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R API client for metexplore3api

Rest API for MetExplore content.

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: 0.23.1
  • Package version: 1.0.0
  • Generator version: 7.9.0
  • 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/GIT_USER_ID/GIT_REPO_ID
cd GIT_REPO_ID
R CMD build .
R CMD check metexplore3api_1.0.0.tar.gz --no-manual
R CMD INSTALL --preclean metexplore3api_1.0.0.tar.gz

Install the package

install.packages("metexplore3api")

To install directly from Github, use devtools:

install.packages("devtools")
library(devtools)
install_github("GIT_USER_ID/GIT_REPO_ID")

To install the package from a local file:

install.packages("metexplore3api_1.0.0.tar.gz", repos = NULL, type = "source")

Usage

library(metexplore3api)

Reformat code

To reformat code using styler, please run the following in the R console:

install.packages("remotes")
remotes::install_github("r-lib/[email protected]")
library("styler")
style_dir()

Documentation for API Endpoints

All URIs are relative to https://metexplore.toulouse.inrae.fr/metexplore3-api

Class Method HTTP request Description
AnalysesApi AddAnalysis POST /analyses add Analysis
AnalysesApi DelAnalysis DELETE /analyses delete Analysis
AnalysesApi GetAnalyses GET /analyses get Analyses
AnalysesApi UpdateAnalysis PATCH /analyses update Analysis
AnalysisDataApi AddAnalysisData POST /analysis_data add AnalysisData
AnalysisDataApi DelAnalysisData DELETE /analysis_data delete AnalysisData
AnalysisDataApi GetAnalysisData GET /analysis_data get AnalysisData
AnalysisDataApi UpdateAnalysisData PATCH /analysis_data update AnalysisData
ApiAppsApi AddApp POST /apiapps add an app and generate a token
ApiAppsApi DelApiApp DELETE /apiapps delete an api app. Requires admin authentification
ApiAppsApi GetApiApps GET /apiapps get api apps
ApiAppsApi UpdateApiApp PATCH /apiapps update Api App
AppsApi GETAPPS GET /apps get MetExplore apps
CollectionApi ADDCOLLECTION POST /collections add Metabolic Network Collection
CollectionApi DELCOLLECTION DELETE /collections delete a Metabolic Network Collection
CollectionApi GETCOLLECTIONS GET /collections get Metabolic Network Collections
CollectionsApi UPDATECOLLECTION PATCH /collections update a Metabolic Network Collection
CompartmentsApi COUNTCOMPARTMENTS GET /compartments/count count number of compartments in a network
CompartmentsApi DELCOMPARTMENT DELETE /compartments Delete a Compartment from a Network
CompartmentsApi GETCOMPARTMENTS GET /compartments get compartments in a network
CompartmentsApi POSTCOMPARTMENT POST /compartments add a compartment in a Network
CompartmentsApi UPDATECOMPARTMENT PATCH /compartments update a compartment
DefaultApi Root GET / Root of metexplore3-api
EnzymesApi COUNTENZYMES GET /enzymes/count count ligns Enzyme
EnzymesApi DELENZYME DELETE /enzymes del Enzyme
EnzymesApi GETENZYMES GET /enzymes get Enzyme
EnzymesApi POSTENZYME POST /enzymes add Enzyme
EnzymesApi UPDATEENZYME PATCH /enzymes update Enzyme
ExportSbmlApi EXPORTSBML GET /export/sbml Export a network into an SBML file
FiltersApi GetFilter POST /filter filter identifiers of metabolic entities by ids of other metabolic entities
GenesApi COUNTGENES GET /genes/count get the number of genes for one network
GenesApi DELGENE DELETE /genes del Gene
GenesApi GETGENES GET /genes get Gene
GenesApi POSTGENE POST /genes add Gene
GenesApi UPDATEGENE PATCH /genes update Gene
ImportSbmlApi IMPORTSBML POST /import/sbml Import an SBML file
JobsApi GETJOBS GET /jobs get jobs
MappingApi MAPPINGGENESIDS POST /mapping/genes/ids Map genes ids onto a metabolic Network
MappingApi MAPPINGMETABOLITESIDS POST /mapping/metabolites/ids Map metabolic ids onto a metabolic Network
MappingApi MAPPINGREACTIONSIDS POST /mapping/reactions/ids Map reactions ids onto a metabolic Network
MappingAnalysesApi AddMappingAnalyses POST /analyses/mapping add Mapping Analysis
MappingAnalysesApi DelMappingAnalyses DELETE /analyses/mapping delete Mapping Analysis
MappingAnalysesApi GetMappingAnalyses GET /analyses/mapping get mapping Analysis
MappingAnalysesApi UpdateMappingAnalysis PATCH /analyses/mapping update mapping Analysis
MatchingApiApi PostMatchingApi POST /matching_api get compounds IDs
MetabolitesApi COUNTMETABOLITES GET /metabolites/count get the number of metabolites in a network
MetabolitesApi DELMETABOLITE DELETE /metabolites del Metabolite
MetabolitesApi GETMETABOLITES GET /metabolites get Metabolite
MetabolitesApi POSTMETABOLITE POST /metabolites add Metabolite
MetabolitesApi UPDATEMETABOLITE PATCH /metabolites update Metabolite
NetworkApi DELNETWORK DELETE /networks delete a Metabolic Network
NetworksApi ADDNETWORK POST /networks add a Network
NetworksApi GETNETWORKS GET /networks Get all networks
NetworksApi UPDATENETWORK PATCH /networks update a Metabolic Networ
PathwaysApi COUNTPATHWAYS GET /pathways/count get the number of pathways in a network
PathwaysApi DELPATHWAY DELETE /pathways del Pathway
PathwaysApi GETPATHWAYS GET /pathways get Pathway
PathwaysApi POSTPATHWAY POST /pathways add Pathway
PathwaysApi UPDATEPATHWAY PATCH /pathways update Pathway
ProteinsApi COUNTPROTEINS GET /proteins/count get the number of proteins for a network
ProteinsApi DELPROTEIN DELETE /proteins del Protein
ProteinsApi GETPROTEINS GET /proteins get Protein
ProteinsApi POSTPROTEIN POST /proteins add Protein
ProteinsApi UPDATEPROTEIN PATCH /proteins update Protein
ReactionsApi COUNTREACTIONS GET /reactions/count get the number of reactions in a network
ReactionsApi DELREACTION DELETE /reactions delete Reaction
ReactionsApi GETREACTIONS GET /reactions get Reaction
ReactionsApi POSTREACTION POST /reactions add Reaction
ReactionsApi UPDATEREACTION PATCH /reactions update Reaction
StepsApi AddSteps POST /steps add step
StepsApi DelStep DELETE /steps Remove a step
StepsApi GetSteps GET /steps Get specific step of an analysis
StepsApi UpdateSteps PATCH /steps update Step
UsersApi UserCreate POST /users/create Create user into the system
UsersApi UserLogin POST /users/login Logs user into the system
UsersApi UserTokenLogin POST /users/token_login Logs user into the system with a token

Documentation for Models

Documentation for Authorization

Authentication schemes defined for the API:

userAuth

  • Type: Bearer authentication
  • Bearer Format: JWT

appAuth

  • Type: API key
  • API key parameter name: x-app-key
  • Location: HTTP header

Author

[email protected]

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