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

View source: R/brapi_post_observationunits.R

brapi_post_observationunits

R Documentation

post /observationunits

Description

Add new Observation Units

Usage

brapi_post_observationunits(
  con = NULL,
  additionalInfo = list(),
  externalReferences = "",
  germplasmDbId = "",
  germplasmName = "",
  locationDbId = "",
  locationName = "",
  observationUnitName = "",
  observationUnitPUI = "",
  observationUnitPosition = list(),
  programDbId = "",
  programName = "",
  seedLotDbId = "",
  studyDbId = "",
  studyName = "",
  treatments = "",
  trialDbId = "",
  trialName = ""
)

Arguments

`con`	list; required: TRUE; BrAPI connection object
`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.
`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.
`germplasmDbId`	character; required: FALSE; Unique germplasm (accession) identifier for the observation unit.
`germplasmName`	character; required: FALSE; Human readable germplasm name for the observation unit. It can be the preferred name and does not have to be unique.
`locationDbId`	character; required: FALSE; The identifier, which uniquely identifies a location, associated with this study.
`locationName`	character; required: FALSE; The human readable name of a location associated with this study.
`observationUnitName`	character; required: FALSE; A human readable name for an observation unit.
`observationUnitPUI`	character; required: FALSE; A Permanent Unique Identifier for an observation unit. MIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible.
`observationUnitPosition`	list; required: FALSE; All positional and layout information related to this Observation Unit. MIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) or level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. Levels of observation must be consistent with those listed in the Study section. The `observationUnitPosition` list can contain the following elements: `entryType` character; required: FALSE; The type of entry for this observation unit, possible values: "CHECK"\|"TEST" \|"FILLER". `geoCoordinates` 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 `geoCcoordinates` 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 `geoCoordinates` list is to use the geojsonR package. The Examples section shows how to create a `geoCoordinates` list object for a point and a polygon geometry. `observationLevel` list; required: FALSE; The exact level and level code of an observation unit. MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.". The `observationLevel` list can contain the following elements: `levelCode` character; required: FALSE; An identifier code for this level tag. Identify this observation unit by each level of the hierarchy, where it exists. `levelName` character; required: FALSE; A name for this level. `levelOrder` integer; required: FALSE; Defines where that level exists in the hierarchy of levels. Level Order's lower numbers are at the top of the hierarchy (i.e. field -> 1) and higher numbers are at the bottom of the hierarchy (i.e. plant -> 9). `observationLevelRelationships` data.frame; required: FALSE; Data.frame of observation levels to indicate the granularity level at which the measurements are taken. Each row in the data.frame defines the level code, level name (`levelName`), and the level order, as integer, where that level exists in the hierarchy of levels. `levelOrders` lower numbers are at the top of the hierarchy (i.e. field -> 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). `levelCode` is an identifier code for this level tag. Identify this observation unit by each level of the hierarchy, where it exists. `positionCoordinateX` character; required: FALSE; The X position coordinate for an observation unit. Different systems may use different coordinate systems. `positionCoordinateXType` character; required: FALSE; The type of positional coordinate used. Must be one of the following values: `LONGITUDE` - ISO 6709 standard, WGS84 geodetic datum. `LATITUDE` - ISO 6709 standard, WGS84 geodetic datum. `PLANTED_ROW` - The physical planted row number `PLANTED_INDIVIDUAL` - The physical counted number, could be independent or within a planted row. `GRID_ROW` - The row index number of a square grid overlay `GRID_COL` - The column index number of a square grid overlay `MEASURED_ROW` - The distance in meters from a defined 0-th row `MEASURED_COL` - The distance in meters from a defined 0-th column `positionCoordinateY` charcter; required: FALSE; The Y position coordinate for an observation unit. Different systems may use different coordinate systems. `positionCoordinateYType` character; required: FALSE; The type of positional coordinate used. Must be one of the following values: `LONGITUDE` - ISO 6709 standard, WGS84 geodetic datum. `LATITUDE` - ISO 6709 standard, WGS84 geodetic datum. `PLANTED_ROW` - The physical planted row number `PLANTED_INDIVIDUAL` - The physical counted number, could be independent or within a planted row. `GRID_ROW` - The row index number of a square grid overlay `GRID_COL` - The column index number of a square grid overlay `MEASURED_ROW` - The distance in meters from a defined 0-th row `MEASURED_COL` - The distance in meters from a defined 0-th column The Examples section shows an example of how to construct the `observationUnitPosition` argument as a list.
`programDbId`	character; required: FALSE; The identifier, which uniquely identifies a program.
`programName`	character; required: FALSE; The human readable name of a program.
`seedLotDbId`	character; required: FALSE; The unique identifier for the originating Seed Lot.
`studyDbId`	character; required: FALSE; The identifier, which uniquely identifies a study within the given database server.
`studyName`	character; required: FALSE; The human readable name for a study.
`treatments`	data.frame; required: FALSE; Data.frame of treatments applied to an observation unit. MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. Each row in the `treatments` data.frame should contain the following columns: `factor` character; required: TRUE; The type of treatment/factor. e.g. 'fertilizer', 'inoculation', 'irrigation', etc. MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor. `modality` character; required: TRUE; The treatment/factor description. e.g. 'low fertilizer', 'yellow rust inoculation', 'high water', etc. MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor.
`trialDbId`	character; required: FALSE; The identifier, which uniquely identifies a trial.
`trialName`	character; required: FALSE; The human readable name of a trial.

Details

Add new Observation Units

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
additionalInfo <- list(dummyData = "TRUE",
                       example = "post_observationunits")
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"))
germplasmDbId <- "germplasm2"
germplasmName <- "Tomatillo Fantastico"
locationDbId <- "location_01"
locationName <- "Location 1"
observationUnitName <- "Plot 1"
observationUnitPUI <- "doi:10.12345/plot/1a9afc14"

## Create a geoCoordinates list object as element for the
## observationUnitPosition list
library(geojsonR)
## Point geometry
init <- TO_GeoJson$new()
pointGeometry <- list()
pointData <- c(-76.46313, # longitude
                42.44423, # latitude
                     123) # altitude
pointGeometry[["geometry"]] <- init$Point(data = pointData,
                                          stringify = FALSE)
pointGeometry[["type"]] <- "Feature"
##
## Polygon geometry with an exterior ring only
init <- TO_GeoJson$new()
## Individual polygon points are provided as c(longitude, latitude, altitude)
polygonData <- list(list(c(-76.476949, 42.447274, 123), # exterior ring (rectangle)
                         c(-76.474429, 42.447258, 123),
                         c(-76.474428, 42.446193, 123),
                         c(-76.476961, 42.446211, 123),
                         c(-76.476949, 42.447274, 123)))
polygonGeometry <- list()
polygonGeometry[["geometry"]] <- init$Polygon(data = polygonData,
                                              stringify = FALSE)
polygonGeometry[["type"]] <- "Feature"

## Create the observationUnitPosition list object
observationUnitPosition <- list(
  entryType = "TEST",
  geoCoordinates = pointGeometry,
  observationLevel = list(
    levelCode = "plot_1",
    levelName = "plot",
    levelOrder =  4),
  observationLevelRelationships = data.frame(
    levelCode  = c("fieldA", "rep1", "block1"),
    levelName  = c("field", "rep", "block"),
    levelOrder = c(1, 2, 3)),
  positionCoordinateX = "1",
  positionCoordinateXType = "PLANTED_ROW",
  positionCoordinateY = "1",
  positionCoordinateYType = "PLANTED_INDIVIDUAL"
)
programDbId <- "program1"
programName <- "The BrAPI Breeding Program"
seedLotDbId <- "seed_lot2"
studyDbId <- "study1"
studyName <- "Paw paw 2013 yield trial"
treatments <- data.frame(
  factor   = c("fertilizer", "irrigation"),
  modality = c("high fertilizer", "low water"))
trialDbId <- "trial1"
trialName <- "Peru Yield Trial 1"

## Make the POST /observationunits call
brapi_post_observationunits(
  con = con,
  additionalInfo = additionalInfo,
  externalReferences = externalReferences,
  germplasmDbId = germplasmDbId,
  germplasmName = germplasmName,
  locationDbId = locationDbId,
  locationName = locationName,
  observationUnitName = observationUnitName,
  observationUnitPUI = observationUnitPUI,
  observationUnitPosition = observationUnitPosition,
  programDbId = programDbId,
  programName = programName,
  seedLotDbId = seedLotDbId,
  studyDbId = studyDbId,
  studyName = studyName,
  treatments = treatments,
  trialDbId = trialDbId,
  trialName = trialName)


## End(Not run)

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