ncbi-datasets-pyclient 18.4.0__py3-none-any.whl → 18.13.0__py3-none-any.whl

ncbi/datasets/openapi/api/organelle_api.py

@@ -3,10 +3,9 @@
 """
     NCBI Datasets API
 
-    ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time. 
+    ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability. 
 
     The version of the OpenAPI document: v2
-    Contact: help@ncbi.nlm.nih.gov
     Generated by OpenAPI Generator (https://openapi-generator.tech)
 
     Do not edit the class manually.

ncbi/datasets/openapi/api/prokaryote_api.py

@@ -3,10 +3,9 @@
 """
     NCBI Datasets API
 
-    ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time. 
+    ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability. 
 
     The version of the OpenAPI document: v2
-    Contact: help@ncbi.nlm.nih.gov
     Generated by OpenAPI Generator (https://openapi-generator.tech)
 
     Do not edit the class manually.
@@ -44,10 +43,10 @@ class ProkaryoteApi:
     @validate_call
     def download_prokaryote_gene_package(
         self,
-        accessions: Annotated[List[StrictStr], Field(description="WP prokaryote protein accession")],
-        include_annotation_type: Annotated[Optional[List[V2Fasta]], Field(description="Select additional types of annotation to include in the data package.  If unset, no annotation is provided.")] = None,
+        accessions: Annotated[List[StrictStr], Field(description="One or more RefSeq non-redundant protein accessions (preceded by `WP_`)")],
+        include_annotation_type: Annotated[Optional[List[V2Fasta]], Field(description="Specify which sequence files to include in the data package.")] = None,
         gene_flank_config_length: Optional[StrictInt] = None,
-        taxon: Annotated[Optional[StrictStr], Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree")] = None,
+        taxon: Annotated[Optional[StrictStr], Field(description="Limit gene sequences and the genome assemblies described by the [annotation report file](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/) to the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.")] = None,
         filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
         _request_timeout: Union[
             None,
@@ -62,17 +61,17 @@ class ProkaryoteApi:
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> bytearray:
-        """Get a prokaryote gene dataset by RefSeq protein accession
+        """Get a prokaryote gene data package by RefSeq protein accession
 
-        Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession.
+        Download a prokaryote gene data package including sequence, annotation and data reports by RefSeq non-redundant protein accession.
 
-        :param accessions: WP prokaryote protein accession (required)
+        :param accessions: One or more RefSeq non-redundant protein accessions (preceded by `WP_`) (required)
         :type accessions: List[str]
-        :param include_annotation_type: Select additional types of annotation to include in the data package.  If unset, no annotation is provided.
+        :param include_annotation_type: Specify which sequence files to include in the data package.
         :type include_annotation_type: List[V2Fasta]
         :param gene_flank_config_length:
         :type gene_flank_config_length: int
-        :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree
+        :param taxon: Limit gene sequences and the genome assemblies described by the [annotation report file](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/) to the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.
         :type taxon: str
         :param filename: Output file name.
         :type filename: str
@@ -127,10 +126,10 @@ class ProkaryoteApi:
     @validate_call
     def download_prokaryote_gene_package_with_http_info(
         self,
-        accessions: Annotated[List[StrictStr], Field(description="WP prokaryote protein accession")],
-        include_annotation_type: Annotated[Optional[List[V2Fasta]], Field(description="Select additional types of annotation to include in the data package.  If unset, no annotation is provided.")] = None,
+        accessions: Annotated[List[StrictStr], Field(description="One or more RefSeq non-redundant protein accessions (preceded by `WP_`)")],
+        include_annotation_type: Annotated[Optional[List[V2Fasta]], Field(description="Specify which sequence files to include in the data package.")] = None,
         gene_flank_config_length: Optional[StrictInt] = None,
-        taxon: Annotated[Optional[StrictStr], Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree")] = None,
+        taxon: Annotated[Optional[StrictStr], Field(description="Limit gene sequences and the genome assemblies described by the [annotation report file](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/) to the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.")] = None,
         filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
         _request_timeout: Union[
             None,
@@ -145,17 +144,17 @@ class ProkaryoteApi:
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> ApiResponse[bytearray]:
-        """Get a prokaryote gene dataset by RefSeq protein accession
+        """Get a prokaryote gene data package by RefSeq protein accession
 
-        Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession.
+        Download a prokaryote gene data package including sequence, annotation and data reports by RefSeq non-redundant protein accession.
 
-        :param accessions: WP prokaryote protein accession (required)
+        :param accessions: One or more RefSeq non-redundant protein accessions (preceded by `WP_`) (required)
         :type accessions: List[str]
-        :param include_annotation_type: Select additional types of annotation to include in the data package.  If unset, no annotation is provided.
+        :param include_annotation_type: Specify which sequence files to include in the data package.
         :type include_annotation_type: List[V2Fasta]
         :param gene_flank_config_length:
         :type gene_flank_config_length: int
-        :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree
+        :param taxon: Limit gene sequences and the genome assemblies described by the [annotation report file](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/) to the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.
         :type taxon: str
         :param filename: Output file name.
         :type filename: str
@@ -210,10 +209,10 @@ class ProkaryoteApi:
     @validate_call
     def download_prokaryote_gene_package_without_preload_content(
         self,
-        accessions: Annotated[List[StrictStr], Field(description="WP prokaryote protein accession")],
-        include_annotation_type: Annotated[Optional[List[V2Fasta]], Field(description="Select additional types of annotation to include in the data package.  If unset, no annotation is provided.")] = None,
+        accessions: Annotated[List[StrictStr], Field(description="One or more RefSeq non-redundant protein accessions (preceded by `WP_`)")],
+        include_annotation_type: Annotated[Optional[List[V2Fasta]], Field(description="Specify which sequence files to include in the data package.")] = None,
         gene_flank_config_length: Optional[StrictInt] = None,
-        taxon: Annotated[Optional[StrictStr], Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree")] = None,
+        taxon: Annotated[Optional[StrictStr], Field(description="Limit gene sequences and the genome assemblies described by the [annotation report file](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/) to the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.")] = None,
         filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
         _request_timeout: Union[
             None,
@@ -228,17 +227,17 @@ class ProkaryoteApi:
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> RESTResponseType:
-        """Get a prokaryote gene dataset by RefSeq protein accession
+        """Get a prokaryote gene data package by RefSeq protein accession
 
-        Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession.
+        Download a prokaryote gene data package including sequence, annotation and data reports by RefSeq non-redundant protein accession.
 
-        :param accessions: WP prokaryote protein accession (required)
+        :param accessions: One or more RefSeq non-redundant protein accessions (preceded by `WP_`) (required)
         :type accessions: List[str]
-        :param include_annotation_type: Select additional types of annotation to include in the data package.  If unset, no annotation is provided.
+        :param include_annotation_type: Specify which sequence files to include in the data package.
         :type include_annotation_type: List[V2Fasta]
         :param gene_flank_config_length:
         :type gene_flank_config_length: int
-        :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree
+        :param taxon: Limit gene sequences and the genome assemblies described by the [annotation report file](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/) to the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.
         :type taxon: str
         :param filename: Output file name.
         :type filename: str
@@ -391,9 +390,9 @@ class ProkaryoteApi:
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> bytearray:
-        """Get a prokaryote gene dataset by RefSeq protein accession by POST
+        """Get a prokaryote gene data package by RefSeq protein accession
 
-        Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession by POST.
+        Download a prokaryote gene data package including sequence, annotation and data reports by RefSeq non-redundant protein accession.
 
         :param v2_prokaryote_gene_request: (required)
         :type v2_prokaryote_gene_request: V2ProkaryoteGeneRequest
@@ -462,9 +461,9 @@ class ProkaryoteApi:
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> ApiResponse[bytearray]:
-        """Get a prokaryote gene dataset by RefSeq protein accession by POST
+        """Get a prokaryote gene data package by RefSeq protein accession
 
-        Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession by POST.
+        Download a prokaryote gene data package including sequence, annotation and data reports by RefSeq non-redundant protein accession.
 
         :param v2_prokaryote_gene_request: (required)
         :type v2_prokaryote_gene_request: V2ProkaryoteGeneRequest
@@ -533,9 +532,9 @@ class ProkaryoteApi:
         _headers: Optional[Dict[StrictStr, Any]] = None,
         _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
     ) -> RESTResponseType:
-        """Get a prokaryote gene dataset by RefSeq protein accession by POST
+        """Get a prokaryote gene data package by RefSeq protein accession
 
-        Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession by POST.
+        Download a prokaryote gene data package including sequence, annotation and data reports by RefSeq non-redundant protein accession.
 
         :param v2_prokaryote_gene_request: (required)
         :type v2_prokaryote_gene_request: V2ProkaryoteGeneRequest