R/createNewACASExperiment.R

In mcneilco/racas: R Package for ACAS

createNewACASExperiment <- function(metaData, protocol, lsTransaction, pathToGenericDataFormatExcelFile) {
  # creates an experiment using the metaData
  # 
  # Args:
  #   metaData:               A data.frame including "Experiment Name", "Scientist", "Notebook", "Page", and "Assay Date"
  #   protocol:               A list that is a protocol
  #   lsTransaction:          A list that is a lsTransaction tag
  #
  # Returns:
  #  A list that is an experiment
  
#   experimentStates <- list()
#   
#   # Store the metaData in experiment values
#   experimentValues <- list()
#   experimentValues[[length(experimentValues)+1]] <- createStateValue(valueType = "stringValue",
#                                                                      valueKind = "notebook",
#                                                                      stringValue = metaData$Notebook[1])
#   if (!is.null(metaData$Page)) {
#     experimentValues[[length(experimentValues)+1]] <- createStateValue(valueType = "stringValue",
#                                                                        valueKind = "notebook page",
#                                                                        stringValue = metaData$Page[1])
#   }
#   experimentValues[[length(experimentValues)+1]] <- createStateValue(valueType = "dateValue",
#                                                                      valueKind = "completion date",
#                                                                      dateValue = as.numeric(format(as.Date(metaData$"Assay Date"[1]), "%s"))*1000)
#   experimentValues[[length(experimentValues)+1]] <- createStateValue(valueType = "stringValue",
#                                                                      valueKind = "status",
#                                                                      stringValue = "Approved")
#   experimentValues[[length(experimentValues)+1]] <- createStateValue(valueType = "stringValue",
#                                                                      valueKind = "analysis status",
#                                                                      stringValue = "complete")
#   experimentValues[[length(experimentValues)+1]] <- createStateValue(valueType = "clobValue",
#                                                                      valueKind = "analysis result html",
#                                                                      stringValue = "<p>Analysis completed in Galileo</p>")
#   
#   if (!is.null(metaData$Project)) {
#     experimentValues[[length(experimentValues)+1]] <- createStateValue(valueType = "stringValue",
#                                                                        valueKind = "project",
#                                                                        stringValue = metaData$Project[1])
#   }
#   
#   # Create an experiment state for metadata
#   experimentStates[[length(experimentStates)+1]] <- createExperimentState(experimentValues=experimentValues,
#                                                                           lsTransaction = lsTransaction, 
#                                                                           recordedBy=metaData$Scientist[1], 
#                                                                           stateType="metadata", 
#                                                                           stateKind="experiment metadata")
#   
#   # Create a label for the experiment name
#   experimentLabels <- list()
#   experimentLabels[[length(experimentLabels)+1]] <- createExperimentLabel(lsTransaction = lsTransaction, 
#                                                                           recordedBy=metaData$Scientist[1], 
#                                                                           labelType="name", 
#                                                                           labelKind="experiment name",
#                                                                           labelText=metaData$"Experiment Name"[1],
#                                                                           preferred=TRUE)
#   # Create the experiment
#   experiment <- createExperiment(lsTransaction = lsTransaction, 
#                                  protocol = protocol,
#                                  kind = "Galileo ETL",
#                                  shortDescription="experiment created by galileo etl",  
#                                  recordedBy=metaData$Scientist[1], 
#                                  experimentLabels=experimentLabels,
#                                  experimentStates=experimentStates)
#   
#   # Save the experiment to the server
#   experiment <- saveExperiment(experiment)
#   
#   return(experiment)
}