brapi_post_scales: post /scales

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

post /scales

Description

Add new Scales

Usage

brapi_post_scales(
  con = NULL,
  additionalInfo = list(),
  dataType = "",
  decimalPlaces = 0,
  externalReferences = "",
  ontologyReference = list(),
  scaleName = "",
  validValues = list()
)

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.
dataType	character; required: FALSE; Class of the scale, entries can be: "Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed. "Date" - The date class is for events expressed in a time format, 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. "Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months. "Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories. "Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches. "Ordinal" - Ordinal scales are scales composed of ordered categories. "Text" - A free text is used to express the trait.
decimalPlaces	integer; required: FALSE; For numerical, number of decimal places to be reported.
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.
ontologyReference	list; required: FALSE; MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology. (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). The ontolgyReference list should/can contain the following elements: documentationLinks data.frame; required: FALSE; Links to various ontology documentation. Each row in the documentationLinks data.frame should contain the following columns: URL character; required: FALSE; A uniform resource locator specified as a valid uniform resource identifier (URI), e.g. http://purl.obolibrary.org/obo/ro.owl type character; required: FALSE; one of "OBO"| "RDF"|"WEBPAGE". ontologyDbId character; required: TRUE; Ontology database unique identifier. ontologyName character; required: TRUE; Ontology name, e.g. the Crop Ontology. version character; required: FALSE; Ontology version (no specific format). The Examples section shows an example of how to construct the ontologyReference argument as a list.
scaleName	character; required: FALSE; Name of the scale. MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable.
validValues	list; required: FALSE; Valid values for the scale. The validValues list can contain the following elements: categories data.frame; required: FALSE; data.frame of possible values with optional labels. Each row in the categories data.frame must have the following columns: label character; required: FALSE; A text label for a category. value character; required: FALSE; The actual value for a category. max integer; required: FALSE; Maximum value (used for field data capture control) for numerical and date scales. min integer; required: FALSE; Minimum value (used for field data capture control) for numerical and date scales. The Examples section shows an example of how to construct the validValues argument as a list.

Details

Create new scale objects in the database

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_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_observations_observationDbId(), brapi_put_observationunits_observationUnitDbId(), brapi_put_scales_scaleDbId(), brapi_put_traits_traitDbId(), brapi_put_variables_observationVariableDbId()

Other Scales: brapi_get_scales_scaleDbId(), brapi_get_scales(), brapi_put_scales_scaleDbId()

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
## Create function argument values
additionalInfo <- list(dummyData = "TRUE",
                       example = "post_scales")
dataType <- "Numerical"
decimalPlaces <- 2
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"))
ontologyReference <- list(
  documentationLinks = data.frame(
    URL = c("http://purl.obolibrary.org/obo/ro.owl",
            "https://en.wikipedia.org/wiki/Scale"),
    type = c("OBO",
             "WEBPAGE")),
  ontologyDbId = "ontology_attribute1",
  ontologyName = "Ontology.org",
  version = "17")
scaleName <- "Meters"
validValues <- list(
  categories = data.frame(
    label = c("low", "medium", "high"),
    value = c("0", "5", "10")),
  max = 9999,
  min = 2)
## Add the new scale
brapi_post_scales(con = con,
                  additionalInfo = additionalInfo,
                  dataType = dataType,
                  decimalPlaces = decimalPlaces,
                  externalReferences = externalReferences,
                  ontologyReference = ontologyReference,
                  scaleName = scaleName,
                  validValues = validValues)


## End(Not run)

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