brapi_post_vendor_plates: post /vendor/plates

In mverouden/brapir-v1: Client to Access BrAPI Compliant Plant Breeding Databases

post /vendor/plates

Description

Submit a new set of Sample data

Usage

brapi_post_vendor_plates(
  con = NULL,
  clientId = "",
  numberOfSamples = 0,
  plates = "",
  sampleType = ""
)

Arguments

con	list; required: TRUE; BrAPI connection object
clientId	character; required: TRUE; A unique, alpha-numeric ID which identifies the client to the vendor. Used to connect the order to the contract, billing, and contact info.; default: "".
numberOfSamples	integer; required: TRUE; The total number of samples contained in this request. Used for billing and basic validation of the request.; default: 0.
plates	data.frame; required: TRUE, with default: ""; data.frame object of new plates to be submitted to a vendor. Each row in the data.frame describes one submitted plate. The plates argument data.frame requires to contain the following columns per submited plate: clientPlateBarcode vector of type character; Optional value of the barcode attached to each submitted plate. clientPlateId vector of type character; The Id which uniquely identifies each plate to the client making the request. sampleSubmissionFormat vector of type character; Identifier for the plate formats of submitted plates, usually "PLATE_96" for a 96 well plate or "TUBES" for plateless format. samples list of data.frame objects; Each data.frame in this list describes the samples on a submitted plate. Therefore, each row in one data.frame is describing one sample on a specific submitted plate. The data.frame containing the sample information per plate requires to contain the following columns: clientSampleBarCode vector of type character; Optional value of the barcode attached to each sample on a plate. clientSampleId vector of type character; The ID which uniquely identifies each sample on a plate to the client making the request. column vector of type character; The Column identifier for each samples location in a plate. comments vector of type character; Generic comments about each sample on a plate for the vendor. organismName vector of type character; Scientific organism name for each sample on a plate. row vector The Row identifier for each samples location in a plate. speciesName vector of type character; Scientific species name for each sample on a plate. tissueType vector of type character; The type of tissue in each sample on a plate. List of accepted tissue types can be found in the Vendor Specifiations. well vector of type character; The Well identifier for each samples location in the plate. Usually a concatenation of row and column as specified above. concentration data.frame; data.frame with the same number of rows as the number of samples on a plate and requires the following specified columns: units vector of type character; concentration units per sample on a plate concentration vector of type numeric; concentration values per sample on a plate taxonomyOntologyReference data.frame; Taxonomy Ontology Reference details for each sample individually on a plate. The data.frame requires the following specified columns: ontologyID vector of type character; Taxonomy Ontology Identifier per individual sample on a plate. ontologyPrefix vector of type character; Taxonomy Ontology Prefix per sample on a plate. ontologyTerm vector of type character; Taxonomy Ontology Term per sample on a plate. tissueTypeOntologyRefence data.frame; Tissue Type Ontology Reference details for each sample individually on a plate. The data.frame requires the following columns to be specified: ontologyID vector of type character; Tissue Type Ontology Identifier per sample on a plate. ontologyPrefix vector of type character; Tissue Type Ontology Prefix per sample on a plate. ontologyTerm vector of type character; Tissue Type Ontology Term per sample on a plate. volume data.frame; data.frame with the same number of rows as the number of samples on a plate and requires the following specified columns: units vector of type character; volume units per sample on a plate. value vector of type numeric; volume values per sample on a plate. The Examples Section shows an example of how to construct the plates argument as a data.frame object.
sampleType	character; required: TRUE; The type of Samples being submitted; default: "", possible values "DNA" | "RNA" | "Tissue"

Details

Submit a new set of Sample data

Value

data.frame containing the submissionId

Author(s)

brapir generator package

References

BrAPI SwaggerHub

See Also

Other brapi_1.3: brapi_get_allelematrices_search(), brapi_get_allelematrices(), brapi_get_attributes_categories(), brapi_get_attributes(), brapi_get_breedingmethods_breedingMethodDbId(), brapi_get_breedingmethods(), brapi_get_calls(), brapi_get_commoncropnames(), brapi_get_germplasm_germplasmDbId_attributes(), brapi_get_germplasm_germplasmDbId_markerprofiles(), brapi_get_germplasm_germplasmDbId_mcpd(), brapi_get_germplasm_germplasmDbId_pedigree(), brapi_get_germplasm_germplasmDbId_progeny(), brapi_get_germplasm_germplasmDbId(), brapi_get_germplasm(), brapi_get_images_imageDbId(), brapi_get_images(), brapi_get_lists_listDbId(), brapi_get_lists(), brapi_get_locations_locationDbId(), brapi_get_locations(), brapi_get_maps_mapDbId_positions_linkageGroupName(), brapi_get_maps_mapDbId_positions(), brapi_get_maps_mapDbId(), brapi_get_maps(), brapi_get_markerprofiles_markerProfileDbId(), brapi_get_markerprofiles(), brapi_get_markers_markerDbId(), brapi_get_markers(), brapi_get_methods_methodDbId(), brapi_get_methods(), brapi_get_observationlevels(), brapi_get_observationunits(), brapi_get_ontologies(), brapi_get_people_personDbId(), brapi_get_people(), brapi_get_programs(), brapi_get_samples_sampleDbId(), brapi_get_samples(), brapi_get_scales_scaleDbId(), brapi_get_scales(), brapi_get_search_germplasm_searchResultsDbId(), brapi_get_search_images_searchResultsDbId(), brapi_get_search_markers_searchResultsDbId(), brapi_get_search_observationtables_searchResultsDbId(), brapi_get_search_observationunits_searchResultsDbId(), brapi_get_search_programs_searchResultsDbId(), brapi_get_search_samples_searchResultsDbId(), brapi_get_search_studies_searchResultsDbId(), brapi_get_search_variables_searchResultsDbId(), brapi_get_seasons(), brapi_get_studies_studyDbId_germplasm(), brapi_get_studies_studyDbId_layouts(), brapi_get_studies_studyDbId_observations(), brapi_get_studies_studyDbId_observationunits(), brapi_get_studies_studyDbId_observationvariables(), brapi_get_studies_studyDbId_table(), brapi_get_studies_studyDbId(), brapi_get_studies(), brapi_get_studytypes(), brapi_get_traits_traitDbId(), brapi_get_traits(), brapi_get_trials_trialDbId(), brapi_get_trials(), brapi_get_variables_observationVariableDbId(), brapi_get_variables(), 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_plates_submissionId(), brapi_get_vendor_specifications(), brapi_post_allelematrices_search(), brapi_post_images(), brapi_post_lists_listDbId_items(), brapi_post_lists(), brapi_post_methods(), brapi_post_people(), brapi_post_phenotypes(), brapi_post_scales(), brapi_post_search_germplasm(), brapi_post_search_images(), brapi_post_search_markers(), brapi_post_search_observationtables(), brapi_post_search_observationunits(), brapi_post_search_programs(), brapi_post_search_samples(), brapi_post_search_studies(), brapi_post_search_variables(), brapi_post_studies_studyDbId_table(), brapi_post_traits(), brapi_post_vendor_orders(), brapi_put_images_imageDbId_imagecontent(), brapi_put_images_imageDbId(), brapi_put_lists_listDbId(), brapi_put_methods_methodDbId(), brapi_put_people_personDbId(), brapi_put_samples(), brapi_put_scales_scaleDbId(), brapi_put_studies_studyDbId_layouts(), brapi_put_studies_studyDbId_observations(), brapi_put_studies_studyDbId_observationunits(), brapi_put_traits_traitDbId()

Other Vendor: 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_plates_submissionId(), brapi_get_vendor_specifications(), brapi_post_vendor_orders()

Examples

## Not run: 

# Create a connection object
con <- brapi_db()$testserver

# Create an example data.frame plates object containing two plates
# * one 96 well plate ("PLATE_96")
# * one plateless format ("TUBES")
plates = data.frame(
clientPlateBarcode = c("plateBarcode01", "plateBarcode02"),
clientPlateId = c("plateId01", "plateId02"),
sampleSubmissionFormat = c("PLATE_96", "TUBES"))

# Specify samples of PlateId01
samplesPlateId01 <- data.frame(
  clientSampleBarCode = c("sampleBarcode0101", "sampleBarcode0102"),
  clientSampleId = c("sampleId0101", "sampleId0102"),
  column = c("01", "12"),
  comments = c("commentS0101", "commentS0102"),
  organismName = c("oName0101", "oName0102"),
  row = c("A", "H"),
  speciesName = c("sName0101", "sName0102"),
  tissueType = c("tType0101", "tType0102"),
  well = c("A01", "H12"))
samplesPlateId01[["concentration"]] <- data.frame(
  units = c("cUnit0101", "cUnit0101"),
  concentration = c(0.0, 0.0))
samplesPlateId01[["taxonomyOntologyReference"]] <- data.frame(
  ontologyID = c("taxOnId0101", "taxOnRefId0102"),
  ontologyPrefix = c("taxOnPrefix0101", "taxOnPrefix0102"),
  ontologyTerm = c("taxOnTerm0101", "taxOnTerm0102"))
samplesPlateId01[["tissueTypeOntologyRefence"]] <- data.frame(
  ontologyID = c("tTypeOnId0101", "tTypeOnId0102"),
  ontologyPrefix = c("tTypeOnPrefix0101", "tTypeOnPrefix0102"),
  ontologyTerm = c("tTypeOnTerm0101", "tTypeOnTerm0102"))
samplesPlateId01[["volume"]] <- data.frame(
  units = c("vUnit0101", "vUnit0101"),
  value = c(0.00, 0.00))

# Specify samples of PlateId02
samplesPlateId02 <- data.frame(
  clientSampleBarCode = c("sampleBarcode0201", "sampleBarcode0202"),
  clientSampleId = c("sampleId0201", "sampleId0202"),
  column = c("01", "02"),
  comments = c("commentS0201", "commentS0202"),
  organismName = c("oName0201", "oName0202"),
  row = c("TUBE", "TUBE"),
  speciesName = c("sName0201", "sName0202"),
  tissueType = c("tType0201", "tType0202"),
  well = c("TUBE01", "TUBE02"))
samplesPlateId02[["concentration"]] <- data.frame(
  units = c("cUnit0201", "cUnit0201"),
  concentration = c(0, 0))
samplesPlateId02[["taxonomyOntologyReference"]] <- data.frame(
  ontologyID = c("taxOnId0201", "taxOnRefId0202"),
  ontologyPrefix = c("taxOnPrefix0201", "taxOnPrefix0202"),
  ontologyTerm = c("taxOnTerm0201", "taxOnTerm0202"))
samplesPlateId02[["tissueTypeOntologyRefence"]] <- data.frame(
  ontologyID = c("tTypeOnId0201", "tTypeOnId0202"),
  ontologyPrefix = c("tTypeOnPrefix0201", "tTypeOnPrefix0202"),
  ontologyTerm = c("tTypeOnTerm0201", "tTypeOnTerm0202"))
samplesPlateId02[["volume"]] <- data.frame(
  units = c("vUnit0201", "vUnit0201"),
  value = c(0, 0))

# Add samples infomation to the plates object
plates[["samples"]] <- list(samplesPlateId01, samplesPlateId02)

# Make post /vendor/plates call
brapi_post_vendor_plates(con = con,
                         clientId = "BrAPIR",
                         numberOfSamples = 4,
                         plates = plates,
                         sampleType = "DNA")

## End(Not run)

mverouden/brapir-v1 documentation built on April 11, 2022, 9:17 a.m.