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

brapi_post_samples

R Documentation

post /samples

Description

Add new Samples

Usage

brapi_post_samples(
  con = NULL,
  additionalInfo = list(),
  column = as.integer(NA),
  externalReferences = "",
  germplasmDbId = "",
  observationUnitDbId = "",
  plateDbId = "",
  plateName = "",
  programDbId = "",
  row = "",
  sampleBarcode = "",
  sampleDescription = "",
  sampleGroupDbId = "",
  sampleName = "",
  samplePUI = "",
  sampleTimestamp = "",
  sampleType = "",
  studyDbId = "",
  takenBy = "",
  tissueType = "",
  trialDbId = "",
  well = ""
)

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.
`column`	integer; required: FALSE; The Column identifier for this sample's location in the plate.
`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 database identifier for a germplasm (accession).
`observationUnitDbId`	character; required: FALSE; Database identifier, which unique identifies a observation unit.
`plateDbId`	character; required: FALSE; The database identifier, which uniquely identifies a plate of samples.
`plateName`	character; required: FALSE; The human readable name of a plate.
`programDbId`	character; required: FALSE; The datbase identifier, which uniquely identifies a program.
`row`	character; required: FALSE; The Row identifier for this sample's location in the plate.
`sampleBarcode`	character; required: FALSE; A unique identifier physically attached to the sample.
`sampleDescription`	character; required: FALSE; Description of a sample. MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing.
`sampleGroupDbId`	character; required: FALSE; The identifier, which uniquely identifies a group of samples.
`sampleName`	character; required: FALSE; The name of the sample.
`samplePUI`	character; required: FALSE; A permanent unique identifier for the sample (DOI, URL, UUID, etc.). MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible.
`sampleTimestamp`	character; required: FALSE; The date and time a sample was collected from the field. MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested.
`sampleType`	character; required: FALSE; The type of sample taken. e.g. 'DNA', 'RNA', 'Tissue', etc..
`studyDbId`	character; required: FALSE; The database identifier, which uniquely identifies a study.
`takenBy`	character; required: FALSE; The name or identifier of the entity, which took the sample from the field.
`tissueType`	character; required: FALSE; The type of tissue sampled, e.g. 'Leaf', 'Root', etc.. MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology).
`trialDbId`	character; required: FALSE; The database identifier, which uniquely identifies a trial.
`well`	character; required: FALSE; The Well identifier for this sample's location in the plate. Usually a concatenation of Row and Column, or just a number if the samples are not part of an ordered plate.

Details

Call to register the event of a sample being taken. Sample identifier is assigned as a result of the operation and returned in response.

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

Other brapi-genotyping: brapi_get_callsets_callSetDbId_calls(), brapi_get_callsets_callSetDbId(), brapi_get_callsets(), brapi_get_calls(), brapi_get_maps_mapDbId_linkagegroups(), brapi_get_maps_mapDbId(), brapi_get_maps(), brapi_get_markerpositions(), brapi_get_references_referenceDbId_bases(), brapi_get_references_referenceDbId(), brapi_get_referencesets_referenceSetDbId(), brapi_get_referencesets(), brapi_get_references(), brapi_get_samples_sampleDbId(), brapi_get_samples(), brapi_get_search_calls_searchResultsDbId(), brapi_get_search_callsets_searchResultsDbId(), brapi_get_search_markerpositions_searchResultsDbId(), brapi_get_search_references_searchResultsDbId(), brapi_get_search_referencesets_searchResultsDbId(), brapi_get_search_samples_searchResultsDbId(), brapi_get_search_variants_searchResultsDbId(), brapi_get_search_variantsets_searchResultsDbId(), brapi_get_variants_variantDbId_calls(), brapi_get_variants_variantDbId(), brapi_get_variantsets_variantSetDbId_callsets(), brapi_get_variantsets_variantSetDbId_calls(), brapi_get_variantsets_variantSetDbId_variants(), brapi_get_variantsets_variantSetDbId(), brapi_get_variantsets(), brapi_get_variants(), brapi_get_vendor_orders_orderId_plates(), brapi_get_vendor_orders_orderId_results(), brapi_get_vendor_orders_orderId_status(), brapi_get_vendor_orders(), brapi_get_vendor_specifications(), brapi_post_search_callsets(), brapi_post_search_calls(), brapi_post_search_markerpositions(), brapi_post_search_referencesets(), brapi_post_search_references(), brapi_post_search_samples(), brapi_post_search_variantsets(), brapi_post_search_variants(), brapi_post_variantsets_extract(), brapi_put_samples_sampleDbId()

Other Samples: brapi_get_samples_sampleDbId(), brapi_get_samples(), brapi_get_search_samples_searchResultsDbId(), brapi_post_search_samples(), brapi_put_samples_sampleDbId()

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
## Create function argument values
additionalInfo <- list(dummyData = "TRUE",
                       example = "post_samples")
column <- 3
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 <- "germplasm3"
observationUnitDbId <- "observation_unit3"
plateDbId <- "plate1"
plateName <- "Plate 1"
programDbId <- "program1"
row <- "B"
sampleBarcode <- "1234567890"
sampleDescription <- "Fake sample"
sampleGroupDbId <- "sample_group_02"
sampleName <- "Sample 4"
samplePUI <- "doi://40.12345/fake/4423"
sampleTimestamp <- "2012-12-12T12:12:12Z"
sampleType <- "Tissue"
studyDbId <- "study1"
takenBy <- "M. Verouden"
tissueType <- "Stem"
trialDbId <- "trial1"
well <- "B3"
brapi_post_samples(con = con,
                   additionalInfo = additionalInfo,
                   column = column,
                   externalReferences = externalReferences,
                   germplasmDbId = germplasmDbId,
                   observationUnitDbId = observationUnitDbId,
                   plateDbId = plateDbId,
                   plateName = plateName,
                   programDbId = programDbId,
                   row = row,
                   sampleBarcode = sampleBarcode,
                   sampleDescription = sampleDescription,
                   sampleGroupDbId = sampleGroupDbId,
                   sampleName = sampleName,
                   samplePUI = samplePUI,
                   sampleTimestamp = sampleTimestamp,
                   sampleType = sampleType,
                   studyDbId = studyDbId,
                   takenBy = takenBy,
                   tissueType = tissueType,
                   trialDbId = trialDbId,
                   well = well)

## End(Not run)

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