README.md

In sdgamboa/omicidxClientR: R Package Client for OmicIDX

R API client for omicidxClientR

The OmicIDX API documentation is available in three forms:

• RapiDoc
• OpenAPI/Swagger Interactive
• ReDoc (more readable in some ways)

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: 0.99.1
• Package version: 1.0.0
• Build package: org.openapitools.codegen.languages.RClientCodegen

Installation

Prerequisites

Install the dependencies

install.packages("jsonlite")
install.packages("httr")
install.packages("base64enc")

Build the package

git clone https://github.com/sdgamboa/omicidxClientR
cd omicidxClientR
R CMD build .
R CMD check omicidxClientR_1.0.0.tar.gz --no-manual
R CMD INSTALL omicidxClientR_1.0.0.tar.gz

Install the package

install.packages("omicidxClientR")

To install directly from Github, use devtools:

install.packages("devtools")
library(devtools)
install_github("sdgamboa/omicidxClientR")

Usage

library(omicidxClientR)

Documentation for API Endpoints

All URIs are relative to http://localhost

Class | Method | HTTP request | Description ------------ | ------------- | ------------- | ------------- BiosampleApi | BiosampleByAccessionBiosampleSamplesAccessionGet | GET /biosample/samples/{accession} | Biosample By Accession BiosampleApi | BiosamplesBiosampleSamplesGet | GET /biosample/samples | Biosamples BiosampleApi | MappingBiosampleFieldsEntityGet | GET /biosample/fields/{entity} | Mapping DefaultApi | FacetsByIndexFacetsEntityGet | GET /facets/{entity} | Facets By Index SRAApi | ExperimentByAccessionSraExperimentsAccessionGet | GET /sra/experiments/{accession} | Experiment By Accession SRAApi | ExperimentsForSampleSraSamplesAccessionExperimentsGet | GET /sra/samples/{accession}/experiments | Experiments For Sample SRAApi | ExperimentsForStudySraStudiesAccessionExperimentsGet | GET /sra/studies/{accession}/experiments | Experiments For Study SRAApi | ExperimentsSraExperimentsGet | GET /sra/experiments | Experiments SRAApi | MappingSraFieldsEntityGet | GET /sra/fields/{entity} | Mapping SRAApi | RunByAccessionSraRunsAccessionGet | GET /sra/runs/{accession} | Run By Accession SRAApi | RunsForExperimentSraExperimentsAccessionRunsGet | GET /sra/experiments/{accession}/runs | Runs For Experiment SRAApi | RunsForSampleSraSamplesAccessionRunsGet | GET /sra/samples/{accession}/runs | Runs For Sample SRAApi | RunsForStudySraStudiesAccessionRunsGet | GET /sra/studies/{accession}/runs | Runs For Study SRAApi | RunsSraRunsGet | GET /sra/runs | Runs SRAApi | SampleByAccessionSraSamplesAccessionGet | GET /sra/samples/{accession} | Sample By Accession SRAApi | SamplesForStudySraStudiesAccessionSamplesGet | GET /sra/studies/{accession}/samples | Samples For Study SRAApi | SamplesSraSamplesGet | GET /sra/samples | Samples SRAApi | StudiesSraStudiesGet | GET /sra/studies | Studies SRAApi | StudyByAccessionSraStudiesAccessionGet | GET /sra/studies/{accession} | Study By Accession

Documentation for Models

• HTTPValidationError
• ResponseModel
• ResponseStats
• ValidationError

Documentation for Authorization

All endpoints do not require authorization.

Author

sdgamboa/omicidxClientR documentation built on Dec. 22, 2021, 11:12 p.m.