fixes #550, #569, #578

Author: BrapiCoordinatorSelby

Specification/BrAPI-Schema/BrAPI-Core/Study.json

@@ -204,6 +204,12 @@
                         "string"
                     ]
                 },
+                "program": {
+                    "$ref": "Program.json#/$defs/Program",
+                    "description": "A program identifier to search for",
+                    "referencedAttribute": "trials",
+                    "relationshipType": "many-to-one"
+                },
                 "trial": {
                     "$ref": "Trial.json#/$defs/Trial",
                     "description": "The ID which uniquely identifies a trial",

Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json

@@ -2,6 +2,11 @@
     "$defs": {
         "AlleleMatrix": {
             "properties": {
+                "additionalInfo": {
+                    "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.",
+                    "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo",
+					"relationshipType": "one-to-one"
+                },
                 "callSets": {
                     "description": "A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case.",
                     "items": {

Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json

@@ -23,8 +23,6 @@
                 },
                 "column": {
                     "description": "The Column identifier for this `Sample` location in the `Plate`",
-                    "maximum": 12,
-                    "minimum": 1,
                     "type": [
                         "null",
                         "integer"

Specification/BrAPI-Schema/Requests/PlateRequest.json

@@ -96,17 +96,6 @@
                                 "45e1e2d7",
                                 "6cc6dd28"
                             ]
-                        },
-                        "germplasmDbIds": {
-                            "description": "The ID which uniquely identifies a germplasm",
-                            "items": {
-                                "type": "string"
-                            },
-                            "type": "array",
-                            "example": [
-                                "d745e1e2",
-                                "6dd28d74"
-                            ]
                         }
                     }
                 }

Specification/BrAPI-Schema/Requests/SampleRequest.json

@@ -85,17 +85,6 @@
                                 "45e1e2d7",
                                 "6cc6dd28"
                             ]
-                        },
-                        "germplasmDbIds": {
-                            "description": "The ID which uniquely identifies a `Germplasm`",
-                            "items": {
-                                "type": "string"
-                            },
-                            "type": "array",
-                            "example": [
-                                "d745e1e2",
-                                "6dd28d74"
-                            ]
                         }
                     }
                 }