""" 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_virus_type import V1AnnotationForVirusType from ncbi.datasets.openapi.model.v1_download_summary import V1DownloadSummary from ncbi.datasets.openapi.model.v1_table_format import V1TableFormat from ncbi.datasets.openapi.model.v1_tabular_output import V1TabularOutput from ncbi.datasets.openapi.model.v1_virus_availability import V1VirusAvailability from ncbi.datasets.openapi.model.v1_virus_availability_request import V1VirusAvailabilityRequest from ncbi.datasets.openapi.model.v1_virus_data_report_request import V1VirusDataReportRequest from ncbi.datasets.openapi.model.v1_virus_data_report_request_content_type import V1VirusDataReportRequestContentType from ncbi.datasets.openapi.model.v1_virus_dataset_request import V1VirusDatasetRequest from ncbi.datasets.openapi.model.v1_virus_table_field import V1VirusTableField from ncbi.datasets.openapi.model.v1reports_virus_data_report_page import V1reportsVirusDataReportPage class VirusApi(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.sars2_protein_download_endpoint = _Endpoint( settings={ 'response_type': (file_type,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/taxon/sars2/protein/{proteins}/download', 'operation_id': 'sars2_protein_download', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'proteins', 'refseq_only', 'annotated_only', 'released_since', 'updated_since', 'host', 'geo_location', 'complete_only', 'include_annotation_type', 'filename', ], 'required': [ 'proteins', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'proteins': ([str],), 'refseq_only': (bool,), 'annotated_only': (bool,), 'released_since': (datetime,), 'updated_since': (datetime,), 'host': (str,), 'geo_location': (str,), 'complete_only': (bool,), 'include_annotation_type': ([V1AnnotationForVirusType],), 'filename': (str,), }, 'attribute_map': { 'proteins': 'proteins', 'refseq_only': 'refseq_only', 'annotated_only': 'annotated_only', 'released_since': 'released_since', 'updated_since': 'updated_since', 'host': 'host', 'geo_location': 'geo_location', 'complete_only': 'complete_only', 'include_annotation_type': 'include_annotation_type', 'filename': 'filename', }, 'location_map': { 'proteins': 'path', 'refseq_only': 'query', 'annotated_only': 'query', 'released_since': 'query', 'updated_since': 'query', 'host': 'query', 'geo_location': 'query', 'complete_only': 'query', 'include_annotation_type': 'query', 'filename': 'query', }, 'collection_format_map': { 'proteins': 'csv', 'include_annotation_type': 'multi', } }, headers_map={ 'accept': [ 'application/zip', 'application/json' ], 'content_type': [], }, api_client=api_client ) self.sars2_protein_summary_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/taxon/sars2/protein/{proteins}', 'operation_id': 'sars2_protein_summary', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'proteins', 'refseq_only', 'annotated_only', 'released_since', 'updated_since', 'host', 'geo_location', 'complete_only', 'include_annotation_type', ], 'required': [ 'proteins', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'proteins': ([str],), 'refseq_only': (bool,), 'annotated_only': (bool,), 'released_since': (datetime,), 'updated_since': (datetime,), 'host': (str,), 'geo_location': (str,), 'complete_only': (bool,), 'include_annotation_type': ([V1AnnotationForVirusType],), }, 'attribute_map': { 'proteins': 'proteins', 'refseq_only': 'refseq_only', 'annotated_only': 'annotated_only', 'released_since': 'released_since', 'updated_since': 'updated_since', 'host': 'host', 'geo_location': 'geo_location', 'complete_only': 'complete_only', 'include_annotation_type': 'include_annotation_type', }, 'location_map': { 'proteins': 'path', 'refseq_only': 'query', 'annotated_only': 'query', 'released_since': 'query', 'updated_since': 'query', 'host': 'query', 'geo_location': 'query', 'complete_only': 'query', 'include_annotation_type': 'query', }, 'collection_format_map': { 'proteins': 'csv', 'include_annotation_type': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.sars2_protein_table_endpoint = _Endpoint( settings={ 'response_type': (V1TabularOutput,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/taxon/sars2/protein/{proteins}/table', 'operation_id': 'sars2_protein_table', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'proteins', 'refseq_only', 'annotated_only', 'released_since', 'updated_since', 'host', 'geo_location', 'complete_only', 'table_fields', 'format', ], 'required': [ 'proteins', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'proteins': ([str],), 'refseq_only': (bool,), 'annotated_only': (bool,), 'released_since': (datetime,), 'updated_since': (datetime,), 'host': (str,), 'geo_location': (str,), 'complete_only': (bool,), 'table_fields': ([V1VirusTableField],), 'format': (V1TableFormat,), }, 'attribute_map': { 'proteins': 'proteins', 'refseq_only': 'refseq_only', 'annotated_only': 'annotated_only', 'released_since': 'released_since', 'updated_since': 'updated_since', 'host': 'host', 'geo_location': 'geo_location', 'complete_only': 'complete_only', 'table_fields': 'table_fields', 'format': 'format', }, 'location_map': { 'proteins': 'path', 'refseq_only': 'query', 'annotated_only': 'query', 'released_since': 'query', 'updated_since': 'query', 'host': 'query', 'geo_location': 'query', 'complete_only': 'query', 'table_fields': 'query', 'format': 'query', }, 'collection_format_map': { 'proteins': 'csv', 'table_fields': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.virus_accession_availability_endpoint = _Endpoint( settings={ 'response_type': (V1VirusAvailability,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/accession/{accessions}/check', 'operation_id': 'virus_accession_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.virus_accession_availability_post_endpoint = _Endpoint( settings={ 'response_type': (V1VirusAvailability,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/check', 'operation_id': 'virus_accession_availability_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_virus_availability_request', ], 'required': [ 'v1_virus_availability_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_virus_availability_request': (V1VirusAvailabilityRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_virus_availability_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.virus_genome_download_endpoint = _Endpoint( settings={ 'response_type': (file_type,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/taxon/{taxon}/genome/download', 'operation_id': 'virus_genome_download', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'taxon', 'refseq_only', 'annotated_only', 'released_since', 'updated_since', 'host', 'pangolin_classification', 'geo_location', 'complete_only', 'exclude_sequence', 'include_annotation_type', 'filename', ], 'required': [ 'taxon', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'taxon': (str,), 'refseq_only': (bool,), 'annotated_only': (bool,), 'released_since': (datetime,), 'updated_since': (datetime,), 'host': (str,), 'pangolin_classification': (str,), 'geo_location': (str,), 'complete_only': (bool,), 'exclude_sequence': (bool,), 'include_annotation_type': ([V1AnnotationForVirusType],), 'filename': (str,), }, 'attribute_map': { 'taxon': 'taxon', 'refseq_only': 'refseq_only', 'annotated_only': 'annotated_only', 'released_since': 'released_since', 'updated_since': 'updated_since', 'host': 'host', 'pangolin_classification': 'pangolin_classification', 'geo_location': 'geo_location', 'complete_only': 'complete_only', 'exclude_sequence': 'exclude_sequence', 'include_annotation_type': 'include_annotation_type', 'filename': 'filename', }, 'location_map': { 'taxon': 'path', 'refseq_only': 'query', 'annotated_only': 'query', 'released_since': 'query', 'updated_since': 'query', 'host': 'query', 'pangolin_classification': 'query', 'geo_location': 'query', 'complete_only': 'query', 'exclude_sequence': 'query', 'include_annotation_type': 'query', 'filename': 'query', }, 'collection_format_map': { 'include_annotation_type': 'multi', } }, headers_map={ 'accept': [ 'application/zip', 'application/json' ], 'content_type': [], }, api_client=api_client ) self.virus_genome_download_accession_endpoint = _Endpoint( settings={ 'response_type': (file_type,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/accession/{accessions}/genome/download', 'operation_id': 'virus_genome_download_accession', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'refseq_only', 'annotated_only', 'released_since', 'updated_since', 'host', 'pangolin_classification', 'geo_location', 'complete_only', 'exclude_sequence', 'include_annotation_type', 'filename', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'refseq_only': (bool,), 'annotated_only': (bool,), 'released_since': (datetime,), 'updated_since': (datetime,), 'host': (str,), 'pangolin_classification': (str,), 'geo_location': (str,), 'complete_only': (bool,), 'exclude_sequence': (bool,), 'include_annotation_type': ([V1AnnotationForVirusType],), 'filename': (str,), }, 'attribute_map': { 'accessions': 'accessions', 'refseq_only': 'refseq_only', 'annotated_only': 'annotated_only', 'released_since': 'released_since', 'updated_since': 'updated_since', 'host': 'host', 'pangolin_classification': 'pangolin_classification', 'geo_location': 'geo_location', 'complete_only': 'complete_only', 'exclude_sequence': 'exclude_sequence', 'include_annotation_type': 'include_annotation_type', 'filename': 'filename', }, 'location_map': { 'accessions': 'path', 'refseq_only': 'query', 'annotated_only': 'query', 'released_since': 'query', 'updated_since': 'query', 'host': 'query', 'pangolin_classification': 'query', 'geo_location': 'query', 'complete_only': 'query', 'exclude_sequence': 'query', 'include_annotation_type': 'query', 'filename': 'query', }, 'collection_format_map': { 'accessions': 'csv', 'include_annotation_type': 'multi', } }, headers_map={ 'accept': [ 'application/zip', 'application/json' ], 'content_type': [], }, api_client=api_client ) self.virus_genome_download_post_endpoint = _Endpoint( settings={ 'response_type': (file_type,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/genome/download', 'operation_id': 'virus_genome_download_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_virus_dataset_request', 'filename', ], 'required': [ 'v1_virus_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_virus_dataset_request': (V1VirusDatasetRequest,), 'filename': (str,), }, 'attribute_map': { 'filename': 'filename', }, 'location_map': { 'v1_virus_dataset_request': 'body', 'filename': 'query', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/zip', 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.virus_genome_summary_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/taxon/{taxon}/genome', 'operation_id': 'virus_genome_summary', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'taxon', 'refseq_only', 'annotated_only', 'released_since', 'updated_since', 'host', 'pangolin_classification', 'geo_location', 'complete_only', 'exclude_sequence', 'include_annotation_type', ], 'required': [ 'taxon', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'taxon': (str,), 'refseq_only': (bool,), 'annotated_only': (bool,), 'released_since': (datetime,), 'updated_since': (datetime,), 'host': (str,), 'pangolin_classification': (str,), 'geo_location': (str,), 'complete_only': (bool,), 'exclude_sequence': (bool,), 'include_annotation_type': ([V1AnnotationForVirusType],), }, 'attribute_map': { 'taxon': 'taxon', 'refseq_only': 'refseq_only', 'annotated_only': 'annotated_only', 'released_since': 'released_since', 'updated_since': 'updated_since', 'host': 'host', 'pangolin_classification': 'pangolin_classification', 'geo_location': 'geo_location', 'complete_only': 'complete_only', 'exclude_sequence': 'exclude_sequence', 'include_annotation_type': 'include_annotation_type', }, 'location_map': { 'taxon': 'path', 'refseq_only': 'query', 'annotated_only': 'query', 'released_since': 'query', 'updated_since': 'query', 'host': 'query', 'pangolin_classification': 'query', 'geo_location': 'query', 'complete_only': 'query', 'exclude_sequence': 'query', 'include_annotation_type': 'query', }, 'collection_format_map': { 'include_annotation_type': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.virus_genome_summary_accession_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/accession/{accessions}/genome', 'operation_id': 'virus_genome_summary_accession', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'refseq_only', 'annotated_only', 'released_since', 'updated_since', 'host', 'pangolin_classification', 'geo_location', 'complete_only', 'exclude_sequence', 'include_annotation_type', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'refseq_only': (bool,), 'annotated_only': (bool,), 'released_since': (datetime,), 'updated_since': (datetime,), 'host': (str,), 'pangolin_classification': (str,), 'geo_location': (str,), 'complete_only': (bool,), 'exclude_sequence': (bool,), 'include_annotation_type': ([V1AnnotationForVirusType],), }, 'attribute_map': { 'accessions': 'accessions', 'refseq_only': 'refseq_only', 'annotated_only': 'annotated_only', 'released_since': 'released_since', 'updated_since': 'updated_since', 'host': 'host', 'pangolin_classification': 'pangolin_classification', 'geo_location': 'geo_location', 'complete_only': 'complete_only', 'exclude_sequence': 'exclude_sequence', 'include_annotation_type': 'include_annotation_type', }, 'location_map': { 'accessions': 'path', 'refseq_only': 'query', 'annotated_only': 'query', 'released_since': 'query', 'updated_since': 'query', 'host': 'query', 'pangolin_classification': 'query', 'geo_location': 'query', 'complete_only': 'query', 'exclude_sequence': 'query', 'include_annotation_type': 'query', }, 'collection_format_map': { 'accessions': 'csv', 'include_annotation_type': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.virus_genome_summary_post_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/genome', 'operation_id': 'virus_genome_summary_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_virus_dataset_request', ], 'required': [ 'v1_virus_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_virus_dataset_request': (V1VirusDatasetRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_virus_dataset_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.virus_genome_table_endpoint = _Endpoint( settings={ 'response_type': (V1TabularOutput,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/taxon/{taxon}/genome/table', 'operation_id': 'virus_genome_table', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'taxon', 'refseq_only', 'annotated_only', 'released_since', 'updated_since', 'host', 'pangolin_classification', 'geo_location', 'complete_only', 'table_fields', 'format', ], 'required': [ 'taxon', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'taxon': (str,), 'refseq_only': (bool,), 'annotated_only': (bool,), 'released_since': (datetime,), 'updated_since': (datetime,), 'host': (str,), 'pangolin_classification': (str,), 'geo_location': (str,), 'complete_only': (bool,), 'table_fields': ([V1VirusTableField],), 'format': (V1TableFormat,), }, 'attribute_map': { 'taxon': 'taxon', 'refseq_only': 'refseq_only', 'annotated_only': 'annotated_only', 'released_since': 'released_since', 'updated_since': 'updated_since', 'host': 'host', 'pangolin_classification': 'pangolin_classification', 'geo_location': 'geo_location', 'complete_only': 'complete_only', 'table_fields': 'table_fields', 'format': 'format', }, 'location_map': { 'taxon': 'path', 'refseq_only': 'query', 'annotated_only': 'query', 'released_since': 'query', 'updated_since': 'query', 'host': 'query', 'pangolin_classification': 'query', 'geo_location': 'query', 'complete_only': 'query', 'table_fields': 'query', 'format': 'query', }, 'collection_format_map': { 'table_fields': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.virus_reports_by_acessions_endpoint = _Endpoint( settings={ 'response_type': (V1reportsVirusDataReportPage,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/accession/{accessions}/dataset_report', 'operation_id': 'virus_reports_by_acessions', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'filter_refseq_only', 'filter_annotated_only', 'filter_released_since', 'filter_updated_since', 'filter_host', 'filter_pangolin_classification', 'filter_geo_location', 'filter_complete_only', 'returned_content', 'table_fields', 'page_size', 'page_token', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'filter_refseq_only': (bool,), 'filter_annotated_only': (bool,), 'filter_released_since': (datetime,), 'filter_updated_since': (datetime,), 'filter_host': (str,), 'filter_pangolin_classification': (str,), 'filter_geo_location': (str,), 'filter_complete_only': (bool,), 'returned_content': (V1VirusDataReportRequestContentType,), 'table_fields': ([str],), 'page_size': (int,), 'page_token': (str,), }, 'attribute_map': { 'accessions': 'accessions', 'filter_refseq_only': 'filter.refseq_only', 'filter_annotated_only': 'filter.annotated_only', 'filter_released_since': 'filter.released_since', 'filter_updated_since': 'filter.updated_since', 'filter_host': 'filter.host', 'filter_pangolin_classification': 'filter.pangolin_classification', 'filter_geo_location': 'filter.geo_location', 'filter_complete_only': 'filter.complete_only', 'returned_content': 'returned_content', 'table_fields': 'table_fields', 'page_size': 'page_size', 'page_token': 'page_token', }, 'location_map': { 'accessions': 'path', 'filter_refseq_only': 'query', 'filter_annotated_only': 'query', 'filter_released_since': 'query', 'filter_updated_since': 'query', 'filter_host': 'query', 'filter_pangolin_classification': 'query', 'filter_geo_location': 'query', 'filter_complete_only': 'query', 'returned_content': 'query', 'table_fields': 'query', 'page_size': 'query', 'page_token': 'query', }, 'collection_format_map': { 'accessions': 'csv', 'table_fields': 'multi', } }, headers_map={ 'accept': [ 'application/json', 'text/tab-separated-values' ], 'content_type': [], }, api_client=api_client ) self.virus_reports_by_post_endpoint = _Endpoint( settings={ 'response_type': (V1reportsVirusDataReportPage,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus', 'operation_id': 'virus_reports_by_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_virus_data_report_request', ], 'required': [ 'v1_virus_data_report_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_virus_data_report_request': (V1VirusDataReportRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_virus_data_report_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json', 'text/tab-separated-values' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.virus_reports_by_taxon_endpoint = _Endpoint( settings={ 'response_type': (V1reportsVirusDataReportPage,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/virus/taxon/{taxon}/dataset_report', 'operation_id': 'virus_reports_by_taxon', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'taxon', 'filter_refseq_only', 'filter_annotated_only', 'filter_released_since', 'filter_updated_since', 'filter_host', 'filter_pangolin_classification', 'filter_geo_location', 'filter_complete_only', 'returned_content', 'table_fields', 'page_size', 'page_token', ], 'required': [ 'taxon', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'taxon': (str,), 'filter_refseq_only': (bool,), 'filter_annotated_only': (bool,), 'filter_released_since': (datetime,), 'filter_updated_since': (datetime,), 'filter_host': (str,), 'filter_pangolin_classification': (str,), 'filter_geo_location': (str,), 'filter_complete_only': (bool,), 'returned_content': (V1VirusDataReportRequestContentType,), 'table_fields': ([str],), 'page_size': (int,), 'page_token': (str,), }, 'attribute_map': { 'taxon': 'taxon', 'filter_refseq_only': 'filter.refseq_only', 'filter_annotated_only': 'filter.annotated_only', 'filter_released_since': 'filter.released_since', 'filter_updated_since': 'filter.updated_since', 'filter_host': 'filter.host', 'filter_pangolin_classification': 'filter.pangolin_classification', 'filter_geo_location': 'filter.geo_location', 'filter_complete_only': 'filter.complete_only', 'returned_content': 'returned_content', 'table_fields': 'table_fields', 'page_size': 'page_size', 'page_token': 'page_token', }, 'location_map': { 'taxon': 'path', 'filter_refseq_only': 'query', 'filter_annotated_only': 'query', 'filter_released_since': 'query', 'filter_updated_since': 'query', 'filter_host': 'query', 'filter_pangolin_classification': 'query', 'filter_geo_location': 'query', 'filter_complete_only': 'query', 'returned_content': 'query', 'table_fields': 'query', 'page_size': 'query', 'page_token': 'query', }, 'collection_format_map': { 'table_fields': 'multi', } }, headers_map={ 'accept': [ 'application/json', 'text/tab-separated-values' ], 'content_type': [], }, api_client=api_client ) def sars2_protein_download( self, proteins, **kwargs ): """Download SARS-CoV-2 protein and CDS datasets by protein name # noqa: E501 Download SARS-CoV-2 protein datasets # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.sars2_protein_download(proteins, async_req=True) >>> result = thread.get() Args: proteins ([str]): Which proteins to retrieve in the data package Keyword Args: refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] updated_since (datetime): [optional] host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] geo_location (str): Assemblies from this location (country and state, or continent). [optional] complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False include_annotation_type ([V1AnnotationForVirusType]): Select additional types of annotation to include in the data package. If unset, no annotation is provided.. [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['proteins'] = \ proteins 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.sars2_protein_download_endpoint.call_with_http_info(**kwargs) def sars2_protein_summary( self, proteins, **kwargs ): """Summary of SARS-CoV-2 protein and CDS datasets by protein name # noqa: E501 Download a summary of available SARS-CoV-2 protein datasets # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.sars2_protein_summary(proteins, async_req=True) >>> result = thread.get() Args: proteins ([str]): Which proteins to retrieve in the data package Keyword Args: refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] updated_since (datetime): [optional] host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] geo_location (str): Assemblies from this location (country and state, or continent). [optional] complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False include_annotation_type ([V1AnnotationForVirusType]): 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['proteins'] = \ proteins 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.sars2_protein_summary_endpoint.call_with_http_info(**kwargs) def sars2_protein_table( self, proteins, **kwargs ): """Get SARS-CoV-2 protein metadata in a tabular format. # noqa: E501 Get protein metadata in tabular format for SARS-CoV-2 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.sars2_protein_table(proteins, async_req=True) >>> result = thread.get() Args: proteins ([str]): Which proteins to retrieve in the data package Keyword Args: refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] updated_since (datetime): [optional] host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] geo_location (str): Assemblies from this location (country and state, or continent). [optional] complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False table_fields ([V1VirusTableField]): Specify which fields to include in the tabular report. [optional] format (V1TableFormat): Choose download format (tsv, csv or jsonl). [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: V1TabularOutput 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['proteins'] = \ proteins 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.sars2_protein_table_endpoint.call_with_http_info(**kwargs) def virus_accession_availability( self, accessions, **kwargs ): """Check available viruses by accession GET # noqa: E501 Check available viruses GET # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.virus_accession_availability(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): virus sequence 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: V1VirusAvailability 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.virus_accession_availability_endpoint.call_with_http_info(**kwargs) def virus_accession_availability_post( self, v1_virus_availability_request, **kwargs ): """Check available viruses by accession POST # noqa: E501 Check available viruses POST # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.virus_accession_availability_post(v1_virus_availability_request, async_req=True) >>> result = thread.get() Args: v1_virus_availability_request (V1VirusAvailabilityRequest): 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: V1VirusAvailability 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_virus_availability_request'] = \ v1_virus_availability_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.virus_accession_availability_post_endpoint.call_with_http_info(**kwargs) def virus_genome_download( self, taxon, **kwargs ): """Download a coronavirus genome dataset by taxon # noqa: E501 Download a coronavirus genome dataset by taxon # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.virus_genome_download(taxon, async_req=True) >>> result = thread.get() Args: taxon (str): NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank Keyword Args: refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] updated_since (datetime): [optional] host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] pangolin_classification (str): If set, limit results to genomes classified to this lineage by the PangoLearn tool.. [optional] geo_location (str): Assemblies from this location (country and state, or continent). [optional] complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False 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 ([V1AnnotationForVirusType]): Select additional types of annotation to include in the data package. If unset, no annotation is provided.. [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['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.virus_genome_download_endpoint.call_with_http_info(**kwargs) def virus_genome_download_accession( self, accessions, **kwargs ): """Download a coronavirus genome dataset by accession # noqa: E501 Download a coronavirus genome dataset 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.virus_genome_download_accession(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): Accessions accessions = 16; Keyword Args: refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] updated_since (datetime): [optional] host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] pangolin_classification (str): If set, limit results to genomes classified to this lineage by the PangoLearn tool.. [optional] geo_location (str): Assemblies from this location (country and state, or continent). [optional] complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False 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 ([V1AnnotationForVirusType]): Select additional types of annotation to include in the data package. If unset, no annotation is provided.. [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.virus_genome_download_accession_endpoint.call_with_http_info(**kwargs) def virus_genome_download_post( self, v1_virus_dataset_request, **kwargs ): """Get a coronavirus 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.virus_genome_download_post(v1_virus_dataset_request, async_req=True) >>> result = thread.get() Args: v1_virus_dataset_request (V1VirusDatasetRequest): 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_virus_dataset_request'] = \ v1_virus_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.virus_genome_download_post_endpoint.call_with_http_info(**kwargs) def virus_genome_summary( self, taxon, **kwargs ): """Get summary data for Coronaviridae genomes by taxon # noqa: E501 Get summary data and download by command line instructions for Coronaviridae genomes by taxon. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.virus_genome_summary(taxon, async_req=True) >>> result = thread.get() Args: taxon (str): NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank Keyword Args: refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] updated_since (datetime): [optional] host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] pangolin_classification (str): If set, limit results to genomes classified to this lineage by the PangoLearn tool.. [optional] geo_location (str): Assemblies from this location (country and state, or continent). [optional] complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False 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 ([V1AnnotationForVirusType]): 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['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.virus_genome_summary_endpoint.call_with_http_info(**kwargs) def virus_genome_summary_accession( self, accessions, **kwargs ): """Get summary data for Coronaviridae genomes by accession # noqa: E501 Get summary data for Coronaviridae genomes 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.virus_genome_summary_accession(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): Accessions accessions = 16; Keyword Args: refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] updated_since (datetime): [optional] host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] pangolin_classification (str): If set, limit results to genomes classified to this lineage by the PangoLearn tool.. [optional] geo_location (str): Assemblies from this location (country and state, or continent). [optional] complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False 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 ([V1AnnotationForVirusType]): 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.virus_genome_summary_accession_endpoint.call_with_http_info(**kwargs) def virus_genome_summary_post( self, v1_virus_dataset_request, **kwargs ): """Get summary data for Coronaviridae genomes by post # noqa: E501 The 'GET' version 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.virus_genome_summary_post(v1_virus_dataset_request, async_req=True) >>> result = thread.get() Args: v1_virus_dataset_request (V1VirusDatasetRequest): 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_virus_dataset_request'] = \ v1_virus_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.virus_genome_summary_post_endpoint.call_with_http_info(**kwargs) def virus_genome_table( self, taxon, **kwargs ): """Get viral genomic metadata in a tabular format. # noqa: E501 Get viral genomic metadata in tabular format for Coronaviridae genomes by taxon. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.virus_genome_table(taxon, async_req=True) >>> result = thread.get() Args: taxon (str): NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank Keyword Args: refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] updated_since (datetime): [optional] host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] pangolin_classification (str): If set, limit results to genomes classified to this lineage by the PangoLearn tool.. [optional] geo_location (str): Assemblies from this location (country and state, or continent). [optional] complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False table_fields ([V1VirusTableField]): Specify which fields to include in the tabular report. [optional] format (V1TableFormat): Choose download format (tsv, csv or jsonl). [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: V1TabularOutput 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.virus_genome_table_endpoint.call_with_http_info(**kwargs) def virus_reports_by_acessions( self, accessions, **kwargs ): """Get virus metadata by accession # noqa: E501 Get virus metadata by accesion. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines) # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.virus_reports_by_acessions(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): genome sequence accessions Keyword Args: filter_refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False filter_annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False filter_released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] filter_updated_since (datetime): [optional] filter_host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] filter_pangolin_classification (str): If set, limit results to genomes classified to this lineage by the PangoLearn tool.. [optional] filter_geo_location (str): Assemblies from this location (country and state, or continent). [optional] filter_complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False returned_content (V1VirusDataReportRequestContentType): Return either virus genome accessions, or complete virus metadata. [optional] table_fields ([str]): Specify which fields to include in the tabular report. [optional] page_size (int): The maximum number of virus data reports 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 a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` 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: V1reportsVirusDataReportPage 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.virus_reports_by_acessions_endpoint.call_with_http_info(**kwargs) def virus_reports_by_post( self, v1_virus_data_report_request, **kwargs ): """Get virus metadata by POST # noqa: E501 Get virus metadata. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines) # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.virus_reports_by_post(v1_virus_data_report_request, async_req=True) >>> result = thread.get() Args: v1_virus_data_report_request (V1VirusDataReportRequest): 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: V1reportsVirusDataReportPage 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_virus_data_report_request'] = \ v1_virus_data_report_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.virus_reports_by_post_endpoint.call_with_http_info(**kwargs) def virus_reports_by_taxon( self, taxon, **kwargs ): """Get virus metadata by taxon # noqa: E501 Get virus metadata by taxon. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines) # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.virus_reports_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: filter_refseq_only (bool): If true, limit results to RefSeq genomes.. [optional] if omitted the server will use the default value of False filter_annotated_only (bool): If true, limit results to annotated genomes.. [optional] if omitted the server will use the default value of False filter_released_since (datetime): If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'. [optional] filter_updated_since (datetime): [optional] filter_host (str): If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default. [optional] filter_pangolin_classification (str): If set, limit results to genomes classified to this lineage by the PangoLearn tool.. [optional] filter_geo_location (str): Assemblies from this location (country and state, or continent). [optional] filter_complete_only (bool): only include complete genomes.. [optional] if omitted the server will use the default value of False returned_content (V1VirusDataReportRequestContentType): Return either virus genome accessions, or complete virus metadata. [optional] table_fields ([str]): Specify which fields to include in the tabular report. [optional] page_size (int): The maximum number of virus data reports 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 a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` 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: V1reportsVirusDataReportPage 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.virus_reports_by_taxon_endpoint.call_with_http_info(**kwargs)