Refactor of the filter-panel

.github/workflows/check.yaml

@@ -36,6 +36,7 @@ jobs:
     with:
       additional-env-vars: |
         _R_CHECK_CRAN_INCOMING_REMOTE_=false
+        _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=10
       additional-r-cmd-check-params: --as-cran
       enforce-note-blocklist: true
       note-blocklist: |

.gitignore

@@ -1,4 +1,5 @@
 *.Rcheck
+.Rprofile
 *.html
 *.rprof
 *.sas.txt

.pre-commit-config.yaml

@@ -26,7 +26,6 @@ repos:
           - methods
           - bioc::MultiAssayExperiment
           - R6
-          - rlang
           - rtables
           - shinyjs
           - shinyWidgets

DESCRIPTION

@@ -2,15 +2,20 @@ Type: Package
 Package: teal.slice
 Title: Filter Module for `teal` Applications
 Version: 0.3.0.9005
-Date: 2023-06-29
+Date: 2023-07-13
 Authors@R: c(
-    person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")),
-    person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"),
-    person("Nikolas", "Burkoff", , "nikolas.burkoff@roche.com", role = "aut"),
-    person("Mahmoud", "Hallal", , "mahmoud.hallal@roche.com", role = "aut"),
-    person("Maciej", "Nasinski", , "maciej.nasinski@contractors.roche.com", role = "aut"),
-    person("Konrad", "Pagacz", , "konrad.pagacz@contractors.roche.com", role = "aut"),
-    person("Junlue", "Zhao", , "zhaoj88@gene.com", role = "aut"),
+    person("Dawid", "Kaledkowski", email = "dawid.kaledkowski@roche.com", role = c("aut", "cre")),
+    person("Pawel", "Rucki", email = "pawel.rucki@roche.com", role = "aut"),
+    person("Aleksander", "Chlebowski", email = "aleksander.chlebowski@contractors.roche.com", role = "aut"),
+    person("Kartikeya", "Kirar", email = "kartikeya.kirar@businesspartner.roche.com", role = "aut"),
+    person("Marcin", "Kosinski", email = "marcin.kosinski.mk1@roche.com", role = "aut"),
+    person("Chendi", "Liao", email = "chendi.liao@roche.com", role = "rev"),
+    person("Dony", "Unardi", email = "unardid@gene.com", role = "rev"),
+    person("Mahmoud", "Hallal", role = "aut"),
+    person("Nikolas", "Burkoff", role = "aut"),
+    person("Maciej", "Nasinski", role = "aut"),
+    person("Konrad", "Pagacz", role = "aut"),
+    person("Junlue", "Zhao", role = "aut"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
 Description: Filter module for teal applications.
@@ -19,22 +24,24 @@ Depends:
     R (>= 4.0),
     shiny
 Imports:
+    bslib (>= 0.4.0),
     checkmate,
     dplyr,
-    ggplot2,
     grDevices,
+    jsonlite,
+    htmltools,
     lifecycle,
     logger (>= 0.2.0),
     methods,
+    plotly,
     R6,
+    shinycssloaders,
     shinyjs,
-    shinyWidgets (>= 0.5.0),
-    stats,
+    shinyWidgets (>= 0.6.2),
     teal.data (>= 0.1.2.9011),
     teal.logger (>= 0.1.1),
     teal.widgets (>= 0.2.0)
 Suggests:
-    bslib,
     formatters (>= 0.3.1),
     knitr,
     MultiAssayExperiment,

NAMESPACE

@@ -1,7 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(get_supported_filter_varnames,FilteredDataset)
-S3method(get_supported_filter_varnames,MAEFilteredDataset)
+S3method("[",teal_slices)
+S3method(as.list,teal_slice)
+S3method(c,teal_slices)
+S3method(format,teal_slice)
+S3method(format,teal_slices)
+S3method(get_supported_filter_varnames,MultiAssayExperiment)
 S3method(get_supported_filter_varnames,default)
 S3method(get_supported_filter_varnames,matrix)
 S3method(init_filter_state,Date)
@@ -20,33 +24,30 @@ S3method(init_filtered_data,TealData)
 S3method(init_filtered_data,default)
 S3method(init_filtered_dataset,MultiAssayExperiment)
 S3method(init_filtered_dataset,data.frame)
-S3method(resolve_state,default)
-S3method(resolve_state,default_filter)
-S3method(resolve_state,list)
+S3method(print,teal_slice)
+S3method(print,teal_slices)
 S3method(variable_types,DFrame)
 S3method(variable_types,DataTable)
 S3method(variable_types,data.frame)
 S3method(variable_types,default)
 S3method(variable_types,matrix)
 export(FilterPanelAPI)
+export(as.teal_slice)
+export(as.teal_slices)
 export(clear_filter_states)
 export(get_filter_expr)
 export(get_filter_state)
 export(init_filter_states)
 export(init_filtered_data)
 export(init_filtered_dataset)
+export(is.teal_slice)
+export(is.teal_slices)
 export(remove_filter_state)
 export(set_filter_state)
+export(slices_restore)
+export(slices_store)
+export(teal_slice)
+export(teal_slices)
 import(R6)
 import(shiny)
-importFrom(dplyr,filter)
-importFrom(ggplot2,ggplot)
-importFrom(grDevices,rgb)
-importFrom(lifecycle,badge)
-importFrom(logger,log_trace)
 importFrom(methods,is)
-importFrom(shinyWidgets,pickerOptions)
-importFrom(shinyjs,hide)
-importFrom(stats,setNames)
-importFrom(teal.data,dataset)
-importFrom(teal.widgets,optionalSelectInput)

NEWS.md

@@ -1,6 +1,23 @@
 # teal.slice 0.3.0.9005
 
-* Remove `scda` from dependencies.
+### New features
+
+* API is based now on `teal_slices` and `teal_slice` objects.
+* Implemented reactive counts of single filter card to compare filtered and unfiltered variable distributions. See `count_type` in `teal_slices`.
+* Possible now to specify filter based on arbitrary logical expression. See `expr` argument in `teal_slice`. 
+* Possible now to limit choices in single filter card. See `choices` argument in `teal_slice`.
+* Possible now to initialize filter panel without "Add filter variables" panel through `module_add` in `teal_slices`.
+* Possible now to set filter which can't be removed by app user. See `anchored` argument in `teal_slice`.
+* Possible now to set filter which selection remains the same. See `fixed` argument in `teal_slice`.
+* Possible now to limit variable by single level only. See `multuple` argument in `teal_slice`  
+* Changed appearance of filter cards to collapsible accordion.
+* Replaced `sliderInput` with interactive `plotly` to be able to zoom variable distribution.
+
+### Breaking changes
+
+* Setting filters using a list is now deprecated. Use `teal_slices` and `teal_slice` instead.
+* Removed `CDISCFilteredData` and `CDISCFilteredDataset` and implementing `JoinKeys` handling in their parent classes (`FilteredData` and `DefaultFilteredDataset`).
+* Specifying set of filterable columns is done through `include_varnames` and `exclude_varnames`. Specifying `attr(, "filterable")` is hard deprecated.
 
 # teal.slice 0.3.0
 
@@ -13,6 +30,7 @@
 * Added a global turn on/off button for the Filter Panel.
 * Added ability to collapse Active Filter Display panel.
 * Added ability to collapse all filters of an individual dataset.
+* Added fixed filter states.
 
 ### Enhancements
 
@@ -22,12 +40,14 @@
 
 * Fixed an error where the `RangeFilterState` produced an error when using `bootstrap 4`.
 * Fixed a bug that caused the range slider to omit values selected programmatically through the filter API.
+* Fixed a bug where setting incorrect values for Date and Date time ranges caused the app to crash.
 
 ### Miscellaneous
 
 * Calculation of step in slider for `RangeFilterState` now uses `checkmate::test_integerish` instead of `is.integer`.
 * Updated `init_filtered_data` to take into account the removal of `CDISCTealData` from `teal.data` package.
-* Added examples apps for `ChoicesFilterState` and `DFFilterStates`.
+* Added `shinyvalidate` validation for Date and Date time ranges.
+* Added examples apps for `FilterState` child classes and `DFFilterStates`.
 
 # teal.slice 0.2.0
 
@@ -47,10 +67,10 @@
 ### Enhancements
 
 * Redesigned the count bars for filter panel check box inputs.
-* Redesigned the filter panel input for dates to use CSS flexbox.
+* Redesigned the filter panel input for dates to use `CSS flexbox`.
 * Update icons to be compatible with Font Awesome 6.
 * Updates the `FilteredData` method `get_formatted_filter_state` so it no longer appends empty filters.
-* Added clearer installation instructions to README.
+* Added clearer installation instructions to `README`.
 
 ### Breaking changes
 

R/FilterPanelAPI.R

@@ -21,18 +21,18 @@
 #' isolate(fpa$get_filter_state())
 #'
 #' # set a filter state
-#' isolate(
-#'   set_filter_state(
-#'     fpa,
-#'     list(iris = list(Species = list(selected = "setosa", keep_na = TRUE)))
+#' set_filter_state(
+#'   fpa,
+#'   teal_slices(
+#'     teal_slice(dataname = "iris", varname = "Species", selected = "setosa", keep_na = TRUE)
 #'   )
 #' )
 #'
 #' # get the actual filter state --> named list with filters
 #' isolate(fpa$get_filter_state())
 #'
 #' # remove all_filter_states
-#' fpa$remove_all_filter_states()
+#' fpa$clear_filter_states()
 #'
 #' # get the actual filter state --> empty named list
 #' isolate(fpa$get_filter_state())
@@ -44,6 +44,7 @@ FilterPanelAPI <- R6::R6Class( # nolint
     #' @description
     #' Initialize a `FilterPanelAPI` object
     #' @param datasets (`FilteredData`) object.
+    #'
     initialize = function(datasets) {
       checkmate::assert_class(datasets, "FilteredData")
       private$filtered_data <- datasets
@@ -56,78 +57,52 @@ FilterPanelAPI <- R6::R6Class( # nolint
     #' The output list is a compatible input to `set_filter_state`.
     #'
     #' @return `list` with named elements corresponding to `FilteredDataset` objects with active filters.
+    #'
     get_filter_state = function() {
       private$filtered_data$get_filter_state()
     },
 
     #' @description
     #' Sets active filter states.
-    #' @param filter (`named list`)\cr
-    #' nested list of filter selections applied to datasets.
+    #' @param filter (`teal_slices`)
+    #'
+    #' @return `NULL` invisibly
     #'
-    #' @return `NULL`
     set_filter_state = function(filter) {
-      if (private$filtered_data$get_filter_panel_active()) {
-        private$filtered_data$set_filter_state(filter)
-      } else {
-        warning(private$deactivated_msg)
-      }
+      private$filtered_data$set_filter_state(filter)
       invisible(NULL)
     },
 
     #' @description
     #' Remove one or more `FilterState` of a `FilteredDataset` in the `FilteredData` object.
-    #' @param filter (`named list`)\cr
-    #'  nested list of filter selections applied to datasets.
     #'
-    #' @return `NULL`
+    #' @param filter (`teal_slices`)\cr
+    #'   specifying `FilterState` objects to remove;
+    #'   `teal_slice`s may contain only `dataname` and `varname`, other elements are ignored
+    #'
+    #' @return `NULL` invisibly
+    #'
     remove_filter_state = function(filter) {
-      if (private$filtered_data$get_filter_panel_active()) {
-        private$filtered_data$remove_filter_state(filter)
-      } else {
-        warning(private$deactivated_msg)
-      }
+      private$filtered_data$remove_filter_state(filter)
       invisible(NULL)
     },
 
     #' @description Remove all `FilterStates` of the `FilteredData` object.
     #'
     #' @param datanames (`character`)\cr
-    #'  datanames to remove their `FilterStates`;
+    #'  `datanames` to remove their `FilterStates`;
     #'  omit to remove all `FilterStates` in the `FilteredData` object
     #'
-    #' @return `NULL`
-    #'
-    remove_all_filter_states = function(datanames) {
-      if (private$filtered_data$get_filter_panel_active()) {
-        datanames_to_remove <- if (missing(datanames)) private$filtered_data$datanames() else datanames
-        private$filtered_data$remove_all_filter_states(datanames = datanames_to_remove)
-      } else {
-        warning(private$deactivated_msg)
-      }
-      invisible(NULL)
-    },
-    #' @description
-    #' Toggle the state of the global Filter Panel button by running `javascript` code
-    #' to click the toggle button with the `filter_panel_active` id suffix.
-    #' The button id is prefixed with the Filter Panel shiny namespace.
-    #' This button is observed in `srv_filter_panel` method that executes
-    #' `filter_panel_enable()` or `filter_panel_disable()` method depending on the toggle state.
+    #' @return `NULL` invisibly
     #'
-    #' @return `NULL`
-    filter_panel_toggle = function() {
-      shinyjs::runjs(
-        sprintf(
-          '$("#%s-filter_turn_onoff").click();',
-          private$filtered_data$get_filter_panel_ui_id()
-        )
-      )
+    clear_filter_states = function(datanames) {
+      datanames_to_remove <- if (missing(datanames)) private$filtered_data$datanames() else datanames
+      private$filtered_data$clear_filter_states(datanames = datanames_to_remove)
       invisible(NULL)
     }
   ),
   ## __Private Methods ====
   private = list(
-    filtered_data = NULL,
-    deactivated_msg = "Filter Panel is deactivated so the action can not be applied with api."
+    filtered_data = NULL
   )
 )