data_translator.py

import csv

class WormbaseIonChannelCSVTranslator(DataTranslator):
    input_type = WormbaseIonChannelCSVDataSource
    output_type = DataObjectContextDataSource

    def translate(self, data_source):
        res = set([])
        try:
            with open(data_source.csv_file_name, 'r') as csvfile:
                next(csvfile, None)
                csvreader = csv.reader(csvfile, skipinitialspace=True)

                for line in csvreader:
                    channel_name = normalize_cell_name(line[0]).upper()
                    gene_name = line[1].upper()
                    gene_WB_ID = line[2].upper()
                    expression_pattern = line[3]
                    description = line[4]
                    c = Channel(name=str(channel_name))
                    c.gene_name(gene_name)
                    c.gene_WB_ID(gene_WB_ID)
                    c.description(description)
                    patterns = expression_pattern.split(r' | ')
                    regex = re.compile(r' *\[([^\]]+)\] *(.*) *')

                    matches = [regex.match(pat) for pat in patterns]
                    patterns = [ExpressionPattern(wormbaseID=m.group(1),
                                                  description=m.group(2))
                                for m in matches if m is not None]
                    for pat in patterns:
                        c.expression_pattern(pat)
                    res.add(c)
        except Exception:
            traceback.print_exc()
        return res