brapi_put_observations_observationDbId: put /observations/{observationDbId}

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

put /observations/{observationDbId}

Description

Update an existing Observation

Usage

brapi_put_observations_observationDbId(
  con = NULL,
  observationDbId = "",
  additionalInfo = list(),
  collector = "",
  externalReferences = "",
  germplasmDbId = "",
  germplasmName = "",
  observationTimeStamp = "",
  observationUnitDbId = "",
  observationUnitName = "",
  observationVariableDbId = "",
  observationVariableName = "",
  season = list(),
  studyDbId = "",
  uploadedBy = "",
  value = ""
)

Arguments

con	list; required: TRUE; BrAPI connection object
observationDbId	character; required: TRUE; The unique identifier of an observation to update.
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.
collector	character; required: FALSE; The name or identifier of the entity, which collected the observation.
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; The identifier which uniquely identifies a germplasm.
germplasmName	character; required: FALSE; Human readable name of the germplasm. It can be the preferred name and does not have to be unique.
observationTimeStamp	character; required: FALSE; The date and time when the observation was made. 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).
observationUnitDbId	character; required: FALSE; The identifier which uniquely identifies an observation unit.
observationUnitName	character; required: FALSE; A human readable name for an observation unit.
observationVariableDbId	character; required: FALSE; The identifier which uniquely identifies an observation variable.
observationVariableName	character; required: FALSE; A human readable name for an observation variable.
season	list; required: FALSE; Information about the season in which the observation was made. The list can or should contain the following elements: season character; required: FALSE; Name of the season, e.g. 'Spring', 'Q2', 'Season A', etc. seasonDbId character; required: TRUE; Uniquely identifier for the season in which the observation was made. For backward compatibility it can be a string like '2012', '1957-2004'. year integer; required: FALSE; The 4 digit year of the season in which the observation was made. The Examples section shows an example of how to construct the season argument as a list.
studyDbId	character; required: FALSE; The identifier which uniquely identifies a study within the given database server.
uploadedBy	character; required: FALSE; The name or id of the user, who uploaded the observation to the database system.
value	character; required: FALSE; The value of the data collected as an observation.

Details

Update an existing Observation

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

See Also

Other brapi-phenotyping: brapi_get_events(), brapi_get_images_imageDbId(), brapi_get_images(), brapi_get_methods_methodDbId(), brapi_get_methods(), brapi_get_observationlevels(), brapi_get_observations_observationDbId(), brapi_get_observations_table(), brapi_get_observations(), brapi_get_observationunits_observationUnitDbId(), brapi_get_observationunits_table(), brapi_get_observationunits(), brapi_get_ontologies(), brapi_get_scales_scaleDbId(), brapi_get_scales(), brapi_get_search_images_searchResultsDbId(), brapi_get_search_observations_searchResultsDbId(), brapi_get_search_observationunits_searchResultsDbId(), brapi_get_search_variables_searchResultsDbId(), brapi_get_traits_traitDbId(), brapi_get_traits(), brapi_get_variables_observationVariableDbId(), brapi_get_variables(), brapi_post_images(), brapi_post_methods(), brapi_post_observations(), brapi_post_observationunits(), brapi_post_scales(), brapi_post_search_images(), brapi_post_search_observations(), brapi_post_search_observationunits(), brapi_post_search_variables(), brapi_post_traits(), brapi_post_variables(), brapi_put_images_imageDbId_imagecontent(), brapi_put_images_imageDbId(), brapi_put_methods_methodDbId(), brapi_put_observationunits_observationUnitDbId(), brapi_put_scales_scaleDbId(), brapi_put_traits_traitDbId(), brapi_put_variables_observationVariableDbId()

Other Observations: brapi_get_observations_observationDbId(), brapi_get_observations_table(), brapi_get_observations(), brapi_get_search_observations_searchResultsDbId(), brapi_post_observations(), brapi_post_search_observations()

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
additionalInfo <- list(dummyData = "TRUE",
                       example = "post_observations")
collector <- "BrAPIR v2"
externalReferences <-
  data.frame(referenceID = c("doi:10.155454/12341234",
                             "http://purl.obolibrary.org/obo/ro.owl",
                             "75a50e76"),
             referenceSource = c("DOI",
                                 "OBO Library",
                                 "Remote Data Collection Upload Tool"))
germplasmDbId <- "germplasm2"
germplasmName <- "Tomatillo Fantastico"
observationTimeStamp <- "2021-05-11T19:00:00+02:00"
observationUnitDbId <- "observation_unit2"
observationUnitName <- "Plot 2"
observationVariableDbId <- "variable1"
observationVariableName <- "Plant Height"
season <- list(season = "summer",
               seasonDbId = "summer_2013",
               year = 2013)
studyDbId <- "study2"
uploadedBy <- "Maikel (BrAPIR)"
value <- "50"
out <-
  brapi_post_observations(con = con,
                          additionalInfo = additionalInfo,
                          collector = collector,
                          externalReferences = externalReferences,
                          germplasmDbId = germplasmDbId,
                          germplasmName = germplasmName,
                          observationTimeStamp = observationTimeStamp,
                          observationUnitDbId = observationUnitDbId,
                          observationUnitName = observationUnitName,
                          observationVariableDbId = observationVariableDbId,
                          observationVarialbleName = observationVariableName,
                          season = season,
                          studyDbId = studyDbId,
                          uploadedBy = uploadedBy,
                          value = value)
observationDbId <- unique(out$observationDbId)
brapi_put_observations_observationDbId(con = con,
                                       observationDbId = observationDbId,
                                       value = "100")

## End(Not run)

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