Merge pull request #155 from ncbi/release/13.32.0

Release updated docs for 13.32.0

client_docs/python/README.md

@@ -7,7 +7,7 @@ For some larger downloads, you may want to download a [dehydrated bag](https://w
 This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
 - API version: v1
-- Package version: 13.31.0
+- Package version: 13.32.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 
 ## Requirements.

client_docs/python/docs/VirusApi.md

@@ -1192,7 +1192,7 @@ with ncbi.datasets.openapi.ApiClient(configuration) as api_client:
     filter_geo_location = "USA" # str | Assemblies from this location (country and state, or continent) (optional)
     filter_complete_only = True # bool | only include complete genomes. (optional) if omitted the server will use the default value of False
     returned_content = V1VirusDataReportRequestContentType("COMPLETE") # V1VirusDataReportRequestContentType | Return either virus genome accessions, or complete virus metadata (optional)
-    table_fields = ["accession","is_complete","is_annotated"] # [str] | Specify which fields to include in the tabular report (optional)
+    table_fields = ["accession","is-complete","is-annotated"] # [str] | Specify which fields to include in the tabular report (optional)
     page_size = 20 # int | The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results. (optional) if omitted the server will use the default value of 20
     page_token = "page_token_example" # str | A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved. (optional)
 
@@ -1244,7 +1244,7 @@ Name | Type | Description  | Notes
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: application/json, text/tab-separated-values, application/x-tabular
+ - **Accept**: application/json, text/tab-separated-values
 
 
 ### HTTP response details
@@ -1346,7 +1346,7 @@ Name | Type | Description  | Notes
 ### HTTP request headers
 
  - **Content-Type**: application/json
- - **Accept**: application/json, text/tab-separated-values, application/x-tabular
+ - **Accept**: application/json, text/tab-separated-values
 
 
 ### HTTP response details
@@ -1408,7 +1408,7 @@ with ncbi.datasets.openapi.ApiClient(configuration) as api_client:
     filter_geo_location = "USA" # str | Assemblies from this location (country and state, or continent) (optional)
     filter_complete_only = True # bool | only include complete genomes. (optional) if omitted the server will use the default value of False
     returned_content = V1VirusDataReportRequestContentType("COMPLETE") # V1VirusDataReportRequestContentType | Return either virus genome accessions, or complete virus metadata (optional)
-    table_fields = ["accession","is_complete","is_annotated"] # [str] | Specify which fields to include in the tabular report (optional)
+    table_fields = ["accession","is-complete","is-annotated"] # [str] | Specify which fields to include in the tabular report (optional)
     page_size = 20 # int | The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results. (optional) if omitted the server will use the default value of 20
     page_token = "page_token_example" # str | A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved. (optional)
 
@@ -1460,7 +1460,7 @@ Name | Type | Description  | Notes
 ### HTTP request headers
 
  - **Content-Type**: Not defined
- - **Accept**: application/json, text/tab-separated-values, application/x-tabular
+ - **Accept**: application/json, text/tab-separated-values
 
 
 ### HTTP response details

datasets.openapi.yaml

@@ -3002,9 +3002,6 @@ paths:
             text/tab-separated-values:
               schema:
                 type: string
-            application/x-tabular:
-              schema:
-                type: string
         default:
           description: An unexpected error response.
           content:
@@ -3181,8 +3178,8 @@ paths:
           example-0:
             value:
               - accession
-              - is_complete
-              - is_annotated
+              - is-complete
+              - is-annotated
             summary: Virus Genome Fields
       - name: page_size
         description: 'The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.'
@@ -3214,9 +3211,6 @@ paths:
             text/tab-separated-values:
               schema:
                 type: string
-            application/x-tabular:
-              schema:
-                type: string
         default:
           description: An unexpected error response.
           content:
@@ -3389,8 +3383,8 @@ paths:
           example-0:
             value:
               - accession
-              - is_complete
-              - is_annotated
+              - is-complete
+              - is-annotated
             summary: Virus Genome Fields
       - name: page_size
         description: 'The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.'
@@ -3422,9 +3416,6 @@ paths:
             text/tab-separated-values:
               schema:
                 type: string
-            application/x-tabular:
-              schema:
-                type: string
         default:
           description: An unexpected error response.
           content:

pkgs/ncbi-datasets-cli/src/datasets/datasets/DownloadVirusGenomeTaxon.go

@@ -11,13 +11,26 @@ import (
 	openapi "datasets_cli/v1/openapi"
 )
 
+func contains(s []int32, e int32) bool {
+	for _, a := range s {
+		if a == e {
+			return true
+		}
+	}
+	return false
+}
+
 func checkTaxonWithinScope(cli *openapi.APIClient, taxon string) (is_cov bool) {
 	// conservatively set default to true
 	is_cov = true
-	query_min_ord, query_max_ord, err := findTaxonOrd(cli, taxon)
-	if err == nil {
-		cov_min_ord, cov_max_ord, err := findTaxonOrd(cli, "Coronaviridae")
-		if err == nil && (query_min_ord < cov_min_ord || query_max_ord > cov_max_ord) {
+	coronaviridaeTaxId := int32(10239)
+	request := cli.TaxonomyApi.TaxonomyMetadata(nil, []string{taxon})
+	org, resp, err := request.Execute()
+	if err = handleHTTPResponse(resp, err); err == nil {
+		taxNode := org.GetTaxonomyNodes()[0]
+		taxonomy := taxNode.GetTaxonomy()
+		lineage := taxonomy.GetLineage()
+		if !contains(lineage, coronaviridaeTaxId) {
 			is_cov = false
 		}
 	}

pkgs/ncbi-datasets-cli/src/datasets/datasets/SummaryVirusGenomeTaxon.go

@@ -28,16 +28,13 @@ Refer to NCBI's [download and install](https://www.ncbi.nlm.nih.gov/datasets/doc
 	Args: cobra.ExactArgs(1),
 
 	RunE: func(cmd *cobra.Command, args []string) error {
-		processAssmAccArgs(args)
 		request, err := summaryVirusGenomeRequestWithTax(args[0])
 		if err != nil {
 			return err
 		}
-
 		return printViralMetadataWithPost(request)
 	},
 }
 
 func init() {
-
 }