brapi_put_samples_sampleDbId: put /samples/{sampleDbId}

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

put /samples/{sampleDbId}

Description

Update the details of an existing Sample

Usage

brapi_put_samples_sampleDbId(
  con = NULL,
  sampleDbId = "",
  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
sampleDbId	character; required: TRUE; the unique internal database identifier for a sample.
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

Update the details of an existing Sample

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

See Also

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_samples(), 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()

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

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"
## Add a new sample
out <-
 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)
## Obtain the sampleDbId
sampleDbId <- unique(out$sampleDbId)
## Retrieve information about the new sample
brapi_get_samples_sampleDbId(con = con, sampleDbId = sampleDbId)
## Update the new sample information
additionalInfo <- list(dummyData = "TRUE",
                       example = "put_samples_sampleeDbId")
sampleDescription <- "Fake sample with updated information"
sampleName <- "Updated Sample 4"
brapi_put_samples_sampleDbId(con = con,
                             sampleDbId = sampleDbId,
                             additionalInfo = additionalInfo,
                             sampleDescription = sampleDescription,
                             sampleName = sampleName)
## Check the changes
brapi_get_samples_sampleDbId(con = con, sampleDbId = sampleDbId)

## End(Not run)

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