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feat: added formatting function for filter panel classes #28

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merged 12 commits into from
May 17, 2022
Merged

feat: added formatting function for filter panel classes #28

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3020d22
feat: added a method to convert filter state to string
kpagacz May 5, 2022
e37e73c
wip
kpagacz May 5, 2022
a0ab58b
wip
kpagacz May 5, 2022
5d2986f
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kpagacz May 10, 2022
49ab696
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kpagacz May 10, 2022
0ede485
feat: added human-readable string represtations of filtering classes
kpagacz May 12, 2022
ee4f770
Apply suggestions from code review
kpagacz May 13, 2022
7e62953
review no 1
kpagacz May 13, 2022
8205487
fixes
kpagacz May 13, 2022
967a751
added timezone to posixct constructors
kpagacz May 13, 2022
02d3b9c
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kpagacz May 17, 2022
99999c0
Merge branch 'main' into 8_teal.reporter_filter_list_print2@main
kpagacz May 17, 2022
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92 changes: 90 additions & 2 deletions R/FilterState.R
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Original file line number Diff line number Diff line change
Expand Up @@ -354,6 +354,25 @@ FilterState <- R6::R6Class( # nolint
return(invisible(NULL))
},

#' @description
#' Returns a formatted string representing this `FilterState`.
#'
#' @param indent (`numeric(1)`) the number of spaces before after each new line character of the formatted string.
#' Default: 0
#' @return `character(1)` the formatted string
#'
format = function(indent = 0) {
checkmate::assert_number(indent, finite = TRUE, lower = 0)

sprintf(
"%sFiltering on: %s\n%1$s Selected values: %s\n%1$s Include missing values: %s",
format("", width = indent),
self$get_varname(deparse = TRUE),
paste0(format(self$get_selected(), nsmall = 3), collapse = " "),
format(self$get_keep_na())
)
},

#' @description
#' Returns reproducible condition call for current selection relevant
#' for selected variable type.
Expand All @@ -370,7 +389,7 @@ FilterState <- R6::R6Class( # nolint
#' @return (`name` or `character(1)`)
get_dataname = function(deparse = TRUE) {
if (isTRUE(deparse)) {
deparse(private$input_dataname)
deparse1(private$input_dataname)
} else {
private$input_dataname
}
Expand All @@ -397,7 +416,7 @@ FilterState <- R6::R6Class( # nolint
#' @return (`name` or `character(1)`)
get_varname = function(deparse = FALSE) {
if (isTRUE(deparse)) {
deparse(private$varname)
deparse1(private$varname)
} else {
private$varname
}
Expand All @@ -424,6 +443,15 @@ FilterState <- R6::R6Class( # nolint
)
},

#' @description
#' Prints this `FilterState` object
#'
#' @param ... additional arguments to this method
print = function(...) {
cat(shiny::isolate(self$format()))
cat("\n")
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},

#' @description
#' Set if `NA` should be kept
#' @param value (`logical(1)`)\cr
Expand Down Expand Up @@ -1271,6 +1299,26 @@ RangeFilterState <- R6::R6Class( # nolint
return(invisible(self))
},

#' @description
#' Returns a formatted string representing this `LogicalFilterState`.
#'
#' @param indent (`numeric(1)`) the number of spaces before after each new line character of the formatted string.
#' Default: 0
#' @return `character(1)` the formatted string
#'
format = function(indent = 0) {
checkmate::assert_number(indent, finite = TRUE, lower = 0)

sprintf(
"%sFiltering on: %s\n%1$s Selected range: %s - %s\n%1$s Include missing values: %s",
format("", width = indent),
self$get_varname(deparse = TRUE),
format(self$get_selected(), nsmall = 3)[1],
format(self$get_selected(), nsmall = 3)[2],
format(self$get_keep_na())
)
Comment on lines +1311 to +1318
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RangeFilterState handles also Inf

Suggested change
sprintf(
"%sFiltering on: %s\n%1$s Selected range: %s - %s\n%1$s Include missing values: %s",
format("", width = indent),
self$get_varname(deparse = TRUE),
format(self$get_selected(), nsmall = 3)[1],
format(self$get_selected(), nsmall = 3)[2],
format(self$get_keep_na())
)
sprintf(
"%sFiltering on: %s\n%1$s Selected range: %s - %s\n%1$s Include missing values: %s\n%1$s Include infinite values: %s",
format("", width = indent),
self$get_varname(deparse = TRUE),
format(self$get_selected(), nsmall = 3)[1],
format(self$get_selected(), nsmall = 3)[2],
format(self$get_keep_na()),
format(self$get_keep_inf())
)

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I don't think it's consequential for a human readable output to be honest. It was a conscious decision.

},

#' @description
#' Answers the question of whether the current settings and values selected actually filters out any values.
#' @return logical scalar
Expand Down Expand Up @@ -2048,6 +2096,26 @@ DateFilterState <- R6::R6Class( # nolint
return(invisible(self))
},

#' @description
#' Returns a formatted string representing this `DateFilterState`.
#'
#' @param indent (`numeric(1)`) the number of spaces before after each new line character of the formatted string.
#' Default: 0
#' @return `character(1)` the formatted string
#'
format = function(indent = 0) {
checkmate::assert_number(indent, finite = TRUE, lower = 0)

sprintf(
"%sFiltering on: %s\n%1$s Selected range: %s - %s\n%1$s Include missing values: %s",
format("", width = indent),
self$get_varname(deparse = TRUE),
format(self$get_selected()[1], nsmall = 3),
format(self$get_selected()[2], nsmall = 3),
format(self$get_keep_na())
)
},

#' @description
#' Answers the question of whether the current settings and values selected actually filters out any values.
#' @return logical scalar
Expand Down Expand Up @@ -2346,6 +2414,26 @@ DatetimeFilterState <- R6::R6Class( # nolint
return(invisible(self))
},

#' @description
#' Returns a formatted string representing this `DatetimeFilterState`.
#'
#' @param indent (`numeric(1)`) the number of spaces before after each new line character of the formatted string.
#' Default: 0
#' @return `character(1)` the formatted string
#'
format = function(indent = 0) {
checkmate::assert_number(indent, finite = TRUE, lower = 0)
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should these be assert_integerish ?

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The whole method doesn't throw even when passed a fraction but good point. Probably yes.

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it's because format implicitly casts width to an integer XD


sprintf(
"%sFiltering on: %s\n%1$s Selected range: %s - %s\n%1$s Include missing values: %s",
format("", width = indent),
self$get_varname(deparse = TRUE),
format(self$get_selected(), nsmall = 3)[1],
format(self$get_selected(), nsmall = 3)[2],
format(self$get_keep_na())
)
},

#' @description
#' Answers the question of whether the current settings and values selected actually filters out any values.
#' @return logical scalar
Expand Down
132 changes: 119 additions & 13 deletions R/FilterStates.R
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Original file line number Diff line number Diff line change
Expand Up @@ -205,6 +205,24 @@ FilterStates <- R6::R6Class( # nolint
logger::log_trace("Instantiated { class(self)[1] }, dataname: { deparse1(private$input_dataname) }")
invisible(self)
},

#' @description
#' Returns the label of the dataset
#' @return (`character(1)`) the label
get_datalabel = function() {
private$datalabel
},

#' @description
#' Returns the formatted string representing this `FilterStates` object.
#'
#' @param indent (`numeric(1)`) the number of spaces before each line of the representation
#' @return `character(1)` the formatted string
#'
format = function(indent) {
stop("Pure virtual method")
},

#' @description
#' Filter call
#'
Expand Down Expand Up @@ -276,6 +294,15 @@ FilterStates <- R6::R6Class( # nolint
}
},

#' @description
#' Prints this `FilterStates` object
#'
#' @param ... additional arguments to this method
print = function(...) {
cat(shiny::isolate(self$format()))
cat("\n")
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},

#' @description
#' Gets the name of the function used to filter the data in this `FilterStates`.
#'
Expand Down Expand Up @@ -647,14 +674,15 @@ FilterStates <- R6::R6Class( # nolint
)
)

#' Specialization of `FilterStates` for a base `data.frame`.
#' @title `DFFFilterStates`
#' @description Specialization of `FilterStates` for a base `data.frame`.
#'
#' @keywords internal
DFFilterStates <- R6::R6Class( # nolint
classname = "DFFilterStates",
inherit = FilterStates,
public = list(
#' Initializes `DFFilterStates` object
#' @description Initializes `DFFilterStates` object
#'
#' Initializes `DFFilterStates` object by setting `input_dataname`,
#' `output_dataname` and initializing `ReactiveQueue`. This class contains a
Expand Down Expand Up @@ -689,6 +717,22 @@ DFFilterStates <- R6::R6Class( # nolint
)
},

#' @description
#' Returns the formatted string representing this `FilterStates` object.
#'
#' @param indent (`numeric(1)`) the number of spaces before each line of the representation
#' @return `character(1)` the formatted string
format = function(indent = 0) {
checkmate::assert_number(indent, finite = TRUE, lower = 0)

formatted_states <- vapply(
self$queue_get(1L), function(state) state$format(indent = indent),
USE.NAMES = FALSE, FUN.VALUE = character(1)
)
paste(formatted_states, collapse = "\n")
},

#' @description
#' Get function name
#'
#' Get function name used to create filter call.
Expand Down Expand Up @@ -1041,13 +1085,14 @@ DFFilterStates <- R6::R6Class( # nolint
)


#' Specialization of `FilterStates` for `MultiAssayExperiment`.
#' @title `MAEFilterStates`
#' @description Specialization of `FilterStates` for `MultiAssayExperiment`.
#' @keywords internal
MAEFilterStates <- R6::R6Class( # nolint
classname = "MAEFilterStates",
inherit = FilterStates,
public = list(
#' Initialize `MAEFilterStates` object
#' @description Initializes `MAEFilterStates` object
#'
#' Initialize `MAEFilterStates` object
#'
Expand Down Expand Up @@ -1082,11 +1127,24 @@ MAEFilterStates <- R6::R6Class( # nolint
return(invisible(self))
},

#' Get function name
#' @description
#' Returns the formatted string representing this `MAEFilterStates` object.
#'
#' Get function name used to create filter call.
#' For `MAEFilterStates`
#' `MultiAssayExperiment::subsetByColData` is used.
#' @param indent (`numeric(1)`) the number of spaces before each line of the representation
#' @return `character(1)` the formatted string
format = function(indent = 0) {
checkmate::assert_number(indent, finite = TRUE, lower = 0)

if (length(self$queue_get(1L)) > 0) {
formatted_states <- sprintf("%sSubject filters:", format("", width = indent))
for (state in self$queue_get(1L)) formatted_states <- c(formatted_states, state$format(indent = indent + 2))
paste(formatted_states, collapse = "\n")
}
},

#' @description
#' Returns function name used to create filter call.
#' For `MAEFilterStates` `MultiAssayExperiment::subsetByColData` is used.
#' @return `character(1)`
get_fun = function() {
return("MultiAssayExperiment::subsetByColData")
Expand Down Expand Up @@ -1195,7 +1253,8 @@ MAEFilterStates <- R6::R6Class( # nolint
NULL
},

#' @description Remove a variable from the `ReactiveQueue` and its corresponding UI element.
#' @description
#' Removes a variable from the `ReactiveQueue` and its corresponding UI element.
#'
#' @param element_id (`character(1)`)\cr name of `ReactiveQueue` element.
#'
Expand Down Expand Up @@ -1403,13 +1462,14 @@ MAEFilterStates <- R6::R6Class( # nolint
)
)

#' Specialization of `FilterStates` for `SummaryExperiment`.
#' @title `SEFilterStates`
#' @description Specialization of `FilterStates` for `SummaryExperiment`.
#' @keywords internal
SEFilterStates <- R6::R6Class( # nolint
classname = "SEFilterStates",
inherit = FilterStates,
public = list(
#' Initialize `SEFilterStates` object
#' @description Initialize `SEFilterStates` object
#'
#' Initialize `SEFilterStates` object
#'
Expand All @@ -1435,6 +1495,36 @@ SEFilterStates <- R6::R6Class( # nolint
)
},

#' @description
#' Returns the formatted string representing this `MAEFilterStates` object.
#'
#' @param indent (`numeric(1)`) the number of spaces before each line of the representation
#' @return `character(1)` the formatted string
format = function(indent = 0) {
checkmate::assert_number(indent, finite = TRUE, lower = 0)

whitespace_indent <- format("", width = indent)
formatted_states <- c()
if (!is.null(self$queue_get(queue_index = "subset"))) {
formatted_states <- c(formatted_states, paste0(whitespace_indent, " Subsetting:"))
for (state in self$queue_get(queue_index = "subset")) {
formatted_states <- c(formatted_states, state$format(indent = indent + 4))
}
}

if (!is.null(self$queue_get(queue_index = "select"))) {
formatted_states <- c(formatted_states, paste0(whitespace_indent, " Selecting:"))
for (state in self$queue_get(queue_index = "select")) {
formatted_states <- c(formatted_states, state$format(indent = indent + 4))
}
}

if (length(formatted_states) > 0) {
formatted_states <- c(paste0(whitespace_indent, "Assay ", self$get_datalabel(), " filters:"), formatted_states)
paste(formatted_states, collapse = "\n")
}
},

#' @description
#' Server module
#' @param id (`character(1)`)\cr
Expand Down Expand Up @@ -1942,13 +2032,14 @@ SEFilterStates <- R6::R6Class( # nolint
)
)

#' Specialization of `FilterStates` for a base matrix.
#' @title `MatrixFilterStates`
#' @description Specialization of `FilterStates` for a base matrix.
#' @keywords internal
MatrixFilterStates <- R6::R6Class( # nolint
classname = "MatrixFilterStates",
inherit = FilterStates,
public = list(
#' Initialize `MatrixFilterStates` object
#' @description Initialize `MatrixFilterStates` object
#'
#' Initialize `MatrixFilterStates` object
#'
Expand All @@ -1970,6 +2061,21 @@ MatrixFilterStates <- R6::R6Class( # nolint
)
},

#' @description
#' Returns the formatted string representing this `MatrixFilterStates` object.
#'
#' @param indent (`numeric(1)`) the number of spaces before each line of the representation
#' @return `character(1)` the formatted string
format = function(indent = 0) {
checkmate::assert_number(indent, finite = TRUE, lower = 0)

formatted_states <- c()
for (state in self$queue_get(queue_index = "subset")) {
formatted_states <- c(formatted_states, state$format(indent = indent + 2))
}
paste(formatted_states, collapse = "\n")
},

#' @description
#' Server module
#' @param id (`character(1)`)\cr
Expand Down
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