From e66fd18b059bd0ccdb1b4fa838fcbbad879281e7 Mon Sep 17 00:00:00 2001 From: Stu Field Date: Thu, 4 Apr 2024 14:14:33 -0600 Subject: [PATCH] Update Checksums and versions for Annotations Excel files - updated the 7k and 11k file versions - accordingly updated the md5sum checksums - should allow `read_annotations()` to load the individual Excel files - fixes #116 --- R/read-annotations.R | 47 ++++++++++---------------- tests/testthat/test-read-annotations.R | 4 +-- 2 files changed, 20 insertions(+), 31 deletions(-) diff --git a/R/read-annotations.R b/R/read-annotations.R index 7dec7d0..fd64587 100644 --- a/R/read-annotations.R +++ b/R/read-annotations.R @@ -116,22 +116,11 @@ ver_dict <- list( skip = 8L, rows = 5293, cols = 43), - # 11k - # SomaScan_V5.0_11K_Annotated_Content_20240214 - "SL-906-rev3-2024-02" = list(sha = "44352af60dc0152d65f3dad1f0c54abc", - col_serum = c("Serum Scalar v5.0 11K to v4.1 7K", - "Serum Scalar v5.0 11K to v4.0 5K"), - col_plasma = c("Plasma Scalar v5.0 11K to v4.1 7K", - "Plasma Scalar v5.0 11K to v4.0 5K"), - which_serum = c(43, 47), - which_plasma = c(45, 49), - skip = 8L, - rows = 11092, - cols = 51), - # 7k - # SomaScan_V4.1_7K_Annotated_Content_20240214 - "SL-00000571-rev7-2024-02" = list(sha = "ab6ecbce3565c2c6049c0150f653f51b", + # source 7k ---- + # https://menu.somalogic.com + # SomaScan_7K_Annotated_Content.xlsx + "SL-00000571-rev7-2024-02" = list(sha = "0cf00a6afdc1a5cf1f7b8e16cffedccc", col_serum = c("Serum Scalar v4.1 7K to v4.0 5K", "Serum Scalar v4.1 7K to v5.0 11K"), col_plasma = c("Plasma Scalar v4.1 7K to v4.0 5K", @@ -140,18 +129,18 @@ ver_dict <- list( which_plasma = c(45, 49), skip = 8L, rows = 7605, - cols = 50) - # 5k - # SomaScan_V4.0_5K_Annotated_Content_20240216.xlsx - # (may not be released) - # "SL-00000246-revnotreleased-2024-02" = list(sha = "xxxxxx", - # col_serum = c("Serum Scalar v4.0 5K to v4.1 7K", - # "Serum Scalar v4.0 5K to v5.0 11K"), - # col_plasma = c("Plasma Scalar v4.0 5K to v4.1 7K", - # "Plasma Scalar v4.0 5K to v5.0 11K"), - # which_serum = c(43, 47), - # which_plasma = c(45, 49), - # skip = 8L, - # rows = 5293, - # cols = 50) + cols = 50), + # source 11k ---- + # https://menu.somalogic.com + # SomaScan_11K_Annotated_Content.xlsx + "SL-00000906-rev4-2024-03" = list(sha = "f4f42681780a03d2972215f355748064", + col_serum = c("Serum Scalar v5.0 11K to v4.1 7K", + "Serum Scalar v5.0 11K to v4.0 5K"), + col_plasma = c("Plasma Scalar v5.0 11K to v4.1 7K", + "Plasma Scalar v5.0 11K to v4.0 5K"), + which_serum = c(43, 47), + which_plasma = c(45, 49), + skip = 8L, + rows = 11092, + cols = 51) ) diff --git a/tests/testthat/test-read-annotations.R b/tests/testthat/test-read-annotations.R index 05dfd0b..767ae67 100644 --- a/tests/testthat/test-read-annotations.R +++ b/tests/testthat/test-read-annotations.R @@ -8,8 +8,8 @@ test_that("`ver_dict` is updated and correct", { "SL-12345678-rev0-2021-01", "SL-00000571-rev2-2021-06", "SL-00000246-rev5-2021-06", - "SL-906-rev3-2024-02", - "SL-00000571-rev7-2024-02")) + "SL-00000571-rev7-2024-02", + "SL-00000906-rev4-2024-03")) }) test_that("`getAnnoVer()` parses the version correctly", {