R API client for metexplore3api

Rest API for MetExplore content.

Installation

Prerequisites

Install the dependencies

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

Install the package

To install directly from Github:

install.packages("remotes") 
remotes::install_github("MetExplore/metexplore3api_client_r")

To install the package from a local file:

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

Usage

library(metexplore3api)

  # Spécifier l'identifiant du réseau
  network_id <- 1
  
  ###########################
  ### Genes
  ###########################
    
  # #Créer une instance de la classe GenesApi
  api <- GenesApi$new()

  # Appel de l’API pour récuperer les genes du réseau
  result <- api$GETGENES(network_id)
  results <- result$results


  df_genes <- data.frame(
    name = sapply(result$results, function(x) if (!is.null(x$name)) x$name else NA),
    identifier = sapply(result$results, function(x) if (!is.null(x$db_identifier)) x$db_identifier else NA),
    stringsAsFactors = FALSE)

  View(df_genes)

  ###########################
  ### Proteins
  ###########################
  api <- ProteinsApi$new()
  result <- api$GETPROTEINS(NULL,network_id,NULL)
  results <- result$results


  df_proteins <- data.frame(
    name = sapply(result$results, function(x) if (!is.null(x$name)) x$name else NA),
    identifier = sapply(result$results, function(x) if (!is.null(x$db_identifier)) x$name else NA),
    stringsAsFactors = FALSE)

  View(df_proteins)


  ###########################
  ### Enzymes
  ###########################

  api <- EnzymesApi$new()
  #print(api$GETENZYMES)
  result <- api$GETENZYMES(network_id)
  results <- result$results


  df_enzymes <- data.frame(
    name = sapply(result$results, function(x) if (!is.null(x$name)) x$name else NA),
    identifier = sapply(result$results, function(x) if (!is.null(x$db_identifier)) x$db_identifier else NA),
    stringsAsFactors = FALSE)

  View(df_enzymes)

  ###########################
  ### Reactions
  ###########################

  api <- ReactionsApi$new()

  result <- api$GETREACTIONS(network_id)
  results <- result$results


  df_reactions <- data.frame(
    name = sapply(result$results, function(x) if (!is.null(x$name)) x$name else NA),
    identifier = sapply(result$results, function(x) if (!is.null(x$db_identifier)) x$db_identifier else NA),
    ec   = sapply(result$results, function(x) if (!is.null(x$ec)) x$ec else NA),
    stringsAsFactors = FALSE)

  View(df_reactions)
  
  ###########################
  ### Metabolites
  ###########################

  api <- MetabolitesApi$new()
  response <- api$GETMETABOLITESWithHttpInfo(id_network = network_id)
  if (response$status_code >= 200 && response$status_code < 300) {
     json <- response$response_as_text()
     parsed <- jsonlite::fromJSON(json, simplifyDataFrame = TRUE)
  }
  else {
     stop("Erreur lors de l'appel API : ", response$status_code)
  }
  df_metabolites <- parsed$results
  View(df_metabolites)
  
  ###########################
  ### Pathways
  ###########################
  
  api <- PathwaysApi$new()

  result <- api$GETPATHWAYS(NULL,network_id, NULL)
  results <- result$results


  df_pathways <- data.frame(
    name = sapply(result$results, function(x) if (!is.null(x$name)) x$name else NA),
    identifier = sapply(result$results, function(x) if (!is.null(x$db_identifier)) x$db_identifier else NA),
    stringsAsFactors = FALSE)

  View(df_pathways)

Documentation for API Endpoints

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

Class	Method	HTTP request	Description
EnzymesApi	GETENZYMES	GET /enzymes	get Enzyme
GenesApi	GETGENES	GET /genes	get Gene
MetabolitesApi	GETMETABOLITES	GET /metabolites	get Metabolite
PathwaysApi	GETPATHWAYS	GET /pathways	get Pathway
ProteinsApi	GETPROTEINS	GET /proteins	get Protein
ReactionsApi	GETREACTIONS	GET /reactions	get Reaction

Author

[email protected]