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

ncbi/datasets/openapi/models/v2_download_summary_dehydrated.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_file_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_hydrated.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_element_flank_config.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 V2ElementFlankConfig(BaseModel):
+    """
+    V2ElementFlankConfig
+    """ # noqa: E501
+    length: Optional[StrictInt] = None
+    __properties: ClassVar[List[str]] = ["length"]
+
+    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 V2ElementFlankConfig 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 V2ElementFlankConfig from a dict"""
+        if obj is None:
+            return None
+
+        if not isinstance(obj, dict):
+            return cls.model_validate(obj)
+
+        _obj = cls.model_validate({
+            "length": obj.get("length")
+        })
+        return _obj
+
+

ncbi/datasets/openapi/models/v2_fasta.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_file_file_type.py

@@ -0,0 +1,57 @@
+# 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 V2FileFileType(str, Enum):
+    """
+    V2FileFileType
+    """
+
+    """
+    allowed enum values
+    """
+    UNKNOWN = 'UNKNOWN'
+    FASTA = 'FASTA'
+    GFF3 = 'GFF3'
+    DATA_REPORT = 'DATA_REPORT'
+    ANNOTATION_REPORT = 'ANNOTATION_REPORT'
+    GENOMIC_NUCLEOTIDE_FASTA = 'GENOMIC_NUCLEOTIDE_FASTA'
+    PROTEIN_FASTA = 'PROTEIN_FASTA'
+    GENBANK_FLAT_FILE = 'GENBANK_FLAT_FILE'
+    GENPEPT_FLAT_FILE = 'GENPEPT_FLAT_FILE'
+    README = 'README'
+    PDB_FILE = 'PDB_FILE'
+    CDS_NUCLEOTIDE_FASTA = 'CDS_NUCLEOTIDE_FASTA'
+    RNA_NUCLEOTIDE_FASTA = 'RNA_NUCLEOTIDE_FASTA'
+    DATA_TABLE = 'DATA_TABLE'
+    SEQUENCE_REPORT = 'SEQUENCE_REPORT'
+    GTF = 'GTF'
+    PROKARYOTE_GENE_DATA_REPORT = 'PROKARYOTE_GENE_DATA_REPORT'
+    PROKARYOTE_GENE_LOCATION_DATA_REPORT = 'PROKARYOTE_GENE_LOCATION_DATA_REPORT'
+    GENOMIC_NUCLEOTIDE_WITH_FLANK_FASTA = 'GENOMIC_NUCLEOTIDE_WITH_FLANK_FASTA'
+    BIOSAMPLE_REPORT = 'BIOSAMPLE_REPORT'
+    CATALOG = 'CATALOG'
+    TAXONOMY_NAMES_REPORT = 'TAXONOMY_NAMES_REPORT'
+
+    @classmethod
+    def from_json(cls, json_str: str) -> Self:
+        """Create an instance of V2FileFileType from a JSON string"""
+        return cls(json.loads(json_str))
+
+

ncbi/datasets/openapi/models/v2_gene_chromosome_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_gene_chromosome_summary_reply_gene_chromosome_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_gene_chromosome_summary_request.py

@@ -0,0 +1,89 @@
+# 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 V2GeneChromosomeSummaryRequest(BaseModel):
+    """
+    V2GeneChromosomeSummaryRequest
+    """ # noqa: E501
+    taxon: Optional[StrictStr] = None
+    annotation_name: Optional[StrictStr] = None
+    __properties: ClassVar[List[str]] = ["taxon", "annotation_name"]
+
+    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 V2GeneChromosomeSummaryRequest 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 V2GeneChromosomeSummaryRequest from a dict"""
+        if obj is None:
+            return None
+
+        if not isinstance(obj, dict):
+            return cls.model_validate(obj)
+
+        _obj = cls.model_validate({
+            "taxon": obj.get("taxon"),
+            "annotation_name": obj.get("annotation_name")
+        })
+        return _obj
+
+

ncbi/datasets/openapi/models/v2_gene_counts_by_taxon_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_gene_counts_by_taxon_reply_gene_type_and_count.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_gene_counts_by_taxon_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_gene_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.
@@ -18,12 +17,13 @@ import pprint
 import re  # noqa: F401
 import json
 
-from pydantic import BaseModel, ConfigDict, StrictInt, StrictStr
+from pydantic import BaseModel, ConfigDict, StrictBool, StrictInt, StrictStr
 from typing import Any, ClassVar, Dict, List, Optional
 from ncbi.datasets.openapi.models.v2_gene_dataset_reports_request_content_type import V2GeneDatasetReportsRequestContentType
 from ncbi.datasets.openapi.models.v2_gene_dataset_reports_request_symbols_for_taxon import V2GeneDatasetReportsRequestSymbolsForTaxon
 from ncbi.datasets.openapi.models.v2_gene_type import V2GeneType
 from ncbi.datasets.openapi.models.v2_include_tabular_header import V2IncludeTabularHeader
+from ncbi.datasets.openapi.models.v2_sort_field import V2SortField
 from typing import Optional, Set
 from typing_extensions import Self
 
@@ -31,7 +31,7 @@ class V2GeneDatasetReportsRequest(BaseModel):
     """
     V2GeneDatasetReportsRequest
     """ # noqa: E501
-    returned_content: Optional[V2GeneDatasetReportsRequestContentType] = None
+    returned_content: Optional[V2GeneDatasetReportsRequestContentType] = V2GeneDatasetReportsRequestContentType.COMPLETE
     gene_ids: Optional[List[StrictInt]] = None
     accessions: Optional[List[StrictStr]] = None
     symbols_for_taxon: Optional[V2GeneDatasetReportsRequestSymbolsForTaxon] = None
@@ -39,13 +39,15 @@ class V2GeneDatasetReportsRequest(BaseModel):
     locus_tags: Optional[List[StrictStr]] = None
     table_fields: Optional[List[StrictStr]] = None
     table_format: Optional[StrictStr] = None
-    include_tabular_header: Optional[V2IncludeTabularHeader] = None
+    include_tabular_header: Optional[V2IncludeTabularHeader] = V2IncludeTabularHeader.INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY
     page_size: Optional[StrictInt] = None
     page_token: Optional[StrictStr] = None
     query: Optional[StrictStr] = None
     types: Optional[List[V2GeneType]] = None
     accession_filter: Optional[List[StrictStr]] = None
-    __properties: ClassVar[List[str]] = ["returned_content", "gene_ids", "accessions", "symbols_for_taxon", "taxon", "locus_tags", "table_fields", "table_format", "include_tabular_header", "page_size", "page_token", "query", "types", "accession_filter"]
+    tax_search_subtree: Optional[StrictBool] = None
+    sort: Optional[List[V2SortField]] = None
+    __properties: ClassVar[List[str]] = ["returned_content", "gene_ids", "accessions", "symbols_for_taxon", "taxon", "locus_tags", "table_fields", "table_format", "include_tabular_header", "page_size", "page_token", "query", "types", "accession_filter", "tax_search_subtree", "sort"]
 
     model_config = ConfigDict(
         populate_by_name=True,
@@ -89,6 +91,13 @@ class V2GeneDatasetReportsRequest(BaseModel):
         # override the default output from pydantic by calling `to_dict()` of symbols_for_taxon
         if self.symbols_for_taxon:
             _dict['symbols_for_taxon'] = self.symbols_for_taxon.to_dict()
+        # override the default output from pydantic by calling `to_dict()` of each item in sort (list)
+        _items = []
+        if self.sort:
+            for _item_sort in self.sort:
+                if _item_sort:
+                    _items.append(_item_sort.to_dict())
+            _dict['sort'] = _items
         return _dict
 
     @classmethod
@@ -101,7 +110,7 @@ class V2GeneDatasetReportsRequest(BaseModel):
             return cls.model_validate(obj)
 
         _obj = cls.model_validate({
-            "returned_content": obj.get("returned_content"),
+            "returned_content": obj.get("returned_content") if obj.get("returned_content") is not None else V2GeneDatasetReportsRequestContentType.COMPLETE,
             "gene_ids": obj.get("gene_ids"),
             "accessions": obj.get("accessions"),
             "symbols_for_taxon": V2GeneDatasetReportsRequestSymbolsForTaxon.from_dict(obj["symbols_for_taxon"]) if obj.get("symbols_for_taxon") is not None else None,
@@ -109,12 +118,14 @@ class V2GeneDatasetReportsRequest(BaseModel):
             "locus_tags": obj.get("locus_tags"),
             "table_fields": obj.get("table_fields"),
             "table_format": obj.get("table_format"),
-            "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,
             "page_size": obj.get("page_size"),
             "page_token": obj.get("page_token"),
             "query": obj.get("query"),
             "types": obj.get("types"),
-            "accession_filter": obj.get("accession_filter")
+            "accession_filter": obj.get("accession_filter"),
+            "tax_search_subtree": obj.get("tax_search_subtree"),
+            "sort": [V2SortField.from_dict(_item) for _item in obj["sort"]] if obj.get("sort") is not None else None
         })
         return _obj
 

ncbi/datasets/openapi/models/v2_gene_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.
@@ -29,7 +28,6 @@ class V2GeneDatasetReportsRequestContentType(str, Enum):
     """
     COMPLETE = 'COMPLETE'
     IDS_ONLY = 'IDS_ONLY'
-    PRODUCT = 'PRODUCT'
     COUNTS_ONLY = 'COUNTS_ONLY'
 
     @classmethod

ncbi/datasets/openapi/models/v2_gene_dataset_reports_request_symbols_for_taxon.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_gene_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.
@@ -32,13 +31,13 @@ class V2GeneDatasetRequest(BaseModel):
     """ # noqa: E501
     gene_ids: Optional[List[StrictInt]] = None
     include_annotation_type: Optional[List[V2Fasta]] = None
-    returned_content: Optional[V2GeneDatasetRequestContentType] = None
+    returned_content: Optional[V2GeneDatasetRequestContentType] = V2GeneDatasetRequestContentType.COMPLETE
     fasta_filter: Optional[List[StrictStr]] = None
     accession_filter: Optional[List[StrictStr]] = None
     aux_report: Optional[List[V2GeneDatasetRequestGeneDatasetReportType]] = None
     tabular_reports: Optional[List[V2GeneDatasetRequestGeneDatasetReportType]] = None
     table_fields: Optional[List[StrictStr]] = None
-    table_report_type: Optional[V2GeneDatasetRequestGeneDatasetReportType] = None
+    table_report_type: Optional[V2GeneDatasetRequestGeneDatasetReportType] = V2GeneDatasetRequestGeneDatasetReportType.DATASET_REPORT
     __properties: ClassVar[List[str]] = ["gene_ids", "include_annotation_type", "returned_content", "fasta_filter", "accession_filter", "aux_report", "tabular_reports", "table_fields", "table_report_type"]
 
     model_config = ConfigDict(
@@ -94,13 +93,13 @@ class V2GeneDatasetRequest(BaseModel):
         _obj = cls.model_validate({
             "gene_ids": obj.get("gene_ids"),
             "include_annotation_type": obj.get("include_annotation_type"),
-            "returned_content": obj.get("returned_content"),
+            "returned_content": obj.get("returned_content") if obj.get("returned_content") is not None else V2GeneDatasetRequestContentType.COMPLETE,
             "fasta_filter": obj.get("fasta_filter"),
             "accession_filter": obj.get("accession_filter"),
             "aux_report": obj.get("aux_report"),
             "tabular_reports": obj.get("tabular_reports"),
             "table_fields": obj.get("table_fields"),
-            "table_report_type": obj.get("table_report_type")
+            "table_report_type": obj.get("table_report_type") if obj.get("table_report_type") is not None else V2GeneDatasetRequestGeneDatasetReportType.DATASET_REPORT
         })
         return _obj
 

ncbi/datasets/openapi/models/v2_gene_dataset_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_gene_dataset_request_gene_dataset_report_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_gene_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_gene_links_reply_gene_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 V2GeneLinksReplyGeneLink(BaseModel):
     V2GeneLinksReplyGeneLink
     """ # noqa: E501
     gene_id: Optional[StrictInt] = None
-    gene_link_type: Optional[V2GeneLinksReplyGeneLinkType] = None
+    gene_link_type: Optional[V2GeneLinksReplyGeneLinkType] = V2GeneLinksReplyGeneLinkType.DEFAULT
     resource_link: Optional[StrictStr] = None
     resource_id: Optional[StrictStr] = None
     __properties: ClassVar[List[str]] = ["gene_id", "gene_link_type", "resource_link", "resource_id"]
@@ -86,7 +85,7 @@ class V2GeneLinksReplyGeneLink(BaseModel):
 
         _obj = cls.model_validate({
             "gene_id": obj.get("gene_id"),
-            "gene_link_type": obj.get("gene_link_type"),
+            "gene_link_type": obj.get("gene_link_type") if obj.get("gene_link_type") is not None else V2GeneLinksReplyGeneLinkType.DEFAULT,
             "resource_link": obj.get("resource_link"),
             "resource_id": obj.get("resource_id")
         })

ncbi/datasets/openapi/models/v2_gene_links_reply_gene_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.
@@ -27,6 +26,7 @@ class V2GeneLinksReplyGeneLinkType(str, Enum):
     """
     allowed enum values
     """
+    DEFAULT = 'DEFAULT'
     GENE_LINK = 'GENE_LINK'
     GDV_LINK = 'GDV_LINK'
     ORTHOLOG_LINK = 'ORTHOLOG_LINK'

ncbi/datasets/openapi/models/v2_gene_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.