v2.1 clean up

plantbreeding · Jun 21, 2022 · 5e3257a · 5e3257a
1 parent 72887c3
commit 5e3257a
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Showing 17 changed files with 36 additions and 24 deletions.
diff --git a/Specification/BrAPI-Core/ServerInfo/ServerInfo_GET.yaml b/Specification/BrAPI-Core/ServerInfo/ServerInfo_GET.yaml
@@ -46,8 +46,7 @@ paths:
           $ref: '#/components/schemas/ContentTypes'
       - description: |-
           **Deprecated in v2.1** Please use `contentType`. Github issue number #443
-
-          The data format supported by the call.
+          <br>The data format supported by the call.
         deprecated: true
         in: query
         name: dataType

diff --git a/Specification/BrAPI-Genotyping/Calls/Schemas/Call.yaml b/Specification/BrAPI-Genotyping/Calls/Schemas/Call.yaml
@@ -86,6 +86,7 @@ components:
         genotype:
           $ref: '#/components/schemas/ListValue'
         genotype_likelihood:
+          deprecated: true
           description: |-
             **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491             
             <br>The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec.

diff --git a/Specification/BrAPI-Genotyping/Calls/Schemas/ListValue.yaml b/Specification/BrAPI-Genotyping/Calls/Schemas/ListValue.yaml
@@ -6,6 +6,7 @@ paths: {}
 components:
   schemas:
     ListValue:
+      deprecated: true
       type: object
       description: |-
         **Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491             
@@ -14,6 +15,7 @@ components:
       properties:
         values:
           type: array
+          deprecated: true
           description: |-
             **Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491             
             <br>Repeated field of dynamically typed values.

diff --git a/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml b/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml
@@ -14,11 +14,20 @@ components:
         This is equivalent to a row in VCF.
       properties:
         alternate_bases:
+          deprecated: true
+          description: |-
+            **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549
+            <br>The bases that appear instead of the reference bases. Multiple alternate alleles are possible.
+          items:
+            type: string
+          type: array
+          example: ['T', 'TAC']
+        alternateBases:
           description: The bases that appear instead of the reference bases. Multiple alternate alleles are possible.
           items:
             type: string
           type: array
-          example: ['TAGGATTGAGCTCTATAT']
+          example: ['T', 'TAC']
         additionalInfo:
           additionalProperties:
             type: string
@@ -92,7 +101,7 @@ components:
         referenceBases:
           description: The reference bases for this variant. They start at the given start position.
           type: string
-          example: TAGGATTGAGCTCTATAT
+          example: A
         referenceSetDbId:
           description: The unique identifier for a ReferenceSet
           type: string

diff --git a/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml b/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml
@@ -29,6 +29,7 @@ components:
             type: integer
             example: 1500
           referenceDbId:
+            deprecated: true
             description: |-
               **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472
               <br/>Only return variants on this reference.

diff --git a/Specification/BrAPI-Germplasm/Crosses/Schemas/CrossNewRequest.yaml b/Specification/BrAPI-Germplasm/Crosses/Schemas/CrossNewRequest.yaml
@@ -52,8 +52,7 @@ components:
         pollinationTimeStamp: 
           description: |-
             **Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265 
-
-            the timestamp when the pollination took place
+            <br>The timestamp when the pollination took place
           type: string
           format: date-time
           deprecated: true

diff --git a/Specification/BrAPI-Phenotyping/Events/Schemas/Event.yaml b/Specification/BrAPI-Phenotyping/Events/Schemas/Event.yaml
@@ -81,6 +81,7 @@ components:
               type: string
               example: '2018-10-08T18:15:11Z'
         date:
+          deprecated: true
           description: |-
             **Deprecated in v2.1** Please use `eventDateRange.discreteDates`. Github issue number #440             
             <br>A list of dates when the event occurred
@@ -136,12 +137,14 @@ components:
                 type: string
                 example: Standard V-Ripper (TI001)
               key:
+                deprecated: true
                 description: |-
                   **Deprecated in v2.1** Please use `name`. Github issue number #440             
                   <br>Specifies the relationship between the event and the given property. E.g. fertilizer, operator
                 type: string
                 example: operator
               rdfValue:
+                deprecated: true
                 description: |-
                   **Deprecated in v2.1** Please use `code`. Github issue number #440             
                   <brThe type of the value given above, e.g. http://xmlns.com/foaf/0.1/Agent

diff --git a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_Table_GET.yaml b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_Table_GET.yaml
@@ -94,14 +94,13 @@ paths:
           type: string
       - description: |-
           **Deprecated in v2.1** Please use `observationUnitLevelName`. Github issue number #464 
-
-          The type of the observationUnit. Returns only the observation unit of the specified type; 
-          the parent levels ID can be accessed through observationUnitStructure. 
+          <br>The type of the observationUnit. Returns only the observation unit of the specified type; the parent levels ID can be accessed through observationUnitStructure. 
         in: query
         name: observationLevel
         required: false
         schema:
           type: string
+        deprecated: true
       - $ref: '#/components/parameters/observationUnitLevelName'
       - $ref: '#/components/parameters/observationUnitLevelOrder'
       - $ref: '#/components/parameters/observationUnitLevelCode'

diff --git a/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml b/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml
@@ -96,14 +96,13 @@ paths:
           type: string
       - description: |-
           **Deprecated in v2.1** Please use `observationUnitLevelName`. Github issue number #464 
-
-          The type of the observationUnit. Returns only the observation unit of the specified type; 
-          the parent levels ID can be accessed through observationUnitStructure. 
+          <br>The type of the observationUnit. Returns only the observation unit of the specified type; the parent levels ID can be accessed through observationUnitStructure. 
         in: query
         name: observationLevel
         required: false
         schema:
           type: string
+        deprecated: true
       - description: Permanent unique identifier which references the search results
         in: query
         name: searchResultsDbId

diff --git a/Specification/BrAPI-Phenotyping/Observations/Schemas/SeasonObs.yaml b/Specification/BrAPI-Phenotyping/Observations/Schemas/SeasonObs.yaml
@@ -18,8 +18,7 @@ components:
           deprecated: true
           description: |-
             **Deprecated in v2.1** Please use `seasonName`. Github issue number #456 
-
-            Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.
+            <br>Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.
           type: string
           example: Spring
         seasonDbId:

diff --git a/Specification/Components/Parameters/externalReferences.yaml b/Specification/Components/Parameters/externalReferences.yaml
@@ -10,8 +10,7 @@ components:
       name: externalReferenceID
       description:  |-
         **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 
-
-        An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)
+        <br>An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)
       in: query
       required: false
       schema:

diff --git a/Specification/Components/Schemas/ExternalReferences.yaml b/Specification/Components/Schemas/ExternalReferences.yaml
@@ -20,8 +20,7 @@ components:
             deprecated: true
             description: |-
               **Deprecated in v2.1** Please use `referenceId`. Github issue number #460 
-
-              The external reference ID. Could be a simple string or a URI.
+              <br>The external reference ID. Could be a simple string or a URI.
             type: string
           referenceId:
             description: The external reference ID. Could be a simple string or a URI.

diff --git a/Specification/Components/Schemas/ScaleBaseClass.yaml b/Specification/Components/Schemas/ScaleBaseClass.yaml
@@ -66,15 +66,14 @@ components:
             max:
               description: |-
                 **Deprecated in v2.1** Please use `maximumValue`. Github issue number #450 
-
-                Maximum value for numerical scales. Typically used for data capture control and QC.
+                <br>Maximum value for numerical scales. Typically used for data capture control and QC.
               type: integer
               example: 9999
               deprecated: true
             min:
               description: |-
                 **Deprecated in v2.1** Please use `minimumValue`. Github issue number #450 
-                <br/>Minimum value for numerical scales. Typically used for data capture control and QC.
+                <br>Minimum value for numerical scales. Typically used for data capture control and QC.
               type: integer
               example: 2
               deprecated: true

diff --git a/...on/Components/Schemas/SearchRequestSchemas/SearchRequestParametersExternalReferences.yaml b/...on/Components/Schemas/SearchRequestSchemas/SearchRequestParametersExternalReferences.yaml
@@ -12,8 +12,7 @@ components:
           deprecated: true
           description:  |-
             **Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 
-
-            List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)
+            <br>List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)
           items:
             type: string
           type: array

diff --git a/...ification/Components/Schemas/SearchRequestSchemas/SearchRequestParametersTokenPaging.yaml b/...ification/Components/Schemas/SearchRequestSchemas/SearchRequestParametersTokenPaging.yaml
@@ -9,6 +9,7 @@ components:
       type: object
       properties:
         pageToken:
+          deprecated: true
           description: |-
             **Deprecated in v2.1** Please use `page`. Github issue number #451 
             <br>Used to request a specific page of data to be returned.

diff --git a/...ion/Components/Schemas/SearchRequestSchemas/SearchRequestParametersVariableBaseClass.yaml b/...ion/Components/Schemas/SearchRequestSchemas/SearchRequestParametersVariableBaseClass.yaml
@@ -18,7 +18,7 @@ components:
           studyDbId:  
             description: |-
               **Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 
-              The unique ID of a studies to filter on
+              <br>The unique ID of a studies to filter on
             deprecated: true
             type: array
             items:

diff --git a/Specification/Components/Schemas/metadata.yaml b/Specification/Components/Schemas/metadata.yaml
@@ -79,6 +79,7 @@ components:
       allOf:
       - $ref: '#/components/schemas/basePagination'
       - type: object
+        deprecated: true
         description: |-
           **Deprecated in v2.1** Please use `page`. Github issue number #451 
           <br>The pagination object is applicable only when the payload contains a "data" key. It describes the pagination of the data contained in the "data" array, as a way to identify which subset of data is being returned. 
@@ -87,18 +88,21 @@ components:
         - nextPageToken
         properties:
           nextPageToken:
+            deprecated: true
             description: |- 
               **Deprecated in v2.1** Please use `page`. Github issue number #451 
               <br>The string token used to query the next page of data.
             type: string
             example: cb668f63
           currentPageToken:
+            deprecated: true
             description: |- 
               **Deprecated in v2.1** Please use `page`. Github issue number #451 
               <br>The string token used to query the current page of data.
             type: string
             example: 48bc6ac1
           prevPageToken:
+            deprecated: true
             description: |- 
               **Deprecated in v2.1** Please use `page`. Github issue number #451 
               <br>The string token used to query the previous page of data.