Add tests for annotator-cli.R

analyses/long-format-table-utils/annotator/tests/test_annotator_cli.R

@@ -0,0 +1,398 @@
+# The working directory is the directory that contains this test R file, if this
+# file is executed by test_dir
+#
+# testthat package is loaded, if this file is executed by test_dir
+context("test_annotator_cli.R")
+
+
+working_input_tsv_path <- "test_data/test_long_format_table.tsv"
+
+# Add [] after reading to be compatible with readr >= 1.3.1, otherwise the tests
+# will fail on readr >= 1.3.1 as found by @NHJohnson at
+# <https://github.com/PediatricOpenTargets/OpenPedCan-analysis/pull/56
+#  #issuecomment-885188592>
+#
+# readr 1.3.1 returns spec_tbl_df subclass, which becomes tbl_df after any
+# subsetting
+#
+# Ref: https://www.tidyverse.org/blog/2018/12/readr-1-3-1/#tibble-subclass
+long_format_tibble <- readr::read_tsv(
+  working_input_tsv_path,
+  col_types = readr::cols(.default = readr::col_character()))[]
+
+inspected_annotated_long_format_tibble <- readr::read_tsv(
+  "test_data/inspected_annotated_test_long_format_table.tsv",
+  col_types = readr::cols(.default = readr::col_character()),
+  na = c("NA"), quoted_na = FALSE, trim_ws = FALSE)[]
+
+# to save intermediate files
+scratch_dir <- "test_scratch"
+annotator_cli_path <- file.path("..", "annotator-cli.R")
+annotator_cli_output_path <- file.path(
+  scratch_dir, "annotated_test_long_format_table.tsv")
+
+# Test cases
+#
+# Helper function to run annotator CLI
+run_cli_get_tibble <- function(columns_to_add,
+                               input_table_path,
+                               output_table_path) {
+  run_command <- function(cmd_str) {
+    # ignore.stderr = TRUE avoids printing when testing
+    #
+    # intern = TRUE captures output as return value
+    #
+    # If a command fails, only a warning is generated, so expect warning when
+    # testing
+    #
+    # Future updates could parse warning messages to determine whether it is
+    # failed by the CLI or other issues
+    out <- system(cmd_str, ignore.stderr = TRUE, intern = TRUE)
+    return(out)
+  }
+  if (is.null(columns_to_add)) {
+    # run without -c
+    run_command(paste0(
+      "Rscript --vanilla ../annotator-cli.R -r ",
+      " -i ", input_table_path,
+      " -o ", output_table_path))
+  } else {
+    columns_to_add_opt_val <- paste0(
+      "'", paste(columns_to_add, collapse = ","), "'")
+    run_command(paste0(
+      "Rscript --vanilla ../annotator-cli.R ",
+      "-r -c ", columns_to_add_opt_val,
+      " -i ", input_table_path,
+      " -o ", output_table_path))
+  }
+
+  # the file may not be created due to CLI call failure
+  if (file.exists(output_table_path)) {
+    ann_tibble <- readr::read_tsv(
+      output_table_path,
+      col_types = readr::cols(.default = readr::col_character()),
+      na = c("NA"), quoted_na = FALSE, trim_ws = FALSE)[]
+
+    # clean up, so other tests will not be affected
+    file.remove(output_table_path)
+    return(ann_tibble)
+  } else {
+    return(NULL)
+  }
+}
+
+# Add package prefix for auto completion purpose only
+#
+# Test standard usecase
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path),
+  inspected_annotated_long_format_tibble)
+
+# Test annotation order
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("RMTL", "Gene_type", "OncoKB_cancer_gene",
+                       "OncoKB_oncogene_TSG", "Gene_full_name",
+                       "Protein_RefSeq_ID", "EFO", "MONDO"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path),
+  inspected_annotated_long_format_tibble[,
+    c("Gene_symbol", "Gene_Ensembl_ID", "Disease", "cohort", "tpm_mean", "RMTL",
+      "Gene_type", "OncoKB_cancer_gene", "OncoKB_oncogene_TSG",
+      "Gene_full_name", "Protein_RefSeq_ID", "EFO", "MONDO")])
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("MONDO", "RMTL", "EFO"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path),
+  inspected_annotated_long_format_tibble[,
+    c("Gene_symbol", "Gene_Ensembl_ID", "Disease", "cohort", "tpm_mean",
+      "MONDO", "RMTL", "EFO")])
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("RMTL", "EFO", "MONDO"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path),
+  inspected_annotated_long_format_tibble[,
+    c("Gene_symbol", "Gene_Ensembl_ID", "Disease", "cohort", "tpm_mean",
+      "RMTL", "EFO", "MONDO")])
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("RMTL", "Protein_RefSeq_ID", "Gene_full_name"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path),
+  inspected_annotated_long_format_tibble[,
+    c("Gene_symbol", "Gene_Ensembl_ID", "Disease", "cohort", "tpm_mean",
+      "RMTL", "Protein_RefSeq_ID", "Gene_full_name")])
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("OncoKB_oncogene_TSG", "OncoKB_cancer_gene", "MONDO"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path),
+  inspected_annotated_long_format_tibble[,
+    c("Gene_symbol", "Gene_Ensembl_ID", "Disease", "cohort", "tpm_mean",
+      "OncoKB_oncogene_TSG", "OncoKB_cancer_gene", "MONDO")])
+
+# Return same table if no annotation to add
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = "",
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path),
+  long_format_tibble)
+
+# Error on duplicated annotation columns
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = c("OncoKB_oncogene_TSG", "OncoKB_oncogene_TSG", "MONDO"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path))
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = c("OncoKB_oncogene_TSG", "MONDO", "MONDO"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path))
+
+# Error on non-available annotation columns
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = c("NOT_AVAILABLE", "MONDO", "MONDO"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path))
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = c("NOT_AVAILABLE"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path))
+
+# Error on missing required columns
+req_col_missing_tbl_path <- file.path(
+  scratch_dir, "test_missing_req_col_long_format_table.tsv")
+
+readr::write_tsv(
+  dplyr::select(long_format_tibble, -Gene_symbol),
+  req_col_missing_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = req_col_missing_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+
+readr::write_tsv(
+  dplyr::select(long_format_tibble, -Gene_Ensembl_ID),
+  req_col_missing_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = req_col_missing_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+
+readr::write_tsv(
+  dplyr::select(long_format_tibble, -Disease),
+  req_col_missing_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = req_col_missing_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+
+readr::write_tsv(
+  dplyr::select(long_format_tibble, -Gene_symbol, -Gene_Ensembl_ID),
+  req_col_missing_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = req_col_missing_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+
+readr::write_tsv(
+  dplyr::select(long_format_tibble, -Gene_symbol, -Gene_Ensembl_ID, -Disease),
+  req_col_missing_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = req_col_missing_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+
+readr::write_tsv(
+  dplyr::select(long_format_tibble, -Gene_Ensembl_ID, -Disease),
+  req_col_missing_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = req_col_missing_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+
+# Error on requiring existing annotation columns
+ann_col_exist_tbl_path <- file.path(
+  scratch_dir, "test_ann_col_exist_long_format_table.tsv")
+
+readr::write_tsv(
+  dplyr::select(inspected_annotated_long_format_tibble, -EFO),
+  ann_col_exist_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = ann_col_exist_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+readr::write_tsv(
+  inspected_annotated_long_format_tibble,
+  ann_col_exist_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = NULL,
+    input_table_path = ann_col_exist_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+
+readr::write_tsv(
+  dplyr::select(inspected_annotated_long_format_tibble, -EFO),
+  ann_col_exist_tbl_path)
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = c("EFO", "MONDO"),
+    input_table_path = ann_col_exist_tbl_path,
+    output_table_path = annotator_cli_output_path))
+
+
+# Error on duplicated annotation columns
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = c("EFO", "EFO"),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path))
+
+# Error on non character annotation columns
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = c(1),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path))
+
+testthat::expect_warning(
+  run_cli_get_tibble(
+    columns_to_add = c(TRUE),
+    input_table_path = working_input_tsv_path,
+    output_table_path = annotator_cli_output_path))
+
+
+# No error on requiring non-existing annotation columns
+#
+# Relocate to last, so the order is expected. Adapted from
+# https://stackoverflow.com/a/43902237/4638182. The dplyr::relocate is not
+# available in the Docker image
+#
+# The behavior of testthat::expect_equal changed at some point. The Docker
+# image/container version does not check column order, whereas the latest
+# version checks.
+req_non_existing_ann_tbl_path <- file.path(
+  scratch_dir, "test_req_non_existing_ann_long_format_table.tsv")
+
+readr::write_tsv(
+  dplyr::select(
+    inspected_annotated_long_format_tibble, -EFO, -OncoKB_cancer_gene),
+  req_non_existing_ann_tbl_path)
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("EFO", "OncoKB_cancer_gene"),
+    input_table_path = req_non_existing_ann_tbl_path,
+    output_table_path = annotator_cli_output_path),
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -EFO, -OncoKB_cancer_gene,
+    EFO, OncoKB_cancer_gene))
+
+
+readr::write_tsv(
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -EFO, -OncoKB_cancer_gene, -OncoKB_oncogene_TSG),
+  req_non_existing_ann_tbl_path)
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("EFO", "OncoKB_cancer_gene"),
+    input_table_path = req_non_existing_ann_tbl_path,
+    output_table_path = annotator_cli_output_path),
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -OncoKB_oncogene_TSG, -EFO, -OncoKB_cancer_gene,
+    EFO, OncoKB_cancer_gene))
+
+
+readr::write_tsv(
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -MONDO, -OncoKB_cancer_gene, -Protein_RefSeq_ID, -RMTL),
+  req_non_existing_ann_tbl_path)
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("MONDO", "OncoKB_cancer_gene", "Protein_RefSeq_ID"),
+    input_table_path = req_non_existing_ann_tbl_path,
+    output_table_path = annotator_cli_output_path),
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -RMTL, -MONDO, -OncoKB_cancer_gene, -Protein_RefSeq_ID,
+    MONDO, OncoKB_cancer_gene, Protein_RefSeq_ID))
+
+
+readr::write_tsv(
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -EFO, -OncoKB_oncogene_TSG, -Gene_full_name, -RMTL),
+  req_non_existing_ann_tbl_path)
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("EFO", "OncoKB_oncogene_TSG", "Gene_full_name"),
+    input_table_path = req_non_existing_ann_tbl_path,
+    output_table_path = annotator_cli_output_path),
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -RMTL, -EFO, -OncoKB_oncogene_TSG, -Gene_full_name,
+    EFO, OncoKB_oncogene_TSG, Gene_full_name))
+
+
+readr::write_tsv(
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -EFO, -OncoKB_oncogene_TSG, -Gene_full_name, -RMTL, -Gene_type),
+  req_non_existing_ann_tbl_path)
+
+testthat::expect_equal(
+  run_cli_get_tibble(
+    columns_to_add = c("EFO", "OncoKB_oncogene_TSG", "Gene_full_name",
+                       "Gene_type"),
+    input_table_path = req_non_existing_ann_tbl_path,
+    output_table_path = annotator_cli_output_path),
+  dplyr::select(
+    inspected_annotated_long_format_tibble,
+    -RMTL, -EFO, -OncoKB_oncogene_TSG, -Gene_full_name, -Gene_type,
+    EFO, OncoKB_oncogene_TSG, Gene_full_name, Gene_type))