r-sdk: R SDK for flywheel.io

devtools::use_package("httr")
devtools::use_package("jsonlite")

library(httr)
library(jsonlite)



flywheel = function(APIKEY=NULL)
{

  if (!requireNamespace("httr", quietly = TRUE)) {
    stop("library httr is needed for this function to work. Please install it.",
         call. = FALSE)
  }
  if (!requireNamespace("jsonlite", quietly = TRUE)) {
    stop("library jsonlite is needed for this function to work. Please install it.",
         call. = FALSE)
  }

  ## Get the environment for this
  ## instance of the function.
  thisEnv <- environment()

  api_key <- ""
  base_url <- ""
  debug_mode <- FALSE


  ## Create the list used to represent an
  ## object for this class
  me <- list(

    ## Define the environment where this list is defined so
    ## that I can refer to it later.
    thisEnv = thisEnv,

    ## Define the accessors for the data fields.
    getEnv = function()
    {
      return(get("thisEnv",thisEnv))
    },

    getApiKey = function()
    {
      return(get("api_key",thisEnv))
    },

    setApiKey = function(value)
    {
      return(assign("api_key",value,thisEnv))
    },

    getBaseURL = function()
    {
      return(get("base_url",thisEnv))
    },

    setBaseURL = function(value)
    {
      return(assign("base_url",value,thisEnv))
    },

    setDebugMode = function(value)
    {
      return(assign("debug_mode",value,thisEnv))
    },

    getDebugMode = function()
    {
      return(get("debug_mode",thisEnv))
    },

    getFlywheel = function(endpoint) {
      protocol <- "https://"
      baseURL <- this$getBaseURL()
      apiKey <- this$getApiKey()
      authHeader <- paste("scitran-user ",apiKey,sep="")
      url <- paste(protocol,baseURL,"/api/",endpoint,sep="")
      #print(this$getDebugMode())
      #print(this$getDebugMode()==TRUE)
      if (this$getDebugMode()==TRUE) {
        print(url)
        print(authHeader)
      }
      response = GET(url, add_headers(Authorization = authHeader))
      contentType <- headers(response)['content-type']
      if (this$getDebugMode()==TRUE) {
        print(response)
        print(contentType)
      }
      #jsonDataFrame = fromJSON(content(response,as = "text"), simplifyDataFrame=TRUE)
      result <- content(response,as = "text")
      if (this$getDebugMode()==TRUE) {
        if (contentType=="application/json; charset=utf-8") print(prettify(result, indent = 4))
      }
      return(result)
    },

    putFlywheel = function(endpoint, payload) {
      protocol <- "https://"
      baseURL <- this$getBaseURL()
      apiKey <- this$getApiKey()
      authHeader <- paste("scitran-user ",apiKey,sep="")
      url <- paste(protocol,baseURL,"/api/",endpoint,sep="")
      if (this$getDebugMode()==TRUE) {
        print(url)
        print(authHeader)
      }
      response = PUT(url, body=payload, add_headers(Authorization = authHeader), content_type_json(), verbose())
      if (this$getDebugMode()==TRUE) {
        print(payload)
        print(response)
      }
      #jsonDataFrame = fromJSON(content(response,as = "text"), simplifyDataFrame=TRUE)
      result = content(response,as = "text")
      #print(prettify(result, indent = 4))
      return(result)
    },

    getCurrentUser = function() {
      return(this$getFlywheel("users/self"))
    },

    getAllUsers = function() {
      return(this$getFlywheel("users"))
    },

    getUser = function(key) {
      endpoint = paste("users/",key, sep="")
      return(this$getFlywheel(endpoint))
    },

    getAllGroups = function() {
      return(this$getFlywheel("groups"))
    },

    getGroup = function(key) {
      endpoint = paste("groups/",key, sep="")
      return(this$getFlywheel(endpoint))
    },

    getAllProjects = function() {
      return(this$getFlywheel("projects"))
    },

    getProject = function(key) {
      endpoint = paste("projects/",key, sep="")
      return(this$getFlywheel(endpoint))
    },

    getProjectByName = function(project_name) {
      projects_df <- fromJSON(this$getAllProjects(), simplifyDataFrame=TRUE)
      return(projects_df[projects_df$label==project_name,])
    },

    getProjectIdByName = function(project_name) {
      project_df <- this$getProjectByName(project_name)
      return(project_df$'_id')
    },

    getProjectsDataFrame = function() {
      projects_df <- fromJSON(this$getAllProjects(),  simplifyDataFrame=TRUE)
      return(projects_df)
    },

    getProjectSessions = function(key) {
      endpoint = paste("projects/",key, "/sessions", sep="")
      return(this$getFlywheel(endpoint))
    },

    getProjectSessionsDataFrame = function(project_id) {
      sessions_df <- fromJSON(this$getProjectSessions(project_id),  simplifyDataFrame=TRUE)
      return(sessions_df)
    },

    putProjectInfo = function(project, json) {
      endpoint = paste("projects/",project, sep="")
      payload = paste(' { "info": ', json, '}')
      return(this$putFlywheel(endpoint, payload))
    },

    putProjectInfoKey = function(project, key, value) {
      payload = paste(' { "',key, '": ', toJSON(value, auto_unbox=TRUE), '}', sep="")
      print(payload)
      return(this$putProjectInfo(project, payload))
    },

    getProjectFileUrl = function(project, filename) {
      endpoint = paste("projects/", project, "/files/", filename, "?ticket=", sep="")
      response <- this$getFlywheel(endpoint)
      result = fromJSON(response)
      url <- paste("https://",this$getBaseURL(),"/api/","projects/", project, "/files/", filename, "?ticket=",result$ticket, sep="")
      return(url)
    },

    getProjectAnalysisFileUrl = function(project, analysis, filename) {
      endpoint = paste("projects/", project, "/analyses/", analysis, "/files/", filename, "?ticket=", sep="")
      response <- this$getFlywheel(endpoint)
      result = fromJSON(response)
      url <- paste("https://",this$getBaseURL(),"/api/","projects/", project, "/analyses/", analysis, "/files/", filename, "?ticket=",result$ticket, sep="")
      return(url)
    },

    getAllSessions = function() {
      return(this$getFlywheel("sessions"))
    },

    getSession = function(key) {
      endpoint = paste("sessions/",key, sep="")
      return(this$getFlywheel(endpoint))
    },

    getSessionByName = function(session_label) {
      sessions_df <- fromJSON(this$getAllSessions(), simplifyDataFrame=TRUE)
      return(sessions_df[sessions_df$label==session_label,])
    },

    getSessionIdByName = function(session_label) {
      session_df <- this$getSessionByName(session_label)
      return(session_df$'_id')
    },

    getSessionsDataFrame = function(project_id) {
      sessions_df <- fromJSON(this$getAllProjects(),  simplifyDataFrame=TRUE)
      return(projects_df)
    },

    getSessionAnalysis = function(session, analysis) {
      endpoint = paste("sessions/", session, "/analyses/", analysis, sep="")
      return(this$getFlywheel(endpoint))
    },

    getSessionAnalysisFile = function(session, analysis, filename) {
      endpoint = paste("sessions/", session, "/analyses/", analysis, "/files/", filename, "?view=true", sep="")
      return(this$getFlywheel(endpoint))
    },

    getSessionAnalysisFileUrl = function(session, analysis, filename) {
      endpoint = paste("sessions/", session, "/analyses/", analysis, "/files/", filename, "?ticket=", sep="")
      response <- this$getFlywheel(endpoint)
      result = fromJSON(response)
      url <- paste("https://",this$getBaseURL(),"/api/","sessions/", session, "/analyses/", analysis, "/files/", filename, "?ticket=",result$ticket, sep="")
      return(url)
    },

    getSessionFileUrl = function(session, filename) {
      endpoint = paste("sessions/", session, "/files/", filename, "?ticket=", sep="")
      response <- this$getFlywheel(endpoint)
      result = fromJSON(response)
      url <- paste("https://",this$getBaseURL(),"/api/","sessions/", session, "/files/", filename, "?ticket=",result$ticket, sep="")
      return(url)
    },

    putSessionInfo = function(session, json) {
      endpoint = paste("sessions/",session, sep="")
      payload = paste(' { "info": ', json, '}')
      return(this$putFlywheel(endpoint, payload))
    },

    putSessionInfoKey = function(session, key, value) {
      payload = paste(' { "',key, '": ', toJSON(value, auto_unbox=TRUE), '}', sep="")
      print(payload)
      return(this$putSessionInfo(session, payload))
    },

    putSubjectInfo = function(session, value) {
      endpoint = paste("sessions/",session, sep="")
      payload = paste('{ "subject": { "info": ', value, '}}')
      return(this$putFlywheel(endpoint, payload))
    },

    putSubjectInfoKey = function(session, key, value) {
      payload = paste(' { "',key, '": ', toJSON(value, auto_unbox=TRUE), '}', sep="")
      print(payload)
      return(this$putSubjectInfo(session, payload))
    },

    getAllAcquisitions = function() {
      return(this$getFlywheel("acquisitions"))
    },

    getAcquisition = function(key) {
      endpoint = paste("acquisitions/",key, sep="")
      return(this$getFlywheel(endpoint))
    },

    getAcquisitionFileUrl = function(acquisition, filename) {
      endpoint = paste("acquisitions/", acquisition, "/files/", filename, "?ticket=", sep="")
      response <- this$getFlywheel(endpoint)
      result = fromJSON(response)
      url <- paste("https://",this$getBaseURL(),"/api/","acquisitions/", acquisition, "/files/", filename, "?ticket=",result$ticket, sep="")
      return(url)
    },

    putAcquisitionInfo = function(acquisition, json) {
      endpoint = paste("acquisitions/",acquisition, sep="")
      payload = paste(' { "info": ', json, '}')
      return(this$putFlywheel(endpoint, payload))
    },

    putAcquisitionInfoKey = function(acquisition, key, value) {
      payload = paste(' { "',key, '": ', toJSON(value, auto_unbox=TRUE), '}', sep="")
      print(payload)
      return(this$putAcquisitionInfo(acquisition, payload))
    },

    getAcquisitionAnalysis = function(acquisition, analysis) {
      endpoint = paste("acquisitions/", acquisition, "/analyses/", analysis, sep="")
      return(this$getFlywheel(endpoint))
    },

    getAcquisitionAnalysisFileUrl = function(acquisition, analysis, filename) {
      endpoint = paste("acquisitions/", acquisition, "/analyses/", analysis, "/files/", filename, "?ticket=", sep="")
      response <- this$getFlywheel(endpoint)
      result = fromJSON(response)
      url <- paste("https://",this$getBaseURL(),"/api/","acquisitions/", acquisition, "/analyses/", analysis, "/files/", filename, "?ticket=",result$ticket, sep="")
      return(url)
    },

    getAllCollections = function() {
      return(this$getFlywheel("collections"))
    },

    getCollection = function(key) {
      endpoint = paste("collections/",key, sep="")
      return(this$getFlywheel(endpoint))
    },

    getCollectionByName = function(collection_name) {
      collections_df <- fromJSON(this$getAllCollections(), simplifyDataFrame=TRUE)
      return(collections_df[collections_df$label==collection_name,])
    },

    getCollectionIdByName = function(collection_name) {
      collection_df <- this$getCollectionByName(collection_name)
      return(collection_df$'_id')
    },

    getCollectionsDataFrame = function() {
      collections_df <- fromJSON(this$getAllCollections(),  simplifyDataFrame=TRUE)
      return(collections_df)
    },

    getCollectionSessions = function(key) {
      endpoint = paste("collections/",key, "/sessions", sep="")
      return(this$getFlywheel(endpoint))
    },

    getCollectionSessionsDataFrame = function(collection_id) {
      sessions_df <- fromJSON(this$getCollectionSessions(collection_id),  simplifyDataFrame=TRUE)
      return(sessions_df)
    },

    putCollectionInfo = function(collection, json) {
      endpoint = paste("collections/",collection, sep="")
      payload = paste(' { "info": ', json, '}')
      return(this$putFlywheel(endpoint, payload))
    },

    putCollectionInfoKey = function(collection, key, value) {
      payload = paste(' { "',key, '": ', toJSON(value, auto_unbox=TRUE), '}', sep="")
      print(payload)
      return(this$putCollectionInfo(collection, payload))
    },

    getCollectionFileUrl = function(collection, filename) {
      endpoint = paste("collections/", collection, "/files/", filename, "?ticket=", sep="")
      response <- this$getFlywheel(endpoint)
      result = fromJSON(response)
      url <- paste("https://",this$getBaseURL(),"/api/","collections/", collection, "/files/", filename, "?ticket=",result$ticket, sep="")
      return(url)
    },

    getCollectionAnalysisFileUrl = function(collection, analysis, filename) {
      endpoint = paste("collections/", collection, "/analyses/", analysis, "/files/", filename, "?ticket=", sep="")
      response <- this$getFlywheel(endpoint)
      result = fromJSON(response)
      url <- paste("https://",this$getBaseURL(),"/api/","collections/", collection, "/analyses/", analysis, "/files/", filename, "?ticket=",result$ticket, sep="")
      return(url)
    },

    getAllGears = function() {
      return(this$getFlywheel("gears"))
    },

    getGear = function(key) {
      endpoint = paste("gears/",key, sep="")
      return(this$getFlywheel(endpoint))
    },

    getVersion = function() {
      return(this$getFlywheel("version"))
    },

    apikey = function(APIKEY) {
      if (!is.null(APIKEY)) {
        result <- unlist(strsplit(APIKEY, ":"))
        if (length(result)==2) {
          this$setBaseURL(result[1])
        } else if (length(result)==3) {
          this$setBaseURL(paste(result[1], result[2], sep=":"))
        } else {
          stop("Bad APIKEY")
        }
        this$setApiKey(APIKEY)
        this$getCurrentUser()
      }
    }

  )

  ## Define the value of the list within the current environment.
  assign('this',me,envir=thisEnv)

  # capture APIKEY and base_url if APIKEY provided  - "connect"
  this$apikey(APIKEY)


  ## Set the name for the class
  class(me) <- append(class(me),"Flywheel")
  return(me)
}