brapi_put_methods_methodDbId: put /methods/{methodDbId}

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

put /methods/{methodDbId}

Description

Update an existing Method

Usage

brapi_put_methods_methodDbId(
  con = NULL,
  methodDbId = "",
  additionalInfo = list(),
  bibliographicalReference = "",
  description = "",
  externalReferences = "",
  formula = "",
  methodClass = "",
  methodName = "",
  ontologyReference = list()
)

Arguments

con	list; required: TRUE; BrAPI connection object
methodDbId	character; required: TRUE; The unique identifier of the method to update details of.
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.
bibliographicalReference	character; required: FALSE; Bibliographical reference describing the method. MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method.
description	character; required: FALSE; Method description. MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number).
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.
formula	character; required: FALSE; For computational methods, i.e. when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation.
methodClass	character; required: FALSE; Method class (examples: "Measurement", "Counting", "Estimation", "Computation", etc.).
methodName	character; required: FALSE; Human readable name for the method. MIAPPE V1.1 (DM-88) Method Name of the method of observation.
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.

Details

Update the details of an existing method.

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

Other Methods: brapi_get_methods_methodDbId(), brapi_get_methods(), brapi_post_methods()

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
additionalInfo <- list(dummyData = "TRUE",
                       example = "post_methods")
bibliographicalReference <- "Smith, 1893, Really Cool Paper, Popular Journal"
description <- "Discriminant for root finding of quadratic functions"
externalReferences <-
  data.frame(referenceID = c("doi:10.155454/12341234",
                             "http://purl.obolibrary.org/obo/ro.owl",
                             "75a50e76"),
             referenceSource = c("DOI",
                                 "OBO Library",
                                 "Remote Data Collection Upload Tool"))
formula <- "b^2 - 4ad"
methodClass <- "Computation"
methodName <- "Discrimenant"
ontologyReference <- list(
  documentationLinks = data.frame(
    URL = c("http://purl.obolibrary.org/obo/ro.owl",
            "https://en.wikipedia.org/wiki/Discriminant"),
    type = c("OBO",
             "WEBPAGE")),
  ontologyDbId = "ontology_attribute1",
  ontologyName = "Ontology.org",
  version = "17")
## Add the new method
out <- brapi_post_methods(
 con = con,
 additionalInfo = additionalInfo,
 bibliographicalReference = bibliographicalReference,
 description = description,
 externalReferences = externalReferences,
 formula = formula,
 methodClass = methodClass,
 methodName = methodName,
 ontologyReference = ontologyReference)
## Obtain the methodDbId
methodDbId <- unique(out$methodDbId)
## Retrieve information about the new method
brapi_get_methods_methodDbId(con = con, methodDbId = methodDbId)
## Update the new method by correcting typographical errors
brapi_put_methods_methodDbId(con = con,
                             methodDbId = methodDbId,
                             additionalInfo = list(
                               dummyData = "TRUE",
                               example = "put_methods_methodDbId"),
                             formula = "b^2 - 4ac",
                             methodName = "Discriminant")

## End(Not run)

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