brapir-v2: Client to Access BrAPI Compliant Plant Breeding Databases

brapi_post_locations

R Documentation

post /locations

Description

Create new Locations

Usage

brapi_post_locations(
  con = NULL,
  abbreviation = "",
  additionalInfo = list(),
  coordinateDescription = "",
  coordinateUncertainty = "",
  coordinates = list(),
  countryCode = "",
  countryName = "",
  documentationURL = "",
  environmentType = "",
  exposure = "",
  externalReferences = "",
  instituteAddress = "",
  instituteName = "",
  locationName = "",
  locationType = "",
  siteStatus = "",
  slope = "",
  topography = ""
)

Arguments

`con`	list; required: TRUE; BrAPI connection object
`abbreviation`	character; required: FALSE; An abbreviation which represents this location
`additionalInfo`	list; required: FALSE; Additional arbitrary information. If provided use the following construct list(additionalProp1 = "string", additionalProp2 = "string", additionalProp3 = "string"). The Examples section shows an example on how to construct the `additionalInfo` argument as a list.
`coordinateDescription`	character; required: FALSE; Describes the precision and landmarks of the coordinate values used for this location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc).
`coordinateUncertainty`	character; required: FALSE; Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.
`coordinates`	list; required: FALSE; One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. A coordinate position MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element and is specified in meters. The `coordinates` list MUST contain the following two elements: `geometry` as a list; required: TRUE; A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed . The Point geometry is described by exactly two elements: `coordinates` as a vector of type character; required: TRUE; A point position containing two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. `type` as a character; required: TRUE; Literally specified as "Point" The Polygon geometry is described by exactly two elements: `coordinates` as a list; required : TRUE; List of linear rings, where each linear ring is a list of at least four positions with the first equal to the last. The first linear ring specifies the exterior ring, and each subsequent ring an interior ring. `type` as a character; required: TRUE; Literally specified as "Polygon". `type` as a character; required: TRUE; Literally specified as "Feature". The easiest way in R to construct the `coordinates` list is to use the geojsonR package. The Examples section shows how to create a `coordinates` list object for a point and a polygon geometry.
`countryCode`	character; required: FALSE; ISO_3166-1_alpha-3 specification MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.
`countryName`	character; required: FALSE; The full name of the country where this location is MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.
`documentationURL`	character; required: FALSE; A URL to the human readable documentation of this object.
`environmentType`	character; required: FALSE; Describes the general type of environment of the location. (ex. forest, field, nursery, etc).
`exposure`	character; required: FALSE: Describes the level of protection /exposure for things like sun light and wind.
`externalReferences`	data.frame; required: FALSE; A data.frame of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. The `externalReferences` argument data.frame should contain the following columns: `referenceID` character; required: TRUE; The external reference ID. Could be a simple string or a URI. `referenceSource` character; required: TRUE; An identifier for the source system or database of this reference. The Examples section shows an example of how to construct the `externalReferences` argument as a data.frame.
`instituteAddress`	character; required: FALSE; The street address of the institute representing this location. MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.
`instituteName`	character; required: FALSE; Each institute/laboratory can have several experimental field. MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.
`locationName`	character; required: FALSE; A human readable name for this location. MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc., where the experiment took place.
`locationType`	character; required: FALSE; The type of location this represents (ex. Breeding Location, Storage Location, etc.).
`siteStatus`	character; required: FALSE: Description of the accessibility of the location (ex. Public, Private)
`slope`	character; required: FALSE; Describes the approximate slope (height/distance) of the location.
`topography`	character; required: FALSE; Describes the topography of the land at the location. (ex. Plateau, Cirque, Hill, Valley, etc.)

Details

Add new locations to database

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
abbreviation <- "L1"
additionalInfo <- list(dummyData = "True", example = "post_locations")
coordinateDescription <- "North East corner of greenhouse"
coordinateUncertainty <- "20"
## Load geojsonR package
library(geojsonR)
## Create a coordinates list object
## Point geometry
init <- TO_GeoJson$new()
pointGeometry <- list()
pointData <- c(-76.506042, # longitude
                42.417373, # lattitude
                      123) # altitude
pointGeometry[["geometry"]] <- init$Point(data = pointData,
                                          stringify = FALSE)
pointGeometry[["type"]] <- "Feature"
##
## Polygon geometry with an exterior and one interior ring
init <- TO_GeoJson$new()
## Individual polygon points are provided as c(longitude, latitude, altitude)
polygonData <- list(list(c(-76.476949, 42.447274, 123), # exterior ring (rectangle)
                         c(-76.474429, 42.447258, 123),
                         c(-76.474428, 42.446193, 123),
                         c(-76.476961, 42.446211, 123),
                         c(-76.476949, 42.447274, 123)),
                    list(c(-76.476733, 42.446916), # interior ring (triangle)
                         c(-76.475810, 42.447154),
                         c(-76.476306, 42.446281),
                         c(-76.476733, 42.446916)))
polygonGeometry <- list()
polygonGeometry[["geometry"]] <- init$Polygon(data = polygonData,
                                              stringify = FALSE)
polygonGeometry[["type"]] <- "Feature"
countryCode <- "PER"
countryName <- "Peru"
documentationURL <- "https://brapi.org"
environmentType <- "Nursery"
exposure <- "Structure, no exposure"
externalReferences <-
  data.frame(referenceID = c("doi:10.155454/12341234",
                             "http://purl.obolibrary.org/obo/ro.owl",
                             "75a50e76"),
             referenceSource = c("DOI",
                                 "OBO Library",
                                 "Remote Data Collection Upload Tool"))
instituteAddress <- "71 Pilgrim Avenue Chevy Chase MD 20815"
instituteName <- "Plant Science Institute"
locationName <- "Location 1"
locationType <- "Storage Location"
siteStatus <- "Private"
slope <- "0"
topography <- "Valley"

brapi_post_locations(con = con,
                     abbreviation = abbreviation,
                     additionalInfo = additionalInfo,
                     coordinateDescription = coordinateDescription,
                     coordinateUncertainty = coordinateUncertainty,
                     coordinates = pointGeometry,
                     countryCode = countryCode,
                     countryName = countryName,
                     documentationURL = documentationURL,
                     environmentType = environmentType,
                     exposure = exposure,
                     externalReferences = externalReferences,
                     instituteAddress = instituteAddress,
                     instituteName = instituteName,
                     locationName = locationName,
                     locationType = locationType,
                     siteStatus = siteStatus,
                     slope = slope,
                     topography = topography)

## End(Not run)

mverouden/brapir-v2 documentation built on April 22, 2022, 9:24 a.m.