tests/testthat/test-ID.mapping.R

In chemokine/OmicsSBGN: Overlay omics data onto SBGN pathway diagram

library(SBGNview)
library(testthat)
context("test-ID.mapping")
test.id.mapping = function(
                  species 
                  ,input.types 
                  ,output.types 
                  ,example.ids
                  ,mol.type){
    n = 0
    for(i in seq_len(length(input.types))){
       input.type = input.types[i]
       for(j in seq_len(length(output.types))){
           output.type = output.types[j]
           for(k in seq_len(length(species))){
               species.run = species[k]
               if(identical(input.type,output.type)){
                  next()
               }
               n = n+1
               message("\n\n\n\n\n Checking:  ",n," ",mol.type," ",input.type," ",output.type," ",species.run,"\n\n")
                id.map = try(
                              load.mapping.table(
                                      output.type = output.type
                                      ,input.type = input.type
                                      ,cpd.or.gene = mol.type
                                      ,species = species.run
                                      ,limit.to.ids = example.ids[[input.type]][[species.run]]
                              )[[1]][[1]]
                              ,silent = TRUE
                          )
                # if(!nrow(id.map)>0){
                #     stop()
                # }
                expect_that(nrow(id.map)>0, is_true() )
           }
       }
    }
  return(invisible(0))
}

example.ids = list(
        ENTREZID = list(mmu = c(26395,14693)
                        ,hsa = c(29085,10993))
        ,ENSEMBL = list(hsa = c("ENSG00000156006","ENSG00000244593")
                        ,mmu = c("ENSMUSG00000002997", "ENSMUSG00000004455") )
        ,KO = list(hsa = c( "K01847", "K00921" )
                        ,mmu = c( "K01847", "K00921" ) )
        ,chebi = list(cpd = c("10036","10049","18420","48828"))
        ,CompoundName = list(cpd = c("tyrosine", "(+-)-epinephrine"
                                     ,"1,3, 7-Trimethyluric acid"
                                     ,"(1S)-3,7,7-trimethylbicyclo[4.1.0]hept-3-ene")
                             )
        
        ,kegg.ligand = list(cpd = c("C00451","C00186","C11382","C06304"))
)

test.gene = function(){
    # species = c("hsa","mmu")
    # input.types = c("ENTREZID","KO","ENSEMBL")
    # output.types = c("pathwayCommons","metacyc.SBGN","pathway.id")
    species = c("hsa")
    input.types = c("ENTREZID")
    output.types = c("pathwayCommons")
    mol.type = "gene"
    test.id.mapping(
        species  = species
        ,input.types  = input.types
        ,output.types = output.types
        ,mol.type = mol.type
        ,example.ids = example.ids
    )
}

test.compound = function(){
    species = c("cpd")
    input.types = c("chebi","CompoundName","kegg.ligand")
    output.types = c("pathwayCommons","metacyc.SBGN","pathway.id")
    mol.type = "compound"
    test.id.mapping(
        species  = species
        ,input.types  = input.types
        ,output.types = output.types
        ,mol.type = mol.type
        ,example.ids = example.ids
    )
}


test.gene()
# test.compound()