<gh_stars>1-10
#!/usr/bin/env python
import re
import sys

from EPPs.common import GenerateHamiltonInputEPP, InvalidStepError


class GenerateHamiltonInputNTP(GenerateHamiltonInputEPP):
    """"Generate a CSV containing the necessary information to normalise the libraries in a NTP plate"""
    _use_load_config = False  # prevent the loading of the config
    # Define the column headers that will be used in the Hamilton input file
    csv_column_headers = ['Input Plate', 'Input Well', 'Output Plate', 'Output Well', 'Library Volume',
                          'RSB Barcode', 'RSB Volume']
    # Define the output file
    output_file_name = 'KAPA_NORMALISE_LIBRARIES.csv'

    # Define the number of input containers that are permitted
    _max_nb_input_containers = 1

    # Define the number of output containers that are permitted
    _max_nb_output_containers = 1

    # the script is only compatible with 1 output for each input i.e. replicates are not allowed
    _nb_analytes_per_input = 1

    def _generate_csv_dict(self):
        # csv_dict will be a dictionary that consists of the lines to be present in the Hamilton input file.
        csv_dict = {}

        # find the lot number, i.e. barcode, of the RSB reagent.
        RSB_template = "LP[0-9]{7}-RSB"
        reagent_lots = list(self.process.step.reagent_lots)

        rsb_barcode = None
        for lot in reagent_lots:
            if re.match(RSB_template, lot.lot_number):
                rsb_barcode = lot.lot_number

        if not rsb_barcode:
                raise InvalidStepError('Please assign RSB lot before generating Hamilton input.')


        # find all the inputs for the step that are analytes (i.e. samples and not associated files)
        for input_art in self.artifacts:
            if input_art.type == 'Analyte':
                output = self.process.outputs_per_input(input_art.id, Analyte=True)[0]

                # remove semi-colon from locations as this is not compatible with Hamilton Venus software
                input_location = input_art.location[1].replace(':', '')
                output_location = output.location[1].replace(':', '')

                # assemble each line of the Hamilton input file in the correct structure for the Hamilton
                csv_line = [
                    input_art.container.name, input_location, output.container.name, output_location,
                    output.udf['NTP Library Volume (uL)'], rsb_barcode, output.udf['NTP RSB Volume (uL)']
                ]
                # build a dictionary of the lines for the Hamilton input file with a key that facilitates
                # the lines being by input container then column then row
                csv_dict[input_art.location[1]] = csv_line

        return csv_dict


if __name__ == '__main__':
    sys.exit(GenerateHamiltonInputNTP().run())

#!/usr/bin/env python
import re
import sys

from EPPs.common import GenerateHamiltonInputEPP, InvalidStepError


class GenerateHamiltonInputNTP(GenerateHamiltonInputEPP):
    """"Generate a CSV containing the necessary information to normalise the libraries in a NTP plate"""
    _use_load_config = False  # prevent the loading of the config
    # Define the column headers that will be used in the Hamilton input file
    csv_column_headers = ['Input Plate', 'Input Well', 'Output Plate', 'Output Well', 'Library Volume',
                          'RSB Barcode', 'RSB Volume']
    # Define the output file
    output_file_name = 'KAPA_NORMALISE_LIBRARIES.csv'

    # Define the number of input containers that are permitted
    _max_nb_input_containers = 1

    # Define the number of output containers that are permitted
    _max_nb_output_containers = 1

    # the script is only compatible with 1 output for each input i.e. replicates are not allowed
    _nb_analytes_per_input = 1

    def _generate_csv_dict(self):
        # csv_dict will be a dictionary that consists of the lines to be present in the Hamilton input file.
        csv_dict = {}

        # find the lot number, i.e. barcode, of the RSB reagent.
        RSB_template = "LP[0-9]{7}-RSB"
        reagent_lots = list(self.process.step.reagent_lots)

        rsb_barcode = None
        for lot in reagent_lots:
            if re.match(RSB_template, lot.lot_number):
                rsb_barcode = lot.lot_number

        if not rsb_barcode:
                raise InvalidStepError('Please assign RSB lot before generating Hamilton input.')


        # find all the inputs for the step that are analytes (i.e. samples and not associated files)
        for input_art in self.artifacts:
            if input_art.type == 'Analyte':
                output = self.process.outputs_per_input(input_art.id, Analyte=True)[0]

                # remove semi-colon from locations as this is not compatible with Hamilton Venus software
                input_location = input_art.location[1].replace(':', '')
                output_location = output.location[1].replace(':', '')

                # assemble each line of the Hamilton input file in the correct structure for the Hamilton
                csv_line = [
                    input_art.container.name, input_location, output.container.name, output_location,
                    output.udf['NTP Library Volume (uL)'], rsb_barcode, output.udf['NTP RSB Volume (uL)']
                ]
                # build a dictionary of the lines for the Hamilton input file with a key that facilitates
                # the lines being by input container then column then row
                csv_dict[input_art.location[1]] = csv_line

        return csv_dict


if __name__ == '__main__':
    sys.exit(GenerateHamiltonInputNTP().run())
#!/usr/bin/env python "Generate a CSV containing the necessary information to normalise the libraries in a NTP plate # prevent the loading of the config # Define the column headers that will be used in the Hamilton input file # Define the output file # Define the number of input containers that are permitted # Define the number of output containers that are permitted # the script is only compatible with 1 output for each input i.e. replicates are not allowed # csv_dict will be a dictionary that consists of the lines to be present in the Hamilton input file. # find the lot number, i.e. barcode, of the RSB reagent. # find all the inputs for the step that are analytes (i.e. samples and not associated files) # remove semi-colon from locations as this is not compatible with Hamilton Venus software # assemble each line of the Hamilton input file in the correct structure for the Hamilton # build a dictionary of the lines for the Hamilton input file with a key that facilitates # the lines being by input container then column then row