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Genesys PGR
genesysr
Commits
1621e571
Commit
1621e571
authored
Jun 12, 2018
by
Matija Obreza
Browse files
Hide internal functions
parent
cc7fae5f
Changes
2
Hide whitespace changes
Inline
Side-by-side
R/api-client.R
View file @
1621e571
...
...
@@ -77,7 +77,7 @@ authorization <- function(authorization) {
}
#' Ensure that environment has OAuth token
check_auth
<-
function
()
{
.
check_auth
<-
function
()
{
if
(
is.null
(
.genesysEnv
$
Authorization
))
{
warning
(
"You must first authorize with Genesys with user_login() or client_login(...)."
);
}
...
...
@@ -155,8 +155,8 @@ client_login <- function() {
}
api_call
<-
function
(
path
,
method
=
"get"
)
{
check_auth
()
.
api_call
<-
function
(
path
,
method
=
"get"
)
{
.
check_auth
()
resp
<-
httr
::
GET
(
api_url
(
path
),
httr
::
add_headers
(
Authorization
=
.genesysEnv
$
Authorization
)
...
...
@@ -184,8 +184,8 @@ api_url <- function(path) {
paste0
(
.genesysEnv
$
server
,
"/api/v0"
,
path
)
}
get
<-
function
(
path
,
query
=
NULL
)
{
check_auth
()
.
get
<-
function
(
path
,
query
=
NULL
)
{
.
check_auth
()
resp
<-
httr
::
GET
(
api_url
(
path
),
query
=
query
,
httr
::
add_headers
(
Authorization
=
.genesysEnv
$
Authorization
))
...
...
@@ -203,8 +203,8 @@ get <- function(path, query = NULL) {
#' @param content.type Content-Type of the body
#'
#' @return httr response
post
<-
function
(
path
,
query
=
NULL
,
body
=
NULL
,
content.type
=
"application/json"
)
{
check_auth
()
.
post
<-
function
(
path
,
query
=
NULL
,
body
=
NULL
,
content.type
=
"application/json"
)
{
.
check_auth
()
content
<-
jsonlite
::
toJSON
(
body
)
if
(
!
is.null
(
body
)
&&
length
(
body
)
==
0
)
{
# If body is provided, but has length of 0
...
...
R/genesys.R
View file @
1621e571
...
...
@@ -19,7 +19,7 @@
#'
#' @export
me
<-
function
()
{
resp
<-
api_call
(
"/me"
)
resp
<-
.
api_call
(
"/me"
)
message
(
jsonlite
::
toJSON
(
resp
,
pretty
=
TRUE
))
invisible
(
resp
)
}
...
...
@@ -38,9 +38,9 @@ me <- function() {
#' accessions <- fetch_accessions(mcpd_filter(ORIGCTY = c("DEU", "SVN")))
#'
#' @return Paged data structure
fetch_accessions_page
<-
function
(
filters
=
list
(),
page
=
0
,
size
=
1000
,
selector
=
NULL
)
{
.
fetch_accessions_page
<-
function
(
filters
=
list
(),
page
=
0
,
size
=
1000
,
selector
=
NULL
)
{
start_time
<-
as.numeric
(
as.numeric
(
Sys.time
())
*
1000
,
digits
=
15
)
resp
<-
post
(
path
=
"/acn/filter"
,
query
=
list
(
p
=
page
,
l
=
size
),
body
=
filters
)
resp
<-
.
post
(
path
=
"/acn/filter"
,
query
=
list
(
p
=
page
,
l
=
size
),
body
=
filters
)
if
(
httr
::
status_code
(
resp
)
!=
200
)
{
stop
(
"Genesys responded with HTTP status code "
,
httr
::
status_code
(
resp
),
". Expected 200."
)
}
...
...
@@ -80,11 +80,11 @@ fetch_accessions_page <- function(filters = list(), page = 0, size = 1000, selec
fetch_accessions
<-
function
(
filters
=
list
(),
page
=
NULL
,
size
=
1000
,
selector
=
NULL
,
at.least
=
NULL
)
{
if
(
!
is.null
(
page
))
{
# Fetch page
return
(
fetch_accessions_page
(
filters
,
page
,
size
,
selector
));
return
(
.
fetch_accessions_page
(
filters
,
page
,
size
,
selector
));
}
# Fetch first page to determine number of records
paged
<-
fetch_accessions_page
(
filters
,
page
=
0
,
size
,
selector
)
paged
<-
.
fetch_accessions_page
(
filters
,
page
=
0
,
size
,
selector
)
pages
<-
paged
$
totalPages
for
(
page
in
1
:
pages
)
{
...
...
@@ -93,7 +93,7 @@ fetch_accessions <- function(filters = list(), page = NULL, size = 1000, selecto
message
(
paste
(
"Not requesting data after page"
,
.MAX_ALLOWED_PAGES
,
"Stopping."
))
break
}
p
<-
fetch_accessions_page
(
filters
,
page
,
size
,
selector
)
p
<-
.
fetch_accessions_page
(
filters
,
page
,
size
,
selector
)
paged
$
content
<-
c
(
paged
$
content
,
p
$
content
)
paged
$
last
<-
p
$
last
...
...
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