inst/runscripts/Consensus_Wrapper.R

In Sage-Bionetworks/metanetwork: Network meta analysis

# Calling in Libraries ----------------------------------------------------

library(dplyr, quietly = TRUE)
library(glmnet, quietly = TRUE)
library(randomForest, quietly = TRUE)
library(Hmisc, quietly = TRUE)
library(lars, quietly = TRUE)
library(WGCNA, quietly = TRUE)
library(synapser, quietly = TRUE)
library(metanetwork, quietly = TRUE)
library(githubr, quietly = TRUE)
library(c3net, quietly = TRUE)
library(config, quietly = TRUE)
library(optparse, quietly = TRUE)
library(data.table, quietly = TRUE)
library(parmigene, quietly = TRUE)
library(WGCNA, quietly = TRUE)
library(reader, quietly = TRUE)
# Obtaining the data - From User --------------------------------------------

option_list <- list(make_option(c("-u","--synapse_user"), type="character", action = "store",
                                help = "Synapse User name"),
                    make_option(c("-p","--synapse_pass"), type="character", action = "store",
                                help = "Synapse User Password"),
                    make_option(c("-c","--config_file"), type="character", action = "store",
                                help = "Path to the complete config file"))
req_args <- parse_args(OptionParser(option_list=option_list))


# Obtaining the data - From Synapse --------------------------------------------

#Setting up the cofig file
Sys.setenv(R_CONFIG_ACTIVE = "default")
config <- config::get(file = req_args$config_file)

#Linking with Project
synLogin(email = req_args$synapse_user, password = req_args$synapse_pass)
input_file = synGet(config$input_profile$input_proj_id,downloadLocation = config$input_profile$temp_input_loc)
fileName = input_file$path
project = Project(config$input_profile$project_id)
project <- synStore(project)


outputpath = config$input_profile$temp_storage_loc
networkFolderId = config$input_profile$input_folderid
pattern_id = config$input_profile$pattern_id
run_id = config$input_profile$run_id
network_names = c('c3net','mrnet','wgcna',
                  'lassoAIC','lassoBIC','lassoCV1se','lassoCVmin','ridgeAIC','ridgeBIC','ridgeCV1se','ridgeCVmin',
                  'sparrowZ','sparrow2Z','tigress','genie3')

child_obj <- synapser::synGetChildren(as.character(networkFolderId), includeTypes = list('folder'))
child_list <- as.list(child_obj)
child_names = c()
for(k in 1:length(child_list)){
    temp_name = child_list[k]
    temp_name = unlist(temp_name)
    nn = temp_name['name']
    nn = as.character(nn)
    child_names = c(child_names,nn)
}

  #child_names <- lapply(child_list, `[[`, 1)
  #child_names <- unlist(child_names)
out_list <- list()
print(length(child_names))
for(ent in 1:length(child_names)){
  print('st1')
  temp_l = synGetChildren(child_list[[ent]]$id)
  temp_list = temp_l$asList()
  print(temp_list)
  temp_names = c()
  temp_ids = c()
  for(k in 1:length(temp_list)){
    temp_name = temp_list[k]
    temp_name = unlist(temp_name)
    nn = temp_name['name']
    nn = as.character(nn)
    temp_names = c(temp_names,nn)
    nn = as.character(temp_name['id'])
    temp_ids = c(temp_ids,nn)
  }
  ## - wgcnaSoftThresholdNetwork.csv
  ## - wgcnaTopologicalOverlapMatrixNetwork

  # temp_names <- lapply(temp_list, `[[`, 1)
  # temp_names <- unlist(temp_names)
  if(child_names[ent] == 'wgcna'){
    temp_name_search <- c('wgcna Topological Overlap Matrix Networ','wgcna Soft Threshold Network')
    temp_names_ids <- c( grep(temp_name_search[1], temp_names), grep(temp_name_search[2], temp_names))
  }else{
    temp_name_search = paste0(child_names[[ent]],pattern_id)
    temp_names_ids <- grep(temp_name_search, temp_names)
  }
  #temp_names_ids <- grep(temp_name_search, temp_names)
  cat(paste0(temp_names[temp_names_ids],' \n'))
  id_t = temp_ids[temp_names_ids]
  if(length(id_t) == 0){
    cat(paste0('No match for ',temp_name_search,' \n'))
  }else{
    #cat(paste0(id_t,' \n'))
    for( id in id_t){
      temp <- synGet(id, downloadLocation = outputpath)
      out_list <- append(out_list, temp)
    }
  }
}
message('Buildig Consensus Networks')
outputpath <- gsub( '//', '/', paste0(outputpath,'/'))
buildConsensus(outputpath = outputpath, networkFolderId = networkFolderId,
  pattern_id = run_id, fileName = fileName,
  bar = out_list, iscsv = config$input_profile$is_csv)


# Obtaining the data - For provenance --------------------------------------------

activity <- synapser::synGet(config$input_profile$project_id)

dataFolder <- Folder('Consensus',parent = config$input_profile$project_id)
dataFolder <- synStore(dataFolder)

#file <- File(path = paste0(outputpath,'rankConsensusNetwork.csv'), parent = dataFolder)
#file <- synStore(file)
#file2 <- File(path = paste0(outputpath,'bicNetworks.rda'), parent = dataFolder)
#file2 <- synStore(file2)
all.annotations <- NULL
try(
  all.annotations <- synGetAnnotations(config$input_profile$input_synid), 
  silent = TRUE
)
checkAnnotations <- function(annotations, config){
  
  namer <- c("data_type", "resource_type", "metadata_type", "ismodelsystem", "ismultispecimen",
    "fileformat", "grant", "species", "organ", "tissue", "study", "consortium", "assay" )
  names(namer) <- c('dataType', 'resourceType', 'metadataType', 'isModelSystem', 'isMultiSpecimen', 
    'fileFormat', 'grant', 'species', 'organ', 'tissue', 'study', 'consortium' , 'assay')

  annot_default <- list(
    dataType = NULL,
    resourceType = NULL,
    metadataType = NULL,
    isModelSystem = NULL,
    isMultiSpecimen = NULL,
    fileFormat = NULL,
    grant = NULL,
    species = NULL,
    organ = NULL,
    tissue = NULL,
    study = NULL,
    consortium = NULL,
    assay = NULL
  )
  for (item in names(annot_default)){
    if (!is.null(config$provenance$annotations[[namer[[item]]]])){
      annot_default[[item]] = config$provenance$annotations[[namer[[item]]]]
    }
    else if ( !is.null(annotations) & !is.null(annotations[[item]])){
      annot_default[[item]] = annotations[[item]]
    }
  }
  return(annot_default)
}

all.annotations <- checkAnnotations(all.annotations,config)

thisRepo = NULL
thisFile = NULL

try(
  thisRepo <- githubr::getRepo(
    repository = config$provenance$code_annotations$repository,
    ref = config$provenance$code_annotations$ref,
    refName = config$provenance$code_annotations$ref_name
  ), silent = TRUE
)
try(
  thisFile <- githubr::getPermlink(
    repository = thisRepo,
    repositoryPath = config$provenance$code_annotations$repository_path
  ), silent = TRUE
)
# Push Config File to synaopse
ENRICH_OBJ <- synapser::synStore( synapser::File(
  path = req_args$config_file,
  name = 'Consensus Config',
  parentId = dataFolder$properties$id),
  used = config$input_profile$input_synid,
  activityName = config$provenance$activity_name,
  executed = thisFile,
  activityDescription = config$provenance$activity_description
)
config_syn <- ENRICH_OBJ$properties$id

ENRICH_OBJ <- synapser::synStore( synapser::File(
  path = paste0(outputpath,'bicNetworks.rda'),
  name = 'bicNetworks',
  parentId = dataFolder$properties$id),
  used = c(config$input_profile$input_synid,config_syn),
  activityName = config$provenance$activity_name,
  executed = thisFile,
  activityDescription = config$provenance$activity_description
)

synapser::synSetAnnotations(ENRICH_OBJ, annotations = all.annotations)


ENRICH_OBJ <- synapser::synStore( synapser::File(
  path = paste0(outputpath,'rankConsensusNetwork.csv'),
  name = 'RankConsensusNetwork',
  parentId = dataFolder$properties$id),
  used = c(config$input_profile$input_synid,config_syn),
  activityName = config$provenance$activity_name,
  executed = thisFile,
  activityDescription = config$provenance$activity_description
)

synapser::synSetAnnotations(ENRICH_OBJ, annotations = all.annotations)

# Formatting the network to md5 format --------------------------------------------

md5Command <- paste0('md5sum ', paste0(outputpath,'rankConsensusNetwork.csv'))
md5 <- strsplit(system(md5Command, intern = TRUE), '  ')[[1]][1]
cat(md5, '\n', file = paste0(outputpath,config$output_profile$md5_output_path), sep = '')

ENRICH_OBJ <- synapser::synStore( synapser::File(
  path = paste0(outputpath,config$output_profile$md5_output_path),
  name = 'RankConsensusNet_MD5',
  parentId = dataFolder$properties$id),
  used = c(config$input_profile$input_synid,config_syn),
  activityName = config$provenance$activity_name,
  executed = thisFile,
  activityDescription = config$provenance$activity_description
)

synapser::synSetAnnotations(ENRICH_OBJ, annotations = all.annotations)

#if((!is.na(config$computing_specs$heavy_ncores)) || (!is.na(config$computing_specs$medium_ncores))){
#  mpi.quit(save = "no")
#}