From d1f7215f3c41b6e112f31199d824d89648b80904 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 30 Apr 2024 11:49:57 -0400 Subject: [PATCH 1/3] bump x.y.z version to even y prior to creation of RELEASE_3_19 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index df557bb3..85868153 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: gDRutils Type: Package Title: A package with helper functions for processing drug response data -Version: 1.1.11 +Version: 1.2.0 Date: 2024-04-15 Authors@R: c(person("Bartosz", "Czech", role=c("aut"), comment = c(ORCID = "0000-0002-9908-3007")), From 29cb67a17274d8021b08419157b3a02400b1a979 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 30 Apr 2024 11:49:57 -0400 Subject: [PATCH 2/3] bump x.y.z version to odd y following creation of RELEASE_3_19 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 85868153..4e714c41 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: gDRutils Type: Package Title: A package with helper functions for processing drug response data -Version: 1.2.0 +Version: 1.3.0 Date: 2024-04-15 Authors@R: c(person("Bartosz", "Czech", role=c("aut"), comment = c(ORCID = "0000-0002-9908-3007")), From 06bb1802c17cd33aa953596abd50d853ec9835f8 Mon Sep 17 00:00:00 2001 From: Marcin Kamianowski Date: Tue, 28 May 2024 15:34:20 +0200 Subject: [PATCH 3/3] fix: move test helper files --- inst/test_settings.json | 29 ++++ inst/test_settings_2.json | 129 ++++++++++++++++++ .../test-convert_mae_se_assay_to_dt.R | 2 +- tests/testthat/test-json_const.R | 2 +- tests/testthat/test-utils.R | 2 +- 5 files changed, 161 insertions(+), 3 deletions(-) create mode 100644 inst/test_settings.json create mode 100644 inst/test_settings_2.json diff --git a/inst/test_settings.json b/inst/test_settings.json new file mode 100644 index 00000000..5cb70579 --- /dev/null +++ b/inst/test_settings.json @@ -0,0 +1,29 @@ +{ + "DICT": { + "fifty_lower_limit": 0.0001, + "fifty_upper_limit": 30, + "max_upper_limit": 1.1, + "range_lower_limit": -0.1 + }, + "DICT_WITH_LOGICAL": { + "axisTitleText": true, + "titleText": true + }, + "DICT_WITH_LISTS": { + "GR AOC within set range": [ + 0, + 1 + ], + "RV AOC within set range": [ + 0, + 1 + ] + }, + "LIST": [ + "rId", + "cId", + "r Id", + "c Id" + ], + "STRING": "fixed" +} diff --git a/inst/test_settings_2.json b/inst/test_settings_2.json new file mode 100644 index 00000000..77d3ae37 --- /dev/null +++ b/inst/test_settings_2.json @@ -0,0 +1,129 @@ +{ + "FILTERED_OUT_COLS_COMBOS": [ + "rId", + "cId", + "r Id", + "c Id" + ], + "FIXED_PREFIX": "fixed", + "METRIC_WISH_LIST": [ + "GR50", + "IC50", + "GR Max", + "E Max", + "EC50", + "GR Mean", + "RV Mean", + "GR AOC within set range", + "RV AOC within set range" + ], + "METRIC_WISH_LIST_CURVE": [ + "GR value", + "Relative Viability" + ], + "METRICS_TRANSFORMED": [ + "GR50", + "IC50", + "EC50" + ], + "SUPPORTED_FILE_TYPES_AUTO": [ + "text/tsv", + "text/tab-separated-values", + ".csv", + ".xlsx", + ".tsv" + ], + "SUPPORTED_FILE_TYPES_MANIFEST": [ + "text/tsv", + "text/tab-separated-values", + "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" + ], + "SUPPORTED_FILE_TYPES_TREATMENT": [ + "text/tsv", + "text/tab-separated-values", + "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" + ], + "SUPPORTED_FILE_TYPES_RAWDATA": [ + "text/csv", + "text/tsv", + "text/tab-separated-values", + "text/tab-separated-values,text/plain", + "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" + ], + "VIS_COLS_NORM": [ + "drug_name", + "drug_moa", + "drug_name2", + "drug_moa2", + "drug_name3", + "drug_moa3", + "cellline_name", + "cellline_tissue", + "cellline_subtype", + "UserCellLineDesignation", + "GR value", + "Relative Viability", + "CorrectedReadout", + "drug", + "drug2", + "drug3", + "cellline", + "cellline_ref_div_time", + "concentration", + "concentration2", + "concentration3" + ], + "VIS_COLS_AVG": [ + "drug_name", + "drug_moa", + "drug_name2", + "drug_moa2", + "drug_name3", + "drug_moa3", + "cellline_name", + "cellline_tissue", + "cellline_subtype", + "UserCellLineDesignation", + "GR value", + "Relative Viability", + "Std GR value", + "Std Relative Viability", + "drug", + "drug2", + "drug3", + "cellline", + "cellline_ref_div_time", + "concentration", + "concentration2", + "concentration3" + ], + "VIS_COLS_METRICS": [ + "drug_name", + "drug_moa", + "drug_name2", + "drug_moa2", + "drug_name3", + "drug_moa3", + "cellline_name", + "cellline_tissue", + "cellline_subtype", + "UserCellLineDesignation", + "Data Source", + "GR AOC", + "RV AOC", + "RV Mean", + "GR Mean", + "IC50", + "GR50", + "E Max", + "GR Max", + "E Inf", + "GR Inf", + "drug", + "drug2", + "drug3", + "cellline", + "cellline_ref_div_time", + "Highest log10(conc.)" + ] +} \ No newline at end of file diff --git a/tests/testthat/test-convert_mae_se_assay_to_dt.R b/tests/testthat/test-convert_mae_se_assay_to_dt.R index 48c2bd3d..77e77ffc 100644 --- a/tests/testthat/test-convert_mae_se_assay_to_dt.R +++ b/tests/testthat/test-convert_mae_se_assay_to_dt.R @@ -200,7 +200,7 @@ test_that("convert_mae_assay_to_dt works as expected", { test_that("convert_se_assay_to_custom_dt works fine", { - json_path <- system.file(package = "gDRcomponents", "settings.json") + json_path <- system.file(package = "gDRutils", "test_settings_2.json") s <- get_settings_from_json(json_path = json_path) se <- get_synthetic_data("finalMAE_small")[[1]] diff --git a/tests/testthat/test-json_const.R b/tests/testthat/test-json_const.R index ad6b2db2..686ad9e8 100644 --- a/tests/testthat/test-json_const.R +++ b/tests/testthat/test-json_const.R @@ -5,7 +5,7 @@ test_that("get_settings_from_json works as expected", { "Assertion on 'json_path' failed" ) json_path <- - system.file(package = "gDRcomponents", "test_settings.json") + system.file(package = "gDRutils", "test_settings.json") expect_error( get_settings_from_json(s = "no_such_entry", json_path = json_path), "Assertion on 's' failed" diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R index bd64ff73..5089afb3 100644 --- a/tests/testthat/test-utils.R +++ b/tests/testthat/test-utils.R @@ -468,7 +468,7 @@ test_that("get_additional_variables works as expected", { test_that("convert_se_assay_to_custom_dt works fine", { - json_path <- system.file(package = "gDRcomponents", "settings.json") + json_path <- system.file(package = "gDRutils", "test_settings_2.json") s <- get_settings_from_json(json_path = json_path) se <- get_synthetic_data("finalMAE_small")[[1]]