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

ncbi/datasets/openapi/models/v2_gene_pubmed_ids_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, StrictInt
+from typing import Any, ClassVar, Dict, List, Optional
+from typing import Optional, Set
+from typing_extensions import Self
+
+class V2GenePubmedIdsRequest(BaseModel):
+    """
+    V2GenePubmedIdsRequest
+    """ # noqa: E501
+    gene_ids: Optional[StrictInt] = None
+    __properties: ClassVar[List[str]] = ["gene_ids"]
+
+    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 V2GenePubmedIdsRequest 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 V2GenePubmedIdsRequest from a dict"""
+        if obj is None:
+            return None
+
+        if not isinstance(obj, dict):
+            return cls.model_validate(obj)
+
+        _obj = cls.model_validate({
+            "gene_ids": obj.get("gene_ids")
+        })
+        return _obj
+
+

ncbi/datasets/openapi/models/v2_gene_pubmed_ids_response.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, Field, StrictInt
+from typing import Any, ClassVar, Dict, List, Optional
+from typing import Optional, Set
+from typing_extensions import Self
+
+class V2GenePubmedIdsResponse(BaseModel):
+    """
+    V2GenePubmedIdsResponse
+    """ # noqa: E501
+    pubmed_ids: Optional[List[StrictInt]] = Field(default=None, alias="pubmedIds")
+    __properties: ClassVar[List[str]] = ["pubmedIds"]
+
+    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 V2GenePubmedIdsResponse 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 V2GenePubmedIdsResponse from a dict"""
+        if obj is None:
+            return None
+
+        if not isinstance(obj, dict):
+            return cls.model_validate(obj)
+
+        _obj = cls.model_validate({
+            "pubmedIds": obj.get("pubmedIds")
+        })
+        return _obj
+
+

ncbi/datasets/openapi/models/v2_gene_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_genome_annotation_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.
@@ -41,8 +40,8 @@ class V2GenomeAnnotationRequest(BaseModel):
     include_annotation_type: Optional[List[V2GenomeAnnotationRequestAnnotationType]] = None
     page_size: Optional[StrictInt] = None
     table_fields: Optional[List[StrictStr]] = None
-    table_format: Optional[V2GenomeAnnotationRequestGenomeAnnotationTableFormat] = None
-    include_tabular_header: Optional[V2IncludeTabularHeader] = None
+    table_format: Optional[V2GenomeAnnotationRequestGenomeAnnotationTableFormat] = V2GenomeAnnotationRequestGenomeAnnotationTableFormat.NO_TABLE
+    include_tabular_header: Optional[V2IncludeTabularHeader] = V2IncludeTabularHeader.INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY
     page_token: Optional[StrictStr] = None
     __properties: ClassVar[List[str]] = ["accession", "annotation_ids", "symbols", "locations", "gene_types", "search_text", "sort", "include_annotation_type", "page_size", "table_fields", "table_format", "include_tabular_header", "page_token"]
 
@@ -114,8 +113,8 @@ class V2GenomeAnnotationRequest(BaseModel):
             "include_annotation_type": obj.get("include_annotation_type"),
             "page_size": obj.get("page_size"),
             "table_fields": obj.get("table_fields"),
-            "table_format": obj.get("table_format"),
-            "include_tabular_header": obj.get("include_tabular_header"),
+            "table_format": obj.get("table_format") if obj.get("table_format") is not None else V2GenomeAnnotationRequestGenomeAnnotationTableFormat.NO_TABLE,
+            "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,
             "page_token": obj.get("page_token")
         })
         return _obj

ncbi/datasets/openapi/models/v2_genome_annotation_request_annotation_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.
@@ -27,6 +26,7 @@ class V2GenomeAnnotationRequestAnnotationType(str, Enum):
     """
     allowed enum values
     """
+    DEFAULT = 'DEFAULT'
     GENOME_FASTA = 'GENOME_FASTA'
     RNA_FASTA = 'RNA_FASTA'
     PROT_FASTA = 'PROT_FASTA'

ncbi/datasets/openapi/models/v2_genome_annotation_request_genome_annotation_table_format.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_genome_annotation_table_summary_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_http_body.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_image_size.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_include_tabular_header.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_micro_bigge_dataset_request.py

@@ -0,0 +1,96 @@
+# 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 ncbi.datasets.openapi.models.v2_element_flank_config import V2ElementFlankConfig
+from ncbi.datasets.openapi.models.v2_micro_bigge_dataset_request_file_type import V2MicroBiggeDatasetRequestFileType
+from typing import Optional, Set
+from typing_extensions import Self
+
+class V2MicroBiggeDatasetRequest(BaseModel):
+    """
+    V2MicroBiggeDatasetRequest
+    """ # noqa: E501
+    opaque_solr_query: Optional[StrictStr] = None
+    files: Optional[List[V2MicroBiggeDatasetRequestFileType]] = None
+    element_flank_config: Optional[V2ElementFlankConfig] = None
+    __properties: ClassVar[List[str]] = ["opaque_solr_query", "files", "element_flank_config"]
+
+    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 V2MicroBiggeDatasetRequest 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,
+        )
+        # override the default output from pydantic by calling `to_dict()` of element_flank_config
+        if self.element_flank_config:
+            _dict['element_flank_config'] = self.element_flank_config.to_dict()
+        return _dict
+
+    @classmethod
+    def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
+        """Create an instance of V2MicroBiggeDatasetRequest from a dict"""
+        if obj is None:
+            return None
+
+        if not isinstance(obj, dict):
+            return cls.model_validate(obj)
+
+        _obj = cls.model_validate({
+            "opaque_solr_query": obj.get("opaque_solr_query"),
+            "files": obj.get("files"),
+            "element_flank_config": V2ElementFlankConfig.from_dict(obj["element_flank_config"]) if obj.get("element_flank_config") is not None else None
+        })
+        return _obj
+
+

ncbi/datasets/openapi/models/v2_micro_bigge_dataset_request_file_type.py

@@ -0,0 +1,39 @@
+# 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 V2MicroBiggeDatasetRequestFileType(str, Enum):
+    """
+    V2MicroBiggeDatasetRequestFileType
+    """
+
+    """
+    allowed enum values
+    """
+    ELEMENT_FASTA = 'element_fasta'
+    ELEMENT_FLANK_FASTA = 'element_flank_fasta'
+    CONTIG_FASTA = 'contig_fasta'
+    PROTEIN_FASTA = 'protein_fasta'
+
+    @classmethod
+    def from_json(cls, json_str: str) -> Self:
+        """Create an instance of V2MicroBiggeDatasetRequestFileType from a JSON string"""
+        return cls(json.loads(json_str))
+
+

ncbi/datasets/openapi/models/v2_mol_type.py

@@ -0,0 +1,40 @@
+# 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 V2MolType(str, Enum):
+    """
+    V2MolType
+    """
+
+    """
+    allowed enum values
+    """
+    MOL_UNSPECIFIED = 'MOL_UNSPECIFIED'
+    MOL_DNA = 'MOL_DNA'
+    MOL_RNA = 'MOL_RNA'
+    MOL_PROTEIN = 'MOL_PROTEIN'
+    MOL_NA = 'MOL_NA'
+
+    @classmethod
+    def from_json(cls, json_str: str) -> Self:
+        """Create an instance of V2MolType from a JSON string"""
+        return cls(json.loads(json_str))
+
+

ncbi/datasets/openapi/models/v2_organelle_download_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_organelle_metadata_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.
@@ -40,11 +39,11 @@ class V2OrganelleMetadataRequest(BaseModel):
     last_release_date: Optional[datetime] = None
     tax_exact_match: Optional[StrictBool] = None
     sort: Optional[List[V2OrganelleSort]] = None
-    returned_content: Optional[V2OrganelleMetadataRequestContentType] = None
+    returned_content: Optional[V2OrganelleMetadataRequestContentType] = V2OrganelleMetadataRequestContentType.COMPLETE
     page_size: Optional[StrictInt] = None
     page_token: Optional[StrictStr] = None
-    table_format: Optional[V2OrganelleMetadataRequestOrganelleTableFormat] = None
-    include_tabular_header: Optional[V2IncludeTabularHeader] = None
+    table_format: Optional[V2OrganelleMetadataRequestOrganelleTableFormat] = V2OrganelleMetadataRequestOrganelleTableFormat.ORGANELLE_TABLE_FORMAT_NO_TABLE
+    include_tabular_header: Optional[V2IncludeTabularHeader] = V2IncludeTabularHeader.INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY
     __properties: ClassVar[List[str]] = ["taxons", "accessions", "organelle_types", "first_release_date", "last_release_date", "tax_exact_match", "sort", "returned_content", "page_size", "page_token", "table_format", "include_tabular_header"]
 
     model_config = ConfigDict(
@@ -112,11 +111,11 @@ class V2OrganelleMetadataRequest(BaseModel):
             "last_release_date": obj.get("last_release_date"),
             "tax_exact_match": obj.get("tax_exact_match"),
             "sort": [V2OrganelleSort.from_dict(_item) for _item in obj["sort"]] if obj.get("sort") is not None else None,
-            "returned_content": obj.get("returned_content"),
+            "returned_content": obj.get("returned_content") if obj.get("returned_content") is not None else V2OrganelleMetadataRequestContentType.COMPLETE,
             "page_size": obj.get("page_size"),
             "page_token": obj.get("page_token"),
-            "table_format": obj.get("table_format"),
-            "include_tabular_header": obj.get("include_tabular_header")
+            "table_format": obj.get("table_format") if obj.get("table_format") is not None else V2OrganelleMetadataRequestOrganelleTableFormat.ORGANELLE_TABLE_FORMAT_NO_TABLE,
+            "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
         })
         return _obj
 

ncbi/datasets/openapi/models/v2_organelle_metadata_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_organelle_metadata_request_organelle_table_format.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_organelle_sort.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 V2OrganelleSort(BaseModel):
     V2OrganelleSort
     """ # noqa: E501
     var_field: Optional[StrictStr] = Field(default=None, alias="field")
-    direction: Optional[V2SortDirection] = None
+    direction: Optional[V2SortDirection] = V2SortDirection.SORT_DIRECTION_UNSPECIFIED
     __properties: ClassVar[List[str]] = ["field", "direction"]
 
     model_config = ConfigDict(
@@ -84,7 +83,7 @@ class V2OrganelleSort(BaseModel):
 
         _obj = cls.model_validate({
             "field": obj.get("field"),
-            "direction": obj.get("direction")
+            "direction": obj.get("direction") if obj.get("direction") is not None else V2SortDirection.SORT_DIRECTION_UNSPECIFIED
         })
         return _obj
 

ncbi/datasets/openapi/models/v2_organism_query_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.
@@ -31,8 +30,8 @@ class V2OrganismQueryRequest(BaseModel):
     """ # noqa: E501
     organism_query: Optional[StrictStr] = None
     taxon_query: Optional[StrictStr] = None
-    tax_rank_filter: Optional[V2OrganismQueryRequestTaxRankFilter] = None
-    taxon_resource_filter: Optional[V2OrganismQueryRequestTaxonResourceFilter] = None
+    tax_rank_filter: Optional[V2OrganismQueryRequestTaxRankFilter] = V2OrganismQueryRequestTaxRankFilter.SPECIES
+    taxon_resource_filter: Optional[V2OrganismQueryRequestTaxonResourceFilter] = V2OrganismQueryRequestTaxonResourceFilter.TAXON_RESOURCE_FILTER_ALL
     exact_match: Optional[StrictBool] = None
     __properties: ClassVar[List[str]] = ["organism_query", "taxon_query", "tax_rank_filter", "taxon_resource_filter", "exact_match"]
 
@@ -89,8 +88,8 @@ class V2OrganismQueryRequest(BaseModel):
         _obj = cls.model_validate({
             "organism_query": obj.get("organism_query"),
             "taxon_query": obj.get("taxon_query"),
-            "tax_rank_filter": obj.get("tax_rank_filter"),
-            "taxon_resource_filter": obj.get("taxon_resource_filter"),
+            "tax_rank_filter": obj.get("tax_rank_filter") if obj.get("tax_rank_filter") is not None else V2OrganismQueryRequestTaxRankFilter.SPECIES,
+            "taxon_resource_filter": obj.get("taxon_resource_filter") if obj.get("taxon_resource_filter") is not None else V2OrganismQueryRequestTaxonResourceFilter.TAXON_RESOURCE_FILTER_ALL,
             "exact_match": obj.get("exact_match")
         })
         return _obj

ncbi/datasets/openapi/models/v2_organism_query_request_tax_rank_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.