Apply automatic changes

Author: daveneti

Specification/BrAPI-Core/Studies/README.md

@@ -677,11 +677,42 @@ type EventsSearchResponse {
   searchResultsDbId: String
 }
 
+type ExperimentFactor {
+  """
+  The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc
+  
+  MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
+  """
+  factor: String
+  "The PUI of the factor which may link to an ontology."
+  factorPUI: String
+  """
+  The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc
+  
+  MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
+  """
+  modalities: [Modality]
+}
+
 type ExperimentalDesign {
-  "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."
+  "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"
   PUI: String
   "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'."
   description: String
+  "The factors used in the experimental design."
+  experimentFactors: [ExperimentFactor]
+  "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."
+  experimentalDesignPUI: String
+  "Is the first replication random."
+  firstRepRand: Boolean
+  "How the trial is layout in the field."
+  layoutPattern: String
+  "The type of randomization use to create the experimental design."
+  randomizationType: String
+  "The number of rows in a plot."
+  rowsPerPlot: Float
+  "The size of the sets in the design."
+  setSize: Float
   "Experimental design associated with a study"
   study: Study
 }
@@ -1408,6 +1439,17 @@ type MethodListResponse {
   page: PageInfo
 }
 
+type Modality {
+  """
+  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. 
+  """
+  modality: String
+  "The PUI of the modality which may link to an ontology."
+  modalityPUI: String
+}
+
 type Mutation {
   "Create a new BreedingMethod"
   createBreedingMethod(breedingMethodInput: BreedingMethodInput): BreedingMethod
@@ -2849,12 +2891,16 @@ type Treatment {
   MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
   """
   factor: String
+  "The PUI of the factor which may link to an ontology."
+  factorPUI: String
   """
   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. 
   """
   modality: String
+  "The PUI of the modality which may link to an ontology."
+  modalityPUI: String
   "associated observation Unit"
   observationUnit: ObservationUnit
 }
@@ -3935,11 +3981,42 @@ input EventsInput {
   studyNames: [String]
 }
 
+input ExperimentFactorInput {
+  """
+  The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc
+  
+  MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
+  """
+  factor: String
+  "The PUI of the factor which may link to an ontology."
+  factorPUI: String
+  """
+  The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc
+  
+  MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
+  """
+  modalities: [ModalityInput]
+}
+
 input ExperimentalDesignInput {
-  "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."
+  "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"
   PUI: String
   "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'."
   description: String
+  "The factors used in the experimental design."
+  experimentFactors: [ExperimentFactorInput]
+  "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."
+  experimentalDesignPUI: String
+  "Is the first replication random."
+  firstRepRand: Boolean
+  "How the trial is layout in the field."
+  layoutPattern: String
+  "The type of randomization use to create the experimental design."
+  randomizationType: String
+  "The number of rows in a plot."
+  rowsPerPlot: Float
+  "The size of the sets in the design."
+  setSize: Float
   "Experimental design associated with a study"
   study: StudyInput
 }
@@ -5003,6 +5080,17 @@ input MethodsInput {
   scaleDbIds: [String]
 }
 
+input ModalityInput {
+  """
+  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. 
+  """
+  modality: String
+  "The PUI of the modality which may link to an ontology."
+  modalityPUI: String
+}
+
 input ObservationInput {
   "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."
   additionalInfo: AdditionalInfoInput
@@ -6851,12 +6939,16 @@ input TreatmentInput {
   MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
   """
   factor: String
+  "The PUI of the factor which may link to an ontology."
+  factorPUI: String
   """
   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. 
   """
   modality: String
+  "The PUI of the modality which may link to an ontology."
+  modalityPUI: String
   "associated observation Unit"
   observationUnit: ObservationUnitInput
 }

Specification/BrAPI-Phenotyping/ObservationUnits/README.md

@@ -9149,6 +9149,31 @@
           }
         }
       },
+      "ExperimentFactor" : {
+        "type" : "object",
+        "properties" : {
+          "factor" : {
+            "type" : "string"
+          },
+          "factorPUI" : {
+            "type" : "string"
+          },
+          "modalities" : {
+            "type" : "array",
+            "items" : {
+              "type" : "object",
+              "properties" : {
+                "modality" : {
+                  "type" : "string"
+                },
+                "modalityPUI" : {
+                  "type" : "string"
+                }
+              }
+            }
+          }
+        }
+      },
       "ExperimentalDesign" : {
         "type" : "object",
         "properties" : {
@@ -9158,6 +9183,30 @@
           "description" : {
             "type" : "string"
           },
+          "experimentFactors" : {
+            "type" : "array",
+            "items" : {
+              "$ref" : "#/components/schemas/ExperimentFactor"
+            }
+          },
+          "experimentalDesignPUI" : {
+            "type" : "string"
+          },
+          "firstRepRand" : {
+            "type" : "boolean"
+          },
+          "layoutPattern" : {
+            "type" : "string"
+          },
+          "randomizationType" : {
+            "type" : "string"
+          },
+          "rowsPerPlot" : {
+            "type" : "number"
+          },
+          "setSize" : {
+            "type" : "number"
+          },
           "studyDbId" : {
             "type" : "string"
           },
@@ -12114,8 +12163,8 @@
               "type" : "string"
             }
           },
-          "experimentalDesign" : {
-            "$ref" : "#/components/schemas/ExperimentalDesign"
+          "experimentalDesignPUI" : {
+            "type" : "string"
           },
           "growthFacility" : {
             "$ref" : "#/components/schemas/GrowthFacility"
@@ -12204,8 +12253,8 @@
               "type" : "string"
             }
           },
-          "experimentalDesign" : {
-            "$ref" : "#/components/schemas/ExperimentalDesign"
+          "experimentalDesignPUI" : {
+            "type" : "string"
           },
           "growthFacility" : {
             "$ref" : "#/components/schemas/GrowthFacility"
@@ -12411,9 +12460,15 @@
           "factor" : {
             "type" : "string"
           },
+          "factorPUI" : {
+            "type" : "string"
+          },
           "modality" : {
             "type" : "string"
           },
+          "modalityPUI" : {
+            "type" : "string"
+          },
           "observationUnitDbId" : {
             "type" : "string"
           },