Closes #1659 and #1660 to use gt() instead of kbl() in our functi…

…ons and reports (#1884) * swap kbl with gt * move the formating to allow gsm_gt * get metricTable working in some sort of form * address tests * address warnings of ID not matching file name dont add full path * sawp gsm_gt with gt::gt()
Gilead-BioStats · Oct 14, 2024 · 3fcdbd2 · 3fcdbd2
1 parent 7d79a78
commit 3fcdbd2
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Showing 6 changed files with 18 additions and 27 deletions.
diff --git a/R/Report_MetricCharts.R b/R/Report_MetricCharts.R
@@ -22,7 +22,8 @@ Report_MetricCharts <- function(lCharts, strMetricID = "", overview = FALSE) {
     "barScoreJS",
     "timeSeriesContinuousScoreJS",
     "timeSeriesContinuousMetricJS",
-    "timeSeriesContinuousNumeratorJS"
+    "timeSeriesContinuousNumeratorJS",
+    "metricTable"
   )
 
   chartTypes2 <- c(
@@ -48,7 +49,8 @@ Report_MetricCharts <- function(lCharts, strMetricID = "", overview = FALSE) {
       timeSeriesContinuousMetricJS = paste0(fontawesome::fa("chart-line", fill = "#337ab7"), "  KRI Metric"),
       timeSeriesContinuousNumeratorJS = paste0(fontawesome::fa("chart-line", fill = "#337ab7"), "  Numerator"),
       groupOverviewJS = paste0(fontawesome::fa("table", fill = "#337ab7"), "  Group Overview"),
-      flagOverTimeJS = paste0(fontawesome::fa("table", fill = "#337ab7"), "  Flags Over Time")
+      flagOverTimeJS = paste0(fontawesome::fa("table", fill = "#337ab7"), "  Flags Over Time"),
+      metricTable = paste0(fontawesome::fa("table", fill = "#337ab7"), "  Metric Table")
     )
 
     ##### chart tab /

diff --git a/R/Report_MetricTable.R b/R/Report_MetricTable.R
@@ -41,9 +41,8 @@ Report_MetricTable <- function(
     return("Nothing flagged for this KRI.")
   }
 
-  SummaryTable <- MetricTable %>%
-    kableExtra::kbl(format = "html", escape = FALSE) %>%
-    kableExtra::kable_styling("striped", full_width = FALSE)
+  MetricTable %>%
+    gsm_gt() %>%
+    fmt_sign_rag(columns = "Flag")
 
-  return(SummaryTable)
 }
diff --git a/R/util-MakeMetricTable.R b/R/util-MakeMetricTable.R
@@ -78,7 +78,6 @@ MakeMetricTable <- function(
       desc(abs(.data$Score))
     ) %>%
     dplyr::mutate(
-      Flag = Report_FormatFlag(.data$Flag),
       dplyr::across(
         dplyr::where(is.numeric),
         ~ round(.x, 2)
@@ -95,6 +94,5 @@ MakeMetricTable <- function(
         "Flag"
       ))
     )
-
   return(MetricTable)
 }
diff --git a/R/util-MakeWorkflowList.R b/R/util-MakeWorkflowList.R
@@ -49,6 +49,7 @@ MakeWorkflowList <- function(
     full.names = FALSE,
     recursive = bRecursive
   )
+  names(yaml_files) <-  sub("^.*/", "", names(yaml_files))
 
   # if `strNames` is not null, subset the workflow list to only include
   # files that match the character vector (`strNames`)
@@ -65,10 +66,6 @@ MakeWorkflowList <- function(
     }
   }
 
-  if (is.null(strNames) && strPath == "workflow") {
-    names(yaml_files) <-  sub("^.*/", "", names(yaml_files))
-  }
-
   workflows <- purrr::map2(
     yaml_files,
     names(yaml_files),

diff --git a/inst/report/Report_KRI.Rmd b/inst/report/Report_KRI.Rmd
@@ -21,7 +21,7 @@ knitr::opts_chunk$set(warning = FALSE, message = FALSE)
 
 ```{r, results='asis', echo=FALSE, message=FALSE, warning=FALSE}
 library(gsm)
-library(kableExtra)
+library(gt)
 
 setup <- Report_Setup(
   dfGroups =  params$dfGroups, 
@@ -137,9 +137,6 @@ for (i in unique(params$dfMetrics$MetricID)) {
     overview = FALSE
   )
 
- params$lCharts[[lMetric$MetricID]]$metricTable %>%
-   cat
-
 }
 
 ```
@@ -148,11 +145,10 @@ for (i in unique(params$dfMetrics$MetricID)) {
 ```{r, echo=FALSE, results='asis'}
 #print dfMetrics table
 params$dfMetrics %>%
-kbl(format="html", escape=FALSE) %>%
-kable_styling ("striped", full_width = FALSE) %>%
-cat
+  gt::gt()
 
 ```
+
 ```{r echo=FALSE}
 group_dropdown <- system.file('report', 'lib', 'overallGroupDropdown.js', package = "gsm")
 dropdown_drag <- system.file('report', 'lib', 'dragOverallGroupDropdown.js', package = "gsm")

diff --git a/tests/testthat/test-Report_MetricTable.R b/tests/testthat/test-Report_MetricTable.R
@@ -8,25 +8,24 @@ test_that("Correct data structure when proper dataframe is passed", {
   reportingResults_filt <- reportingResults %>%
     dplyr::filter(MetricID == unique(reportingResults$MetricID)[1])
   result <- Report_MetricTable(reportingResults_filt, reportingGroups)
-  expect_s3_class(result, "kableExtra")
-  expect_true(grepl("<table", result))
-  expect_true(grepl("162", result))
-  expect_true(grepl("Kimler", result))
+  expect_s3_class(result, "gt_tbl")
+  expect_true(any(grepl("162", result)))
+  expect_true(any(grepl("Kimler", result)))
 })
 
 test_that("Flag filtering works correctly", {
   reportingResults_filt <- reportingResults %>%
     dplyr::filter(MetricID == unique(reportingResults$MetricID)[1])
   result <- Report_MetricTable(reportingResults_filt, reportingGroups)
-  expect_s3_class(result, "kableExtra")
-  expect_false(grepl("Nkaujiaong", result))
+  expect_s3_class(result, "gt_tbl")
+  expect_false(any(grepl("Nkaujiaong", result)))
 })
 
 test_that("Score rounding works correctly", {
   reportingResults_filt <- reportingResults %>%
     dplyr::filter(MetricID == unique(reportingResults$MetricID)[1])
   result <- Report_MetricTable(reportingResults_filt, reportingGroups)
-  expect_true(grepl("0.05", result))
+  expect_true(any(grepl("0.05", result)))
 })
 
 test_that("Errors out when multiple MetricIDs passed in", {
@@ -37,5 +36,5 @@ test_that("Runs with just results with NULL group argument", {
   reportingResults_filt <- reportingResults %>%
     dplyr::filter(MetricID == unique(reportingResults$MetricID)[1])
   result <- Report_MetricTable(reportingResults_filt)
-  expect_s3_class(result, "kableExtra")
+  expect_s3_class(result, "gt_tbl")
 })