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

View source: R/brapi_post_search_observations.R

brapi_post_search_observations

R Documentation

post /search/observations

Description

Submit a search request for Observations

Usage

brapi_post_search_observations(
  con = NULL,
  externalReferenceIDs = "",
  externalReferenceSources = "",
  germplasmDbIds = "",
  germplasmNames = "",
  locationDbIds = "",
  locationNames = "",
  observationDbIds = "",
  observationLevelRelationships = "",
  observationLevels = "",
  observationTimeStampRangeEnd = "",
  observationTimeStampRangeStart = "",
  observationUnitDbIds = "",
  observationVariableDbIds = "",
  observationVariableNames = "",
  page = 0,
  pageSize = 1000,
  programDbIds = "",
  programNames = "",
  seasonDbIds = "",
  studyDbIds = "",
  studyNames = "",
  trialDbIds = "",
  trialNames = ""
)

Arguments

`con`	list; required: TRUE; BrAPI connection object
`externalReferenceIDs`	vector of type character; required: FALSE; List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter); default: "", when using multiple values supply as c("value1", "value2").
`externalReferenceSources`	vector of type character; required: FALSE; List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter); default: "", when using multiple values supply as c("value1", "value2").
`germplasmDbIds`	vector of type character; required: FALSE; List of unique database identifiers, which uniquely identify germplasm to search for; default: "", when using multiple values supply as c( "value1", "value2").
`germplasmNames`	vector of type character; required: FALSE; List of human readable names to identify germplasm to search for; default: "", when using multiple values supply as c("value1", "value2").
`locationDbIds`	vector of type character; required: FALSE; The unique location identifier(s) to search for; default: "", when using multiple values supply as c("value1", "value2").
`locationNames`	vector of type character; required: FALSE; A human readable location name(s) to search for; default: "", when using multiple values supply as c("value1", "value2").
`observationDbIds`	vector of type character; required: FALSE; The unique database identifier(s) of an observation(s) to search for; default: "", when using multiple values supply as c("value1", "value2").
`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. The Examples section shows an example of how to construct the `observationLevelRelationships` argument as a data.frame.
`observationLevels`	data.frame; required: FALSE; A data.frame of Observation levels, which indicate the granularity level at which the measurements are taken. The `observationLevels` argument data.frame can contain the following columns: `levelName` character; required: FALSE; A name for this level. `levelOrder` interger; required: FALSE; `levelOrder` defines, where that level exists in the hierarchy of levels. `levelOrder`'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). The Examples section shows an example of how to construct the `observationLevels` argument as a data.frame.
`observationTimeStampRangeEnd`	character; required: FALSE; Time stamp to end the range for observations to filter on. Coded in the ISO 8601 standard extended format, where date, time and time zone information needs to be provided (check for example https://www.w3.org/TR/NOTE-datetime).
`observationTimeStampRangeStart`	character; required: FALSE; Time stamp to start the range for observations to filter on. Coded in the ISO 8601 standard extended format, where date, time and time zone information needs to be provided (check for example https://www.w3.org/TR/NOTE-datetime).
`observationUnitDbIds`	vector of type character; required: FALSE; The unique database identifier of an observation unit; default: "", when using multiple values supply as c("value1", "value2").
`observationVariableDbIds`	vector of type character; required: FALSE; The unique database identifiers of Variables to search for; default: "", when using multiple values supply as c("value1", "value2").
`observationVariableNames`	vector of type character; required: FALSE; The names of Variables to search for; default: "", when using multiple values supply as c("value1", "value2").
`page`	integer; required: FALSE; Used to request a specific page of data to be returned. The page indexing starts at 0 (the first page is `page = 0`). Default is `0`.
`pageSize`	integer; required: FALSE; The size of the pages to be returned. Default is `1000`.
`programDbIds`	vector of type character; required: FALSE; Unique program database identifiers to search for; default: "", when using multiple values supply as c("value1", "value2").
`programNames`	vector of type character; required: FALSE; A program names to search for; default: "", when using multiple values supply as c("value1", "value2").
`seasonDbIds`	vector of type character; required: FALSE; Unique season database identifier(s) to search for; default: "", when using multiple values supply as c("value1", "value2").
`studyDbIds`	vector of type character; required: FALSE; List of unique database study identifiers to search for; default: "", when using multiple values supply as c("value1", "value2").
`studyNames`	vector of type character; required: FALSE; List of study names to filter search results; default: "", when using multiple values supply as c("value1", "value2").
`trialDbIds`	vector of type character; required: FALSE; The identifiers, which uniquely identify trials to search for; default: "", when using multiple values supply as c("value1", "value2").
`trialNames`	vector of type character; required: FALSE; The human readable names of trials to search for; default: "", when using multiple values supply as c("value1", "value2").

Details

Submit a search request for Observations. Function will return either the search results (Status 200 for an immediate response) or a searchResultsDbId (Status 202 for both a saved and an asynchronous search).

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
observationLevelRelationships <- data.frame(
  levelCode  = c("fieldA", "rep1", "block1"),
  levelName  = c("field", "rep", "block"),
  levelOrder = c(1, 2, 3))
observationLevels <-
  data.frame(levelName = c("field", "block", "plot"),
             levelOrder = c(0, 1, 2))

# Immediate Response Example
brapi_post_search_observations(con = con,
                               germplasmDbIds = c("germplasm1",
                                                  "germplasm2",
                                                  "germplasm3"))

# Saved or Asynchronous Search Response Example
brapi_post_search_observations(
  con = con,
  externalReferenceIDs = "https://brapi.org/specification",
  externalReferenceSources = "BrAPI Doc",
  germplasmDbIds = c("germplasm1",
                     "germplasm2",
                     "germplasm3"),
  page = 0,
  pageSize = 1000)

## End(Not run)

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