Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

annotate data_manager/data_manager.py @ 2:4af4e175db0d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 04825a097d217d30deb5fcb6906fe718023e25b6"
author iuc
date Tue, 28 Apr 2020 03:57:59 -0400
parents 926847693e4d
children bdd8632fa9fb
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fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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1 import argparse
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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2 import datetime
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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3 import json
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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4 import os
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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5 import shutil
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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6 import tarfile
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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7 import zipfile
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926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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8 try:
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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9 # For Python 3.0 and later
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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10 from urllib.request import Request, urlopen
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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11 except ImportError:
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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12 # Fall back to Python 2 imports
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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13 from urllib2 import Request, urlopen
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fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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16 def url_download(url, workdir):
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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17 file_path = os.path.join(workdir, 'download.dat')
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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18 if not os.path.exists(workdir):
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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19 os.makedirs(workdir)
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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20 src = None
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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21 dst = None
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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22 try:
1
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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23 req = Request(url)
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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24 src = urlopen(req)
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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25 with open(file_path, 'wb') as dst:
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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26 while True:
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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27 chunk = src.read(2**10)
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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28 if chunk:
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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29 dst.write(chunk)
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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30 else:
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
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31 break
0
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32 finally:
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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33 if src:
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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34 src.close()
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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35 if tarfile.is_tarfile(file_path):
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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36 fh = tarfile.open(file_path, 'r:*')
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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37 elif zipfile.is_zipfile(file_path):
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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38 fh = zipfile.ZipFile(file_path, 'r')
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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39 else:
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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40 return
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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41 fh.extractall(workdir)
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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42 os.remove(file_path)
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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44
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45 def main(args):
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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46 workdir = os.path.join(os.getcwd(), 'taxonomy')
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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47 url_download(args.url, workdir)
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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48 data_manager_entry = {}
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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49 data_manager_entry['value'] = args.name.lower()
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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50 data_manager_entry['name'] = args.name
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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51 data_manager_entry['path'] = '.'
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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52 data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry))
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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53 params = json.loads(open(args.output).read())
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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54 target_directory = params['output_data'][0]['extra_files_path']
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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55 os.mkdir(target_directory)
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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56 output_path = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy'))
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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57 for filename in os.listdir(workdir):
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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58 shutil.move(os.path.join(output_path, filename), target_directory)
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4af4e175db0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 04825a097d217d30deb5fcb6906fe718023e25b6"
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59 with open(args.output, 'w') as out:
4af4e175db0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 04825a097d217d30deb5fcb6906fe718023e25b6"
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60 out.write(json.dumps(data_manager_json, sort_keys=True))
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61
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62
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63 if __name__ == '__main__':
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64 parser = argparse.ArgumentParser(description='Create data manager json.')
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
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65 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
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66 parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID')
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
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67 parser.add_argument('--url', dest='url', action='store', default='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz', help='Download URL')
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
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68 args = parser.parse_args()
926847693e4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
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69
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70 main(args)