI-Core/Program.json
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Expand Up @@ -179,7 +179,10 @@
"description": "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies.",
"type": "object",
"brapi-metadata": {
"primaryModel": true
"primaryModel": true,
"controlledVocabularyProperties": [
"commonCropName"
]
}
}
},
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1 change: 1 addition & 0 deletions Specification/BrAPI-Schema/BrAPI-Core/Study.json
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Expand Up @@ -353,6 +353,7 @@
"brapi-metadata": {
"primaryModel": true,
"controlledVocabularyProperties": [
"observationLevels",
"studyType"
]
}
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9 changes: 8 additions & 1 deletion Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json
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Expand Up @@ -161,6 +161,10 @@
"null",
"array"
]
},
"extract": {
"description": "Will perform a search for `Calls` which match the search criteria in `variantSetsExtractRequest`. The results of the search will be used to create a new `VariantSet` on the server. The new `VariantSet` will be returned.",
"$ref": "VariantSet.json#/$defs/VariantSet"
}
},
"required": [
Expand All @@ -170,7 +174,10 @@
"description": "A VariantSet is a collection of variants and variant calls intended to be analyzed together.",
"type": "object",
"brapi-metadata": {
"primaryModel": true
"primaryModel": true,
"actionProperties": [
"extract"
]
}
},
"Analysis": {
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2 changes: 1 addition & 1 deletion Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json
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Expand Up @@ -85,7 +85,7 @@
"description": "The record of an event where material was moved in or out of a particular SeedLot",
"type": "object",
"brapi-metadata": {
"primaryModel": false
"primaryModel": true
}
}
},
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9 changes: 7 additions & 2 deletions Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json
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Expand Up @@ -41,6 +41,11 @@
"title": "ExternalReferences",
"type": "array"
},
"imageContent": {
"description": "The unique identifier of an image",
"type": "string",
"format": "binary"
},
"imageDbId": {
"description": "The unique identifier of an image",
"type": "string"
Expand Down Expand Up @@ -128,8 +133,8 @@
"$ref": "Observation.json#/$defs/Observation"
},
"referencedAttribute": "images",
"relationshipType": "many-to-many",
"type": "array"
"relationshipType": "one-to-many",
"type": ["null", "array"]
}
},
"required": [
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294 changes: 294 additions & 0 deletions Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json
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Expand Up @@ -167,6 +167,300 @@
"brapi-metadata": {
"primaryModel": true
}
},
"ObservationTable": {
"type": "object",
"properties": {
"data": {
"description": "The 2D matrix of observation data. ObservationVariables and other metadata are the columns, ObservationUnits are the rows.",
"type": "array",
"items": {
"type": "array",
"items": {
"type": "string"
}
},
"example": [
[
"2019-09-10T18:13:27.223Z",
"f3a8a3db",
"Plant Alpha",
"0fe3e48b",
"2017 Plant Study",
"06307ec0",
"A0043001",
"76.50106681",
"42.44409301",
"2017",
"Field_1",
"Plot_11",
"SubPlot_111",
"Plant_1111",
"Pot_1111",
"Block_11",
"Entry_11",
"Rep_11",
"25.3",
"",
"",
""
],
[
"2019-09-10T18:14:27.223Z",
"f3a8a3db",
"Plant Alpha",
"0fe3e48b",
"2017 Plant Study",
"06307ec0",
"A0043001",
"76.50106681",
"42.44409301",
"2017",
"Field_1",
"Plot_11",
"SubPlot_111",
"Plant_1111",
"Pot_1111",
"Block_11",
"Entry_11",
"Rep_11",
"",
"3",
"",
""
],
[
"2019-09-10T18:15:54.868Z",
"05d1b011",
"Plant Beta",
"0fe3e48b",
"2017 Plant Study",
"59d435cd",
"A0043002",
"76.50106683",
"42.44409301",
"2017",
"Field_1",
"Plot_11",
"SubPlot_112",
"Plant_1122",
"Pot_1122",
"Block_11",
"Entry_11",
"Rep_12",
"27.9",
"",
"",
""
],
[
"2019-09-10T18:16:54.868Z",
"05d1b011",
"Plant Beta",
"0fe3e48b",
"2017 Plant Study",
"59d435cd",
"A0043002",
"76.50106683",
"42.44409301",
"2017",
"Field_1",
"Plot_11",
"SubPlot_112",
"Plant_1122",
"Pot_1122",
"Block_11",
"Entry_11",
"Rep_12",
"",
"1",
"",
""
],
[
"2019-09-10T18:17:34.433Z",
"67e2d87c",
"Plant Gamma",
"0fe3e48b",
"2017 Plant Study",
"06307ec0",
"A0043001",
"76.50106681",
"42.44409356",
"2017",
"Field_1",
"Plot_12",
"SubPlot_123",
"Plant_1233",
"Pot_1233",
"Block_12",
"Entry_12",
"Rep_11",
"",
"3",
"",
""
],
[
"2019-09-10T18:18:34.433Z",
"67e2d87c",
"Plant Gamma",
"0fe3e48b",
"2017 Plant Study",
"06307ec0",
"A0043001",
"76.50106681",
"42.44409356",
"2017",
"Field_1",
"Plot_12",
"SubPlot_123",
"Plant_1233",
"Pot_1233",
"Block_12",
"Entry_12",
"Rep_11",
"25.5",
"",
"",
""
],
[
"2019-09-10T18:19:15.629Z",
"d98d0d4c",
"Plant Epsilon",
"0fe3e48b",
"2017 Plant Study",
"59d435cd",
"A0043002",
"76.50106683",
"42.44409356",
"2017",
"Field_1",
"Plot_12",
"SubPlot_124",
"Plant_1244",
"Pot_1244",
"Block_12",
"Entry_12",
"Rep_12",
"28.9",
"",
"",
""
],
[
"2019-09-10T18:20:15.629Z",
"d98d0d4c",
"Plant Epsilon",
"0fe3e48b",
"2017 Plant Study",
"59d435cd",
"A0043002",
"76.50106683",
"42.44409356",
"2017",
"Field_1",
"Plot_12",
"SubPlot_124",
"Plant_1244",
"Pot_1244",
"Block_12",
"Entry_12",
"Rep_12",
"",
"0",
"",
""
]
]
},
"headerRow": {
"description": "<p>The table is REQUIRED to have the following columns</p>\n<ul>\n <li>observationUnitDbId - Each row is related to one Observation Unit</li>\n <li>observationTimeStamp - Each row is has a time stamp for when the observation was taken</li>\n <li>At least one column with an observationVariableDbId</li>\n</ul>\n<p>The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer</p>\n<ul>\n <li>observationUnitName</li>\n <li>studyDbId</li>\n <li>studyName</li>\n <li>germplasmDbId</li>\n <li>germplasmName</li>\n <li>positionCoordinateX</li>\n <li>positionCoordinateY</li>\n <li>year</li>\n</ul>\n<p>The table also may have any number of Observation Unit Hierarchy Level columns. For example:</p>\n<ul>\n <li>field</li>\n <li>plot</li>\n <li>sub-plot</li>\n <li>plant</li>\n <li>pot</li>\n <li>block</li>\n <li>entry</li>\n <li>rep</li>\n</ul>\n<p>The JSON representation provides a pair of extra arrays for defining the headers of the table. \nThe first array \"headerRow\" will always contain \"observationUnitDbId\" and any or all of the OPTIONAL column header names. \nThe second array \"observationVariables\" contains the names and DbIds for the Observation Variables represented in the table. \nBy appending the two arrays, you can construct the complete header row of the table. </p>",
"items": {
"description": "valid header fields",
"enum": [
"observationTimeStamp",
"observationUnitDbId",
"observationUnitName",
"studyDbId",
"studyName",
"germplasmDbId",
"germplasmName",
"positionCoordinateX",
"positionCoordinateY",
"year",
"field",
"plot",
"sub-plot",
"plant",
"pot",
"block",
"entry",
"rep"
],
"type": "string"
},
"type": "array",
"example": [
"observationTimeStamp",
"observationUnitDbId",
"observationUnitName",
"studyDbId",
"studyName",
"germplasmDbId",
"germplasmName",
"positionCoordinateX",
"positionCoordinateY",
"year",
"field",
"plot",
"sub-plot",
"plant",
"pot",
"block",
"entry",
"rep"
]
},
"observationVariables": {
"description": "The list of observation variables which have values recorded for them in the data matrix. Append to the 'headerRow' for complete header row of the table.",
"type": "array",
"items": {
"type": "object",
"properties": {
"observationVariableDbId": {
"description": "Variable unique identifier",
"type": "string",
"example": "367aa1a9"
},
"observationVariableName": {
"description": "Variable name (usually a short name)",
"type": "string",
"example": "Plant height"
}
}
},
"example": [
{
"observationVariableDbId": "367aa1a9",
"observationVariableName": "Plant height"
},
{
"observationVariableDbId": "2acb934c",
"observationVariableName": "Carotenoid"
},
{
"observationVariableDbId": "85a21ce1",
"observationVariableName": "Root color"
},
{
"observationVariableDbId": "46f590e5",
"observationVariableName": "Virus severity"
}
]
}
}
}
},
"$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json",
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