#####################################################
### Transformation script that registers samples  ###
###   if they are not already in LabKey.          ###
### Created by: Hannah Brakke                     ###
#####################################################

#load needed packages (assuming they are already installed on your server)
library(Rlabkey); library(readxl)

################################################
# Read in the run properties and results data. #
################################################

run.props = labkey.transform.readRunPropertiesFile("${runInfo}");

# save the important run.props as separate variables
run.data.file = labkey.transform.getRunPropertyValue(run.props, "runDataFile");
run.output.file = run.props$val3[run.props$name == "runDataFile"];
error.file = labkey.transform.getRunPropertyValue(run.props, "errorsFile");

# read in the results data file content
run.data = read.delim(run.data.file, header=TRUE, sep="\t", stringsAsFactors = FALSE);

###########################################################
# Now that the file is loaded, perform the transformation #
###########################################################


### If you want to transform any of your assay data, do it here. 


### Now register samples that don't exist in LabKey but are in your assay file
### Include lineage of these samples to a parent sample type

### Configure API key, base URL, and folder path in the lines below:

myApiKey = "YOUR_API_KEY_HERE" ### Paste your API key between the quotes

labkey.setDefaults(apiKey=myApiKey)

## pull the sample type information
myBaseUrl = "http://localhost:8080/labkey" ### Define your baseUrl
myFolderPath = "/Tutorials/AssayTransform" ### Define your folder path
mySchemaName = "samples"
myChildQueryName = "childSamples" #define the child sample type name
myParentQueryName = "parentSamples" #define the parent sample type name

#load the child sample data
childData= labkey.selectRows(
  baseUrl= myBaseUrl, 
  folderPath= myFolderPath, 
  schemaName= mySchemaName, 
  queryName= myChildQueryName,
  colSelect="Name" #we only care about the name to register samples
)

#load the parent sample data
parentData= labkey.selectRows(
  baseUrl= myBaseUrl, 
  folderPath= myFolderPath, 
  schemaName= mySchemaName, 
  queryName= myParentQueryName,
  colSelect="Name" #we only care about the name to register the lineage
)

### Determine if the sample ID in your assay matches with your sample type (this assumes you have a column called sampleID)

#match the child sample type IDs with my assay IDs
childmatches = match(run.data$sampleID, childData$Name, nomatch=NA)
parentmatches = match(run.data$parentID, parentData$Name, nomatch=NA)

#create an empty data frame to load sample IDs and the sample parent
rowsToInsert = setNames(data.frame(matrix(ncol = 2, nrow = 0)), c("Name","MaterialInputs/parentSamples")) #change the parentSamples to your parent sample name

for(i in 1:nrow(run.data)){
    if(is.na(childmatches[i]) == TRUE && is.na(parentmatches[i]) == TRUE){
      #if there is no sampleID registered or a parent ID registered, error out
      stop("If the sampleId isn't registered, the parent sample must be registered. Please register a sample Id or a parent sample.")
    }else if(is.na(childmatches[i]) == TRUE && is.na(parentmatches[i]) == FALSE){
      rowsToInsert[i,] = c(run.data$sampleID[i],run.data$parentID[i])
  }
}

#remove rows with NA    
rowsToInsert =na.omit(rowsToInsert)
      
#insert new samples
labkey.insertRows(
  baseUrl= myBaseUrl, 
  folderPath=myFolderPath, 
  schemaName= mySchemaName, 
  queryName= myChildQueryName,
  toInsert = rowsToInsert)


###########################################################
# Write the transformed data to the output file location. #
###########################################################

# write the new set of run data out to an output file
write.table(run.data, file=run.output.file, sep="\t", na="", row.names=FALSE, quote=FALSE)

# print the ending time for the transform script
writeLines(paste("nProcessing end time:",Sys.time(),sep=" "))