Description Usage Arguments Details Examples
View source: R/uploadEnvDataRequest.R
Upload an Env-Data request for Annotation
1 2 3 4 5 6 7 | uploadEnvDataRequest(
csv.file,
xml.file,
login = NULL,
password = NULL,
link.file = "annotation_status_link.url"
)
|
csv.file |
Location and name of |
xml.file |
Location and name of |
link.file |
name of link to access status and final annotated data |
login, password |
login and password for EnvData (NOT the same as MoveBank login and password) |
The function will fill out the data annotation form on the EnvData annotation tool at http://www.bioinfo.mpg.de/orn-gateway/services2.jsp. It will also create a link to the status report of the annotation request, and will attempt to automatically open that page.
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 | # specify names of data file to annotate (e.g. output of grid) and xml file with the request
csv.file <- "../sandbox/testdata.csv"
xml.file <- "../sandbox/testrequest.xml"
# create a gridded dataset
lats <- seq(38.8, 39.0, length = 40)
lons <- seq(-77.12, -76.91, length = 40)
start <- ymd("2014-01-01")
finish <- ymd("2014-01-01")
createEnvDataGrid(lats, lons, start, finish, 0,
savefile = TRUE,
fileout = csv.file)
# create an xml request
createEnvDataRequest(request_name = "TestRequest",
type_name = "aster/ASTGTM2",
variable_name = "dem",
interpolation_type = "bilinear",
dist_func_spatial="geodetic",
email = email,
savefile = TRUE,
fileout = xml.file)
# send the request to the server
uploadEnvDataRequest(csv.file, xml.file,
link.file = "annotation_status_link.url")
|
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