def validate_data(time_series_data, errors):
  gene_locus_regex = re.compile("^BSU[0-9]+|^BSU_misc_RNA_[0-9]+|^VMG_[0-9]+_[0-9]+(_c)?")
  # Column headers encode timepoint, value type, biological replicates, technical replicates
  column_header_regex = re.compile("^(\+|-)?[0-9]+::(value|mean|median|std|var|error|iqr)::b.+::t.+")
  dataLines = time_series_data.getRawDataLines()
  lineCount = 0
  for line in dataLines:
    # The header needs to be GeneLocus
    if lineCount is 0:
      if line[0] != "GeneLocus":
        errors.append(createFileValidationError("The first data column must be 'GeneLocus'"))
        break
      lineCount = lineCount + 1
      has_human_readable = line[1] == "HumanReadable"
      
      if has_human_readable:
        range_start = 2
      else:
        range_start = 1
      for i in range(range_start, len(line)):
        if not column_header_regex.match(line[i].lower()):
          errors.append(createFileValidationError("Column " + str(i) + " header must be of the format Timepoint::(value|mean|median|std|var|error|iqr)::Biological Replicates::Technical Replicates, (instead of " + line[i] + ")."))
      continue

    # The compound id should be one of these forms
    gene_locus = line[0]
    if not gene_locus_regex.match(gene_locus):
      errors.append(createFileValidationError("Line " + str(lineCount + 1) + ", column 1 must be of the format 'BSU#', 'BSU_misc_RNA_#', 'VMG_#_#', or 'VMG_#_#_c' (instead of " + gene_locus + ")."))
    lineCount = lineCount + 1
    
def validate_metadata(time_series_data, errors):
  metadata = time_series_data.getMetadataMap()
  validationHelper = ValidationHelper(metadata, errors)
  
  # validate the strain
  validationHelper.validateStrain()
  
  # validate the header format
  validationHelper.validateExplicitHeaderFormat("TIME::VALUE_TYPE")
  
  # validate the timepoint type
  validationHelper.validateControlledVocabularyProperty("TIMEPOINT TYPE", 
    "time point type", ['EX', 'IN', 'SI'], "'EX', 'IN', 'SI'")

  # validate the cell location    
  validationHelper.validateControlledVocabularyProperty("CELL LOCATION",
     "cell location", ['CE', 'ES', 'ME', 'CY', 'NC'], "'CE', 'ES', 'ME', 'CY', 'NC'")

  # validate the value unit
  validationHelper.validateControlledVocabularyProperty("VALUE UNIT", 
    "value unit", ['MM', 'UM', 'PERCENT', 'RATIOT1', 'RATIOCS', 'AU', 'DIMENSIONLESS', 'FMOL/UG'], "'mM', 'uM', 'Percent', 'RatioT1', 'RatioCs', 'AU', 'Dimensionless', 'fmol/ug'")
  
  # validate the scale
  validationHelper.validateControlledVocabularyProperty("SCALE", "scale",
    ['LIN', 'LOG2', 'LOG10', 'LN'], "'lin', 'log2', 'log10', 'ln'")

def validate_data_set_file(file):
  errors = []
  time_series_data = create_time_series_excel(file.getAbsolutePath())
  if time_series_data is None:
    errors.append(createFileValidationError(file.getName() + " is not an Excel file."))
    return errors
    
  # validate the metadata
  validate_metadata(time_series_data, errors)
      
  # validate the data
  validate_data(time_series_data, errors)
  
  return errors