added nullable: true to remaining

Author: Guy Davenport

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

@@ -120,6 +120,7 @@ components:
             
             MIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study
           type: string
+          nullable: true
           example: INRA's Walnut Genetic Resources Observation at Kenya
         studyCode:
           description: A short human readable code for a study
@@ -134,6 +135,7 @@ components:
         studyType:
           description: The type of study being performed. ex. "Yield Trial", etc
           type: string
+          nullable: true
           example: Phenotyping
         trialDbId:
           description: The ID which uniquely identifies a trial

Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrix.yaml

@@ -19,33 +19,39 @@ components:
         pagination:
           description: Pagination for the matrix
           type: array
+          nullable: true
           items:
             type: object
             properties:
               dimension:
                 description: The dimension of the matrix being paginated
                 type: string
+                nullable: true
                 enum:
                 - CALLSETS
                 - VARIANTS
                 example: VARIANTS
               pageSize: 
                 description: the maximum number of elements per page in this dimension of the matrix
                 type: integer
+                nullable: true
                 example: 500
               page: 
                 description: the requested page number (zero indexed) 
                 type: integer
+                nullable: true
                 example: 0
               totalCount:
                 description: The total number of elements that are available on the server and match the requested query parameters. 
                 type: integer
+                nullable: true
                 example: 10000
               totalPages:
                 description: |-
                   The total number of pages of elements available on the server. This should be calculated with the following formula. 
                   <br/>totalPages = CEILING( totalCount / requested_page_size)
                 type: integer
+                nullable: true
                 example: 20
           example:
             -  dimension: VARIANTS
@@ -73,19 +79,22 @@ components:
         variantDbIds: 
           description: A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix.
           type: array
+          nullable: true
           items:
             type: string
           example: ['feb54257', 'feb40355', 'feb40323']
         dataMatrices:
           description: The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the "callSetDbIds" as columns and the "variantDbIds" as rows.
           type: array
+          nullable: true
           items:
             description: This is a single data matrix. It could be the allele matrix or an additional layer of metadata associated with each genotype value.
             type: object
             properties:
               dataType:
                 description: The type of field represented in this data matrix. This is intended to help parse the data out of JSON.
                 type: string
+                nullable: true
                 enum:
                 - string
                 - integer
@@ -97,16 +106,19 @@ components:
                   The name of the field represented in this data matrix. The key word "Genotype" is reserved for the allele matrix. Examples of other metadata matrices include: "Genotype Quality", "Read Depth", and "Haplotype Quality"
                   <br> This maps to a FORMAT field in the VCF file standard.
                 type: string
+                nullable: true
                 example: Genotype
               dataMatrixAbbreviation:
                 description: |-
                   The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word "GT" is reserved for the allele matrix. Examples of other metadata matrices include: "GQ", "RD", and "HQ"
                   <br> This maps to a FORMAT field in the VCF file standard.
                 type: string
+                nullable: true
                 example: GT
               dataMatrix:
                 description: The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the "callSetDbIds" as columns and the "variantDbIds" as rows.
                 type: array
+                nullable: true
                 items:
                   description: An array of rows in the data matrix
                   type: array
@@ -135,16 +147,20 @@ components:
         expandHomozygotes: 
           description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false)
           type: boolean
+          nullable: true
           example: true
         sepPhased:
           description: The string used as a separator for phased allele calls.
           type: string
+          nullable: true
           example: '|'
         sepUnphased:
           description: The string used as a separator for unphased allele calls.
           type: string
+          nullable: true
           example: '/'
         unknownString:
           description: The string used as a representation for missing data.
           type: string
+          nullable: true
           example: '.'

Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml

@@ -93,7 +93,7 @@ components:
     positionRange:
       name: positionRange
       description: |-
-        The postion range to search
+        The position range to search
         <br/> Uses the format "contig:start-end" where "contig" is the chromosome or contig name, "start" is  
         the starting position of the range, and "end" is the ending position of the range
         <br> Example: CRHOM_1:12000-14000

Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml

@@ -11,6 +11,7 @@ components:
         pagination:
           description: Pagination for the matrix
           type: array
+          nullable: true
           items:
             type: object
             properties:
@@ -53,13 +54,15 @@ components:
           description: |-
             `dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.
           type: array
+          nullable: true
           items:
             type: string
           example: ['Genotype', 'Read Depth']
         dataMatrixAbbreviations:
           description: |-
             `dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.
           type: array
+          nullable: true
           items:
             type: string
           example: ['GT', 'RD']
@@ -70,30 +73,35 @@ components:
             Uses the format "<chrom>:<start>-<end>" where <chrom> is the chromosome name, <start> is 
             the starting position of the range, and <end> is the ending position of the range
           type: array
+          nullable: true
           items:
             type: string
           example: [ '20:1000-35000', '20:87000-125000' ]
         germplasmNames:
           description: A list of human readable `Germplasm` names
           type: array
+          nullable: true
           items:
             type: string
           example: [ 'a03202ec', '274e4f63' ]
         germplasmPUIs:
           description: A list of permanent unique identifiers associated with `Germplasm`
           type: array
+          nullable: true
           items:
             type: string
           example: [ 'a03202ec', '274e4f63' ]
         germplasmDbIds:
           description: A list of IDs which uniquely identify `Germplasm` within the given database server 
           type: array
+          nullable: true
           items:
             type: string
           example: [ 'a03202ec', '274e4f63' ]
         sampleDbIds:
           description: A list of IDs which uniquely identify `Samples` within the given database server 
           type: array
+          nullable: true
           items:
             type: string
           example: [ 'a03202ec', '274e4f63' ]
@@ -106,28 +114,34 @@ components:
         variantDbIds: 
           description: A list of IDs which uniquely identify `Variants` within the given database server 
           type: array
+          nullable: true
           items:
             type: string
           example: [ 'bba0b258', 'ff97d4f0' ]
         variantSetDbIds: 
           description: A list of IDs which uniquely identify `VariantSets` within the given database server 
           type: array
+          nullable: true
           items:
             type: string
           example: [ '407c0508', '49e24dfc' ]
         expandHomozygotes:
           description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false)
           type: boolean
+          nullable: true
           example: true
         sepPhased:
           description: The string used as a separator for phased allele calls.
           type: string
+          nullable: true
           example: '|'
         sepUnphased:
           description: The string used as a separator for unphased allele calls.
           type: string
+          nullable: true
           example: '/'
         unknownString:
           description: The string used as a representation for missing data.
           type: string
+          nullable: true
           example: '.'

Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml

@@ -21,15 +21,19 @@ components:
             type: string
           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.
           type: object
+          nullable: true
         externalReferences: 
           $ref: '#/components/schemas/ExternalReferences'
+          nullable: true
         sampleDbId:
           description: The Biosample entity the call set data was generated from.
           type: string
+          nullable: true
           example: 5e50e11d
         created:
           description: The date this call set was created
           type: string
+          nullable: true
           format: date-time
         callSetDbId:
           description: The ID which uniquely identifies a CallSet within the given database server 
@@ -38,19 +42,23 @@ components:
         callSetName:
           description: The human readable name which identifies a germplasm within the given database server 
           type: string
+          nullable: true
           example: Sample_123_DNA_Run_456
         updated:
           description: The time at which this call set was last updated
           type: string
+          nullable: true
           format: date-time
         studyDbId:
           description: The ID which uniquely identifies a study within the given database server
           type: string
+          nullable: true
           example: 708149c1
         variantSetDbIds:
           description: The IDs of the variantSets this callSet has calls in.
           items:
             type: string
           type: array
+          nullable: true
           example: [ 'cfd3d60f', 'a4e8bfe9' ]
 

Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml

@@ -19,30 +19,35 @@ components:
           sampleDbIds:
             description: A list of IDs which uniquely identify `Samples` within the given database server 
             type: array
+            nullable: true
             items:
               type: string
             example: [ '758d3f6d', '39c0a3f7']
           sampleNames:
             description: A list of human readable names associated with `Samples`
             type: array
+            nullable: true
             items:
               type: string
             example: [ 'Sample_123', 'Sample_789' ]
           callSetDbIds: 
             description: A list of IDs which uniquely identify `CallSets` within the given database server 
             type: array
+            nullable: true
             items:
               type: string
             example: [ '6c7486b2', '49c36a73']
           callSetNames:
             description: A list of human readable names associated with `CallSets`
             type: array
+            nullable: true
             items:
               type: string
             example: [ 'Sample_123_DNA_Run_456', 'Sample_789_DNA_Run_101' ]
           variantSetDbIds: 
             description: A list of IDs which uniquely identify `VariantSets` within the given database server 
             type: array
+            nullable: true
             items:
               type: string
             example: [ '8a9a8972', '32a2649a']

Specification/BrAPI-Genotyping/Calls/Schemas/Call.yaml

@@ -26,6 +26,7 @@ components:
             type: string
           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.
           type: object
+          nullable: true
         callSetDbId:
           description: |-
             The ID of the call set this variant call belongs to.

Specification/BrAPI-Genotyping/Calls/Schemas/CallsListResponse.yaml

@@ -34,17 +34,21 @@ components:
                   expandHomozygotes: 
                     description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false)
                     type: boolean
+                    nullable: true
                     example: true
                   sepPhased:
                     description: The string used as a separator for phased allele calls.
                     type: string
+                    nullable: true
                     example: '|'
                   sepUnphased:
                     description: The string used as a separator for unphased allele calls.
                     type: string
+                    nullable: true
                     example: '/'
                   unknownString:
                     description: The string used as a representation for missing data.
                     type: string
+                    nullable: true
                     example: '.'
 

Specification/BrAPI-Genotyping/Calls/Schemas/CallsSearchRequest.yaml

@@ -13,34 +13,41 @@ components:
           callSetDbIds:
             description: A list of IDs which uniquely identify `CallSets` within the given database server 
             type: array
+            nullable: true
             items:
               type: string
             example: [ 'a03202ec', '274e4f63' ]
           variantDbIds: 
             description: A list of IDs which uniquely identify `Variant` within the given database server 
             type: array
+            nullable: true
             items:
               type: string
             example: [ 'bba0b258', 'ff97d4f0' ]
           variantSetDbIds: 
             description: A list of IDs which uniquely identify `VariantSets` within the given database server 
             type: array
+            nullable: true
             items:
               type: string
             example: [ '407c0508', '49e24dfc' ]
           expandHomozygotes:
             description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false)
             type: boolean
+            nullable: true
             example: true
           sepPhased:
             description: The string used as a separator for phased allele calls.
             type: string
+            nullable: true
             example: '|'
           sepUnphased:
             description: The string used as a separator for unphased allele calls.
             type: string
+            nullable: true
             example: '/'
           unknownString:
             description: The string used as a representation for missing data.
             type: string
+            nullable: true
             example: '.'