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Fix attribution display in pick_phylopic #105

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Mar 12, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ Encoding: UTF-8
LazyData: true
biocViews:
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
RoxygenNote: 7.3.1
Depends:
R (>= 4.0)
Imports:
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1 change: 1 addition & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

* Added add_phylopic_legend (#83)
* Added permalink generation option to get_attribution (#81)
* Fix pick_phylopic attribution display bug (#104)
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Should it be reported in NEWS.md if we introduced the bug and fixed the bug between releases?

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Maybe not, I guess many users don't use the development version?

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Yeah, I doubt many people do, and I think this might just cause more confusion for those that don't (not that too many people are going to read the changelog anyways).


# rphylopic 1.3.0

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16 changes: 12 additions & 4 deletions R/pick_phylopic.R
Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,10 @@ utils::globalVariables(c("x", "y", "uuid", "label"))
#' @param auto \code{numeric}. This argument allows the user to automate input
#' into the menu choice. If the input value is `1`, the first returned image
#' will be selected. If the input value is `2`, requested images will be
#' automatically cycled through with the final image returned. If `NULL`
#' (default), the user must interactively respond to the called menu.
#' automatically cycled through with the final image returned. If the input
#' value is `3`, a list of attribution information for each image is
#' returned (this functionality is principally intended for testing). If
#' `NULL` (default), the user must interactively respond to the called menu.
#'
#' @return A [Picture][grImport2::Picture-class] object is returned. The uuid of
#' the selected image is saved as the "uuid" attribute of the returned object
Expand Down Expand Up @@ -60,8 +62,8 @@ utils::globalVariables(c("x", "y", "uuid", "label"))
pick_phylopic <- function(name = NULL, n = 5, uuid = NULL, view = 1,
filter = NULL, auto = NULL) {
# Error handling
if (!is.null(auto) && !auto %in% c(1, 2)) {
stop("`auto` must be of value: NULL, 1, or 2")
if (!is.null(auto) && !auto %in% c(1, 2, 3)) {
stop("`auto` must be of value: NULL, 1, 2, or 3")
}
if (!is.numeric(view)) {
stop("`view` must be of class numeric.")
Expand All @@ -75,8 +77,10 @@ pick_phylopic <- function(name = NULL, n = 5, uuid = NULL, view = 1,
grid.newpage()
grid.picture(img)
# Add text for attribution
att <- att[[1]][[1]]
att_string <- paste0("Contributor: ", att$contributor, "\n",
"Created: ", att$created, "\n",
"Attribution: ", att$attribution, "\n",
"License: ", att$license)
grid.text(label = att_string,
x = 0.96, y = 0.92,
Expand Down Expand Up @@ -126,6 +130,7 @@ pick_phylopic <- function(name = NULL, n = 5, uuid = NULL, view = 1,
}
# Get attribution data
att <- lapply(uuids[[i]], get_attribution)
att <- lapply(att, function(x) x[[1]][[1]])
# Attribution text
n_spaces <- 3 + floor(log10(length(att) + 1))
att_string <- lapply(att, function(x) {
Expand Down Expand Up @@ -174,6 +179,9 @@ pick_phylopic <- function(name = NULL, n = 5, uuid = NULL, view = 1,
m <- n_plotted + 1
} else if (auto == 1) {
m <- 1
} else if (auto == 3) {
names(att) <- sapply(att, function(x) x$image_uuid)
return(att)
}
}

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6 changes: 4 additions & 2 deletions man/pick_phylopic.Rd

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5 changes: 5 additions & 0 deletions tests/testthat/test-pick_phylo.R
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,11 @@ test_that("pick_phylopic works", {
expect_true(is(pick_phylopic(name = "Bacteria", n = 13,
view = 5, auto = 2),
"Picture"))

# Test attribution information
expect_equal(
length(pick_phylopic(name = "Scleractinia", n = 4, view = 4, auto = 3)),
4)

# Expect warning
expect_warning(pick_phylopic(name = "Acropora cervicornis", n = 10))
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