Mercurial > repos > recetox > data_manager_recetox_metabolite_fetcher

annotate data_manager/recetox_metabolite_fetcher.py @ 0:953dd78a34d3 draft default tip

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"planemo upload commit be4b24b2dacc3f23538068d5a6082bca246f6887"
author recetox
date Tue, 25 Aug 2020 11:15:49 +0000
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1 import os
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2 import errno
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3
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4 from argparse import ArgumentParser
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5 from datetime import datetime
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6 from json import dumps, loads
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7 from urllib.parse import urlparse
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8 from shutil import copy
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9
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10
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11 def main(args):
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12 with open(args.data_manager_json, 'r') as json_in:
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13 data_manager_input = loads(json_in.read())
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14 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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15
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16 try:
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17 os.mkdir(target_directory)
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18 except OSError as exc:
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19 if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
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20 pass
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21 else:
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22 raise
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23
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24 date = str(datetime.now())
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25 base = urlparse(args.database_url).hostname.split('.')[-2]
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26 name = f'{base}_{date}'.replace(' ', '_')
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27
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28 if base not in ['hmdb', 't3db']:
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29 raise NameError('Unknown database')
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30
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31 src = os.path.join(args.tool_data_dir, f'{base}.h5')
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32 dst = os.path.join(target_directory, f'{name}.h5')
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33 copy(src, dst)
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34
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35 data_table_entry = {
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36 'data_tables': {
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37 'recetox_metabolite_databases' : [
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38 {
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39 "value": name,
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40 "name": name,
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41 "date": date,
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42 "path": f'{name}.h5',
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43 }
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44 ]
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45 }
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46 }
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47
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48 with open(args.data_manager_json, 'w') as json_out:
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49 json_out.write(dumps(data_table_entry))
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50
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51
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52 if __name__ == "__main__":
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53 parser = ArgumentParser()
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54 parser.add_argument('--tool_data_dir')
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55 parser.add_argument('--database_url')
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56 parser.add_argument('--data_manager_json')
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57 main(parser.parse_args())