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pre-build.R
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pre-build.R
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# Run this script prior to building site to:
# * Scrape publication information and generate publication pages
# * Update authors.yml based on publication information
# * Search for author images and update authors.yml
library(yaml)
library(tidyverse)
library(here)
library(cli)
library(jsonlite)
library(rvest)
library(pdftools)
library(magick)
source(here("funs.R"))
# Directories
pub_yml <- read_yaml("pubs.yml")
pub_dir <- "pubs"
img_dir <- here("images")
pdf_dir <- here("docs")
# PUBLICATIONS ----
# * Scrape missing publication information and update pubs.yml
# * Add missing authors to authors.yml
# * Associate publications with projects based on authors.yml
# * Create directories and write index.qmd page for each publication
# * Write index.qmd page for each atlas
# Check for duplicated publications
dup_pubs <- pub_yml %>%
map_chr(pluck, "pubmed") %>%
duplicated()
# Create index.qmd for each pub entry
projs <- names(read_yaml("projects.yml"))
pub_yml_new <- pub_yml[!dup_pubs] %>%
map(
.create_pub_page,
athr_yml_file = "authors.yml",
out_dir = here(pub_dir),
img_dir = img_dir,
proj_order = projs
)
# Write updated pubs.yml
# this will have info scraped from pubmed
if (!identical(pub_yml, pub_yml_new)) {
pub_yml_new %>%
write_yaml(here("pubs.yml"))
}
# Create pages for atlases
atlas_pubs <- pub_yml_new %>%
keep(~ !is.null(pluck(.x, "links", "atlas"))) %>%
map(
.create_pub_page,
athr_yml_file = "authors.yml",
out_dir = here("atlases"),
img_dir = img_dir,
proj_order = projs,
atlas = TRUE
)
# INVESTIGATORS ----
# Check for image and update authors.yml if image is found
athr_yml <- read_yaml("authors.yml")
athr_yml_new <- athr_yml %>%
imap(~ {
if (is.null(.x$image)) {
img_nm <- .y %>%
str_to_lower() %>%
str_replace_all(" ", "-")
img <- dir(img_dir, str_c("^", img_nm, "\\."), full.names = TRUE)
if (length(img) > 1) img <- img[[1]]
img <- str_remove(img, here())
if (!is_empty(img)) .x$image <- img
# Remove image path if it does not exist
} else if (!file.exists(str_remove(.x$image, "^/"))) {
.x$image <- NULL
}
.x
})
if (!identical(athr_yml, athr_yml_new)) {
athr_yml_new %>%
write_yaml(here("authors.yml"))
}
# TIMELINE ----
# Filter for authors to label
lab_athr <- athr_yml_new %>%
keep(~ !is.null(.x$project)) %>%
names()
tl_dat <- pub_yml_new %>%
map_dfr(~ {
athrs <- .x$authors
athrs <- athrs[athrs %in% lab_athr]
athrs <- str_extract(athrs, "[^ ]+$")
tibble(
key = .x$key,
date = as.Date(str_c(.x$year, "-01-01")),
proj = str_c(str_to_title(.x$project), collapse = ", "),
authors = str_c(athrs, collapse = ", "),
pmid = str_extract(.x$pubmed, "[0-9]+(/|)$")
)
})
# Format publication data
tl_dat <- tl_dat %>%
mutate(
pmid = str_remove(pmid, "/$"),
pmid = str_c("PMID", pmid),
year = as.character(year(date)),
url = file.path(pub_dir, key)
) %>%
pivot_longer(c(proj, pmid), values_to = "lab") %>%
mutate(
style = ifelse(name == "pmid", "bold", "normal"),
style = map(style, ~ list(`font-weight` = .x))
)
# Save as json file
tl_dat %>%
write_json("timeline.json")