ncbi-datasets-pyclient

NCBI Datasets is a resource that lets you easily gather data from NCBI.

The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.

This Python package is automatically generated by the OpenAPI Generator project:

API version: v2
Package version: v18.37.0
Generator version: 7.25.0
Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 3.10+

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

pip install git+https://github.com/misialq/ncbi-datasets-pyclient.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/misialq/ncbi-datasets-pyclient.git)

Then import the package:

import ncbi.datasets.openapi

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

Then import the package:

import ncbi.datasets.openapi

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

import ncbi.datasets.openapi
from ncbi.datasets.openapi.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://api.ncbi.nlm.nih.gov/datasets/v2
# See configuration.py for a list of all supported configuration parameters.
configuration = ncbi.datasets.openapi.Configuration(
    host = "https://api.ncbi.nlm.nih.gov/datasets/v2"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: ApiKeyAuthHeader
configuration.api_key['ApiKeyAuthHeader'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['ApiKeyAuthHeader'] = 'Bearer'


# Enter a context with an instance of the API client
with ncbi.datasets.openapi.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ncbi.datasets.openapi.BioSampleApi(api_client)
    accessions = ['SAMN15960293'] # List[str] | 

    try:
        # Get BioSample dataset reports by accession(s)
        api_response = api_instance.bio_sample_dataset_report(accessions)
        print("The response of BioSampleApi->bio_sample_dataset_report:\n")
        pprint(api_response)
    except ApiException as e:
        print("Exception when calling BioSampleApi->bio_sample_dataset_report: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to https://api.ncbi.nlm.nih.gov/datasets/v2

Class	Method	HTTP request	Description
BioSampleApi	bio_sample_dataset_report	GET /biosample/accession/{accessions}/biosample_report	Get BioSample dataset reports by accession(s)
GeneApi	download_gene_package	GET /gene/id/{gene_ids}/download	Get a gene data package by GeneID
GeneApi	download_gene_package_post	POST /gene/download	Get a gene data package
GeneApi	gene_chromosome_summary	GET /gene/taxon/{taxon}/annotation/{annotation_name}/chromosome_summary	Get gene counts per chromosome by taxon and annotation name
GeneApi	gene_counts_for_taxon	GET /gene/taxon/{taxon}/counts	Get gene counts by taxon
GeneApi	gene_counts_for_taxon_by_post	POST /gene/taxon/counts	Get gene counts by taxon
GeneApi	gene_dataset_report	POST /gene/dataset_report	Get a gene data report
GeneApi	gene_dataset_report_by_accession	GET /gene/accession/{accessions}/dataset_report	Get a gene data report by RefSeq nucleotide or protein accession
GeneApi	gene_dataset_report_by_tax_and_symbol	GET /gene/symbol/{symbols}/taxon/{taxon}/dataset_report	Get a gene data report by symbol and taxon
GeneApi	gene_dataset_reports_by_id	GET /gene/id/{gene_ids}/dataset_report	Get a gene data report by GeneID
GeneApi	gene_dataset_reports_by_locus_tag	GET /gene/locus_tag/{locus_tags}/dataset_report	Get a gene data report by locus tag
GeneApi	gene_dataset_reports_by_taxon	GET /gene/taxon/{taxon}/dataset_report	Get a gene data report by taxon
GeneApi	gene_download_summary_by_id	GET /gene/id/{gene_ids}/download_summary	Get a download summary of a gene data package by GeneID
GeneApi	gene_download_summary_by_post	POST /gene/download_summary	Get a download summary of a gene data package
GeneApi	gene_expression_report	POST /gene/expression_report	Get a gene expression report
GeneApi	gene_expression_reports_by_id	GET /gene/id/{gene_ids}/expression_report	Get a gene expression report by GeneID
GeneApi	gene_links_by_id	GET /gene/id/{gene_ids}/links	Get gene links by GeneID
GeneApi	gene_links_by_id_by_post	POST /gene/links	Get gene links by GeneID
GeneApi	gene_metadata_by_accession	GET /gene/accession/{accessions}	Get gene metadata by RefSeq Accession
GeneApi	gene_metadata_by_post	POST /gene	Get gene metadata as JSON
GeneApi	gene_metadata_by_tax_and_symbol	GET /gene/symbol/{symbols}/taxon/{taxon}	Get gene metadata by gene symbol
GeneApi	gene_orthologs_by_id	GET /gene/id/{gene_id}/orthologs	Get a gene data report for a gene ortholog set by GeneID
GeneApi	gene_orthologs_by_post	POST /gene/orthologs	Get a gene data report for a gene ortholog set by GeneID
GeneApi	gene_product_report	POST /gene/product_report	Get a gene product report
GeneApi	gene_product_report_by_accession	GET /gene/accession/{accessions}/product_report	Get a gene product report by RefSeq nucleotide or protein accession
GeneApi	gene_product_report_by_tax_and_symbol	GET /gene/symbol/{symbols}/taxon/{taxon}/product_report	Get a gene product report by symbol and taxon
GeneApi	gene_product_reports_by_id	GET /gene/id/{gene_ids}/product_report	Get a gene product report by GeneID
GeneApi	gene_product_reports_by_locus_tags	GET /gene/locus_tag/{locus_tags}/product_report	Get a gene product report by locus tag
GeneApi	gene_product_reports_by_taxon	GET /gene/taxon/{taxon}/product_report	Get a gene product report by taxon
GeneApi	gene_reports_by_id	GET /gene/id/{gene_ids}	Get gene reports by GeneID
GeneApi	gene_reports_by_taxon	GET /gene/taxon/{taxon}	Get gene reports by taxonomic identifier
GenomeApi	annotation_report_facets_by_accession	GET /genome/accession/{accession}/annotation_summary	Get genome annotation report summary information by genome assembly accession
GenomeApi	annotation_report_facets_by_post	POST /genome/annotation_summary	Get genome annotation report summary information by genome assembly accession
GenomeApi	assembly_accessions_for_sequence_accession	GET /genome/sequence_accession/{accession}/sequence_assemblies	Get a genome assembly accession for a nucleotide sequence accession
GenomeApi	assembly_accessions_for_sequence_accession_by_post	POST /genome/sequence_assemblies	Get a genome assembly accession for a nucleotide sequence accession
GenomeApi	assembly_revision_history_by_get	GET /genome/accession/{accession}/revision_history	Get a revision history for a genome assembly by genome assembly accession
GenomeApi	assembly_revision_history_by_post	POST /genome/revision_history	Get a revision history for a genome assembly by genome assembly accession
GenomeApi	check_assembly_availability	GET /genome/accession/{accessions}/check	Check the validity of a genome assembly accession
GenomeApi	check_assembly_availability_post	POST /genome/check	Check the validity of a genome assembly accession
GenomeApi	checkm_histogram_by_taxon	GET /genome/taxon/{species_taxon}/checkm_histogram	Get CheckM histogram data by species taxon
GenomeApi	checkm_histogram_by_taxon_by_post	POST /genome/checkm_histogram	Get CheckM histogram data by species taxon
GenomeApi	download_assembly_package	GET /genome/accession/{accessions}/download	Get a genome data package by genome assembly accession
GenomeApi	download_assembly_package_post	POST /genome/download	Get a genome data package by genome assembly accession
GenomeApi	download_genome_annotation_package	GET /genome/accession/{accession}/annotation_report/download	Get a genome annotation data package by genome assembly accession
GenomeApi	download_genome_annotation_package_by_post	POST /genome/annotation_report/download	Get a genome annotation data package by genome assembly accession
GenomeApi	genome_annotation_download_summary	GET /genome/accession/{accession}/annotation_report/download_summary	Get a download summary (preview) of a genome annotation data package by genome assembly accession
GenomeApi	genome_annotation_download_summary_by_post	POST /genome/annotation_report/download_summary	Get a download summary (preview) of a genome annotation data package by genome assembly accession
GenomeApi	genome_annotation_report	GET /genome/accession/{accession}/annotation_report	Get genome annotation reports by genome assembly accession
GenomeApi	genome_annotation_report_by_post	POST /genome/annotation_report	Get genome annotation reports by genome assembly accession
GenomeApi	genome_dataset_report	GET /genome/accession/{accessions}/dataset_report	Get a genome assembly report by genome assembly accession
GenomeApi	genome_dataset_report_by_post	POST /genome/dataset_report	Get a genome assembly report
GenomeApi	genome_dataset_reports_by_assembly_name	GET /genome/assembly_name/{assembly_names}/dataset_report	Get genome assembly reports by assembly name
GenomeApi	genome_dataset_reports_by_bioproject	GET /genome/bioproject/{bioprojects}/dataset_report	Get genome assembly reports by BioProject accession
GenomeApi	genome_dataset_reports_by_biosample_id	GET /genome/biosample/{biosample_ids}/dataset_report	Get genome assembly reports by BioSample accession
GenomeApi	genome_dataset_reports_by_taxon	GET /genome/taxon/{taxons}/dataset_report	Get a genome assembly report by taxon
GenomeApi	genome_dataset_reports_by_wgs	GET /genome/wgs/{wgs_accessions}/dataset_report	Get a genome assembly data report by WGS accession
GenomeApi	genome_download_summary	GET /genome/accession/{accessions}/download_summary	Get a download summary (preview) of a genome data package by genome assembly accession
GenomeApi	genome_download_summary_by_post	POST /genome/download_summary	Get a download summary (preview) of a genome data package by genome assembly accession
GenomeApi	genome_links_by_accession	GET /genome/accession/{accessions}/links	Get assembly links by genome assembly accession
GenomeApi	genome_links_by_accession_by_post	POST /genome/links	Get assembly links by genome assembly accession
GenomeApi	genome_sequence_report	GET /genome/accession/{accession}/sequence_reports	Get a genome sequence report by genome assembly accession
GenomeApi	genome_sequence_report_by_post	POST /genome/sequence_reports	Get a genome sequence report by genome assembly accession
OrganelleApi	download_organelle_package	GET /organelle/accession/{accessions}/download	Get an organelle data package by nucleotide accession
OrganelleApi	download_organelle_package_by_post	POST /organelle/download	Get an organelle data package
OrganelleApi	organelle_datareport_by_accession	GET /organelle/accessions/{accessions}/dataset_report	Get an organelle data report by nucleotide accession
OrganelleApi	organelle_datareport_by_post	POST /organelle/dataset_report	Get an organelle data report
OrganelleApi	organelle_datareport_by_taxon	GET /organelle/taxon/{taxons}/dataset_report	Get an organelle data report by taxon
ProkaryoteApi	download_prokaryote_gene_package	GET /protein/accession/{accessions}/download	Get a prokaryote gene data package by RefSeq protein accession
ProkaryoteApi	download_prokaryote_gene_package_post	POST /protein/accession/download	Get a prokaryote gene data package by RefSeq protein accession
TaxonomyApi	download_taxonomy_package	GET /taxonomy/taxon/{tax_ids}/download	Get a taxonomy data package by Taxonomy ID
TaxonomyApi	download_taxonomy_package_by_post	POST /taxonomy/download	Get a taxonomy data package by Taxonomy ID
TaxonomyApi	get_biocollections	POST /taxonomy/biocollections/dataset_report	Get a biocollection report by collection ID or code
TaxonomyApi	get_biocollections_by_get	GET /taxonomy/biocollections/id/{collection_ids}/dataset_report	Get a biocollection report by collection ID or code
TaxonomyApi	tax_name_query	GET /taxonomy/taxon_suggest/{taxon_query}	Get a list of taxonomy names and IDs by partial taxonomic name
TaxonomyApi	tax_name_query_by_post	POST /taxonomy/taxon_suggest	Get a list of taxonomy names and IDs by partial taxonomic name
TaxonomyApi	taxonomy_data_report	GET /taxonomy/taxon/{taxons}/dataset_report	Get a taxonomy data report by taxon
TaxonomyApi	taxonomy_data_report_post	POST /taxonomy/dataset_report	Get a taxonomy data report by taxon
TaxonomyApi	taxonomy_filtered_subtree	GET /taxonomy/taxon/{taxons}/filtered_subtree	Get a filtered taxonomic subtree by taxon
TaxonomyApi	taxonomy_filtered_subtree_post	POST /taxonomy/filtered_subtree	Get a filtered taxonomic subtree by taxon
TaxonomyApi	taxonomy_image	GET /taxonomy/taxon/{taxon}/image	Get a taxonomy image by taxon
TaxonomyApi	taxonomy_image_metadata	GET /taxonomy/taxon/{taxon}/image/metadata	Get taxonomy image metadata by Taxonomy ID
TaxonomyApi	taxonomy_image_metadata_post	POST /taxonomy/image/metadata	Get taxonomy image metadata by Taxonomy ID
TaxonomyApi	taxonomy_image_post	POST /taxonomy/image	Get a taxonomy image by taxon
TaxonomyApi	taxonomy_links	GET /taxonomy/taxon/{taxon}/links	Get external links by Taxonomy ID
TaxonomyApi	taxonomy_links_by_post	POST /taxonomy/links	Get external links by Taxonomy ID
TaxonomyApi	taxonomy_metadata	GET /taxonomy/taxon/{taxons}	Use taxonomic identifiers to get taxonomic metadata
TaxonomyApi	taxonomy_metadata_post	POST /taxonomy	Get taxonomy metadata by taxon
TaxonomyApi	taxonomy_names	GET /taxonomy/taxon/{taxons}/name_report	Get a taxonomy names report by taxon
TaxonomyApi	taxonomy_names_post	POST /taxonomy/name_report	Get a taxonomy names report by taxon
TaxonomyApi	taxonomy_related_ids	GET /taxonomy/taxon/{tax_id}/related_ids	Get child nodes, and optionally parent nodes, for a given taxon by Taxonomy ID
TaxonomyApi	taxonomy_related_ids_post	POST /taxonomy/related_ids	Get child nodes, and optionally parent nodes, for a given taxon by Taxonomy ID
VersionApi	version	GET /version	Retrieve service version
VirusApi	sars2_protein_download	GET /virus/taxon/sars2/protein/{proteins}/download	Get a SARS-CoV-2 protein data package by protein name
VirusApi	sars2_protein_download_post	POST /virus/taxon/sars2/protein/download	Get a SARS-CoV-2 protein data package
VirusApi	sars2_protein_summary	GET /virus/taxon/sars2/protein/{proteins}	Get a download summary of a SARS-CoV-2 protein data package by protein name
VirusApi	sars2_protein_summary_by_post	POST /virus/taxon/sars2/protein	Get a download summary of a SARS-CoV-2 protein data package by protein name
VirusApi	sars2_protein_table	GET /virus/taxon/sars2/protein/{proteins}/table	Get SARS-CoV-2 protein metadata in a tabular format by protein name
VirusApi	virus_accession_availability	GET /virus/accession/{accessions}/check	Check the validity of a virus genome nucleotide accession
VirusApi	virus_accession_availability_post	POST /virus/check	Check the validity of a virus genome nucleotide accession
VirusApi	virus_annotation_reports_by_acessions	GET /virus/accession/{accessions}/annotation_report	Get a virus annotation report by nucleotide accession
VirusApi	virus_annotation_reports_by_post	POST /virus/annotation_report	Get a virus annotation report
VirusApi	virus_annotation_reports_by_taxon	GET /virus/taxon/{taxon}/annotation_report	Get a virus annotation report by taxon
VirusApi	virus_genome_download	GET /virus/taxon/{taxon}/genome/download	Get a virus genome data package by taxon
VirusApi	virus_genome_download_accession	GET /virus/accession/{accessions}/genome/download	Get a virus genome data package by nucleotide accession
VirusApi	virus_genome_download_post	POST /virus/genome/download	Get a virus genome data package
VirusApi	virus_genome_summary	GET /virus/taxon/{taxon}/genome	Get a download summary of a virus genome data package by taxon
VirusApi	virus_genome_summary_by_post	POST /virus/genome	Get a download summary of a virus genome data package
VirusApi	virus_genome_table	GET /virus/taxon/{taxon}/genome/table	Get virus genome metadata in a tabular format
VirusApi	virus_reports_by_acessions	GET /virus/accession/{accessions}/dataset_report	Get a virus data report by nucleotide accession
VirusApi	virus_reports_by_post	POST /virus	Get a virus data report
VirusApi	virus_reports_by_taxon	GET /virus/taxon/{taxon}/dataset_report	Get a virus data report by taxon

Documentation For Models

Documentation For Authorization

Authentication schemes defined for the API:

ApiKeyAuth

Type: API key
API key parameter name: api_key
Location: URL query string

ApiKeyAuthHeader

Type: API key
API key parameter name: api-key
Location: HTTP header

Author

Metadata

Release files for ncbi-datasets-pyclient 18.37.0

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