removed v1 references

hms-dbmi-cellenics · Jul 25, 2022 · d1dc483 · d1dc483
1 parent 2758efb
commit d1dc483
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Showing 3 changed files with 11 additions and 63 deletions.
diff --git a/pipeline-runner/R/gem2s-1-download_user_files.R b/pipeline-runner/R/gem2s-1-download_user_files.R
@@ -12,45 +12,6 @@ download_and_store <- function(bucket, key, file_path, s3) {
   writeBin(body, con = file_path)
 }
 
-#' Download user files from S3
-#'
-#' @param input The input params received from the api
-#' @param originals_bucket The bucket where the sample files are
-#' @param input_dir A string, where the s3 object is going to be stored
-#' @param s3 S3 aws client
-#'
-#' @export
-#'
-get_gem2s_file_v1 <- function(input, originals_bucket, input_dir, s3) {
-  project_id <- input$projectId
-  sample_ids <- unlist(input$sampleIds)
-  sample_ids <- sort(sample_ids)
-
-
-  unlink(input_dir, recursive = TRUE)
-
-  for (sample_id in sample_ids) {
-    message("\nSample --> ", sample_id)
-
-    res <- s3$list_objects(
-      Bucket = originals_bucket,
-      Prefix = file.path(project_id, sample_id)
-    )
-
-    keys <- unlist(lapply(res$Contents, `[[`, "Key"))
-
-    for (gem_key in keys) {
-      message("GEM key: ", gem_key)
-      fname <- basename(gem_key)
-
-      # Preparing directories
-      local_fpath <- file.path(input_dir, sample_id, fname)
-
-      download_and_store(originals_bucket, gem_key, local_fpath, s3)
-    }
-  }
-}
-
 #' Download user files from S3
 #'
 #' @param input The input params received from the api
@@ -61,7 +22,7 @@ get_gem2s_file_v1 <- function(input, originals_bucket, input_dir, s3) {
 #'
 #' @export
 #'
-get_gem2s_file_v2 <- function(input, originals_bucket, input_dir, s3) {
+get_gem2s_file <- function(input, originals_bucket, input_dir, s3) {
   project_id <- input$projectId
   sample_ids <- input$sampleIds
   sample_s3_paths <- input$sampleS3Paths
@@ -73,7 +34,7 @@ get_gem2s_file_v2 <- function(input, originals_bucket, input_dir, s3) {
     for (file_type in file_types_by_technology[[technology]]) {
       s3_path <- sample_s3_paths[[sample_id]][[file_type]]
 
-      local_fpath <- file.path(input_dir, sample_id, file_names_v1[[file_type]])
+      local_fpath <- file.path(input_dir, sample_id, file_names[[file_type]])
       download_and_store(originals_bucket, s3_path, local_fpath, s3)
     }
   }
@@ -92,11 +53,7 @@ get_gem2s_file_v2 <- function(input, originals_bucket, input_dir, s3) {
 download_user_files <- function(input, pipeline_config, prev_out = list(), input_dir= "/input") {
   s3 <- paws::s3(config = pipeline_config$aws_config)
 
-  if (input$apiVersion == "v1") {
-    get_gem2s_file_v1(input, pipeline_config$originals_bucket, input_dir, s3)
-  } else if (input$apiVersion == "v2") {
-    get_gem2s_file_v2(input, pipeline_config$originals_bucket, input_dir, s3)
-  }
+  get_gem2s_file(input, pipeline_config$originals_bucket, input_dir, s3)
 
   config <- list(
     name = input$experimentName,

diff --git a/pipeline-runner/data-raw/sysdata.R b/pipeline-runner/data-raw/sysdata.R
@@ -16,7 +16,7 @@ file_types_by_technology <- list(
   "10x" = list("barcodes10x", "features10x", "matrix10x")
 )
 
-file_names_v1 <- list(
+file_names <- list(
   barcodes10x = "barcodes.tsv.gz",
   features10x = "features.tsv.gz",
   matrix10x = "matrix.mtx.gz"
@@ -37,7 +37,7 @@ IDS_IDS <- "ids_ids"
 usethis::use_data(
   gem2s,
   DEBUG_PATH,
-  file_names_v1,
+  file_names,
   file_types_by_technology,
   SYM_IDS,
   SYM_SYM,

diff --git a/pipeline-runner/init.R b/pipeline-runner/init.R
@@ -27,7 +27,7 @@ buildActivityArn <- function(aws_region, aws_account_id, activity_id) {
     return(activity_arn)
 }
 
-load_config <- function(development_aws_server, api_version = "v1") {
+load_config <- function(development_aws_server) {
     label_path <- "/etc/podinfo/labels"
     aws_account_id <- Sys.getenv("AWS_ACCOUNT_ID", unset="242905224710")
     aws_region <- Sys.getenv("AWS_DEFAULT_REGION", unset="eu-west-1")
@@ -107,18 +107,10 @@ load_config <- function(development_aws_server, api_version = "v1") {
     config[["plot_data_bucket"]] <- paste("plots-tables", config$cluster_env, config$aws_account_id, sep = "-")
     config[["cell_sets_bucket"]] <- paste("cell-sets", config$cluster_env, config$aws_account_id, sep = "-")
     config[["debug_bucket"]] <- paste("biomage-pipeline-debug", config$cluster_env, config$aws_account_id, sep = "-")
-
-    if (api_version == "v1") {
-        config[["sns_topic"]] <- paste(
-            paste("arn:aws:sns", config$aws_region, config$aws_account_id, "work-results", sep = ":"),
-            config$cluster_env, config$sandbox_id, sep = "-"
-        )
-    } else if (api_version == "v2") {
-        config[["sns_topic"]] <- paste(
-            paste("arn:aws:sns", config$aws_region, config$aws_account_id, "work-results", sep = ":"),
-            config$cluster_env, config$sandbox_id, "v2", sep = "-"
-        )
-    }
+    config[["sns_topic"]] <- paste(
+        paste("arn:aws:sns", config$aws_region, config$aws_account_id, "work-results", sep = ":"),
+        config$cluster_env, config$sandbox_id, "v2", sep = "-"
+    )
 
     return(config)
 }
@@ -227,7 +219,6 @@ call_data_processing <- function(task_name, input, pipeline_config) {
     #need this for embed_and_cluster
     config$api_url <- pipeline_config$api_url
     config$auth_JWT <- input$authJWT
-    config$api_version <- input$apiVersion
 
     if (!exists("scdata")) {
         message("No single-cell data has been loaded, reloading from S3...")
@@ -411,7 +402,7 @@ init <- function() {
 
         tryCatchLog({
                 # Refresh pipeline_config with the new task input
-                pipeline_config <- load_config(input$server, api_version = input$apiVersion)
+                pipeline_config <- load_config(input$server)
 
                 wrapper(input, pipeline_config)