Merge branch 'main' into register_handlers

Signed-off-by: Pawel Rucki <[email protected]>
insightsengineering · Mar 11, 2024 · 453865f · 453865f
2 parents bdc4d5d + b3a2b6f
commit 453865f
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diff --git a/.github/ISSUE_TEMPLATE/release.yaml → .github/ISSUE_TEMPLATE/release.yml b/.github/ISSUE_TEMPLATE/release.yaml → .github/ISSUE_TEMPLATE/release.yml
@@ -18,12 +18,10 @@ body:
       description: Any PRs or issues that this release is blocked by.
       placeholder: Add a list of blocking PRs or issues here.
       value: |
-        ### PRs
-
+        #### PRs
         - [ ] PR 1
 
-        ### Issues
-
+        #### Issues
         - [ ] Issue 1
     validations:
       required: true
@@ -48,46 +46,48 @@ body:
       description: The steps to be taken in order to create a release.
       placeholder: Steps to create a release.
       value: |
-        ### Prepare the release
-
+        #### Prepare the release
         - [ ] Create a new release candidate branch
         `git checkout -b release-candidate-vX.Y.Z`
         - [ ] Update NEWS.md file: make sure it reflects a holistic summary of what has changed in the package, check README.
         - [ ] Remove the additional fields (`Remotes`) from the DESCRIPTION file where applicable.
         - [ ] Make sure that the minimum dependency versions are updated in the DESCRIPTION file for the package.
-        - [ ] Increase versioned dependency on {package name} to >=X.Y.Z.
+          - [ ] Increase versioned dependency on {package name} to >=X.Y.Z.
         - [ ] Commit your changes and create the PR on GitHub (add "[skip vbump]" in the PR title). Add all updates, commit, and push changes:
-        `# Make the necessary modifications to your files
-        # Stage the changes
-        git add <files your modified>
-        # Commit the changes
-        git commit -m "[skip vbump] <Your commit message>"
-        git push origin release-candidate-vX.Y.Z`
+          ```r
+          # Make the necessary modifications to your files
+          # Stage the changes
+          git add <files your modified>
+          # Commit the changes
+          git commit -m "[skip vbump] <Your commit message>"
+          git push origin release-candidate-vX.Y.Z
+          ```
 
-        ### Test the release
 
+        #### Test the release
         - [ ] Execute the manual tests on Shiny apps that are deployed on various hosting providers (Posit connect and shinyapps.io) - track the results in GitHub issue (Applicable only for frameworks that use Shiny).
         - [ ] Monitor integration tests, if integration fails, create priority issues on the board.
         - [ ] Execute UAT tests (Optional).
 
-        ### Validation loop
 
-        Note: This section is applicable only for regulatory packages.
+        #### Validation loop
+
+        **Note:** This section is applicable only for regulatory packages.
 
         - [ ] Tag the update(s) as a release candidate vX.Y.Z-rc<iteration-number> (e.g. v0.5.3-rc1) on the release candidate branch (release-candidate-vX.Y.Z).
-          `# Create rc tag for submission for internal validation
+          ```r
+          # Create rc tag for submission for internal validation
           git tag vX.Y.Z-rc<iteration number>
-          git push origin vX.Y.Z-rc<iteration number>`
+          git push origin vX.Y.Z-rc<iteration number>
+          ```
         - [ ] Submit the package for internal validation.
         - [ ] Address any feedback (internal validation/user testing), retag the package as a release candidate vX.Y.Z-rc(n+1). Repeat the submission for internal validation if necessary.
         - [ ] Get the package validated.
 
-        ### Tag the release
-
+        #### Tag the release
         - [ ] If the additional fields were removed, add them back in a separate PR, and then merge the PR back to main (add "[skip vbump]" in the PR title). If nothing was removed just merge the PR you created in the "Prepare the release" section to `main`. Note the commit hash of the merged commit. **Note:** additional commits might be added to the `main` branch by a bot or an automation - we do **NOT** want to tag this commit.
 
-        #### Make sure of the following before continuing with the release:
-
+        ##### Make sure of the following before continuing with the release:
         - [ ] CI checks are passing in GH.
         - [ ] Shiny apps are deployable and there are no errors/warnings (Applicable only for frameworks that use Shiny).
 
@@ -99,7 +99,7 @@ body:
           3. Push the tag to make the final release.
           `git push origin vX.Y.Z`
         - [ ] Update downstream package dependencies to (>=X.Y.Z) in {package name}.
-        Note: Once the release tag is created, the package is automatically published to internal repositories.
+        **Note:** Once the release tag is created, the package is automatically published to internal repositories.
   - type: textarea
     id: post-release
     attributes:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9027
+    rev: v0.4.0
     hooks:
       - id: style-files
         name: Style code with `styler`
@@ -15,25 +15,28 @@ repos:
       - id: roxygenize
         name: Regenerate package documentation
         additional_dependencies:
+          - teal.data # missing
+          - insightsengineering/teal.slice # missing
+          - insightsengineering/goshawk
+          - shiny
+          - insightsengineering/teal
+          - insightsengineering/teal.transform
           - checkmate
-          - digest
+          - colourpicker
           - dplyr
+          - DT
           - ggplot2
-          - glue
           - grDevices
           - lifecycle
-          - magrittr
           - methods
-          - bioc::MultiAssayExperiment
-          - R6
           - rlang
-          - rtables
           - shinyjs
-          - shinyWidgets
+          - shinyvalidate
           - stats
-          - bioc::SummarizedExperiment
-          - utils
-          - yaml
+          - teal.code
+          - teal.logger
+          - teal.reporter
+          - teal.widgets
       - id: spell-check
         name: Check spelling with `spelling`
         exclude: >

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.goshawk
 Title: Longitudinal Visualization `teal` Modules
-Version: 0.1.15.9006
-Date: 2023-12-13
+Version: 0.1.15.9012
+Date: 2024-02-20
 Authors@R: c(
     person("Nick", "Paszty", , "[email protected]", role = c("aut", "cre")),
     person("Dawid", "Kaledkowski", , "[email protected]", role = "aut"),
@@ -25,6 +25,9 @@ Description: Modules that produce web interfaces through which
     variables, Limit of Quantification flag variable (LOQFL) is expected
     with levels 'Y', 'N' or NA.
 License: Apache License 2.0 | file LICENSE
+URL: https://insightsengineering.github.io/teal.goshawk/,
+    https://github.com/insightsengineering/teal.goshawk/
+BugReports: https://github.com/insightsengineering/teal.goshawk/issues
 Depends:
     goshawk (>= 0.1.15),
     R (>= 3.6),
@@ -65,4 +68,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.goshawk 0.1.15.9006
+# teal.goshawk 0.1.15.9012
 
 ### Breaking Changes
 * Adapted all modules to use `teal_data` objects.

diff --git a/R/teal_goshawk.R b/R/teal_goshawk.R
@@ -5,8 +5,6 @@
 #' The data used for teal.goshawk have some constraints.
 #' It must contain the columns `AVISITCD`, `BASE`, `BASE2`, `AVALU`, `LBSTRESC`, `LOQFL`, `CHG2`, and `PCHG2`.
 #'
-#' @docType package
-#'
 #' @name teal_goshawk
 #'
 #' @import goshawk
@@ -17,4 +15,4 @@
 #' @importFrom rlang .data sym
 #' @importFrom teal.transform choices_selected
 #' @keywords internal
-NULL
+"_PACKAGE"
diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R
@@ -108,7 +108,7 @@
 #'   attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
 #'
 #'   # add LLOQ and ULOQ variables
-#'   ALB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
+#'   ALB_LOQS <- goshawk:::h_identify_loq_values(ADLB, "LOQFL")
 #'   ADLB <- dplyr::left_join(ADLB, ALB_LOQS, by = "PARAM")
 #' })
 #'
@@ -210,7 +210,8 @@ tm_g_gh_boxplot <- function(label,
       plot_height = plot_height,
       plot_width = plot_width,
       hline_vars_colors = hline_vars_colors,
-      hline_vars_labels = hline_vars_labels
+      hline_vars_labels = hline_vars_labels,
+      module_args = args
     ),
     ui = ui_g_boxplot,
     ui_args = args
@@ -251,16 +252,7 @@ ui_g_boxplot <- function(id, ...) {
         selected = a$trt_group$selected,
         multiple = FALSE
       ),
-      templ_ui_params_vars(
-        ns,
-        xparam_choices = a$param$choices,
-        xparam_selected = a$param$selected,
-        xparam_label = "Select a Biomarker",
-        xchoices = a$xaxis_var$choices,
-        xselected = a$xaxis_var$selected,
-        ychoices = a$yaxis_var$choices,
-        yselected = a$yaxis_var$selected
-      ),
+      uiOutput(ns("axis_selections")),
       teal.widgets::optionalSelectInput(
         ns("facet_var"),
         label = "Facet by",
@@ -324,13 +316,30 @@ srv_g_boxplot <- function(id,
                           plot_height,
                           plot_width,
                           hline_vars_colors,
-                          hline_vars_labels) {
+                          hline_vars_labels,
+                          module_args) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    output$axis_selections <- renderUI({
+      env <- shiny::isolate(as.list(data()@env))
+      resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
+      resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
+      resolved_param <- teal.transform::resolve_delayed(module_args$param, env)
+      templ_ui_params_vars(
+        session$ns,
+        xparam_choices = resolved_param$choices,
+        xparam_selected = resolved_param$selected,
+        xparam_label = module_args$"Select a Biomarker",
+        xchoices = resolved_x$choices,
+        xselected = resolved_x$selected,
+        ychoices = resolved_y$choices,
+        yselected = resolved_y$selected
+      )
+    })
     # reused in all modules
     anl_q_output <- constr_anl_q(
       session, input, data, dataname,

diff --git a/R/tm_g_gh_correlationplot.R b/R/tm_g_gh_correlationplot.R
@@ -130,7 +130,7 @@
 #'   attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
 #'
 #'   # add LLOQ and ULOQ variables
-#'   ADLB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
+#'   ADLB_LOQS <- goshawk:::h_identify_loq_values(ADLB, "LOQFL")
 #'   ADLB <- dplyr::left_join(ADLB, ADLB_LOQS, by = "PARAM")
 #' })
 #'
@@ -259,7 +259,8 @@ tm_g_gh_correlationplot <- function(label,
       hline_vars_colors = hline_vars_colors,
       hline_vars_labels = hline_vars_labels,
       vline_vars_colors = vline_vars_colors,
-      vline_vars_labels = vline_vars_labels
+      vline_vars_labels = vline_vars_labels,
+      module_args = args
     ),
     ui = ui_g_correlationplot,
     ui_args = args
@@ -284,13 +285,7 @@ ui_g_correlationplot <- function(id, ...) {
         selected = a$trt_group$selected,
         multiple = FALSE
       ),
-      templ_ui_params_vars(
-        ns,
-        xparam_choices = a$xaxis_param$choices, xparam_selected = a$xaxis_param$selected,
-        xchoices = a$xaxis_var$choices, xselected = a$xaxis_var$selected,
-        yparam_choices = a$yaxis_param$choices, yparam_selected = a$yaxis_param$selected,
-        ychoices = a$yaxis_var$choices, yselected = a$yaxis_var$selected
-      ),
+      uiOutput(ns("axis_selections")),
       templ_ui_constraint(ns, "X-Axis Data Constraint"), # required by constr_anl_q
       if (length(a$hline_vars) > 0) {
         teal.widgets::optionalSelectInput(
@@ -375,13 +370,33 @@ srv_g_correlationplot <- function(id,
                                   hline_vars_colors,
                                   hline_vars_labels,
                                   vline_vars_colors,
-                                  vline_vars_labels) {
+                                  vline_vars_labels,
+                                  module_args) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    output$axis_selections <- renderUI({
+      env <- shiny::isolate(as.list(data()@env))
+      resolved_x_param <- teal.transform::resolve_delayed(module_args$xaxis_param, env)
+      resolved_x_var <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
+      resolved_y_param <- teal.transform::resolve_delayed(module_args$yaxis_param, env)
+      resolved_y_var <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
+      templ_ui_params_vars(
+        session$ns,
+        xparam_choices = resolved_x_param$choices,
+        xparam_selected = resolved_x_param$selected,
+        xchoices = resolved_x_var$choices,
+        xselected = resolved_x_var$selected,
+        yparam_choices = resolved_y_param$choices,
+        yparam_selected = resolved_y_param$selected,
+        ychoices = resolved_y_var$choices,
+        yselected = resolved_y_var$selected
+      )
+    })
+
     iv_r <- reactive({
       iv <- shinyvalidate::InputValidator$new()
 

diff --git a/R/tm_g_gh_density_distribution_plot.R b/R/tm_g_gh_density_distribution_plot.R
@@ -166,7 +166,8 @@ tm_g_gh_density_distribution_plot <- function(label, # nolint
       color_manual = color_manual,
       color_comb = color_comb,
       plot_height = plot_height,
-      plot_width = plot_width
+      plot_width = plot_width,
+      module_args = args
     ),
     ui = ui_g_density_distribution_plot,
     ui_args = args
@@ -201,11 +202,7 @@ ui_g_density_distribution_plot <- function(id, ...) {
         selected = a$trt_group$selected,
         multiple = FALSE
       ),
-      templ_ui_params_vars(
-        ns,
-        xparam_choices = a$param$choices, xparam_selected = a$param$selected, xparam_label = "Select a Biomarker",
-        xchoices = a$xaxis_var$choices, xselected = a$xaxis_var$selected
-      ),
+      uiOutput(ns("axis_selections")),
       templ_ui_constraint(ns, label = "Data Constraint"),
       ui_arbitrary_lines(id = ns("hline_arb"), a$hline_arb, a$hline_arb_label, a$hline_arb_color),
       teal.widgets::panel_group(
@@ -263,13 +260,28 @@ srv_g_density_distribution_plot <- function(id, # nolint
                                             color_manual,
                                             color_comb,
                                             plot_height,
-                                            plot_width) {
+                                            plot_width,
+                                            module_args) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    output$axis_selections <- renderUI({
+      env <- shiny::isolate(as.list(data()@env))
+      resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
+      resolved_param <- teal.transform::resolve_delayed(module_args$param, env)
+      templ_ui_params_vars(
+        session$ns,
+        xparam_choices = resolved_param$choices,
+        xparam_selected = resolved_param$selected,
+        xparam_label = "Select a Biomarker",
+        xchoices = resolved_x$choices,
+        xselected = resolved_x$selected
+      )
+    })
+
     anl_q_output <- constr_anl_q(
       session, input, data, dataname,
       param_id = "xaxis_param", param_var = param_var, trt_group = input$trt_group, min_rows = 2