-
Notifications
You must be signed in to change notification settings - Fork 0
/
get_releases.R
153 lines (134 loc) · 4.48 KB
/
get_releases.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
get_release <- function(resource,
limit = 20L,
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE) {
tbl_json <- get(resource_url = resource,
limit = limit,
verbose = verbose,
warnings = warnings,
progress_bar = progress_bar)
tidy_tbls <- as_tidy_tables_releases(tbl_json)
return(tidy_tbls)
}
get_release_by_release_date <-
function(release_date,
limit = 20L,
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE) {
resource <- '/rest/release'
resource_urls <- sprintf("%s/%s", resource, release_date)
purrr::map(
resource_urls,
get_release,
limit = limit,
warnings = warnings,
verbose = verbose,
progress_bar = progress_bar
) %>%
purrr::pmap(dplyr::bind_rows)
}
get_release_current <-
function(limit = 20L,
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE) {
resource_url <- '/rest/release/current'
get_release(resource_url,
limit = limit,
warnings = warnings,
verbose = verbose,
progress_bar = progress_bar)
}
get_release_all <-
function(limit = 20L,
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE) {
resource_url <- '/rest/release/all'
get_release(resource_url,
limit = limit,
warnings = warnings,
verbose = verbose,
progress_bar = progress_bar)
}
#' Get PGS Catalog Releases
#'
#' This function retrieves PGS Catalog release information. Note that the
#' columns \code{pgs_id}, \code{ppm_id} and \code{pgp_id} contain in each
#' element a vector. These columns can be unnested using
#' \code{\link[tidyr]{unnest_longer}} (see Examples).
#'
#' @param date One or more dates formatted as \code{"YYYY-MM-DD"} for respective
#' releases, \code{"latest"} for the latest release, or \code{"all"} for all
#' releases.
#' @param verbose Whether to print information about the underlying requests to
#' the REST API server.
#' @param warnings Whether to print warnings about the underlying requests to
#' the REST API server.
#' @param progress_bar Whether to show a progress bar indicating download
#' progress from the REST API server.
#'
#' @return A data frame where each row is a release. Columns are:
#' \describe{
#' \item{date}{Release date.}
#' \item{n_pgs}{Number of released Polygenic Score (PGS) identifiers
#' (\code{pgs_id}).}
#' \item{n_ppm}{Number of released Performance Metric (PPM) identifiers
#' (\code{ppm_id}).}
#' \item{n_pgp}{Number of released PGS Catalog Publication (PGP) identifiers
#' (\code{pgp_id}).}
#' \item{pgs_id}{Released Polygenic Score (PGS) identifiers.}
#' \item{ppm_id}{Released Performance Metric (PPM) identifiers.}
#' \item{pgp_id}{Released PGS Catalog Publication (PGP) identifiers.}
#' \item{notes}{News about the release.}
#' }
#' @examples
#' \dontrun{
#' # Get the latest release
#' get_releases()
#' get_releases(date = 'latest')
#'
#' # Get all releases
#' get_releases(date = 'all')
#'
#' # Get a specific release by date
#' get_releases(date = '2020-08-19')
#' }
#'
#' @export
get_releases <- function(date = 'latest',
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE) {
if (identical(date, 'latest')) {
tbl <- get_release_current(verbose = verbose,
warnings = warnings,
progress_bar = progress_bar) %>%
coerce_to_s4_releases()
return(tbl)
}
if (identical(date, 'all')) {
tbl <- get_release_all(verbose = verbose,
warnings = warnings,
progress_bar = progress_bar) %>%
coerce_to_s4_releases()
return(tbl)
}
if (all(stringr::str_detect(date, pattern = '^\\d{4}-\\d{2}-\\d{2}$'))) {
tbl <- get_release_by_release_date(
release_date = date,
verbose = verbose,
warnings = warnings,
progress_bar = progress_bar
) %>%
coerce_to_s4_releases()
return(tbl)
}
stop('Argument `date` must be one of:\n',
' - "all": for all releases;\n',
' - "latest": for the most up-to-date release;\n',
' - "YYYY-MM-DD": for a release of a specific date, e.g., "2020-10-19".\n'
)
}