From dc9f82be52cbccf108af3664edbfbb2a4de11783 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Fri, 25 Oct 2024 08:53:50 +0100
Subject: [PATCH 1/9] Allow non-standard datanames in filter data (#622)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

# Pull Request

Fixes https://github.com/insightsengineering/teal/issues/1366

Related:

- https://github.com/insightsengineering/teal/pull/1382
- https://github.com/insightsengineering/teal.slice/pull/622
- https://github.com/insightsengineering/teal.data/pull/340

### Changes description

- Removed assertion on datanames that start with alphabetic character
- [x] Fix problem with JS namespace in filter panel
- [x] Fix crash when filtering using MAE (both SE and Matrix)
- [x ] ~Fix upload of snapshot file that is not compatible~
- [x] Ignore datanames that contain functions, language, expression (and
other non-data objects)
    - https://github.com/insightsengineering/teal/issues/1352

---------

Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
Co-authored-by: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>
---
 DESCRIPTION                                   |   1 +
 R/FilterStates.R                              |  13 +-
 R/FilterStatesMatrix.R                        |   5 +
 R/FilterStatesSE.R                            |   4 +-
 R/FilteredData.R                              |   3 -
 R/FilteredDataset.R                           |   2 +-
 R/utils.R                                     |  78 ++++++++----
 man/check_simple_name.Rd                      |  21 ----
 man/sanitize_id.Rd                            |  23 ++++
 .../testthat/test-DataframeFilteredDataset.R  |   4 +-
 tests/testthat/test-utils.R                   | 111 ++++++++++++++----
 11 files changed, 191 insertions(+), 74 deletions(-)
 delete mode 100644 man/check_simple_name.Rd
 create mode 100644 man/sanitize_id.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 81a89c49e..72ad39930 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -45,6 +45,7 @@ Imports:
     methods,
     plotly (>= 4.9.2.2),
     R6 (>= 2.2.0),
+    rlang (>= 1.0.0),
     shiny (>= 1.6.0),
     shinycssloaders (>= 1.0.0),
     shinyjs,
diff --git a/R/FilterStates.R b/R/FilterStates.R
index 4fceca00d..5ac79756e 100644
--- a/R/FilterStates.R
+++ b/R/FilterStates.R
@@ -57,7 +57,11 @@ FilterStates <- R6::R6Class( # nolint
 
       private$dataname <- dataname
       private$datalabel <- datalabel
-      private$dataname_prefixed <- dataname
+      private$dataname_prefixed <- if (identical(dataname, make.names(dataname))) {
+        dataname
+      } else {
+        sprintf("`%s`", dataname)
+      }
       private$data <- data
       private$data_reactive <- data_reactive
       private$state_list <- reactiveVal()
@@ -165,7 +169,12 @@ FilterStates <- R6::R6Class( # nolint
       )
       if (length(filter_items) > 0L) {
         filter_function <- private$fun
-        data_name <- str2lang(private$dataname_prefixed)
+        data_name <- tryCatch(
+          {
+            str2lang(private$dataname_prefixed)
+          },
+          error = function(e) str2lang(paste0("`", private$dataname_prefixed, "`"))
+        )
         substitute(
           env = list(
             lhs = data_name,
diff --git a/R/FilterStatesMatrix.R b/R/FilterStatesMatrix.R
index 776c1bbc9..d5ed4d136 100644
--- a/R/FilterStatesMatrix.R
+++ b/R/FilterStatesMatrix.R
@@ -35,6 +35,11 @@ MatrixFilterStates <- R6::R6Class( # nolint
       checkmate::assert_matrix(data)
       super$initialize(data, data_reactive, dataname, datalabel)
       private$set_filterable_varnames(include_varnames = colnames(private$data))
+      if (!is.null(datalabel)) {
+        private$dataname_prefixed <- sprintf(
+          "%s[['%s']]", private$dataname_prefixed, datalabel
+        )
+      }
     }
   ),
   private = list(
diff --git a/R/FilterStatesSE.R b/R/FilterStatesSE.R
index 686bb44c4..06e14eac1 100644
--- a/R/FilterStatesSE.R
+++ b/R/FilterStatesSE.R
@@ -39,7 +39,9 @@ SEFilterStates <- R6::R6Class( # nolint
       checkmate::assert_class(data, "SummarizedExperiment")
       super$initialize(data, data_reactive, dataname, datalabel)
       if (!is.null(datalabel)) {
-        private$dataname_prefixed <- sprintf("%s[['%s']]", dataname, datalabel)
+        private$dataname_prefixed <- sprintf(
+          "%s[['%s']]", private$dataname_prefixed, datalabel
+        )
       }
     },
 
diff --git a/R/FilteredData.R b/R/FilteredData.R
index 9b56ee937..c36227c80 100644
--- a/R/FilteredData.R
+++ b/R/FilteredData.R
@@ -307,9 +307,6 @@ FilteredData <- R6::R6Class( # nolint
     set_dataset = function(data, dataname) {
       checkmate::assert_string(dataname)
       logger::log_debug("FilteredData$set_dataset setting dataset, name: { dataname }")
-      # to include it nicely in the Show R Code;
-      # the UI also uses `datanames` in ids, so no whitespaces allowed
-      check_simple_name(dataname)
 
       parent_dataname <- teal.data::parent(private$join_keys, dataname)
       keys <- private$join_keys[dataname, dataname]
diff --git a/R/FilteredDataset.R b/R/FilteredDataset.R
index 998f5f4d8..2ffefe420 100644
--- a/R/FilteredDataset.R
+++ b/R/FilteredDataset.R
@@ -30,7 +30,7 @@ FilteredDataset <- R6::R6Class( # nolint
     #' @return Object of class `FilteredDataset`, invisibly.
     #'
     initialize = function(dataset, dataname, keys = character(0), label = attr(dataset, "label", exact = TRUE)) {
-      check_simple_name(dataname)
+      checkmate::assert_string(dataname)
       logger::log_debug("Instantiating { class(self)[1] }, dataname: { dataname }")
       checkmate::assert_character(keys, any.missing = FALSE)
       checkmate::assert_character(label, null.ok = TRUE)
diff --git a/R/utils.R b/R/utils.R
index 725f5a8c9..caceb09c5 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,28 +1,3 @@
-#' Test whether variable name can be used within `Show R Code`
-#'
-#' Variable names containing spaces are problematic and must be wrapped in backticks.
-#' Also, they should not start with a number as `R` may silently make it valid by changing it.
-#' Therefore, we only allow alphanumeric characters with underscores.
-#' The first character of the `name` must be an alphabetic character and can be followed by alphanumeric characters.
-#'
-#' @md
-#'
-#' @param name (`character`) vector of names to check
-#' @return Returns `NULL` or raises error.
-#' @keywords internal
-#'
-check_simple_name <- function(name) {
-  checkmate::assert_character(name, min.len = 1, any.missing = FALSE)
-  if (!grepl("^[[:alpha:]][a-zA-Z0-9_]*$", name, perl = TRUE)) {
-    stop(
-      "name '",
-      name,
-      "' must only contain alphanumeric characters (with underscores)",
-      " and the first character must be an alphabetic character"
-    )
-  }
-}
-
 #' Include `JS` files from `/inst/js/` package directory to application header
 #'
 #' `system.file` should not be used to access files in other packages, it does
@@ -81,3 +56,56 @@ make_c_call <- function(choices) {
   if (length(private$session_bindings) > 0) lapply(private$session_bindings, function(x) x$destroy())
   invisible(NULL)
 }
+
+
+
+#' Encodes ids to be used in JavaScript and Shiny
+#'
+#' @description
+#' Replaces non-ASCII characters into a format that can be used in HTML,
+#' JavaScript and Shiny.
+#'
+#' When the id has a character that is not allowed, it is replaced with `"_"`
+#' and a 4 character hash of the original id is added to the start of the
+#' resulting id.
+#'
+#'
+#' @param id (`character(1)`) The id string.
+#'
+#' @return Sanitized string that removes special characters and spaces.
+#'
+#' @keywords internal
+sanitize_id <- function(id) {
+  pattern_escape <- "[^0-9A-Za-z_]"
+
+  id_new <- gsub(pattern_escape, "_", id)
+  hashes <- vapply(id[id != id_new], rlang::hash, character(1), USE.NAMES = FALSE)
+
+  id[id != id_new] <- paste0("h", substr(hashes, 1, 4), "_", id_new[id != id_new])
+  id
+}
+
+#' `NS` wrapper to sanitize ids for shiny
+#'
+#' Special characters and spaces are not allowed in shiny ids (in JS)
+#'
+#' @noRd
+NS <- function(namespace, id = NULL) { # nolint: object_name.
+  if (!missing(id)) {
+    return(shiny::NS(namespace, sanitize_id(id)))
+  }
+
+  function(id) {
+    shiny::NS(namespace, sanitize_id(id))
+  }
+}
+
+#' `moduleServer` wrapper to sanitize ids for shiny
+#'
+#' Special characters and spaces are not allowed in shiny ids (in JS)
+#'
+#' @noRd
+moduleServer <- function(id, module, session = getDefaultReactiveDomain()) { # nolint: object_name.
+  id <- sanitize_id(id)
+  shiny::moduleServer(id, module, session)
+}
diff --git a/man/check_simple_name.Rd b/man/check_simple_name.Rd
deleted file mode 100644
index b8472b5fb..000000000
--- a/man/check_simple_name.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{check_simple_name}
-\alias{check_simple_name}
-\title{Test whether variable name can be used within \verb{Show R Code}}
-\usage{
-check_simple_name(name)
-}
-\arguments{
-\item{name}{(\code{character}) vector of names to check}
-}
-\value{
-Returns \code{NULL} or raises error.
-}
-\description{
-Variable names containing spaces are problematic and must be wrapped in backticks.
-Also, they should not start with a number as \code{R} may silently make it valid by changing it.
-Therefore, we only allow alphanumeric characters with underscores.
-The first character of the \code{name} must be an alphabetic character and can be followed by alphanumeric characters.
-}
-\keyword{internal}
diff --git a/man/sanitize_id.Rd b/man/sanitize_id.Rd
new file mode 100644
index 000000000..7a67ebd69
--- /dev/null
+++ b/man/sanitize_id.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{sanitize_id}
+\alias{sanitize_id}
+\title{Encodes ids to be used in JavaScript and Shiny}
+\usage{
+sanitize_id(id)
+}
+\arguments{
+\item{id}{(\code{character(1)}) The id string.}
+}
+\value{
+Sanitized string that removes special characters and spaces.
+}
+\description{
+Replaces non-ASCII characters into a format that can be used in HTML,
+JavaScript and Shiny.
+
+When the id has a character that is not allowed, it is replaced with \code{"_"}
+and a 4 character hash of the original id is added to the start of the
+resulting id.
+}
+\keyword{internal}
diff --git a/tests/testthat/test-DataframeFilteredDataset.R b/tests/testthat/test-DataframeFilteredDataset.R
index 7ab9f8b65..d90987aa9 100644
--- a/tests/testthat/test-DataframeFilteredDataset.R
+++ b/tests/testthat/test-DataframeFilteredDataset.R
@@ -4,7 +4,9 @@ testthat::test_that("constructor accepts data.frame object with a dataname", {
   testthat::expect_error(DataframeFilteredDataset$new(dataset = head(iris)), "argument .+ missing, with no default")
   testthat::expect_error(DataframeFilteredDataset$new(dataname = "iris"), "argument .+ missing, with no default")
   testthat::expect_error(DataframeFilteredDataset$new(dataset = as.list(iris)), "Assertion on 'dataset' failed")
-  testthat::expect_error(DataframeFilteredDataset$new(dataset = iris, dataname = iris), "Assertion on 'name' failed")
+  testthat::expect_error(
+    DataframeFilteredDataset$new(dataset = iris, dataname = iris), "Assertion on 'dataname' failed"
+  )
 })
 
 testthat::test_that("filter_states list is initialized with single `FilterStates` element named filter", {
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 91cb3a6aa..6d9d542fd 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -1,25 +1,96 @@
-# check_simple_name ----
-test_that("check_simple_name behaves as expected", {
-  testthat::expect_silent(check_simple_name("aas2df"))
-  testthat::expect_silent(check_simple_name("ADSL"))
-  testthat::expect_silent(check_simple_name("ADSLmodified"))
-  testthat::expect_silent(check_simple_name("a1"))
-  testthat::expect_silent(check_simple_name("ADSL_modified"))
-  testthat::expect_silent(check_simple_name("ADSL_filtered"))
-  testthat::expect_silent(check_simple_name("FILTERED_ADSL"))
-  testthat::expect_silent(check_simple_name("FILTERED"))
-  testthat::expect_silent(check_simple_name("ADSLFILTERED"))
-  testthat::expect_silent(check_simple_name("a_1_2_b_"))
-
-  testthat::expect_error(check_simple_name("1a"), "name '.+' must only contain alphanumeric characters")
-  testthat::expect_error(check_simple_name("ADSL.modified"), "name '.+' must only contain alphanumeric characters")
-  testthat::expect_error(check_simple_name("a1..."), "name '.+' must only contain alphanumeric characters")
-  testthat::expect_error(check_simple_name("a a"), "name '.+' must only contain alphanumeric characters")
-  testthat::expect_error(check_simple_name("_A_b"), "name '.+' must only contain alphanumeric characters")
-})
-
 # make_c_call ----
 testthat::test_that("make_c_call", {
   testthat::expect_identical(make_c_call(1:3), quote(c(1L, 2L, 3L)))
   testthat::expect_identical(make_c_call(1), 1)
 })
+
+# sanitize_id ----
+testthat::describe("sanitize_id", {
+  testthat::it("should replace dots with `_` when id is otherwise valid", {
+    id <- "a.b"
+    ns <- teal.slice:::NS("app")
+    testthat::expect_identical(
+      ns(id),
+      paste0("app-h", substr(rlang::hash(id), 1, 4), "_a_b")
+    )
+  })
+
+  testthat::it("should take vector input", {
+    id <- c("a.b", "a", "b", " c")
+    ns <- teal.slice:::NS("app")
+    testthat::expect_identical(
+      ns(id),
+      c(
+        paste0("app-h", substr(rlang::hash(id[1]), 1, 4), "_a_b"),
+        "app-a",
+        "app-b",
+        paste0("app-h", substr(rlang::hash(id[4]), 1, 4), "__c")
+      )
+    )
+  })
+
+  testthat::it("should allow for integer input", {
+    id <- c(1L, 2L, 3L)
+    ns <- teal.slice:::NS("app")
+    testthat::expect_identical(
+      ns(id),
+      c("app-1", "app-2", "app-3")
+    )
+  })
+
+  testthat::it("should replace non-ASCII characters in middle of id with `_`", {
+    id <- "a$b"
+    ns <- teal.slice:::NS("app")
+    testthat::expect_identical(
+      ns(id),
+      paste0("app-h", substr(rlang::hash(id), 1, 4), "_a_b")
+    )
+  })
+
+  # Test using moduleServer to access the sanitized id
+  testthat::it("should replace non-ASCII characters in the start/end of id with `_`", {
+    id <- "%a bad symbol$"
+    id2 <- "a&b#"
+    id_from_module <- shiny::withReactiveDomain(
+      MockShinySession$new(),
+      teal.slice:::moduleServer(id, function(input, output, session) session$ns("a_good_name"))
+    )
+
+    testthat::expect_identical(
+      id_from_module,
+      paste0("h", substr(rlang::hash(id), 1, 4), "__a_bad_symbol_-a_good_name")
+    )
+  })
+
+  testthat::it("should replace all quotes characters with `_`", {
+    id <- " a.b.c\"d`e'j"
+    testthat::expect_identical(
+      teal.slice:::NS("app", id),
+      paste0("app-h", substr(rlang::hash(id), 1, 4), "__a_b_c_d_e_j")
+    )
+  })
+
+  testthat::it("should replace all escape characters from JQuery selectors", {
+    forbidden <- " !\"#$%&'()*+,./:;<=>?@[\\]^`{|}~]"
+    testthat::expect_identical(
+      teal.slice:::NS("app", forbidden),
+      paste0(
+        "app-h",
+        substr(rlang::hash(forbidden), 1, 4),
+        paste(rep("_", nchar(forbidden) + 1), collapse = "")
+      )
+    )
+  })
+
+  testthat::it("should replace UTF characters outside the allowed range", {
+    id <- "\U41\U05E\U30\U5F\U7A\U1F4AA" # "A:circumflex_accent:0_z:flexed_biceps:
+    testthat::expect_identical(
+      teal.slice:::NS("app", id),
+      paste0(
+        "app-h",
+        substr(rlang::hash(id), 1, 4),
+        "_A_0_z_"
+      )
+    )
+  })
+})

From c9cede08330d87ba9156ba28204542c15b70e4bc Mon Sep 17 00:00:00 2001
From: averissimo <averissimo@users.noreply.github.com>
Date: Fri, 25 Oct 2024 07:55:02 +0000
Subject: [PATCH 2/9] [skip actions] Bump version to 0.5.1.9013

---
 .pre-commit-config.yaml | 2 +-
 DESCRIPTION             | 4 ++--
 NEWS.md                 | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 69e978ae5..6bed6a537 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 ---
 # All available hooks: https://pre-commit.com/hooks.html
 # R specific hooks: https://github.com/lorenzwalthert/precommit
-default_stages: [commit]
+default_stages: [pre-commit]
 default_language_version:
   python: python3
 repos:
diff --git a/DESCRIPTION b/DESCRIPTION
index 72ad39930..f956b2e92 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.slice
 Title: Filter Module for 'teal' Applications
-Version: 0.5.1.9012
-Date: 2024-09-16
+Version: 0.5.1.9013
+Date: 2024-10-25
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9533-457X")),
diff --git a/NEWS.md b/NEWS.md
index b493de05e..6e5f5577f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.slice 0.5.1.9012
+# teal.slice 0.5.1.9013
 
 ### Enhancements
 

From 912a28133c3556b3daea8c7d591666f9be2aaf72 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 25 Oct 2024 12:26:04 +0200
Subject: [PATCH 3/9] add rmarkdown to VignetteBuilder (#626)

fix nosuggests ci
---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f956b2e92..b326b8702 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -62,7 +62,8 @@ Suggests:
     testthat (>= 3.1.5),
     withr (>= 2.1.0)
 VignetteBuilder:
-    knitr
+    knitr,
+    rmarkdown
 RdMacros:
     lifecycle
 Config/Needs/verdepcheck: rstudio/shiny, rstudio/bslib, mllg/checkmate,

From e07256a0d14e06b6556dc28a221ded65c2e55efc Mon Sep 17 00:00:00 2001
From: pawelru <pawelru@users.noreply.github.com>
Date: Fri, 25 Oct 2024 10:27:14 +0000
Subject: [PATCH 4/9] [skip actions] Bump version to 0.5.1.9014

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b326b8702..3a10b2f11 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: teal.slice
 Title: Filter Module for 'teal' Applications
-Version: 0.5.1.9013
+Version: 0.5.1.9014
 Date: 2024-10-25
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 6e5f5577f..65b8459a5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.slice 0.5.1.9013
+# teal.slice 0.5.1.9014
 
 ### Enhancements
 

From b732c15e22c43291f2e83ac8f4c409ed66f9008c Mon Sep 17 00:00:00 2001
From: Dony Unardi <donyunardi@gmail.com>
Date: Fri, 1 Nov 2024 12:58:44 -0700
Subject: [PATCH 5/9] update min version of testthat and precommit config
 (#627)

Similar with https://github.com/insightsengineering/teal.code/pull/220,
failure in min_isolated pipeline:

https://github.com/insightsengineering/teal.slice/actions/runs/11537362432/job/32114685586#step:9:1346

### Summary:

* Update testthat minimum version due to usage of `testthat::it()` in
DESCRIPTION file:

https://github.com/insightsengineering/teal.slice/blob/main/tests/testthat/test-utils.R#L9

* Add `teal.code` to the pre-commit configuration to allow it to use the
development version when running. This is necessary because the
development version of `teal.data` requires the development version of
`teal.code` to run, and without this, the pre-commit will fail.
---
 .pre-commit-config.yaml | 1 +
 DESCRIPTION             | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6bed6a537..225106070 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -30,6 +30,7 @@ repos:
           - shinycssloaders
           - shinyjs
           - shinyWidgets
+          - insightsengineering/teal.code
           - insightsengineering/teal.data
           - insightsengineering/teal.logger
           - insightsengineering/teal.widgets
diff --git a/DESCRIPTION b/DESCRIPTION
index 3a10b2f11..1abcbb34d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -59,7 +59,7 @@ Suggests:
     MultiAssayExperiment,
     rmarkdown (>= 2.23),
     SummarizedExperiment,
-    testthat (>= 3.1.5),
+    testthat (>= 3.1.8),
     withr (>= 2.1.0)
 VignetteBuilder:
     knitr,

From 25f41015bc1ed8b9c5301b8cf1ae48cbf7c96f2c Mon Sep 17 00:00:00 2001
From: donyunardi <donyunardi@users.noreply.github.com>
Date: Fri, 1 Nov 2024 19:59:56 +0000
Subject: [PATCH 6/9] [skip actions] Bump version to 0.5.1.9015

---
 DESCRIPTION | 4 ++--
 NEWS.md     | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1abcbb34d..1316dbe75 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.slice
 Title: Filter Module for 'teal' Applications
-Version: 0.5.1.9014
-Date: 2024-10-25
+Version: 0.5.1.9015
+Date: 2024-11-01
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9533-457X")),
diff --git a/NEWS.md b/NEWS.md
index 65b8459a5..fe06e0865 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.slice 0.5.1.9014
+# teal.slice 0.5.1.9015
 
 ### Enhancements
 

From a3d9a0f10000a484a534dc1d84184d573a8a21a8 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 4 Nov 2024 15:49:01 +0100
Subject: [PATCH 7/9] Update scheduled.yaml (#628)

Currently the max strategy fails with the following:
```
Error : ! Could not solve package dependencies:
* deps::/tmp/RtmpZGFxMH/filec219ed9d76: Can't install dependency insightsengineering/teal.data
* insightsengineering/teal.data: Can't install dependency teal.code (>= 0.5.0.9011)
```

`teal.code` is an indirect dependency via `teal.data`

Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
---
 .github/workflows/scheduled.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml
index f82c4c325..3c621eb25 100644
--- a/.github/workflows/scheduled.yaml
+++ b/.github/workflows/scheduled.yaml
@@ -38,6 +38,8 @@ jobs:
       strategy: ${{ matrix.test-strategy }}
       additional-env-vars: |
         PKG_SYSREQS_DRY_RUN=true
+      extra-deps: |
+        insightsengineering/teal.code
   branch-cleanup:
     if: >
       github.event_name == 'schedule' || (

From 2c60f56c1b9143d3d10f961ca4ad6070c9b0471e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?=
 <185338939+llrs-roche@users.noreply.github.com>
Date: Thu, 14 Nov 2024 16:15:57 +0100
Subject: [PATCH 8/9] Remove arguments (#630)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

# Pull Request

Fixes #623

After 1 year with an error and with `verify()` in place, it makes sense
to remove them.
I didn't keep any documentation or redirect users to other
functions/examples, (but it is hard for me to guess if users might not
know how to update their code).

The checks will fail due to #629

---------

Signed-off-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com>
---
 NEWS.md                   |  1 +
 R/FilteredData-utils.R    | 16 +---------------
 man/init_filtered_data.Rd |  6 +-----
 3 files changed, 3 insertions(+), 20 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index fe06e0865..ad2375b70 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,6 +3,7 @@
 ### Enhancements
 
 * Reduced the space of the filter panel by not displaying the "add filters" UI in a separate panel.
+* The deprecated parameters `code` and `check` were removed from `init_filtered_data()`.
 
 ### Bug fixes
 
diff --git a/R/FilteredData-utils.R b/R/FilteredData-utils.R
index 6f2e272a3..69df4a96b 100644
--- a/R/FilteredData-utils.R
+++ b/R/FilteredData-utils.R
@@ -4,8 +4,6 @@
 #'
 #' @param x (`named list`) of datasets.
 #' @param join_keys (`join_keys`) see [`teal.data::join_keys()`].
-#' @param code `r lifecycle::badge("deprecated")`
-#' @param check `r lifecycle::badge("deprecated")`
 #'
 #' @return Object of class `FilteredData`.
 #'
@@ -14,21 +12,9 @@
 #' datasets
 #'
 #' @export
-init_filtered_data <- function(x, join_keys = teal.data::join_keys(), code, check) { # nolint
+init_filtered_data <- function(x, join_keys = teal.data::join_keys()) { # nolint
   checkmate::assert_list(x, any.missing = FALSE, names = "unique")
   checkmate::assert_class(join_keys, "join_keys")
-  if (!missing(code)) {
-    lifecycle::deprecate_stop(
-      "0.5.0",
-      "init_filtered_data(code = 'No longer supported')"
-    )
-  }
-  if (!missing(check)) {
-    lifecycle::deprecate_stop(
-      "0.5.0",
-      "init_filtered_data(check = 'No longer supported')"
-    )
-  }
   FilteredData$new(x, join_keys = join_keys)
 }
 
diff --git a/man/init_filtered_data.Rd b/man/init_filtered_data.Rd
index 6994400bf..d07fc8097 100644
--- a/man/init_filtered_data.Rd
+++ b/man/init_filtered_data.Rd
@@ -4,16 +4,12 @@
 \alias{init_filtered_data}
 \title{Initialize \code{FilteredData}}
 \usage{
-init_filtered_data(x, join_keys = teal.data::join_keys(), code, check)
+init_filtered_data(x, join_keys = teal.data::join_keys())
 }
 \arguments{
 \item{x}{(\verb{named list}) of datasets.}
 
 \item{join_keys}{(\code{join_keys}) see \code{\link[teal.data:join_keys]{teal.data::join_keys()}}.}
-
-\item{code}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}}
-
-\item{check}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}}
 }
 \value{
 Object of class \code{FilteredData}.

From 1ba57bade101e0a0f641d11e033849ad303af443 Mon Sep 17 00:00:00 2001
From: llrs-roche <llrs-roche@users.noreply.github.com>
Date: Thu, 14 Nov 2024 15:17:09 +0000
Subject: [PATCH 9/9] [skip actions] Bump version to 0.5.1.9016

---
 .pre-commit-config.yaml | 2 +-
 DESCRIPTION             | 4 ++--
 NEWS.md                 | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 225106070..8743d1e1b 100755
--- 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: v0.4.3.9001
+    rev: v0.4.3.9003
     hooks:
       - id: style-files
         name: Style code with `styler`
diff --git a/DESCRIPTION b/DESCRIPTION
index 1316dbe75..24231c2fb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.slice
 Title: Filter Module for 'teal' Applications
-Version: 0.5.1.9015
-Date: 2024-11-01
+Version: 0.5.1.9016
+Date: 2024-11-14
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9533-457X")),
diff --git a/NEWS.md b/NEWS.md
index ad2375b70..99ea81db1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# teal.slice 0.5.1.9015
+# teal.slice 0.5.1.9016
 
 ### Enhancements