"""
    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_organism_query_request_tax_rank_filter import V1OrganismQueryRequestTaxRankFilter
from ncbi.datasets.openapi.model.v1_organism_query_request_taxon_resource_filter import V1OrganismQueryRequestTaxonResourceFilter
from ncbi.datasets.openapi.model.v1_organism_rank_type import V1OrganismRankType
from ncbi.datasets.openapi.model.v1_sci_name_and_ids import V1SciNameAndIds
from ncbi.datasets.openapi.model.v1_taxonomy_filtered_subtree_request import V1TaxonomyFilteredSubtreeRequest
from ncbi.datasets.openapi.model.v1_taxonomy_filtered_subtree_response import V1TaxonomyFilteredSubtreeResponse
from ncbi.datasets.openapi.model.v1_taxonomy_metadata_request import V1TaxonomyMetadataRequest
from ncbi.datasets.openapi.model.v1_taxonomy_metadata_request_content_type import V1TaxonomyMetadataRequestContentType
from ncbi.datasets.openapi.model.v1_taxonomy_metadata_response import V1TaxonomyMetadataResponse


class TaxonomyApi(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.tax_name_query_endpoint = _Endpoint(
            settings={
                'response_type': (V1SciNameAndIds,),
                'auth': [
                    'ApiKeyAuthHeader'
                ],
                'endpoint_path': '/taxonomy/taxon_suggest/{taxon_query}',
                'operation_id': 'tax_name_query',
                'http_method': 'GET',
                'servers': None,
            },
            params_map={
                'all': [
                    'taxon_query',
                    'tax_rank_filter',
                    'tax_resource_filter',
                ],
                'required': [
                    'taxon_query',
                ],
                'nullable': [
                ],
                'enum': [
                ],
                'validation': [
                ]
            },
            root_map={
                'validations': {
                },
                'allowed_values': {
                },
                'openapi_types': {
                    'taxon_query':
                        (str,),
                    'tax_rank_filter':
                        (V1OrganismQueryRequestTaxRankFilter,),
                    'tax_resource_filter':
                        (V1OrganismQueryRequestTaxonResourceFilter,),
                },
                'attribute_map': {
                    'taxon_query': 'taxon_query',
                    'tax_rank_filter': 'tax_rank_filter',
                    'tax_resource_filter': 'tax_resource_filter',
                },
                'location_map': {
                    'taxon_query': 'path',
                    'tax_rank_filter': 'query',
                    'tax_resource_filter': 'query',
                },
                'collection_format_map': {
                }
            },
            headers_map={
                'accept': [
                    'application/json'
                ],
                'content_type': [],
            },
            api_client=api_client
        )
        self.taxonomy_filtered_subtree_endpoint = _Endpoint(
            settings={
                'response_type': (V1TaxonomyFilteredSubtreeResponse,),
                'auth': [
                    'ApiKeyAuthHeader'
                ],
                'endpoint_path': '/taxonomy/taxon/{taxons}/filtered_subtree',
                'operation_id': 'taxonomy_filtered_subtree',
                'http_method': 'GET',
                'servers': None,
            },
            params_map={
                'all': [
                    'taxons',
                    'specified_limit',
                    'rank_limits',
                ],
                'required': [
                    'taxons',
                ],
                'nullable': [
                ],
                'enum': [
                ],
                'validation': [
                ]
            },
            root_map={
                'validations': {
                },
                'allowed_values': {
                },
                'openapi_types': {
                    'taxons':
                        ([str],),
                    'specified_limit':
                        (bool,),
                    'rank_limits':
                        ([V1OrganismRankType],),
                },
                'attribute_map': {
                    'taxons': 'taxons',
                    'specified_limit': 'specified_limit',
                    'rank_limits': 'rank_limits',
                },
                'location_map': {
                    'taxons': 'path',
                    'specified_limit': 'query',
                    'rank_limits': 'query',
                },
                'collection_format_map': {
                    'taxons': 'csv',
                    'rank_limits': 'multi',
                }
            },
            headers_map={
                'accept': [
                    'application/json'
                ],
                'content_type': [],
            },
            api_client=api_client
        )
        self.taxonomy_filtered_subtree_post_endpoint = _Endpoint(
            settings={
                'response_type': (V1TaxonomyFilteredSubtreeResponse,),
                'auth': [
                    'ApiKeyAuthHeader'
                ],
                'endpoint_path': '/taxonomy/filtered_subtree',
                'operation_id': 'taxonomy_filtered_subtree_post',
                'http_method': 'POST',
                'servers': None,
            },
            params_map={
                'all': [
                    'v1_taxonomy_filtered_subtree_request',
                ],
                'required': [
                    'v1_taxonomy_filtered_subtree_request',
                ],
                'nullable': [
                ],
                'enum': [
                ],
                'validation': [
                ]
            },
            root_map={
                'validations': {
                },
                'allowed_values': {
                },
                'openapi_types': {
                    'v1_taxonomy_filtered_subtree_request':
                        (V1TaxonomyFilteredSubtreeRequest,),
                },
                'attribute_map': {
                },
                'location_map': {
                    'v1_taxonomy_filtered_subtree_request': 'body',
                },
                'collection_format_map': {
                }
            },
            headers_map={
                'accept': [
                    'application/json'
                ],
                'content_type': [
                    'application/json'
                ]
            },
            api_client=api_client
        )
        self.taxonomy_metadata_endpoint = _Endpoint(
            settings={
                'response_type': (V1TaxonomyMetadataResponse,),
                'auth': [
                    'ApiKeyAuthHeader'
                ],
                'endpoint_path': '/taxonomy/taxon/{taxons}',
                'operation_id': 'taxonomy_metadata',
                'http_method': 'GET',
                'servers': None,
            },
            params_map={
                'all': [
                    'taxons',
                    'returned_content',
                ],
                'required': [
                    'taxons',
                ],
                'nullable': [
                ],
                'enum': [
                ],
                'validation': [
                ]
            },
            root_map={
                'validations': {
                },
                'allowed_values': {
                },
                'openapi_types': {
                    'taxons':
                        ([str],),
                    'returned_content':
                        (V1TaxonomyMetadataRequestContentType,),
                },
                'attribute_map': {
                    'taxons': 'taxons',
                    'returned_content': 'returned_content',
                },
                'location_map': {
                    'taxons': 'path',
                    'returned_content': 'query',
                },
                'collection_format_map': {
                    'taxons': 'csv',
                }
            },
            headers_map={
                'accept': [
                    'application/json'
                ],
                'content_type': [],
            },
            api_client=api_client
        )
        self.taxonomy_metadata_post_endpoint = _Endpoint(
            settings={
                'response_type': (V1TaxonomyMetadataResponse,),
                'auth': [
                    'ApiKeyAuthHeader'
                ],
                'endpoint_path': '/taxonomy',
                'operation_id': 'taxonomy_metadata_post',
                'http_method': 'POST',
                'servers': None,
            },
            params_map={
                'all': [
                    'v1_taxonomy_metadata_request',
                ],
                'required': [
                    'v1_taxonomy_metadata_request',
                ],
                'nullable': [
                ],
                'enum': [
                ],
                'validation': [
                ]
            },
            root_map={
                'validations': {
                },
                'allowed_values': {
                },
                'openapi_types': {
                    'v1_taxonomy_metadata_request':
                        (V1TaxonomyMetadataRequest,),
                },
                'attribute_map': {
                },
                'location_map': {
                    'v1_taxonomy_metadata_request': 'body',
                },
                'collection_format_map': {
                }
            },
            headers_map={
                'accept': [
                    'application/json'
                ],
                'content_type': [
                    'application/json'
                ]
            },
            api_client=api_client
        )

    def tax_name_query(
        self,
        taxon_query,
        **kwargs
    ):
        """Get a list of taxonomy names and IDs given a partial taxonomic name  # noqa: E501

        This endpoint retrieves a list of taxonomy names and IDs given a partial taxonomic name of any 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.tax_name_query(taxon_query, async_req=True)
        >>> result = thread.get()

        Args:
            taxon_query (str): NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank

        Keyword Args:
            tax_rank_filter (V1OrganismQueryRequestTaxRankFilter): Set the scope of searched tax ranks. [optional]
            tax_resource_filter (V1OrganismQueryRequestTaxonResourceFilter): [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:
            V1SciNameAndIds
                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_query'] = \
            taxon_query
        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.tax_name_query_endpoint.call_with_http_info(**kwargs)

    def taxonomy_filtered_subtree(
        self,
        taxons,
        **kwargs
    ):
        """Use taxonomic identifiers to get a filtered taxonomic subtree  # noqa: E501

        Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get a filtered taxonomic subtree that includes the full parent lineage and all immediate children from the selected taxonomic ranks in JSON 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.taxonomy_filtered_subtree(taxons, async_req=True)
        >>> result = thread.get()

        Args:
            taxons ([str]):

        Keyword Args:
            specified_limit (bool): Limit to specified species. [optional]
            rank_limits ([V1OrganismRankType]): Limit to the provided ranks.  If empty, accept any rank.. [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:
            V1TaxonomyFilteredSubtreeResponse
                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['taxons'] = \
            taxons
        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.taxonomy_filtered_subtree_endpoint.call_with_http_info(**kwargs)

    def taxonomy_filtered_subtree_post(
        self,
        v1_taxonomy_filtered_subtree_request,
        **kwargs
    ):
        """Use taxonomic identifiers to get a filtered taxonomic subtree by post  # noqa: E501

        Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get a filtered taxonomic subtree that includes the full parent lineage and all immediate children from the selected taxonomic ranks in JSON 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.taxonomy_filtered_subtree_post(v1_taxonomy_filtered_subtree_request, async_req=True)
        >>> result = thread.get()

        Args:
            v1_taxonomy_filtered_subtree_request (V1TaxonomyFilteredSubtreeRequest):

        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:
            V1TaxonomyFilteredSubtreeResponse
                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_taxonomy_filtered_subtree_request'] = \
            v1_taxonomy_filtered_subtree_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.taxonomy_filtered_subtree_post_endpoint.call_with_http_info(**kwargs)

    def taxonomy_metadata(
        self,
        taxons,
        **kwargs
    ):
        """Use taxonomic identifiers to get taxonomic metadata  # noqa: E501

        Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about a taxonomic node including taxonomic identifiers, lineage information, child nodes, and gene and genome counts in JSON 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.taxonomy_metadata(taxons, async_req=True)
        >>> result = thread.get()

        Args:
            taxons ([str]):

        Keyword Args:
            returned_content (V1TaxonomyMetadataRequestContentType): Return either tax-ids alone, or entire taxononmy-metadata records. [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:
            V1TaxonomyMetadataResponse
                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['taxons'] = \
            taxons
        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.taxonomy_metadata_endpoint.call_with_http_info(**kwargs)

    def taxonomy_metadata_post(
        self,
        v1_taxonomy_metadata_request,
        **kwargs
    ):
        """Use taxonomic identifiers to get taxonomic metadata by post  # noqa: E501

        Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about a taxonomic node including taxonomic identifiers, lineage information, child nodes, and gene and genome counts in JSON 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.taxonomy_metadata_post(v1_taxonomy_metadata_request, async_req=True)
        >>> result = thread.get()

        Args:
            v1_taxonomy_metadata_request (V1TaxonomyMetadataRequest):

        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:
            V1TaxonomyMetadataResponse
                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_taxonomy_metadata_request'] = \
            v1_taxonomy_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.taxonomy_metadata_post_endpoint.call_with_http_info(**kwargs)