Go API client for openapi

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

The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a dehydrated zip archive, and retrieve the individual data files at a later time.

Overview

This API client was generated by the OpenAPI Generator project. By using the OpenAPI-spec from a remote server, you can easily generate an API client.

API version: v2alpha
Package version: 1.0.0
Build package: org.openapitools.codegen.languages.GoClientCodegen

Installation

Install the following dependencies:

go get github.com/stretchr/testify/assert
go get golang.org/x/oauth2
go get golang.org/x/net/context

Put the package under your project folder and add the following in import:

import openapi "github.com/GIT_USER_ID/GIT_REPO_ID"

To use a proxy, set the environment variable HTTP_PROXY:

os.Setenv("HTTP_PROXY", "http://proxy_name:proxy_port")

Configuration of Server URL

Default configuration comes with Servers field that contains server objects as defined in the OpenAPI specification.

Select Server Configuration

For using other server than the one defined on index 0 set context value sw.ContextServerIndex of type int.

ctx := context.WithValue(context.Background(), openapi.ContextServerIndex, 1)

Templated Server URL

Templated server URL is formatted using default variables from configuration or from context value sw.ContextServerVariables of type map[string]string.

ctx := context.WithValue(context.Background(), openapi.ContextServerVariables, map[string]string{
	"basePath": "v2",
})

Note, enum values are always validated and all unused variables are silently ignored.

URLs Configuration per Operation

Each operation can use different server URL defined using OperationServers map in the Configuration. An operation is uniquely identified by "{classname}Service.{nickname}" string. Similar rules for overriding default operation server index and variables applies by using sw.ContextOperationServerIndices and sw.ContextOperationServerVariables context maps.

ctx := context.WithValue(context.Background(), openapi.ContextOperationServerIndices, map[string]int{
	"{classname}Service.{nickname}": 2,
})
ctx = context.WithValue(context.Background(), openapi.ContextOperationServerVariables, map[string]map[string]string{
	"{classname}Service.{nickname}": {
		"port": "8443",
	},
})

Documentation for API Endpoints

All URIs are relative to https://api.ncbi.nlm.nih.gov/datasets/v2alpha

Class	Method	HTTP request	Description
BioSampleApi	BioSampleDatasetReport	Get /biosample/accession/{accessions}/biosample_report	Get BioSample dataset reports by accession(s)
GeneApi	DownloadGenePackage	Get /gene/id/{gene_ids}/download	Get a gene dataset by gene ID
GeneApi	DownloadGenePackagePost	Post /gene/download	Get a gene dataset by POST
GeneApi	GeneChromosomeSummary	Get /gene/taxon/{taxon}/annotation/{annotation_name}/chromosome_summary	Get summary of chromosomes for a particular taxon's annotation
GeneApi	GeneCountsForTaxon	Get /gene/taxon/{taxon}/counts	Get gene counts by taxonomic identifier
GeneApi	GeneCountsForTaxonByPost	Post /gene/taxon/counts	Get gene counts by taxonomic identifier
GeneApi	GeneDownloadSummaryById	Get /gene/id/{gene_ids}/download_summary	Get gene download summary by GeneID
GeneApi	GeneDownloadSummaryByPost	Post /gene/download_summary	Get gene download summary
GeneApi	GeneLinksById	Get /gene/id/{gene_ids}/links	Get gene links by gene ID
GeneApi	GeneLinksByIdByPost	Post /gene/links	Get gene links by gene ID
GeneApi	GeneMetadataByAccession	Get /gene/accession/{accessions}	Get gene metadata by RefSeq Accession
GeneApi	GeneMetadataByPost	Post /gene	Get gene metadata as JSON
GeneApi	GeneMetadataByTaxAndSymbol	Get /gene/symbol/{symbols}/taxon/{taxon}	Get gene metadata by gene symbol
GeneApi	GeneOrthologsById	Get /gene/id/{gene_id}/orthologs	Get gene orthologs by gene ID
GeneApi	GeneOrthologsByPost	Post /gene/orthologs	Get gene orthologs by gene ID
GeneApi	GeneReportsById	Get /gene/id/{gene_ids}	Get gene reports by GeneID
GeneApi	GeneReportsByTaxon	Get /gene/taxon/{taxon}	Get gene reports by taxonomic identifier
GenomeApi	AnnotationReportFacets	Get /genome/accession/{accession}/id/{annotation_ids}/annotation_summary	Get genome annotation report summary information
GenomeApi	AnnotationReportFacetsByPost	Post /genome/annotation_summary	Get genome annotation report summary information
GenomeApi	AssemblyAccessionsForSequenceAccession	Get /genome/sequence_accession/{accession}/sequence_assemblies	Get assembly accessions for a sequence accession
GenomeApi	AssemblyAccessionsForSequenceAccessionByPost	Post /genome/sequence_assemblies	Get assembly accessions for a sequence accession
GenomeApi	AssemblyRevisionHistoryByGet	Get /genome/accession/{accession}/revision_history	Get revision history for assembly by accession
GenomeApi	AssemblyRevisionHistoryByPost	Post /genome/revision_history	Get revision history for assembly by accession
GenomeApi	CheckAssemblyAvailability	Get /genome/accession/{accessions}/check	Check the validity of genome accessions
GenomeApi	CheckAssemblyAvailabilityPost	Post /genome/check	Check the validity of many genome accessions in a single request
GenomeApi	CheckmHistogramByTaxon	Get /genome/taxon/{species_taxon}/checkm_histogram	Get CheckM histogram by species taxon
GenomeApi	CheckmHistogramByTaxonByPost	Post /genome/checkm_histogram	Get CheckM histogram by species taxon
GenomeApi	DownloadAssemblyPackage	Get /genome/accession/{accessions}/download	Get a genome dataset by accession
GenomeApi	DownloadAssemblyPackagePost	Post /genome/download	Get a genome dataset by post
GenomeApi	DownloadGenomeAnnotationPackage	Get /genome/accession/{accession}/annotation_report/download	Get an annotation report dataset by accession
GenomeApi	DownloadGenomeAnnotationPackageByPost	Post /genome/annotation_report/download	Get an annotation report dataset by accession
GenomeApi	GenomeAnnotationDownloadSummary	Get /genome/accession/{accession}/annotation_report/download_summary	Preview feature dataset download
GenomeApi	GenomeAnnotationDownloadSummaryByPost	Post /genome/annotation_report/download_summary	Preview feature download by POST
GenomeApi	GenomeAnnotationReport	Get /genome/accession/{accession}/annotation_report	Get genome annotation reports by genome accession
GenomeApi	GenomeAnnotationReportByPost	Post /genome/annotation_report	Get genome annotation reports by genome accession
GenomeApi	GenomeDatasetReport	Get /genome/accession/{accessions}/dataset_report	Get dataset reports by accessions
GenomeApi	GenomeDatasetReportByPost	Post /genome/dataset_report	Get dataset reports by accessions
GenomeApi	GenomeDatasetReportsByAssemblyName	Get /genome/assembly_name/{assembly_names}/dataset_report	Get dataset reports by assembly name (exact)
GenomeApi	GenomeDatasetReportsByBioproject	Get /genome/bioproject/{bioprojects}/dataset_report	Get dataset reports by bioproject
GenomeApi	GenomeDatasetReportsByBiosampleId	Get /genome/biosample/{biosample_ids}/dataset_report	Get dataset reports by biosample id
GenomeApi	GenomeDatasetReportsByTaxon	Get /genome/taxon/{taxons}/dataset_report	Get dataset reports by taxons
GenomeApi	GenomeDatasetReportsByWgs	Get /genome/wgs/{wgs_accessions}/dataset_report	Get dataset reports by wgs accession
GenomeApi	GenomeDownloadSummary	Get /genome/accession/{accessions}/download_summary	Preview genome dataset download
GenomeApi	GenomeDownloadSummaryByPost	Post /genome/download_summary	Preview genome dataset download by POST
GenomeApi	GenomeLinksByAccession	Get /genome/accession/{accessions}/links	Get assembly links by accessions
GenomeApi	GenomeLinksByAccessionByPost	Post /genome/links	Get assembly links by accessions
GenomeApi	GenomeSequenceReport	Get /genome/accession/{accession}/sequence_reports	Get sequence reports by accessions
GenomeApi	GenomeSequenceReportByPost	Post /genome/sequence_reports	Get sequence reports by accessions
OrganelleApi	DownloadOrganellePackage	Get /organelle/accession/{accessions}/download	Get a organelle data package by accesions
OrganelleApi	DownloadOrganellePackageByPost	Post /organelle/download	Get a organelle data package by post
OrganelleApi	OrganelleDatareportByAccession	Get /organelle/accessions/{accessions}/dataset_report	Get Organelle dataset report by accession
OrganelleApi	OrganelleDatareportByPost	Post /organelle/dataset_report	Get Organelle dataset report by http post
OrganelleApi	OrganelleDatareportByTaxon	Get /organelle/taxon/{taxons}/dataset_report	Get Organelle dataset report by taxons
ProkaryoteApi	DownloadProkaryoteGenePackage	Get /protein/accession/{accessions}/download	Get a prokaryote gene dataset by RefSeq protein accession
ProkaryoteApi	DownloadProkaryoteGenePackagePost	Post /protein/accession/download	Get a prokaryote gene dataset by RefSeq protein accession by POST
TaxonomyApi	DownloadTaxonomyPackage	Get /taxonomy/taxon/{tax_ids}/download	Get a taxonomy data package by tax ID
TaxonomyApi	DownloadTaxonomyPackageByPost	Post /taxonomy/download	Get a taxonomy data package by tax_id
TaxonomyApi	TaxNameQuery	Get /taxonomy/taxon_suggest/{taxon_query}	Get a list of taxonomy names and IDs given a partial taxonomic name
TaxonomyApi	TaxNameQueryByPost	Post /taxonomy/taxon_suggest	Get a list of taxonomy names and IDs given a partial taxonomic name
TaxonomyApi	TaxonomyDataReport	Get /taxonomy/taxon/{taxons}/dataset_report	Use taxonomic identifiers to get taxonomic data report
TaxonomyApi	TaxonomyDataReportPost	Post /taxonomy/dataset_report	Use taxonomic identifiers to get taxonomic names data report by post
TaxonomyApi	TaxonomyFilteredSubtree	Get /taxonomy/taxon/{taxons}/filtered_subtree	Use taxonomic identifiers to get a filtered taxonomic subtree
TaxonomyApi	TaxonomyFilteredSubtreePost	Post /taxonomy/filtered_subtree	Use taxonomic identifiers to get a filtered taxonomic subtree by post
TaxonomyApi	TaxonomyImage	Get /taxonomy/taxon/{taxon}/image	Retrieve image associated with a taxonomic identifier
TaxonomyApi	TaxonomyImageMetadata	Get /taxonomy/taxon/{taxon}/image/metadata	Retrieve image metadata associated with a taxonomic identifier
TaxonomyApi	TaxonomyImageMetadataPost	Post /taxonomy/image/metadata	Retrieve image metadata associated with a taxonomic identifier by post
TaxonomyApi	TaxonomyImagePost	Post /taxonomy/image	Retrieve image associated with a taxonomic identifier by post
TaxonomyApi	TaxonomyLinks	Get /taxonomy/taxon/{taxon}/links	Retrieve external links associated with a taxonomic identifier.
TaxonomyApi	TaxonomyLinksByPost	Post /taxonomy/links	Retrieve external links associated with a taxonomic identifier.
TaxonomyApi	TaxonomyMetadata	Get /taxonomy/taxon/{taxons}	Use taxonomic identifiers to get taxonomic metadata
TaxonomyApi	TaxonomyMetadataPost	Post /taxonomy	Use taxonomic identifiers to get taxonomic metadata by post
TaxonomyApi	TaxonomyNames	Get /taxonomy/taxon/{taxons}/name_report	Use taxonomic identifiers to get taxonomic names data report
TaxonomyApi	TaxonomyNamesPost	Post /taxonomy/name_report	Use taxonomic identifiers to get taxonomic names data report by post
TaxonomyApi	TaxonomyRelatedIds	Get /taxonomy/taxon/{tax_id}/related_ids	Use taxonomic identifier to get related taxonomic identifiers, such as children
TaxonomyApi	TaxonomyRelatedIdsPost	Post /taxonomy/related_ids	Use taxonomic identifier to get related taxonomic identifiers, such as children
VersionApi	Version	Get /version	Retrieve service version
VirusApi	Sars2ProteinDownload	Get /virus/taxon/sars2/protein/{proteins}/download	Download SARS-CoV-2 protein and CDS datasets by protein name
VirusApi	Sars2ProteinDownloadPost	Post /virus/taxon/sars2/protein/download	Download SARS-CoV-2 protein and CDS datasets by protein name by POST request
VirusApi	Sars2ProteinSummary	Get /virus/taxon/sars2/protein/{proteins}	Summary of SARS-CoV-2 protein and CDS datasets by protein name
VirusApi	Sars2ProteinSummaryByPost	Post /virus/taxon/sars2/protein	Summary of SARS-CoV-2 protein and CDS datasets by protein name
VirusApi	Sars2ProteinTable	Get /virus/taxon/sars2/protein/{proteins}/table	Get SARS-CoV-2 protein metadata in a tabular format.
VirusApi	VirusAccessionAvailability	Get /virus/accession/{accessions}/check	Check available viruses by accession
VirusApi	VirusAccessionAvailabilityPost	Post /virus/check	Check available viruses by accession
VirusApi	VirusAnnotationReportsByAcessions	Get /virus/accession/{accessions}/annotation_report	Get virus annotation report by accession
VirusApi	VirusAnnotationReportsByPost	Post /virus/annotation_report	Get virus annotation report by POST
VirusApi	VirusAnnotationReportsByTaxon	Get /virus/taxon/{taxon}/annotation_report	Get virus annotation report by taxon
VirusApi	VirusGenomeDownload	Get /virus/taxon/{taxon}/genome/download	Download a virus genome dataset by taxon
VirusApi	VirusGenomeDownloadAccession	Get /virus/accession/{accessions}/genome/download	Download a virus genome dataset by accession
VirusApi	VirusGenomeDownloadPost	Post /virus/genome/download	Get a virus genome dataset by post
VirusApi	VirusGenomeSummary	Get /virus/taxon/{taxon}/genome	Get summary data for virus genomes by taxon
VirusApi	VirusGenomeSummaryByPost	Post /virus/genome	Get summary data for virus genomes by post
VirusApi	VirusGenomeTable	Get /virus/taxon/{taxon}/genome/table	Get virus genome metadata in a tabular format.
VirusApi	VirusReportsByAcessions	Get /virus/accession/{accessions}/dataset_report	Get virus metadata by accession
VirusApi	VirusReportsByPost	Post /virus	Get virus metadata by POST
VirusApi	VirusReportsByTaxon	Get /virus/taxon/{taxon}/dataset_report	Get virus metadata by taxon

Documentation For Models

Documentation For Authorization

ApiKeyAuth

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

Note, each API key must be added to a map of map[string]APIKey where the key is: api_key and passed in as the auth context for each request.

ApiKeyAuthHeader

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

Note, each API key must be added to a map of map[string]APIKey where the key is: api-key and passed in as the auth context for each request.

Documentation for Utility Methods

Due to the fact that model structure members are all pointers, this package contains a number of utility functions to easily obtain pointers to values of basic types. Each of these functions takes a value of the given basic type and returns a pointer to it:

PtrBool
PtrInt
PtrInt32
PtrInt64
PtrFloat
PtrFloat32
PtrFloat64
PtrString
PtrTime

# Packages

# README