Fix #208 and #209 (#210)

* Fix and clean up docs

* Update test and fix

* Update pkgdown index manually

* Fix some logic, including #208

Author: anngvu

R/annotations.R

@@ -53,11 +53,14 @@ annotate_with_manifest <- function(manifest, ignore_na = TRUE, ignore_blank = TR
 #' @param select Vector of properties to selectively copy if present on the entity.
 #' If not specified, will copy over everything, which may not be desirable.
 #' @param update Whether to immediately update or return annotation objects only.
+#' @param as_list Only used when `update=FALSE`; for backwards-compatibility or when
+#' downstream usage of `copy_annotations` expects an R list, return as an R list.
 #' @export
 copy_annotations <- function(entity_from,
                              entity_to,
                              select = NULL,
-                             update = FALSE) {
+                             update = FALSE,
+                             as_list = TRUE) {
 
   .check_login()
 
@@ -74,7 +77,29 @@ copy_annotations <- function(entity_from,
     for(k in select) {
       to_annotations[k] <- from_annotations[k]
     }
-    if(update) .syn$set_annotations(to_annotations) else return(to_annotations)
+    if(update) {
+      .syn$set_annotations(to_annotations)
+    } else if (as_list) {
+      return(.dict_to_list(to_annotations))
+    } else {
+      return(to_annotations)
+    }
   }
 }
 
+
+#' Convert a flat Python Dict to R list
+#'
+#' An internal function used to convert Annotations objects returned by `get_annotations`.
+#'
+#' @param dict A flat Python Dict object.
+.dict_to_list <- function(dict) {
+  if (is.null(names(dict))) {
+    stop("Input must be a named list representing a flat Python dictionary.")
+  }
+  l <- list()
+  for(k in names(dict)) {
+    l[[k]] <- dict[k]
+  }
+  l
+}

R/nextflow_annotation_utils.R

@@ -28,10 +28,10 @@ annotation_rule <- function(outputFrom, which = c("format_as", "annotate_as", "t
     "featureCounts" = list(format_as = function(x) { "txt" }, annotate_as =  "annotate_quantified_expression", template = "bts:ProcessedExpressionTemplate"),
     "SAMtools" = list(format_as = function(x) { substring(x, nchar(x)-2, nchar(x)) }, annotate_as = "annotate_aligned_reads", template = "bts:ProcessedAlignedReadsTemplate"),
     "CNVkit" = list(format_as = function(x) { substring(x, nchar(x)-2, nchar(x)) }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"),
-    "DeepVariant" = list(format_as = function(x) { "vcf" }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"),
-    "Strelka2" = list(format_as = function(x) { "vcf" }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"),
-    "Mutect2" = list(format_as = function(x) { "vcf" }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"),
-    "FreeBayes" = list(format_as = function(x) { "vcf" }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"))
+    "DeepVariant" = list(format_as = function(x) { ifelse(grepl("tbi$", x), "tbi", "vcf") }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"),
+    "Strelka2" = list(format_as = function(x) { ifelse(grepl("tbi$", x), "tbi", "vcf") }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"),
+    "Mutect2" = list(format_as = function(x) { ifelse(grepl("tbi$", x), "tbi", "vcf") }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"),
+    "FreeBayes" = list(format_as = function(x) { ifelse(grepl("tbi$", x), "tbi", "vcf") }, annotate_as = "annotate_called_variants", template = "bts:ProcessedVariantCallsTemplate"))
 
   switch(
     which,
@@ -230,7 +230,7 @@ map_sample_output_sarek <- function(syn_out,
 
       index_fun <- function(x) {
         caller_index <- grep("cnvkit|deepvariant|strelka|mutect|freebayes", x, ignore.case = TRUE)[1]
-        if(!length(caller_index)) stop("Issue with figuring out sample output organization. Is there non-standard output?")
+        if(!length(caller_index)) stop("Issue with inferring sample output organization. Is this non-standard output?")
         file_index <- length(x)
         if((file_index - caller_index) == 1) {
           file_index - 2 # i.e. `VariantCalling/<SAMPLE>/<CALLER>`
@@ -243,7 +243,10 @@ map_sample_output_sarek <- function(syn_out,
       # For nf-sarek tumor somatic variant calling, sample references tumor vs normal from same indiv
       # The sample assigned to the processed data is the tumor sample
       result[, sample := path_extract(path, index_fun = index_fun)]
-      if(grepl("_vs_", first(result$output_name))) result[, sample := gsub("_vs.*", "", sample)]
+      if(.output %in% c("Strelka2", "FreeBayes", "Mutect2") && any(grepl("_vs_", result$sample))) {
+        message("  - Somatic data present.")
+        result[, sample := gsub("_vs.*", "", sample)]
+      }
 
       results[[.output]] <- result
       setattr(results[[.output]], "outputFrom", .output)
@@ -450,6 +453,8 @@ annotate_called_variants <- function(metadata,
         "AnnotatedSomaticVariants"
       } else if(!grepl("_vs_", name) && format == "maf") {
         "AnnotatedGermlineVariants"
+      } else if(format == "tbi") {
+        "dataIndex"
       } else if(format %in% c("cns", "cnn", "cnr", "bed", "pdf", "png")) {
         "CopyNumberVariants"
       } else {
@@ -504,7 +509,6 @@ annotate_with_samtools_stats <- function(meta,
 #' Wrapper for all steps to get manifest for processed product
 #'
 #' @inheritParams map_sample_io
-#' @param
 #' @param workflow_link Workflow link.
 #' @export
 #' @return List `manifest` with manifests for each processed dataset,

_pkgdown.yml

@@ -165,6 +165,7 @@ reference:
   description: Mostly meant to be internal or experimental stuff
 - contents:
   - .delim_string_to_vector
+  - .dict_to_list
   - .replace_string_column_with_stringlist_column
   - .store_rows
   - missing_annotation_email

man/copy_annotations.Rd

@@ -1,4 +1,5 @@
-test_that("Copy annotations works", {
+test_that("Copy annotations works to apply an immediate copy of annotations from one entity to another (update=TRUE)
+          as well as when simply getting a copy of the annotations present as a default R list to work with (update=FALSE)", {
   skip_if_no_synapseclient()
   skip_if_no_login()
 
@@ -18,12 +19,24 @@ test_that("Copy annotations works", {
                                    parent = PARENT_TEST_PROJECT)
   entity_c <- .syn$store(entity_c)
 
-  # when copying all annotations from A->B (default)
+  # when getting a copy of all annotations from A->B (default)
+  copy_of_a_b <- copy_annotations(entity_from = entity_a$properties$id,
+                                  entity_to = entity_b$properties$id,
+                                  select = NULL,
+                                  update = FALSE)
+
+  # when immediately copying all annotations from A->B (default)
   copy_annotations(entity_from = entity_a$properties$id,
                    entity_to = entity_b$properties$id,
                    select = NULL,
                    update = TRUE)
 
+  # when getting a copy of selective annotations from A->C
+  copy_of_a_c <- copy_annotations(entity_from = entity_a$properties$id,
+                                  entity_to = entity_c$properties$id,
+                                  select = c("favorites", "key_not_on_a"),
+                                  update = FALSE)
+
   # when copying selective annotations from A->C
   copy_annotations(entity_from = entity_a$properties$id,
                    entity_to = entity_c$properties$id,
@@ -35,6 +48,8 @@ test_that("Copy annotations works", {
   .syn$delete(entity_a)
   .syn$delete(entity_b)
   .syn$delete(entity_c)
+  testthat::expect_equal(copy_of_a_b, list(after_a = TRUE, favorites = c("raindrops", "whiskers"), foo = "bar"))
+  testthat::expect_equal(copy_of_a_c, list(favorites = c("raindrops", "whiskers")))
   testthat::expect_equal(result_b$foo, "bar")
   testthat::expect_equal(result_b$favorites, c("raindrops", "whiskers"))
   testthat::expect_equal(result_b$after_a, TRUE)
@@ -44,4 +59,3 @@ test_that("Copy annotations works", {
 
 })
 
-