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

ncbi/datasets/openapi/models/v2_assembly_data_report_draft_request.py

@@ -0,0 +1,87 @@
+# coding: utf-8
+
+"""
+    NCBI Datasets API
+
+    ### 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
+    Generated by OpenAPI Generator (https://openapi-generator.tech)
+
+    Do not edit the class manually.
+"""  # noqa: E501
+
+
+from __future__ import annotations
+import pprint
+import re  # noqa: F401
+import json
+
+from pydantic import BaseModel, ConfigDict, StrictStr
+from typing import Any, ClassVar, Dict, List, Optional
+from typing import Optional, Set
+from typing_extensions import Self
+
+class V2AssemblyDataReportDraftRequest(BaseModel):
+    """
+    V2AssemblyDataReportDraftRequest
+    """ # noqa: E501
+    accession: Optional[StrictStr] = None
+    __properties: ClassVar[List[str]] = ["accession"]
+
+    model_config = ConfigDict(
+        populate_by_name=True,
+        validate_assignment=True,
+        protected_namespaces=(),
+    )
+
+
+    def to_str(self) -> str:
+        """Returns the string representation of the model using alias"""
+        return pprint.pformat(self.model_dump(by_alias=True))
+
+    def to_json(self) -> str:
+        """Returns the JSON representation of the model using alias"""
+        # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead
+        return json.dumps(self.to_dict())
+
+    @classmethod
+    def from_json(cls, json_str: str) -> Optional[Self]:
+        """Create an instance of V2AssemblyDataReportDraftRequest from a JSON string"""
+        return cls.from_dict(json.loads(json_str))
+
+    def to_dict(self) -> Dict[str, Any]:
+        """Return the dictionary representation of the model using alias.
+
+        This has the following differences from calling pydantic's
+        `self.model_dump(by_alias=True)`:
+
+        * `None` is only added to the output dict for nullable fields that
+          were set at model initialization. Other fields with value `None`
+          are ignored.
+        """
+        excluded_fields: Set[str] = set([
+        ])
+
+        _dict = self.model_dump(
+            by_alias=True,
+            exclude=excluded_fields,
+            exclude_none=True,
+        )
+        return _dict
+
+    @classmethod
+    def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
+        """Create an instance of V2AssemblyDataReportDraftRequest from a dict"""
+        if obj is None:
+            return None
+
+        if not isinstance(obj, dict):
+            return cls.model_validate(obj)
+
+        _obj = cls.model_validate({
+            "accession": obj.get("accession")
+        })
+        return _obj
+
+

ncbi/datasets/openapi/models/v2_assembly_dataset_availability.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/models/v2_assembly_dataset_descriptors_filter.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.
@@ -34,20 +33,20 @@ class V2AssemblyDatasetDescriptorsFilter(BaseModel):
     V2AssemblyDatasetDescriptorsFilter
     """ # noqa: E501
     reference_only: Optional[StrictBool] = None
-    assembly_source: Optional[V2AssemblyDatasetDescriptorsFilterAssemblySource] = None
+    assembly_source: Optional[V2AssemblyDatasetDescriptorsFilterAssemblySource] = V2AssemblyDatasetDescriptorsFilterAssemblySource.ALL
     has_annotation: Optional[StrictBool] = None
     exclude_paired_reports: Optional[StrictBool] = None
     exclude_atypical: Optional[StrictBool] = None
-    assembly_version: Optional[V2AssemblyDatasetDescriptorsFilterAssemblyVersion] = None
+    assembly_version: Optional[V2AssemblyDatasetDescriptorsFilterAssemblyVersion] = V2AssemblyDatasetDescriptorsFilterAssemblyVersion.CURRENT
     assembly_level: Optional[List[V2reportsAssemblyLevel]] = None
     first_release_date: Optional[datetime] = None
     last_release_date: Optional[datetime] = None
     search_text: Optional[List[StrictStr]] = None
-    is_metagenome_derived: Optional[V2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter] = None
+    is_metagenome_derived: Optional[V2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter] = V2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter.METAGENOME_DERIVED_UNSET
     is_type_material: Optional[StrictBool] = None
     is_ictv_exemplar: Optional[StrictBool] = None
     exclude_multi_isolate: Optional[StrictBool] = None
-    type_material_category: Optional[V2AssemblyDatasetDescriptorsFilterTypeMaterialCategory] = None
+    type_material_category: Optional[V2AssemblyDatasetDescriptorsFilterTypeMaterialCategory] = V2AssemblyDatasetDescriptorsFilterTypeMaterialCategory.NONE
     __properties: ClassVar[List[str]] = ["reference_only", "assembly_source", "has_annotation", "exclude_paired_reports", "exclude_atypical", "assembly_version", "assembly_level", "first_release_date", "last_release_date", "search_text", "is_metagenome_derived", "is_type_material", "is_ictv_exemplar", "exclude_multi_isolate", "type_material_category"]
 
     model_config = ConfigDict(
@@ -102,20 +101,20 @@ class V2AssemblyDatasetDescriptorsFilter(BaseModel):
 
         _obj = cls.model_validate({
             "reference_only": obj.get("reference_only"),
-            "assembly_source": obj.get("assembly_source"),
+            "assembly_source": obj.get("assembly_source") if obj.get("assembly_source") is not None else V2AssemblyDatasetDescriptorsFilterAssemblySource.ALL,
             "has_annotation": obj.get("has_annotation"),
             "exclude_paired_reports": obj.get("exclude_paired_reports"),
             "exclude_atypical": obj.get("exclude_atypical"),
-            "assembly_version": obj.get("assembly_version"),
+            "assembly_version": obj.get("assembly_version") if obj.get("assembly_version") is not None else V2AssemblyDatasetDescriptorsFilterAssemblyVersion.CURRENT,
             "assembly_level": obj.get("assembly_level"),
             "first_release_date": obj.get("first_release_date"),
             "last_release_date": obj.get("last_release_date"),
             "search_text": obj.get("search_text"),
-            "is_metagenome_derived": obj.get("is_metagenome_derived"),
+            "is_metagenome_derived": obj.get("is_metagenome_derived") if obj.get("is_metagenome_derived") is not None else V2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter.METAGENOME_DERIVED_UNSET,
             "is_type_material": obj.get("is_type_material"),
             "is_ictv_exemplar": obj.get("is_ictv_exemplar"),
             "exclude_multi_isolate": obj.get("exclude_multi_isolate"),
-            "type_material_category": obj.get("type_material_category")
+            "type_material_category": obj.get("type_material_category") if obj.get("type_material_category") is not None else V2AssemblyDatasetDescriptorsFilterTypeMaterialCategory.NONE
         })
         return _obj
 

ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_assembly_source.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/models/v2_assembly_dataset_descriptors_filter_assembly_version.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/models/v2_assembly_dataset_descriptors_filter_metagenome_derived_filter.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/models/v2_assembly_dataset_descriptors_filter_type_material_category.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/models/v2_assembly_dataset_reports_request.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.
@@ -41,11 +40,11 @@ class V2AssemblyDatasetReportsRequest(BaseModel):
     tax_exact_match: Optional[StrictBool] = None
     chromosomes: Optional[List[StrictStr]] = None
     table_fields: Optional[List[StrictStr]] = None
-    returned_content: Optional[V2AssemblyDatasetReportsRequestContentType] = None
+    returned_content: Optional[V2AssemblyDatasetReportsRequestContentType] = V2AssemblyDatasetReportsRequestContentType.COMPLETE
     page_size: Optional[StrictInt] = None
     page_token: Optional[StrictStr] = None
     sort: Optional[List[V2SortField]] = None
-    include_tabular_header: Optional[V2IncludeTabularHeader] = None
+    include_tabular_header: Optional[V2IncludeTabularHeader] = V2IncludeTabularHeader.INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY
     table_format: Optional[StrictStr] = None
     __properties: ClassVar[List[str]] = ["taxons", "bioprojects", "biosample_ids", "assembly_names", "wgs_accessions", "accessions", "filters", "tax_exact_match", "chromosomes", "table_fields", "returned_content", "page_size", "page_token", "sort", "include_tabular_header", "table_format"]
 
@@ -120,11 +119,11 @@ class V2AssemblyDatasetReportsRequest(BaseModel):
             "tax_exact_match": obj.get("tax_exact_match"),
             "chromosomes": obj.get("chromosomes"),
             "table_fields": obj.get("table_fields"),
-            "returned_content": obj.get("returned_content"),
+            "returned_content": obj.get("returned_content") if obj.get("returned_content") is not None else V2AssemblyDatasetReportsRequestContentType.COMPLETE,
             "page_size": obj.get("page_size"),
             "page_token": obj.get("page_token"),
             "sort": [V2SortField.from_dict(_item) for _item in obj["sort"]] if obj.get("sort") is not None else None,
-            "include_tabular_header": obj.get("include_tabular_header"),
+            "include_tabular_header": obj.get("include_tabular_header") if obj.get("include_tabular_header") is not None else V2IncludeTabularHeader.INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY,
             "table_format": obj.get("table_format")
         })
         return _obj

ncbi/datasets/openapi/models/v2_assembly_dataset_reports_request_content_type.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/models/v2_assembly_dataset_request.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.
@@ -32,7 +31,7 @@ class V2AssemblyDatasetRequest(BaseModel):
     accessions: Optional[List[StrictStr]] = None
     chromosomes: Optional[List[StrictStr]] = None
     include_annotation_type: Optional[List[V2AnnotationForAssemblyType]] = None
-    hydrated: Optional[V2AssemblyDatasetRequestResolution] = None
+    hydrated: Optional[V2AssemblyDatasetRequestResolution] = V2AssemblyDatasetRequestResolution.FULLY_HYDRATED
     include_tsv: Optional[StrictBool] = None
     __properties: ClassVar[List[str]] = ["accessions", "chromosomes", "include_annotation_type", "hydrated", "include_tsv"]
 
@@ -90,7 +89,7 @@ class V2AssemblyDatasetRequest(BaseModel):
             "accessions": obj.get("accessions"),
             "chromosomes": obj.get("chromosomes"),
             "include_annotation_type": obj.get("include_annotation_type"),
-            "hydrated": obj.get("hydrated"),
+            "hydrated": obj.get("hydrated") if obj.get("hydrated") is not None else V2AssemblyDatasetRequestResolution.FULLY_HYDRATED,
             "include_tsv": obj.get("include_tsv")
         })
         return _obj

ncbi/datasets/openapi/models/v2_assembly_dataset_request_resolution.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/models/v2_assembly_links_reply.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/models/v2_assembly_links_reply_assembly_link.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.
@@ -29,7 +28,7 @@ class V2AssemblyLinksReplyAssemblyLink(BaseModel):
     V2AssemblyLinksReplyAssemblyLink
     """ # noqa: E501
     accession: Optional[StrictStr] = None
-    assembly_link_type: Optional[V2AssemblyLinksReplyAssemblyLinkType] = None
+    assembly_link_type: Optional[V2AssemblyLinksReplyAssemblyLinkType] = V2AssemblyLinksReplyAssemblyLinkType.DEFAULT
     resource_link: Optional[StrictStr] = None
     linked_identifiers: Optional[List[StrictStr]] = None
     __properties: ClassVar[List[str]] = ["accession", "assembly_link_type", "resource_link", "linked_identifiers"]
@@ -86,7 +85,7 @@ class V2AssemblyLinksReplyAssemblyLink(BaseModel):
 
         _obj = cls.model_validate({
             "accession": obj.get("accession"),
-            "assembly_link_type": obj.get("assembly_link_type"),
+            "assembly_link_type": obj.get("assembly_link_type") if obj.get("assembly_link_type") is not None else V2AssemblyLinksReplyAssemblyLinkType.DEFAULT,
             "resource_link": obj.get("resource_link"),
             "linked_identifiers": obj.get("linked_identifiers")
         })

ncbi/datasets/openapi/models/v2_assembly_links_reply_assembly_link_type.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.
@@ -27,13 +26,14 @@ class V2AssemblyLinksReplyAssemblyLinkType(str, Enum):
     """
     allowed enum values
     """
+    DEFAULT = 'DEFAULT'
     GDV_LINK = 'GDV_LINK'
     FTP_LINK = 'FTP_LINK'
     ASSEMBLY_PUBMED = 'ASSEMBLY_PUBMED'
     BLAST_LINK = 'BLAST_LINK'
-    ASSEMBLY_NUCCORE = 'ASSEMBLY_NUCCORE'
     ASSEMBLY_NUCCORE_REFSEQ = 'ASSEMBLY_NUCCORE_REFSEQ'
     ASSEMBLY_NUCCORE_GENBANK = 'ASSEMBLY_NUCCORE_GENBANK'
+    CGV_LINK = 'CGV_LINK'
 
     @classmethod
     def from_json(cls, json_str: str) -> Self:

ncbi/datasets/openapi/models/v2_assembly_links_request.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/models/v2_assembly_revision_history.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/models/v2_assembly_revision_history_request.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/models/v2_assembly_sequence_reports_request.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.
@@ -35,7 +34,7 @@ class V2AssemblySequenceReportsRequest(BaseModel):
     count_assembly_unplaced: Optional[StrictBool] = None
     page_size: Optional[StrictInt] = None
     page_token: Optional[StrictStr] = None
-    include_tabular_header: Optional[V2IncludeTabularHeader] = None
+    include_tabular_header: Optional[V2IncludeTabularHeader] = V2IncludeTabularHeader.INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY
     table_format: Optional[StrictStr] = None
     __properties: ClassVar[List[str]] = ["accession", "chromosomes", "role_filters", "table_fields", "count_assembly_unplaced", "page_size", "page_token", "include_tabular_header", "table_format"]
 
@@ -97,7 +96,7 @@ class V2AssemblySequenceReportsRequest(BaseModel):
             "count_assembly_unplaced": obj.get("count_assembly_unplaced"),
             "page_size": obj.get("page_size"),
             "page_token": obj.get("page_token"),
-            "include_tabular_header": obj.get("include_tabular_header"),
+            "include_tabular_header": obj.get("include_tabular_header") if obj.get("include_tabular_header") is not None else V2IncludeTabularHeader.INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY,
             "table_format": obj.get("table_format")
         })
         return _obj

ncbi/datasets/openapi/models/v2_bio_sample_dataset_reports_request.py

@@ -0,0 +1,87 @@
+# coding: utf-8
+
+"""
+    NCBI Datasets API
+
+    ### 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
+    Generated by OpenAPI Generator (https://openapi-generator.tech)
+
+    Do not edit the class manually.
+"""  # noqa: E501
+
+
+from __future__ import annotations
+import pprint
+import re  # noqa: F401
+import json
+
+from pydantic import BaseModel, ConfigDict, StrictStr
+from typing import Any, ClassVar, Dict, List, Optional
+from typing import Optional, Set
+from typing_extensions import Self
+
+class V2BioSampleDatasetReportsRequest(BaseModel):
+    """
+    V2BioSampleDatasetReportsRequest
+    """ # noqa: E501
+    accessions: Optional[List[StrictStr]] = None
+    __properties: ClassVar[List[str]] = ["accessions"]
+
+    model_config = ConfigDict(
+        populate_by_name=True,
+        validate_assignment=True,
+        protected_namespaces=(),
+    )
+
+
+    def to_str(self) -> str:
+        """Returns the string representation of the model using alias"""
+        return pprint.pformat(self.model_dump(by_alias=True))
+
+    def to_json(self) -> str:
+        """Returns the JSON representation of the model using alias"""
+        # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead
+        return json.dumps(self.to_dict())
+
+    @classmethod
+    def from_json(cls, json_str: str) -> Optional[Self]:
+        """Create an instance of V2BioSampleDatasetReportsRequest from a JSON string"""
+        return cls.from_dict(json.loads(json_str))
+
+    def to_dict(self) -> Dict[str, Any]:
+        """Return the dictionary representation of the model using alias.
+
+        This has the following differences from calling pydantic's
+        `self.model_dump(by_alias=True)`:
+
+        * `None` is only added to the output dict for nullable fields that
+          were set at model initialization. Other fields with value `None`
+          are ignored.
+        """
+        excluded_fields: Set[str] = set([
+        ])
+
+        _dict = self.model_dump(
+            by_alias=True,
+            exclude=excluded_fields,
+            exclude_none=True,
+        )
+        return _dict
+
+    @classmethod
+    def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
+        """Create an instance of V2BioSampleDatasetReportsRequest from a dict"""
+        if obj is None:
+            return None
+
+        if not isinstance(obj, dict):
+            return cls.model_validate(obj)
+
+        _obj = cls.model_validate({
+            "accessions": obj.get("accessions")
+        })
+        return _obj
+
+

ncbi/datasets/openapi/models/v2_catalog_api_version.py

@@ -0,0 +1,38 @@
+# coding: utf-8
+
+"""
+    NCBI Datasets API
+
+    ### 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
+    Generated by OpenAPI Generator (https://openapi-generator.tech)
+
+    Do not edit the class manually.
+"""  # noqa: E501
+
+
+from __future__ import annotations
+import json
+from enum import Enum
+from typing_extensions import Self
+
+
+class V2CatalogApiVersion(str, Enum):
+    """
+    V2CatalogApiVersion
+    """
+
+    """
+    allowed enum values
+    """
+    UNKNOWN = 'UNKNOWN'
+    V1 = 'V1'
+    V2 = 'V2'
+
+    @classmethod
+    def from_json(cls, json_str: str) -> Self:
+        """Create an instance of V2CatalogApiVersion from a JSON string"""
+        return cls(json.loads(json_str))
+
+

ncbi/datasets/openapi/models/v2_dataset_request.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/models/v2_download_summary.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/models/v2_download_summary_available_files.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.