crancheck update

umccr · Dec 1, 2023 · a4b73f7 · a4b73f7
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commit a4b73f7
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Showing 17 changed files with 33 additions and 21 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -26,3 +26,8 @@
 ^\.dvcignore$
 ^\.dockerignore$
 CODE_OF_CONDUCT.md
+
+## inst html
+inst/rmd/umccr_portal/html
+inst/rmd/umccr_workflows/umccrise/html
+inst/rmd/umccr_workflows/bcl_convert/html
diff --git a/R/multiqc.R b/R/multiqc.R
@@ -314,8 +314,9 @@ multiqc_date_fmt <- function(cdate) {
 #'
 #' @examples
 #' \dontrun{
-#' j <- here::here("nogit/warehouse/cttso/2023/05/wfr.ec3748db414f422381e419d367f73eec/dracarys_gds_sync/multiqc_data.json")
-#' multiqc_parse_plots(j, plot_names = c("fastqc_gc_content_mean_sequence_quality_plot", "dragen_coverage_per_contig"))
+#' j <- "dracarys_gds_sync/multiqc_data.json"
+#' multiqc_parse_plots(j, plot_names = c("dragen_coverage_per_contig"))
+#' multiqc_parse_plots(j, plot_names = "everything")
 #' multiqc_parse_plots(j, plot_names = NULL)
 #' }
 #' @export
@@ -428,7 +429,7 @@ multiqc_parse_xyline_plot_contig_cvg <- function(dat) {
 #' @examples
 #' \dontrun{
 #' j1 <- here::here("nogit/bcl_convert/multiqc_data.json")
-#' j2 <- here::here("nogit/warehouse/wgs_tumor_normal/SBJ03197/2023-04-30_0813ce/dracarys_gds_sync/multiqc_data.json")
+#' j2 <- here::here("nogit/dracarys_gds_sync/multiqc_data.json")
 #' j <- j1
 #' j <- j2
 #' multiqc_list_plots(j)

diff --git a/R/portal_meta.R b/R/portal_meta.R
@@ -493,7 +493,7 @@ meta_tso_ctdna_tumor_only <- function(pmeta, status = c("Succeeded")) {
 #' pmeta <- system.file("extdata/portal_meta_top4.csv", package = "dracarys")
 #' (m <- meta_star_alignment(pmeta))
 #' @testexamples
-#' expect_equal(all(c("s3_outdir_star", "LibraryID_tumor") %in% colnames(m)), TRUE)
+#' expect_equal(all(c("s3_outdir_star", "LibraryID") %in% colnames(m)), TRUE)
 #' @export
 meta_star_alignment <- function(pmeta, status = "Succeeded") {
   # retrieve workflow runs with the given type and status
@@ -710,7 +710,7 @@ meta_oncoanalyser_wgts_existing_both <- function(pmeta, status = "Succeeded") {
 #' pmeta <- system.file("extdata/portal_meta_top4.csv", package = "dracarys")
 #' (m <- meta_oncoanalyser_wts(pmeta))
 #' @testexamples
-#' expect_equal(all(c("s3_outdir_oncoanalyser", "LibraryID_tumor", "s3_bam_tumor") %in% colnames(m)), TRUE)
+#' expect_equal(all(c("s3_outdir_oncoanalyser", "LibraryID", "s3_bam") %in% colnames(m)), TRUE)
 #' @export
 meta_oncoanalyser_wts <- function(pmeta, status = "Succeeded") {
   # retrieve workflow runs with the given type and status

diff --git a/R/s3.R b/R/s3.R
@@ -12,7 +12,7 @@
 #' @return A tibble with path, date, file size, file type, and presigned URL if requested.
 #' @examples
 #' \dontrun{
-#' s3dir <- "s3://umccr-primary-data-prod/Accreditation/ALLOCATE-134131/WGS/2021-07-26/umccrised/ALLOCATE-134131__ALLOCATE-134131_MDx150892_Missing/cancer_report_tables"
+#' s3dir <- "s3://umccr-primary-data-prod/cancer_report_tables"
 #' s3_files_list_filter_relevant(s3dir = s3dir, presign = TRUE)
 #' }
 #' @export

diff --git a/R/tso.R b/R/tso.R
@@ -6,7 +6,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' x <- normalizePath("~/icav1/g/production/analysis_data/SBJ00704/tso_ctdna_tumor_only/202311242b9666e0/L2301411/Results/PTC_ctTSO231120_L2301411/dracarys_gds_sync/PTC_ctTSO231120_L2301411_CopyNumberVariants.vcf.gz")
+#' x <- normalizePath("CopyNumberVariants.vcf.gz")
 #' d <- TsoCopyNumberVariantsVcfFile$new(x)
 #' d_parsed <- d$read() # or read(d)
 #' d$write(d_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "tsv")
@@ -50,7 +50,7 @@ TsoCopyNumberVariantsVcfFile <- R6::R6Class(
 #'
 #' @examples
 #' \dontrun{
-#' x <- here::here("nogit/tso/2023-05-30/SBJ00595_L2100178/PTC_SrSqCMM1pc_L2100178_rerun_MergedSmallVariants.vcf.gz")
+#' x <- "MergedSmallVariants.vcf.gz"
 #' d <- TsoMergedSmallVariantsVcfFile$new(x)
 #' d_parsed <- d$read() # or read(d)
 #' d$write(d_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "tsv")

diff --git a/R/utils.R b/R/utils.R
@@ -50,6 +50,7 @@ session_info_tbls <- function(pkgs = NULL) {
 #' Output Format is Valid
 #'
 #' Checks that the specified output format is valid.
+#' @param x Output format.
 #' @export
 dr_output_format_valid <- function(x) {
   format_choices <- c("tsv", "parquet", "delta", "rds")

diff --git a/R/vcf.R b/R/vcf.R
@@ -113,7 +113,7 @@ bcftools_parse_vcf <- function(vcf, only_pass = TRUE) {
 #'
 #' @examples
 #' \dontrun{
-#' vcf_local <- here::here("nogit/tso/2023-05-30/SBJ00595_L2100178/PTC_SrSqCMM1pc_L2100178_rerun_MergedSmallVariants.vcf.gz")
+#' vcf_local <- here::here("MergedSmallVariants.vcf.gz")
 #' r <- c("chr1:115256529-115256529", "chr2:29443613-29443613")
 #' bcftools_parse_vcf_regions(vcf_local, r)
 #' }

diff --git a/inst/rmd/umccr_portal/portal_summary.Rmd b/inst/rmd/umccr_portal/portal_summary.Rmd
@@ -116,8 +116,8 @@ get_sbj_url <- function(x, colour = NULL, account = "pro") {
 # Get metadata for workflows run within the date range
 # options(width = 150)
 fmt1 <- "%Y-%m-%dT%H:%M:%S"
-date_start <- as.POSIXct("2023-11-22T00:00:01", format = fmt1)
-date_end <- as.POSIXct("2023-11-23T23:59:59", format = fmt1)
+date_start <- as.POSIXct("2023-11-27T00:00:01", format = fmt1)
+date_end <- as.POSIXct("2023-11-28T23:59:59", format = fmt1)
 wf_order <- c(
   "bcl_convert",
   "tso_ctdna_tumor_only",
@@ -134,6 +134,7 @@ wf_order <- c(
   "sash"
 )
 
+invisible(capture.output(dracarys:::awsvault_profile("upro")))
 lims_rds <- here(glue("nogit/data_portal/lims/{as.Date(date_end)}.rds"))
 # lims_raw <- dracarys::glims_read()
 # saveRDS(lims_raw, file = lims_rds)

diff --git a/man/TsoCopyNumberVariantsVcfFile.Rd b/man/TsoCopyNumberVariantsVcfFile.Rd
diff --git a/man/TsoMergedSmallVariantsVcfFile.Rd b/man/TsoMergedSmallVariantsVcfFile.Rd
diff --git a/man/bcftools_parse_vcf_regions.Rd b/man/bcftools_parse_vcf_regions.Rd
diff --git a/man/dr_output_format_valid.Rd b/man/dr_output_format_valid.Rd
diff --git a/man/multiqc_parse_bargraph_plot.Rd b/man/multiqc_parse_bargraph_plot.Rd
diff --git a/man/multiqc_parse_plots.Rd b/man/multiqc_parse_plots.Rd
diff --git a/man/s3_files_list_filter_relevant.Rd b/man/s3_files_list_filter_relevant.Rd
diff --git a/tests/testthat/test-roxytest-testexamples-portal_meta.R b/tests/testthat/test-roxytest-testexamples-portal_meta.R
@@ -73,7 +73,7 @@ test_that("Function meta_star_alignment() @ L498", {
 
   pmeta <- system.file("extdata/portal_meta_top4.csv", package = "dracarys")
   (m <- meta_star_alignment(pmeta))
-  expect_equal(all(c("s3_outdir_star", "LibraryID_tumor") %in% colnames(m)), TRUE)
+  expect_equal(all(c("s3_outdir_star", "LibraryID") %in% colnames(m)), TRUE)
 })
 
 
@@ -105,6 +105,6 @@ test_that("Function meta_oncoanalyser_wts() @ L715", {
 
   pmeta <- system.file("extdata/portal_meta_top4.csv", package = "dracarys")
   (m <- meta_oncoanalyser_wts(pmeta))
-  expect_equal(all(c("s3_outdir_oncoanalyser", "LibraryID_tumor", "s3_bam_tumor") %in% colnames(m)), TRUE)
+  expect_equal(all(c("s3_outdir_oncoanalyser", "LibraryID", "s3_bam") %in% colnames(m)), TRUE)
 })
 
diff --git a/tests/testthat/test-roxytest-testexamples-regex.R b/tests/testthat/test-roxytest-testexamples-regex.R
@@ -2,7 +2,7 @@
 
 # File R/regex.R: @testexamples
 
-test_that("Function dr_func_eval() @ L89", {
+test_that("Function dr_func_eval() @ L91", {
 
   mean_1_to_10 <- dr_func_eval("mean", v = c("mean", "sd"))(1:10)
   x <- system.file("extdata/tso/sample705.fragment_length_hist.json.gz", package = "dracarys")