Nothing
tests/testthat/test-dq_report_by_arguments.R
In dataquieR: Data Quality in Epidemiological Research
test_that("dq_report_by error_arguments_test", {
skip_if_not_installed("DT")
skip_if_not_installed("markdown")
skip_if_not_installed("stringdist")
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
skip_on_cran() # slow test
skip_if_offline(host = "dataquality.qihs.uni-greifswald.de")
target <- withr::local_tempdir("testdqareportby")
sd0 <- head(prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
20)
sd0 <- sd0[, head(colnames(sd0), 10)]
md0 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | item_level")
md0 <- md0[md0$VAR_NAMES %in% colnames(sd0), ]
# fewer segments to speed up things.
# can be solved in a more elegant way after
# https://gitlab.com/libreumg/dataquier/-/issues/481
md0$STUDY_SEGMENT <- "STUDY"
expect_warning(expect_warning(dq_report_by(study_data = sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
subgroup = "[v00003] == 106",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm"),
also_print = TRUE),
regexp = "No data available to create the report.+"),
regexp = ".*impossible condition.+")
expect_warning(dq_report_by(study_data = sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
subgroup = "[v00003] > 1",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm1"),
also_print = TRUE),
regexp = "The number of cases did not change after applying the subgroup.+")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_select = "2",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm2"),
also_print = TRUE),
"strata_column is needed for selecting the strata", fixed = TRUE)
expect_message2(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_column = "v00002",
strata_select = "^ma",
selection_type = "regex",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm3"),
also_print = TRUE))
#Label_col and strata not matching
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
label_col = VAR_NAMES,
strata_column = "SEX_0",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm4"),
also_print = TRUE),
regexp = "The strata_column provided does not.+item_level_metadata")
#no existing strata matches the regex
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_column = "v00002",
strata_select = "^hello",
selection_type = "regex",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm5"),
also_print = TRUE),
regexp = "No value or value label.+strata.+select")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_exclude = "1",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm6"),
also_print = TRUE),
"strata_column is needed for excluding the strata", fixed = TRUE)
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
selection_type = "value",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm7"),
also_print = TRUE),
paste0("selection_type can only be specified if strata_select",
" or strata_exclude are present"), fixed = TRUE)
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_column = "SEX_0",
strata_exclude = "1",
selection_type = "values",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm8"),
also_print = TRUE),
paste0('Internal error: The selection_type can only',
' be "value", "v_label", or "regex"'), fixed = TRUE)
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
subgroup = c("[AGE_0]>30", "[SBP_0]>100"),
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm9"),
also_print = TRUE),
paste0("Need exactly one element in argument subgroup, ",
"got 2: [[AGE_0]>30, [SBP_0]>100]"),
fixed = TRUE)
expect_error(dq_report_by(sd0,
meta_data = md0,
input_dir = "test/error",
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm10"),
also_print = TRUE),
regexp = ".+test/error.+does not exist. Provide an.+input_dir.+containing the study data")
expect_error(dq_report_by(sd0,
meta_data = md0,
id_vars = "non-existing",
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm11"),
also_print = TRUE),
regexp = "The id_vars.+non-existing.+is not present in the item_level metadata")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm12"),
strata_column = "SEX_0",
strata_exclude = "female", selection_type = "v_label",
also_print = TRUE),
regexp = "Internal error: No value label.+strata_exclude")
expect_message2(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm13"),
strata_column = "SEX_0",
strata_exclude = "females", selection_type = "v_label",
also_print = TRUE))
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm14"),
strata_column = "SEX_0",
strata_exclude = "^femm", selection_type = "regex",
also_print = TRUE),
regexp = "Internal error: No value or value label.+strata_exclude")
expect_warning(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm15"),
strata_column = "SEX_0",
strata_exclude = "^fem",
also_print = TRUE),
regexp = "The argument selection_type not provided.+expressions")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm16"),
strata_column = "SEX_0", selection_type = "value",
strata_exclude = c("0", "1"),
also_print = TRUE),
regexp = "Internal error: No strata remain.+ones")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
label_col = "VAR_NAMES",
cores = NULL,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm17"),
strata_column = "SEX_0",
also_print = TRUE),
regexp = "The strata_column provided does not correpond.+item_level_metadata")
#remove columns VAR_NAMES from metadata
md1 <- md0[ , !(names(md0) == VAR_NAMES)]
expect_error(dq_report_by(sd0,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm18"),
also_print = TRUE),
regexp = "Did not find the mandatory column.+VAR_NAMES.+in the.+meta_data.+")
#remove columns STUDY_SEGMENT from metadata
md2 <- md0[ , !(names(md0) == STUDY_SEGMENT)]
expect_error(dq_report_by(sd0,
meta_data = md2,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm19"),
also_print = TRUE),
regexp = "No metadata attribute.+STUDY_SEGMENT.+found for segmenting DQ report.")
expect_error(dq_report_by(sd0,
meta_data = md2,
dimensions = "int",
cores = NULL,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm20"),
also_print = TRUE),
regexp = "No information for split provided.+segment_column = NULL.+")
expect_error(dq_report_by(sd0,
meta_data = md2,
dimensions = "int",
cores = NULL,
strata_column = "sex_two",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm21"),
also_print = TRUE),
regexp = "The strata_column provided does not correpond.+item_level_metadata")
expect_message2(dq_report_by(study_data = c("https://dataquality.qihs.uni-greifswald.de/extdata/fortests/ship.RDS",
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
meta_data_v2 ="https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "comb1"),
cores = NULL,
also_print=TRUE,
segment_column = STUDY_SEGMENT,
segment_exclude = c("PHYS_EXAM", "LAB",
"INTERVIEW", "QUESTIONNAIRE"),
strata_column = "v00002",
strata_select = "females",
dimensions = "Integrity",
selection_type = "v_label",
subgroup = "[v00003]<40",
id_vars = "v00001"))
sd1 <- head(prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
20)
expect_message2(dq_report_by(resp_vars = c("v00000", "v00001", "v00002",
"v00003", "v00004", "v00005",
"v00006", "v00018"),
study_data = sd1,
cores = NULL,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "comb2"),
also_print=TRUE,
segment_column = STUDY_SEGMENT,
segment_select = "^STU",
dimensions = "Integrity"))
sd3 <- head(prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
20)
sd3 <- sd3[, head(colnames(sd3), 10)]
md3 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | item_level")
md3 <- md3[md3$VAR_NAMES %in% colnames(sd3), ]
md3$STUDY_SEGMENT <- "STUDY"
md3$DATAFRAMES <- "my_sd"
df3 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | dataframe_level")
df3$DF_ID_REF_TABLE <- NA
df3$DF_RECORD_CHECK <- NA
df3$DF_UNIQUE_ID <- NA
df3$DF_CODE <- "my_sd"
segl3 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | segment_level")
segl3$SEGMENT_ID_TABLE <- NA
segl3$SEGMENT_ID_VARS <- NA
segl3$SEGMENT_RECORD_CHECK<- NA
segl3$SEGMENT_UNIQUE_ROWS <- NA
md3$MISSING_LIST_TABLE <- NA
expect_message2(dq_report_by(sd3,
meta_data = md3,
meta_data_dataframe = df3,
meta_data_segment = segl3,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
segment_select = "^ST",
output_dir = !!file.path(target, "comb3"),
also_print = TRUE))
df3$DF_NAME <- "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"
expect_message2(dq_report_by(meta_data = md3,
meta_data_dataframe = df3,
cores = NULL,
segment_select = "STUDY",
output_dir = !!file.path(target, "comb4"),
also_print = TRUE ))
df3 <- rbind(df3,
data.frame(DF_ELEMENT_COUNT = NA,
DF_RECORD_COUNT = NA,
DF_ID_REF_TABLE = NA,
DF_RECORD_CHECK = NA,
DF_UNIQUE_ID= NA,
DF_ID_VARS = "id",
DF_UNIQUE_ROWS = NA,
DF_CODE = "ship",
DF_NAME = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/ship.RDS"))
expect_message2(dq_report_by(meta_data = md3,
meta_data_dataframe = df3,
cores = NULL,
segment_select = "STUDY",
output_dir = !!file.path(target, "comb5"),
also_print = TRUE ))
md3$REPORT_NAME <- c("A", "B")
expect_message2(dq_report_by(sd3,
meta_data = md3,
dimensions = "int",
cores = NULL,
segment_column = "REPORT_NAME",
segment_select = "A",
output_dir = !!file.path(target, "comb6"),
also_print = TRUE))
expect_error(dq_report_by(sd3,
meta_data = md3,
dimensions = "int",
cores = NULL,
segment_column = "REPORTT_NAME",
output_dir = !!file.path(target, "comb7"),
also_print = TRUE),
regexp = "No metadata.+for segmenting DQ report.")
expect_error(dq_report_by(sd3,
meta_data = md3,
dimensions = "int",
cores = NULL,
strata_column = "non-existent_strata",
output_dir = !!file.path(target, "comb8"),
also_print = TRUE),
regexp = "The strata_column provided.+in the item_level_metadata")
md3 <- md3[, !colnames(md3) %in% "DATAFRAMES"]
df3 <- df3[, !colnames(df3) %in% "DF_CODE"]
expect_warning(dq_report_by(meta_data = md3,
meta_data_dataframe = df3,
cores = NULL,
segment_select = "STUDY",
output_dir = !!file.path(target, "comb9"),
also_print = TRUE ),
regexp = "Because no id variable is available.+duplicated rows.")
#Without LABEL and VARIABLE_ROLE in metadata
sd1 <- head(prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
20)
sd1 <- sd1[, head(colnames(sd1), 10)]
md1 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | item_level")
md1 <- md1[md1$VAR_NAMES %in% colnames(sd1), ]
md1 <- md1[, !colnames(md1) %in% c("LABEL", "VARIABLE_ROLE")]
md1$MISSING_LIST_TABLE <- NA
expect_message2(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_column = NULL,
output_dir = !!file.path(target, "test1"),
also_print = TRUE))
#only segment_select, but from STUDY_SEGMENT
expect_message2(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_select = "PHYS_EXAM",
output_dir = !!file.path(target, "test2"),
also_print = TRUE))
#only segment_select but not present in STUDY_SEGMENT
expect_error(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_select = "THIS_EXAM",
output_dir = !!file.path(target, "test3"),
also_print = TRUE),
regexp = "segment_select values are.+not assigned.")
#only segment_exclude, but from STUDY_SEGMENT
expect_message2(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_exclude = "PHYS_EXAM",
output_dir = !!file.path(target, "test4"),
also_print = TRUE))
#remove all segments with segment_exclude
expect_error(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_column = "STUDY_SEGMENT",
segment_exclude = c("PHYS_EXAM", "STUDY"),
output_dir = !!file.path(target, "test5"),
also_print = TRUE),
regexp = "No segment.+column level left after removing unwanted segments.+")
#only segment_exclude but not present in STUDY_SEGMENT
expect_error(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_exclude = "THIS_EXAM",
output_dir = !!file.path(target, "test6"),
also_print = TRUE),
regexp = "segment_exclude values.+not assigned.")
#no STUDY_SEGMENT and no segment_select provided
#Without LABEL and VARIABLE_ROLE in metadata
md2 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | item_level")
md2 <- md2[md2$VAR_NAMES %in% colnames(sd1), ]
md2 <- md2[, !colnames(md2) %in% "STUDY_SEGMENT"]
md2$MISSING_LIST_TABLE <- NA
expect_error(dq_report_by(study_data = sd1,
meta_data = md2,
dimensions = "int",
cores = NULL,
output_dir = !!file.path(target, "test7"),
also_print = TRUE),
regexp = "No information for split provided..+segment_column = NULL.+")
})
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test_that("dq_report_by error_arguments_test", {
skip_if_not_installed("DT")
skip_if_not_installed("markdown")
skip_if_not_installed("stringdist")
withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
dataquieR.ERRORS_WITH_CALLER = TRUE,
dataquieR.WARNINGS_WITH_CALLER = TRUE,
dataquieR.MESSAGES_WITH_CALLER = TRUE)
skip_on_cran() # slow test
skip_if_offline(host = "dataquality.qihs.uni-greifswald.de")
target <- withr::local_tempdir("testdqareportby")
sd0 <- head(prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
20)
sd0 <- sd0[, head(colnames(sd0), 10)]
md0 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | item_level")
md0 <- md0[md0$VAR_NAMES %in% colnames(sd0), ]
# fewer segments to speed up things.
# can be solved in a more elegant way after
# https://gitlab.com/libreumg/dataquier/-/issues/481
md0$STUDY_SEGMENT <- "STUDY"
expect_warning(expect_warning(dq_report_by(study_data = sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
subgroup = "[v00003] == 106",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm"),
also_print = TRUE),
regexp = "No data available to create the report.+"),
regexp = ".*impossible condition.+")
expect_warning(dq_report_by(study_data = sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
subgroup = "[v00003] > 1",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm1"),
also_print = TRUE),
regexp = "The number of cases did not change after applying the subgroup.+")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_select = "2",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm2"),
also_print = TRUE),
"strata_column is needed for selecting the strata", fixed = TRUE)
expect_message2(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_column = "v00002",
strata_select = "^ma",
selection_type = "regex",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm3"),
also_print = TRUE))
#Label_col and strata not matching
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
label_col = VAR_NAMES,
strata_column = "SEX_0",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm4"),
also_print = TRUE),
regexp = "The strata_column provided does not.+item_level_metadata")
#no existing strata matches the regex
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_column = "v00002",
strata_select = "^hello",
selection_type = "regex",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm5"),
also_print = TRUE),
regexp = "No value or value label.+strata.+select")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_exclude = "1",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm6"),
also_print = TRUE),
"strata_column is needed for excluding the strata", fixed = TRUE)
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
selection_type = "value",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm7"),
also_print = TRUE),
paste0("selection_type can only be specified if strata_select",
" or strata_exclude are present"), fixed = TRUE)
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
strata_column = "SEX_0",
strata_exclude = "1",
selection_type = "values",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm8"),
also_print = TRUE),
paste0('Internal error: The selection_type can only',
' be "value", "v_label", or "regex"'), fixed = TRUE)
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
subgroup = c("[AGE_0]>30", "[SBP_0]>100"),
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm9"),
also_print = TRUE),
paste0("Need exactly one element in argument subgroup, ",
"got 2: [[AGE_0]>30, [SBP_0]>100]"),
fixed = TRUE)
expect_error(dq_report_by(sd0,
meta_data = md0,
input_dir = "test/error",
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm10"),
also_print = TRUE),
regexp = ".+test/error.+does not exist. Provide an.+input_dir.+containing the study data")
expect_error(dq_report_by(sd0,
meta_data = md0,
id_vars = "non-existing",
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm11"),
also_print = TRUE),
regexp = "The id_vars.+non-existing.+is not present in the item_level metadata")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm12"),
strata_column = "SEX_0",
strata_exclude = "female", selection_type = "v_label",
also_print = TRUE),
regexp = "Internal error: No value label.+strata_exclude")
expect_message2(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm13"),
strata_column = "SEX_0",
strata_exclude = "females", selection_type = "v_label",
also_print = TRUE))
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm14"),
strata_column = "SEX_0",
strata_exclude = "^femm", selection_type = "regex",
also_print = TRUE),
regexp = "Internal error: No value or value label.+strata_exclude")
expect_warning(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm15"),
strata_column = "SEX_0",
strata_exclude = "^fem",
also_print = TRUE),
regexp = "The argument selection_type not provided.+expressions")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm16"),
strata_column = "SEX_0", selection_type = "value",
strata_exclude = c("0", "1"),
also_print = TRUE),
regexp = "Internal error: No strata remain.+ones")
expect_error(dq_report_by(sd0,
meta_data = md0,
dimensions = "int",
label_col = "VAR_NAMES",
cores = NULL,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm17"),
strata_column = "SEX_0",
also_print = TRUE),
regexp = "The strata_column provided does not correpond.+item_level_metadata")
#remove columns VAR_NAMES from metadata
md1 <- md0[ , !(names(md0) == VAR_NAMES)]
expect_error(dq_report_by(sd0,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm18"),
also_print = TRUE),
regexp = "Did not find the mandatory column.+VAR_NAMES.+in the.+meta_data.+")
#remove columns STUDY_SEGMENT from metadata
md2 <- md0[ , !(names(md0) == STUDY_SEGMENT)]
expect_error(dq_report_by(sd0,
meta_data = md2,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm19"),
also_print = TRUE),
regexp = "No metadata attribute.+STUDY_SEGMENT.+found for segmenting DQ report.")
expect_error(dq_report_by(sd0,
meta_data = md2,
dimensions = "int",
cores = NULL,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm20"),
also_print = TRUE),
regexp = "No information for split provided.+segment_column = NULL.+")
expect_error(dq_report_by(sd0,
meta_data = md2,
dimensions = "int",
cores = NULL,
strata_column = "sex_two",
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "sm21"),
also_print = TRUE),
regexp = "The strata_column provided does not correpond.+item_level_metadata")
expect_message2(dq_report_by(study_data = c("https://dataquality.qihs.uni-greifswald.de/extdata/fortests/ship.RDS",
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
meta_data_v2 ="https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "comb1"),
cores = NULL,
also_print=TRUE,
segment_column = STUDY_SEGMENT,
segment_exclude = c("PHYS_EXAM", "LAB",
"INTERVIEW", "QUESTIONNAIRE"),
strata_column = "v00002",
strata_select = "females",
dimensions = "Integrity",
selection_type = "v_label",
subgroup = "[v00003]<40",
id_vars = "v00001"))
sd1 <- head(prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
20)
expect_message2(dq_report_by(resp_vars = c("v00000", "v00001", "v00002",
"v00003", "v00004", "v00005",
"v00006", "v00018"),
study_data = sd1,
cores = NULL,
meta_data_v2 = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx",
output_dir = !!file.path(target, "comb2"),
also_print=TRUE,
segment_column = STUDY_SEGMENT,
segment_select = "^STU",
dimensions = "Integrity"))
sd3 <- head(prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
20)
sd3 <- sd3[, head(colnames(sd3), 10)]
md3 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | item_level")
md3 <- md3[md3$VAR_NAMES %in% colnames(sd3), ]
md3$STUDY_SEGMENT <- "STUDY"
md3$DATAFRAMES <- "my_sd"
df3 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | dataframe_level")
df3$DF_ID_REF_TABLE <- NA
df3$DF_RECORD_CHECK <- NA
df3$DF_UNIQUE_ID <- NA
df3$DF_CODE <- "my_sd"
segl3 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | segment_level")
segl3$SEGMENT_ID_TABLE <- NA
segl3$SEGMENT_ID_VARS <- NA
segl3$SEGMENT_RECORD_CHECK<- NA
segl3$SEGMENT_UNIQUE_ROWS <- NA
md3$MISSING_LIST_TABLE <- NA
expect_message2(dq_report_by(sd3,
meta_data = md3,
meta_data_dataframe = df3,
meta_data_segment = segl3,
dimensions = "int",
cores = NULL,
segment_column = STUDY_SEGMENT,
segment_select = "^ST",
output_dir = !!file.path(target, "comb3"),
also_print = TRUE))
df3$DF_NAME <- "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"
expect_message2(dq_report_by(meta_data = md3,
meta_data_dataframe = df3,
cores = NULL,
segment_select = "STUDY",
output_dir = !!file.path(target, "comb4"),
also_print = TRUE ))
df3 <- rbind(df3,
data.frame(DF_ELEMENT_COUNT = NA,
DF_RECORD_COUNT = NA,
DF_ID_REF_TABLE = NA,
DF_RECORD_CHECK = NA,
DF_UNIQUE_ID= NA,
DF_ID_VARS = "id",
DF_UNIQUE_ROWS = NA,
DF_CODE = "ship",
DF_NAME = "https://dataquality.qihs.uni-greifswald.de/extdata/fortests/ship.RDS"))
expect_message2(dq_report_by(meta_data = md3,
meta_data_dataframe = df3,
cores = NULL,
segment_select = "STUDY",
output_dir = !!file.path(target, "comb5"),
also_print = TRUE ))
md3$REPORT_NAME <- c("A", "B")
expect_message2(dq_report_by(sd3,
meta_data = md3,
dimensions = "int",
cores = NULL,
segment_column = "REPORT_NAME",
segment_select = "A",
output_dir = !!file.path(target, "comb6"),
also_print = TRUE))
expect_error(dq_report_by(sd3,
meta_data = md3,
dimensions = "int",
cores = NULL,
segment_column = "REPORTT_NAME",
output_dir = !!file.path(target, "comb7"),
also_print = TRUE),
regexp = "No metadata.+for segmenting DQ report.")
expect_error(dq_report_by(sd3,
meta_data = md3,
dimensions = "int",
cores = NULL,
strata_column = "non-existent_strata",
output_dir = !!file.path(target, "comb8"),
also_print = TRUE),
regexp = "The strata_column provided.+in the item_level_metadata")
md3 <- md3[, !colnames(md3) %in% "DATAFRAMES"]
df3 <- df3[, !colnames(df3) %in% "DF_CODE"]
expect_warning(dq_report_by(meta_data = md3,
meta_data_dataframe = df3,
cores = NULL,
segment_select = "STUDY",
output_dir = !!file.path(target, "comb9"),
also_print = TRUE ),
regexp = "Because no id variable is available.+duplicated rows.")
#Without LABEL and VARIABLE_ROLE in metadata
sd1 <- head(prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData"),
20)
sd1 <- sd1[, head(colnames(sd1), 10)]
md1 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | item_level")
md1 <- md1[md1$VAR_NAMES %in% colnames(sd1), ]
md1 <- md1[, !colnames(md1) %in% c("LABEL", "VARIABLE_ROLE")]
md1$MISSING_LIST_TABLE <- NA
expect_message2(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_column = NULL,
output_dir = !!file.path(target, "test1"),
also_print = TRUE))
#only segment_select, but from STUDY_SEGMENT
expect_message2(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_select = "PHYS_EXAM",
output_dir = !!file.path(target, "test2"),
also_print = TRUE))
#only segment_select but not present in STUDY_SEGMENT
expect_error(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_select = "THIS_EXAM",
output_dir = !!file.path(target, "test3"),
also_print = TRUE),
regexp = "segment_select values are.+not assigned.")
#only segment_exclude, but from STUDY_SEGMENT
expect_message2(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_exclude = "PHYS_EXAM",
output_dir = !!file.path(target, "test4"),
also_print = TRUE))
#remove all segments with segment_exclude
expect_error(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_column = "STUDY_SEGMENT",
segment_exclude = c("PHYS_EXAM", "STUDY"),
output_dir = !!file.path(target, "test5"),
also_print = TRUE),
regexp = "No segment.+column level left after removing unwanted segments.+")
#only segment_exclude but not present in STUDY_SEGMENT
expect_error(dq_report_by(study_data = sd1,
meta_data = md1,
dimensions = "int",
cores = NULL,
segment_exclude = "THIS_EXAM",
output_dir = !!file.path(target, "test6"),
also_print = TRUE),
regexp = "segment_exclude values.+not assigned.")
#no STUDY_SEGMENT and no segment_select provided
#Without LABEL and VARIABLE_ROLE in metadata
md2 <- prep_get_data_frame(
"https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data_v2.xlsx | item_level")
md2 <- md2[md2$VAR_NAMES %in% colnames(sd1), ]
md2 <- md2[, !colnames(md2) %in% "STUDY_SEGMENT"]
md2$MISSING_LIST_TABLE <- NA
expect_error(dq_report_by(study_data = sd1,
meta_data = md2,
dimensions = "int",
cores = NULL,
output_dir = !!file.path(target, "test7"),
also_print = TRUE),
regexp = "No information for split provided..+segment_column = NULL.+")
})
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