""" NCBI Datasets API ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 1 API is considred stable and will not be subject to breaking changes. However, certain endpoints will be [deprecated](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/reference-docs/rest-api/deprecated_apis/), and then sunset as newer versions are published. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/how-tos/genomes/large-download/), and retrieve the individual data files at a later time. # noqa: E501 The version of the OpenAPI document: v1 Generated by: https://openapi-generator.tech """ import re # noqa: F401 import sys # noqa: F401 from ncbi.datasets.openapi.api_client import ApiClient, Endpoint as _Endpoint from ncbi.datasets.openapi.model_utils import ( # noqa: F401 check_allowed_values, check_validations, date, datetime, file_type, none_type, validate_and_convert_types ) from ncbi.datasets.openapi.model.rpc_status import RpcStatus from ncbi.datasets.openapi.model.v1_annotation_for_assembly_type import V1AnnotationForAssemblyType from ncbi.datasets.openapi.model.v1_assembly_dataset_availability import V1AssemblyDatasetAvailability from ncbi.datasets.openapi.model.v1_assembly_dataset_descriptors_filter_assembly_level import V1AssemblyDatasetDescriptorsFilterAssemblyLevel from ncbi.datasets.openapi.model.v1_assembly_dataset_descriptors_filter_assembly_source import V1AssemblyDatasetDescriptorsFilterAssemblySource from ncbi.datasets.openapi.model.v1_assembly_dataset_descriptors_filter_assembly_version import V1AssemblyDatasetDescriptorsFilterAssemblyVersion from ncbi.datasets.openapi.model.v1_assembly_dataset_request import V1AssemblyDatasetRequest from ncbi.datasets.openapi.model.v1_assembly_dataset_request_resolution import V1AssemblyDatasetRequestResolution from ncbi.datasets.openapi.model.v1_assembly_metadata import V1AssemblyMetadata from ncbi.datasets.openapi.model.v1_assembly_metadata_request import V1AssemblyMetadataRequest from ncbi.datasets.openapi.model.v1_assembly_metadata_request_content_type import V1AssemblyMetadataRequestContentType from ncbi.datasets.openapi.model.v1_download_summary import V1DownloadSummary class GenomeApi(object): """NOTE: This class is auto generated by OpenAPI Generator Ref: https://openapi-generator.tech Do not edit the class manually. """ def __init__(self, api_client=None): if api_client is None: api_client = ApiClient() self.api_client = api_client self.assembly_descriptors_by_accessions_endpoint = _Endpoint( settings={ 'response_type': (V1AssemblyMetadata,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/accession/{accessions}', 'operation_id': 'assembly_descriptors_by_accessions', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'filters_reference_only', 'filters_assembly_source', 'filters_has_annotation', 'filters_exclude_atypical', 'filters_assembly_level', 'filters_first_release_date', 'filters_last_release_date', 'filters_search_text', 'page_size', 'page_token', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'filters_reference_only': (bool,), 'filters_assembly_source': (V1AssemblyDatasetDescriptorsFilterAssemblySource,), 'filters_has_annotation': (bool,), 'filters_exclude_atypical': (bool,), 'filters_assembly_level': ([V1AssemblyDatasetDescriptorsFilterAssemblyLevel],), 'filters_first_release_date': (datetime,), 'filters_last_release_date': (datetime,), 'filters_search_text': ([str],), 'page_size': (int,), 'page_token': (str,), }, 'attribute_map': { 'accessions': 'accessions', 'filters_reference_only': 'filters.reference_only', 'filters_assembly_source': 'filters.assembly_source', 'filters_has_annotation': 'filters.has_annotation', 'filters_exclude_atypical': 'filters.exclude_atypical', 'filters_assembly_level': 'filters.assembly_level', 'filters_first_release_date': 'filters.first_release_date', 'filters_last_release_date': 'filters.last_release_date', 'filters_search_text': 'filters.search_text', 'page_size': 'page_size', 'page_token': 'page_token', }, 'location_map': { 'accessions': 'path', 'filters_reference_only': 'query', 'filters_assembly_source': 'query', 'filters_has_annotation': 'query', 'filters_exclude_atypical': 'query', 'filters_assembly_level': 'query', 'filters_first_release_date': 'query', 'filters_last_release_date': 'query', 'filters_search_text': 'query', 'page_size': 'query', 'page_token': 'query', }, 'collection_format_map': { 'accessions': 'csv', 'filters_assembly_level': 'multi', 'filters_search_text': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.assembly_descriptors_by_bioproject_endpoint = _Endpoint( settings={ 'response_type': (V1AssemblyMetadata,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/bioproject/{accessions}', 'operation_id': 'assembly_descriptors_by_bioproject', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'filters_reference_only', 'filters_assembly_source', 'filters_has_annotation', 'filters_exclude_paired_reports', 'filters_exclude_atypical', 'filters_assembly_version', 'filters_assembly_level', 'filters_first_release_date', 'filters_last_release_date', 'filters_search_text', 'returned_content', 'page_size', 'page_token', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'filters_reference_only': (bool,), 'filters_assembly_source': (V1AssemblyDatasetDescriptorsFilterAssemblySource,), 'filters_has_annotation': (bool,), 'filters_exclude_paired_reports': (bool,), 'filters_exclude_atypical': (bool,), 'filters_assembly_version': (V1AssemblyDatasetDescriptorsFilterAssemblyVersion,), 'filters_assembly_level': ([V1AssemblyDatasetDescriptorsFilterAssemblyLevel],), 'filters_first_release_date': (datetime,), 'filters_last_release_date': (datetime,), 'filters_search_text': ([str],), 'returned_content': (V1AssemblyMetadataRequestContentType,), 'page_size': (int,), 'page_token': (str,), }, 'attribute_map': { 'accessions': 'accessions', 'filters_reference_only': 'filters.reference_only', 'filters_assembly_source': 'filters.assembly_source', 'filters_has_annotation': 'filters.has_annotation', 'filters_exclude_paired_reports': 'filters.exclude_paired_reports', 'filters_exclude_atypical': 'filters.exclude_atypical', 'filters_assembly_version': 'filters.assembly_version', 'filters_assembly_level': 'filters.assembly_level', 'filters_first_release_date': 'filters.first_release_date', 'filters_last_release_date': 'filters.last_release_date', 'filters_search_text': 'filters.search_text', 'returned_content': 'returned_content', 'page_size': 'page_size', 'page_token': 'page_token', }, 'location_map': { 'accessions': 'path', 'filters_reference_only': 'query', 'filters_assembly_source': 'query', 'filters_has_annotation': 'query', 'filters_exclude_paired_reports': 'query', 'filters_exclude_atypical': 'query', 'filters_assembly_version': 'query', 'filters_assembly_level': 'query', 'filters_first_release_date': 'query', 'filters_last_release_date': 'query', 'filters_search_text': 'query', 'returned_content': 'query', 'page_size': 'query', 'page_token': 'query', }, 'collection_format_map': { 'accessions': 'csv', 'filters_assembly_level': 'multi', 'filters_search_text': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.assembly_descriptors_by_taxon_endpoint = _Endpoint( settings={ 'response_type': (V1AssemblyMetadata,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/taxon/{taxon}', 'operation_id': 'assembly_descriptors_by_taxon', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'taxon', 'filters_reference_only', 'filters_assembly_source', 'filters_has_annotation', 'filters_exclude_paired_reports', 'filters_exclude_atypical', 'filters_assembly_version', 'filters_assembly_level', 'filters_first_release_date', 'filters_last_release_date', 'filters_search_text', 'tax_exact_match', 'returned_content', 'page_size', 'page_token', ], 'required': [ 'taxon', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'taxon': (str,), 'filters_reference_only': (bool,), 'filters_assembly_source': (V1AssemblyDatasetDescriptorsFilterAssemblySource,), 'filters_has_annotation': (bool,), 'filters_exclude_paired_reports': (bool,), 'filters_exclude_atypical': (bool,), 'filters_assembly_version': (V1AssemblyDatasetDescriptorsFilterAssemblyVersion,), 'filters_assembly_level': ([V1AssemblyDatasetDescriptorsFilterAssemblyLevel],), 'filters_first_release_date': (datetime,), 'filters_last_release_date': (datetime,), 'filters_search_text': ([str],), 'tax_exact_match': (bool,), 'returned_content': (V1AssemblyMetadataRequestContentType,), 'page_size': (int,), 'page_token': (str,), }, 'attribute_map': { 'taxon': 'taxon', 'filters_reference_only': 'filters.reference_only', 'filters_assembly_source': 'filters.assembly_source', 'filters_has_annotation': 'filters.has_annotation', 'filters_exclude_paired_reports': 'filters.exclude_paired_reports', 'filters_exclude_atypical': 'filters.exclude_atypical', 'filters_assembly_version': 'filters.assembly_version', 'filters_assembly_level': 'filters.assembly_level', 'filters_first_release_date': 'filters.first_release_date', 'filters_last_release_date': 'filters.last_release_date', 'filters_search_text': 'filters.search_text', 'tax_exact_match': 'tax_exact_match', 'returned_content': 'returned_content', 'page_size': 'page_size', 'page_token': 'page_token', }, 'location_map': { 'taxon': 'path', 'filters_reference_only': 'query', 'filters_assembly_source': 'query', 'filters_has_annotation': 'query', 'filters_exclude_paired_reports': 'query', 'filters_exclude_atypical': 'query', 'filters_assembly_version': 'query', 'filters_assembly_level': 'query', 'filters_first_release_date': 'query', 'filters_last_release_date': 'query', 'filters_search_text': 'query', 'tax_exact_match': 'query', 'returned_content': 'query', 'page_size': 'query', 'page_token': 'query', }, 'collection_format_map': { 'filters_assembly_level': 'multi', 'filters_search_text': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.check_assembly_availability_endpoint = _Endpoint( settings={ 'response_type': (V1AssemblyDatasetAvailability,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/accession/{accessions}/check', 'operation_id': 'check_assembly_availability', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), }, 'attribute_map': { 'accessions': 'accessions', }, 'location_map': { 'accessions': 'path', }, 'collection_format_map': { 'accessions': 'csv', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.check_assembly_availability_post_endpoint = _Endpoint( settings={ 'response_type': (V1AssemblyDatasetAvailability,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/check', 'operation_id': 'check_assembly_availability_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_assembly_dataset_request', ], 'required': [ 'v1_assembly_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_assembly_dataset_request': (V1AssemblyDatasetRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_assembly_dataset_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.download_assembly_package_endpoint = _Endpoint( settings={ 'response_type': (file_type,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/accession/{accessions}/download', 'operation_id': 'download_assembly_package', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'chromosomes', 'exclude_sequence', 'include_annotation_type', 'hydrated', 'filename', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'chromosomes': ([str],), 'exclude_sequence': (bool,), 'include_annotation_type': ([V1AnnotationForAssemblyType],), 'hydrated': (V1AssemblyDatasetRequestResolution,), 'filename': (str,), }, 'attribute_map': { 'accessions': 'accessions', 'chromosomes': 'chromosomes', 'exclude_sequence': 'exclude_sequence', 'include_annotation_type': 'include_annotation_type', 'hydrated': 'hydrated', 'filename': 'filename', }, 'location_map': { 'accessions': 'path', 'chromosomes': 'query', 'exclude_sequence': 'query', 'include_annotation_type': 'query', 'hydrated': 'query', 'filename': 'query', }, 'collection_format_map': { 'accessions': 'csv', 'chromosomes': 'multi', 'include_annotation_type': 'multi', } }, headers_map={ 'accept': [ 'application/zip', 'application/json' ], 'content_type': [], }, api_client=api_client ) self.download_assembly_package_post_endpoint = _Endpoint( settings={ 'response_type': (file_type,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/download', 'operation_id': 'download_assembly_package_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_assembly_dataset_request', 'filename', ], 'required': [ 'v1_assembly_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_assembly_dataset_request': (V1AssemblyDatasetRequest,), 'filename': (str,), }, 'attribute_map': { 'filename': 'filename', }, 'location_map': { 'v1_assembly_dataset_request': 'body', 'filename': 'query', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/zip', 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.genome_download_summary_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/accession/{accessions}/download_summary', 'operation_id': 'genome_download_summary', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'chromosomes', 'exclude_sequence', 'include_annotation_type', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'chromosomes': ([str],), 'exclude_sequence': (bool,), 'include_annotation_type': ([V1AnnotationForAssemblyType],), }, 'attribute_map': { 'accessions': 'accessions', 'chromosomes': 'chromosomes', 'exclude_sequence': 'exclude_sequence', 'include_annotation_type': 'include_annotation_type', }, 'location_map': { 'accessions': 'path', 'chromosomes': 'query', 'exclude_sequence': 'query', 'include_annotation_type': 'query', }, 'collection_format_map': { 'accessions': 'csv', 'chromosomes': 'multi', 'include_annotation_type': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.genome_download_summary_by_post_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome/download_summary', 'operation_id': 'genome_download_summary_by_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_assembly_dataset_request', ], 'required': [ 'v1_assembly_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_assembly_dataset_request': (V1AssemblyDatasetRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_assembly_dataset_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.genome_metadata_by_post_endpoint = _Endpoint( settings={ 'response_type': (V1AssemblyMetadata,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/genome', 'operation_id': 'genome_metadata_by_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_assembly_metadata_request', ], 'required': [ 'v1_assembly_metadata_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_assembly_metadata_request': (V1AssemblyMetadataRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_assembly_metadata_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) def assembly_descriptors_by_accessions( self, accessions, **kwargs ): """Get genome metadata by accession # noqa: E501 Get detailed metadata for assembled genomes by accession in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.assembly_descriptors_by_accessions(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): Keyword Args: filters_reference_only (bool): If true, only return reference and representative (GCF_ and GCA_) genome assemblies.. [optional] if omitted the server will use the default value of False filters_assembly_source (V1AssemblyDatasetDescriptorsFilterAssemblySource): Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies. [optional] filters_has_annotation (bool): Return only annotated genome assemblies. [optional] if omitted the server will use the default value of False filters_exclude_atypical (bool): If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical. [optional] if omitted the server will use the default value of False filters_assembly_level ([V1AssemblyDatasetDescriptorsFilterAssemblyLevel]): Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.. [optional] filters_first_release_date (datetime): Only return genome assemblies that were released on or after the specified date By default, do not filter.. [optional] filters_last_release_date (datetime): Only return genome assemblies that were released on or before to the specified date By default, do not filter.. [optional] filters_search_text ([str]): Only return results whose fields contain the specified search terms in their taxon, infraspecific, assembly name or submitter fields By default, do not filter. [optional] page_size (int): The maximum number of genome assemblies to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.. [optional] if omitted the server will use the default value of 20 page_token (str): A page token is returned from an `AssemblyMetadataRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyMetadataRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.. [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1AssemblyMetadata If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['accessions'] = \ accessions headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.assembly_descriptors_by_accessions_endpoint.call_with_http_info(**kwargs) def assembly_descriptors_by_bioproject( self, accessions, **kwargs ): """Get genome metadata by bioproject accession # noqa: E501 Get detailed metadata for assembled genomes by bioproject accession in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.assembly_descriptors_by_bioproject(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): Keyword Args: filters_reference_only (bool): If true, only return reference and representative (GCF_ and GCA_) genome assemblies.. [optional] if omitted the server will use the default value of False filters_assembly_source (V1AssemblyDatasetDescriptorsFilterAssemblySource): Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies. [optional] filters_has_annotation (bool): Return only annotated genome assemblies. [optional] if omitted the server will use the default value of False filters_exclude_paired_reports (bool): For paired (GCA/GCF) records, only return the primary record. [optional] if omitted the server will use the default value of False filters_exclude_atypical (bool): If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical. [optional] if omitted the server will use the default value of False filters_assembly_version (V1AssemblyDatasetDescriptorsFilterAssemblyVersion): Return all assemblies, including replaced and suppressed, or only current assemblies. [optional] filters_assembly_level ([V1AssemblyDatasetDescriptorsFilterAssemblyLevel]): Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.. [optional] filters_first_release_date (datetime): Only return genome assemblies that were released on or after the specified date By default, do not filter.. [optional] filters_last_release_date (datetime): Only return genome assemblies that were released on or before to the specified date By default, do not filter.. [optional] filters_search_text ([str]): Only return results whose fields contain the specified search terms in their taxon, infraspecific, assembly name or submitter fields By default, do not filter. [optional] returned_content (V1AssemblyMetadataRequestContentType): Return either assembly accessions, or entire assembly-metadata records. [optional] page_size (int): The maximum number of genome assemblies to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.. [optional] if omitted the server will use the default value of 20 page_token (str): A page token is returned from an `AssemblyMetadataRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyMetadataRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.. [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1AssemblyMetadata If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['accessions'] = \ accessions headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.assembly_descriptors_by_bioproject_endpoint.call_with_http_info(**kwargs) def assembly_descriptors_by_taxon( self, taxon, **kwargs ): """Get genome metadata by taxonomic identifier # noqa: E501 Get detailed metadata on all assembled genomes for a specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.assembly_descriptors_by_taxon(taxon, async_req=True) >>> result = thread.get() Args: taxon (str): NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank Keyword Args: filters_reference_only (bool): If true, only return reference and representative (GCF_ and GCA_) genome assemblies.. [optional] if omitted the server will use the default value of False filters_assembly_source (V1AssemblyDatasetDescriptorsFilterAssemblySource): Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies. [optional] filters_has_annotation (bool): Return only annotated genome assemblies. [optional] if omitted the server will use the default value of False filters_exclude_paired_reports (bool): For paired (GCA/GCF) records, only return the primary record. [optional] if omitted the server will use the default value of False filters_exclude_atypical (bool): If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical. [optional] if omitted the server will use the default value of False filters_assembly_version (V1AssemblyDatasetDescriptorsFilterAssemblyVersion): Return all assemblies, including replaced and suppressed, or only current assemblies. [optional] filters_assembly_level ([V1AssemblyDatasetDescriptorsFilterAssemblyLevel]): Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.. [optional] filters_first_release_date (datetime): Only return genome assemblies that were released on or after the specified date By default, do not filter.. [optional] filters_last_release_date (datetime): Only return genome assemblies that were released on or before to the specified date By default, do not filter.. [optional] filters_search_text ([str]): Only return results whose fields contain the specified search terms in their taxon, infraspecific, assembly name or submitter fields By default, do not filter. [optional] tax_exact_match (bool): If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too. Ignored for assembly_accession request.. [optional] if omitted the server will use the default value of False returned_content (V1AssemblyMetadataRequestContentType): Return either assembly accessions, or entire assembly-metadata records. [optional] page_size (int): The maximum number of genome assemblies to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.. [optional] if omitted the server will use the default value of 20 page_token (str): A page token is returned from an `AssemblyMetadataRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyMetadataRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.. [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1AssemblyMetadata If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['taxon'] = \ taxon headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.assembly_descriptors_by_taxon_endpoint.call_with_http_info(**kwargs) def check_assembly_availability( self, accessions, **kwargs ): """Check the validity of genome accessions # noqa: E501 The 'GET' version of check is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions). The POST operation is provided to allow users to supply a larger number of accessions in a single request. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.check_assembly_availability(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): NCBI genome assembly accessions Keyword Args: _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1AssemblyDatasetAvailability If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['accessions'] = \ accessions headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.check_assembly_availability_endpoint.call_with_http_info(**kwargs) def check_assembly_availability_post( self, v1_assembly_dataset_request, **kwargs ): """Check the validity of many genome accessions in a single request # noqa: E501 The 'GET' version of check is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions). The POST operation is provided to allow users to supply a larger number of accessions in a single request. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.check_assembly_availability_post(v1_assembly_dataset_request, async_req=True) >>> result = thread.get() Args: v1_assembly_dataset_request (V1AssemblyDatasetRequest): Keyword Args: _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1AssemblyDatasetAvailability If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['v1_assembly_dataset_request'] = \ v1_assembly_dataset_request headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.check_assembly_availability_post_endpoint.call_with_http_info(**kwargs) def download_assembly_package( self, accessions, **kwargs ): """Get a genome dataset by accession # noqa: E501 Download a genome dataset including fasta sequence, annotation and a detailed data report by accession. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.download_assembly_package(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): NCBI genome assembly accessions Keyword Args: chromosomes ([str]): The default setting is all chromosome. Specify individual chromosome by string (1,2,MT or chr1,chr2.chrMT). Unplaced sequences are treated like their own chromosome ('Un'). The filter only applies to fasta sequence.. [optional] exclude_sequence (bool): Set to true to omit the genomic sequence.. [optional] if omitted the server will use the default value of False include_annotation_type ([V1AnnotationForAssemblyType]): Select additional types of annotation to include in the data package. If unset, no annotation is provided.. [optional] hydrated (V1AssemblyDatasetRequestResolution): Set to DATA_REPORT_ONLY, to only retrieve data-reports.. [optional] filename (str): Output file name.. [optional] if omitted the server will use the default value of "ncbi_dataset.zip" _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: file_type If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['accessions'] = \ accessions headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.download_assembly_package_endpoint.call_with_http_info(**kwargs) def download_assembly_package_post( self, v1_assembly_dataset_request, **kwargs ): """Get a genome dataset by post # noqa: E501 The 'GET' version of download is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions). The POST operation is provided to allow users to supply a larger number of accessions in a single request. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.download_assembly_package_post(v1_assembly_dataset_request, async_req=True) >>> result = thread.get() Args: v1_assembly_dataset_request (V1AssemblyDatasetRequest): Keyword Args: filename (str): Output file name.. [optional] if omitted the server will use the default value of "ncbi_dataset.zip" _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: file_type If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['v1_assembly_dataset_request'] = \ v1_assembly_dataset_request headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.download_assembly_package_post_endpoint.call_with_http_info(**kwargs) def genome_download_summary( self, accessions, **kwargs ): """Preview genome dataset download # noqa: E501 Get a download summary by accession in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.genome_download_summary(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): NCBI genome assembly accessions Keyword Args: chromosomes ([str]): The default setting is all chromosome. Specify individual chromosome by string (1,2,MT or chr1,chr2.chrMT). Unplaced sequences are treated like their own chromosome ('Un'). The filter only applies to fasta sequence.. [optional] exclude_sequence (bool): Set to true to omit the genomic sequence.. [optional] if omitted the server will use the default value of False include_annotation_type ([V1AnnotationForAssemblyType]): Select additional types of annotation to include in the data package. If unset, no annotation is provided.. [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1DownloadSummary If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['accessions'] = \ accessions headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.genome_download_summary_endpoint.call_with_http_info(**kwargs) def genome_download_summary_by_post( self, v1_assembly_dataset_request, **kwargs ): """Preview genome dataset download by POST # noqa: E501 The 'GET' version of download summary is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions). The POST operation is provided to allow users to supply a larger number of accessions in a single request. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.genome_download_summary_by_post(v1_assembly_dataset_request, async_req=True) >>> result = thread.get() Args: v1_assembly_dataset_request (V1AssemblyDatasetRequest): Keyword Args: _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1DownloadSummary If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['v1_assembly_dataset_request'] = \ v1_assembly_dataset_request headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.genome_download_summary_by_post_endpoint.call_with_http_info(**kwargs) def genome_metadata_by_post( self, v1_assembly_metadata_request, **kwargs ): """Get genome metadata by variety of identifiers # noqa: E501 Get detailed metadata for assembled genomes. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.genome_metadata_by_post(v1_assembly_metadata_request, async_req=True) >>> result = thread.get() Args: v1_assembly_metadata_request (V1AssemblyMetadataRequest): Keyword Args: _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1AssemblyMetadata If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['v1_assembly_metadata_request'] = \ v1_assembly_metadata_request headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.genome_metadata_by_post_endpoint.call_with_http_info(**kwargs)