539 experimental factors added to study add new fields 486

Specification/BrAPI-Core/Studies/Schemas/StudyNewRequest.yaml

@@ -179,20 +179,8 @@ components:
           nullable: true
           example: Irrigation was applied according needs during summer to prevent water stress.
         experimentalDesign:
-          description: The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology
-          type: object
+          $ref: '#/components/schemas/ExperimentalDesign'
           nullable: true
-          properties:
-            description:
-              description: MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be "unknown"/"NA", "aggregated/reduced data", or simply 'none'.
-              type: string
-              nullable: true
-              example: Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information.
-            PUI:
-              description: MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental  design of the study, in the form of an accession number from the Crop Ontology.
-              type: string
-              nullable: true
-              example: CO_715:0000145
         growthFacility:
           description: Short description of the facility in which the study was carried out.
           type: object

Specification/BrAPI-Phenotyping/ObservationUnits/Schemas/ObservationTreatment.yaml

@@ -11,17 +11,28 @@ components:
         factor:
           description: |-
             The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc
-            
+
             MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
           type: string
-          nullable: true
+          deprecated: true
           example: fertilizer
+        factorPUI:
+          description: |-
+            The PUI of the factor which may link to an ontology
+          type: string
+          nullable: true
+          example: test-factor:dia2020-2-nv.fertilizer
         modality:
           description: |-
             The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc
-            
-            MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. 
+
+            MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor.
           type: string
-          nullable: true
+          deprecated: true
           example: low fertilizer
-
+        modalityPUI:
+          description: |-
+            The PUI of the modality which may link to an ontology
+          type: string
+          nullable: true
+          example: test-factor:dia2020-2-nv.lf

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

@@ -393,11 +393,20 @@
         "ExperimentalDesign": {
             "properties": {
                 "PUI": {
+                    "description": "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental  design of the study, in the form of an accession number from the Crop Ontology. **Deprecated in v2.2** Please use `experimentalDesignPUI`. Github issue number #539",
+                    "type": [
+                        "null",
+                        "string"
+                    ],
+                    "deprecated": true
+                },
+                "experimentalDesignPUI": {
                     "description": "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental  design of the study, in the form of an accession number from the Crop Ontology.",
                     "type": [
                         "null",
                         "string"
-                    ]
+                    ],
+                    "examples": ["CO_715:0000145"]
                 },
                 "description": {
                     "description": "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.",
@@ -406,6 +415,56 @@
                         "string"
                     ]
                 },
+                "randomizationType": {
+                    "description": "The type of randomization use to create the experimental design.",
+                    "type": [
+                        "null",
+                        "string"
+                    ],
+                    "examples": ["RCB:Randomize Complete Block"]
+                },
+                "layoutPattern": {
+                    "description": "How the trial is layout in the field.",
+                    "type": [
+                        "null",
+                        "string"
+                    ],
+                    "examples": ["Serpentine"]
+                },
+                "setSize": {
+                    "description": "The size of the sets in the design.",
+                    "type": [
+                        "null",
+                        "number"
+                    ],
+                    "examples": [1]
+                },
+                "rowsPerPlot": {
+                    "description": "The number of rows in a plot.",
+                    "type": [
+                        "null",
+                        "number"
+                    ],
+                    "examples": [1]
+                },
+                "firstRepRand": {
+                    "description": "Is the first replication random.",
+                    "type": [
+                        "null",
+                        "boolean"
+                    ],
+                    "examples": [true]
+                },
+                "experimentFactors": {
+                    "description": "The factors used in the experimental design.",
+                    "items": {
+                        "$ref": "../BrAPI-Core/Study.json#/$defs/ExperimentFactor"
+                    },
+                    "type": [
+                        "null",
+                        "array"
+                    ]
+                },
                 "study": {
                     "description": "Experimental design associated with a study",
                     "$ref": "../BrAPI-Core/Study.json#/$defs/Study",
@@ -420,6 +479,64 @@
                 "primaryModel": false
             }
         },
+        "ExperimentFactor": {
+            "properties": {
+                "factor": {
+                    "description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.",
+                    "type": "string",
+                    "examples": [
+                        "fertilizer"
+                    ]
+                },
+                "factorPUI": {
+                    "description": "The PUI of the factor which may link to an ontology.",
+                    "type": [
+                        "null",
+                        "string"
+                    ],
+                    "examples": [
+                        "test-factor:dia2020-2-nv.fertilizer"
+                    ]
+                },
+                "modalities": {
+                    "description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.",
+                    "items": {
+                        "type": "object",
+                        "properties": {
+                            "modality": {
+                                "description": "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ",
+                                "type": "string",
+                                "examples": [
+                                    "low fertilizer"
+                                ]
+                            },
+                            "modalityPUI": {
+                                "description": "The PUI of the modality which may link to an ontology.",
+                                "type": [
+                                    "null",
+                                    "string"
+                                ],
+                                "examples": [
+                                    "test-factor:dia2020-2-nv.lf"
+                                ]
+                            }
+                        }
+                    },
+                    "type": [
+                        "null",
+                        "array"
+                    ],
+                    "examples": [
+                        "fertilizer"
+                    ]
+                }
+            },
+            "title": "ExperimentFactor",
+            "type": "object",
+            "brapi-metadata": {
+                "primaryModel": false
+            }
+        },
         "GrowthFacility": {
             "properties": {
                 "PUI": {

Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json

@@ -169,7 +169,6 @@
                 "observationUnitDbId"
             ],
             "title": "ObservationUnit",
-            "description": "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples.",
             "type": "object",
             "brapi-metadata": {
                 "primaryModel": true
@@ -284,21 +283,23 @@
                 "primaryModel": false
             }
         },
-        "Treatment": {
+        "ObservationTreatment": {
             "properties": {
                 "factor": {
                     "description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.",
                     "type": [
                         "null",
                         "string"
-                    ]
+                    ],
+                    "examples": ["test-factor:dia2020-2-nv.fertilizer"]
                 },
                 "modality": {
                     "description": "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ",
                     "type": [
                         "null",
                         "string"
-                    ]
+                    ],
+                    "examples": ["test-factor:dia2020-2-nv.lf"]
                 },
                 "observationUnit": {
                     "description": "associated observation Unit",
@@ -307,7 +308,7 @@
                     "referencedAttribute": "treatments"
                 }
             },
-            "title": "Treatment",
+            "title": "ObservationTreatment",
             "description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc. MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.",
             "type": "object",
             "brapi-metadata": {

Specification/Components/Schemas/ExperimentalDesign.yaml

@@ -0,0 +1,96 @@
+info:
+  title: BrAPI
+  version: ''
+openapi: 3.0.0
+paths: {}
+components:
+  schemas:
+    ExperimentalDesign:
+      title: ExperimentalDesign
+      type: object
+      description: |-
+        The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology
+      properties:
+        description:
+          description: MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be "unknown"/"NA", "aggregated/reduced data", or simply 'none'.
+          type: string
+          nullable: true
+          example: Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliest groups based on a prior information.
+        PUI:
+          description: |- 
+            MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental  design of the study, in the form of an accession number from the Crop Ontology.
+
+            **Deprecated in v2.2** Please use `experimentalDesignPUI`. Github issue number #539
+          type: string
+          deprecated: true
+          nullable: true
+          example: CO_715:0000145
+        experimentalDesignPUI:
+          description: MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental  design of the study, in the form of an accession number from the Crop Ontology.
+          type: string
+          nullable: true
+          example: CO_715:0000145
+        randomizationType:
+          description: The type of randomization use to create the experimental design
+          type: string
+          nullable: true
+          example: RCB:Randomize Complete Block
+        layoutPattern:
+          description: How the trial is layout in the field
+          type: string
+          nullable: true
+          example: Serpentine
+        setSize:
+          description: The size of the sets in the design
+          type: number
+          nullable: true
+          example: 1
+        rowsPerPlot:
+          description: The number of rows in a plot
+          type: number
+          nullable: true
+          example: 1
+        firstRepRand:
+          description: Is the first replication random
+          type: boolean
+          nullable: true
+          example: true
+        experimentFactors:
+            description: |-
+              The factors used in the experimental design
+            type: array
+            nullable: true
+            items:
+              type: object
+              title: "ExperimentFactor"
+              properties:
+                factor:
+                  description: |-
+                    The type of treatment/factor. For example 'fertilizer', 'inoculation', 'irrigation', etc
+
+                    MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
+                  type: string
+                  example:  fertilizer
+                factorPUI:
+                  description: |-
+                    The PUI of the factor which may link to an ontology
+                  type: string
+                  nullable: true
+                  example: test-factor:dia2020-2-nv.fertilizer
+                modalities:
+                  items:
+                    type: object
+                    properties:
+                      modality:
+                        description: |-
+                          The treatment/factor modality or level. For example 'low fertilizer', 'yellow rust inoculation', 'high water', etc
+
+                          MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor.
+                        type: string
+                        example: low fertilizer
+                      modalityPUI:
+                        description: |-
+                          The PUI of the modality which may link to an ontology
+                        type: string
+                        nullable: true
+                        example: test-factor:dia2020-2-nv.lf

Specification/Generated/README.md

@@ -1,6 +1,32 @@
 # Generated
 
-The files in this directory are automatically generated by the [Schema Tools](../../generator/README.md) using 
+The files in this directory are automatically generated by the [Schema Tools](https://github.com/plantbreeding/brapi-schema-tools) using 
 a github [action](../../.github/workflows/generate-schema.yml).
 
+## Open API
+
+The generated OpenAPI YAML files by module are 
+* [BrAPI-Core.yaml](BrAPI-Core.yaml)
+* [BrAPI-Genotyping.yaml](BrAPI-Genotyping.yaml)
+* [BrAPI-Germplasm.yaml](BrAPI-Germplasm.yaml)
+* [BrAPI-Phenotyping.yaml](BrAPI-Phenotyping.yaml)
+
+The generated single JSON file from the [JSON Schema](../BrAPI-Schema) is
+* [brapi_generated.json](brapi_generated.json)
+
+The compiled single JSON file from the [YML specification files](../) is 
+* [brapi_generated.json](brapi_generated.json)
+
+The comparison between the generated and compiled JSON file can be found here
+* [brapi_openapi_comparison.md](brapi_openapi_comparison.md)
+
+## GraphQL
+
+The generated GraphQL file from the [JSON Schema](../BrAPI-Schema) is
+* [brapi_generated.graphqls](brapi_generated.graphqls)
+
+## OWL Turtle
+
+The generated OWL Turtle from the [JSON Schema](../BrAPI-Schema) is
+* [brapi_generated.ttl](brapi_generated.ttl)