Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

annotate data_manager/data_manager.py @ 0:fafcd2f5db36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
author devteam
date Thu, 08 Oct 2015 12:14:42 -0400
parents
children 926847693e4d
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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
devteam
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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
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4 import os
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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 sys
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7 import tarfile
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8 import urllib2
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9 import zipfile
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10
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11 parser = argparse.ArgumentParser(description='Create data manager 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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12 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
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13 parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID')
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14 parser.add_argument('--url', dest='url', action='store', default='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz', help='Download URL')
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16 args = parser.parse_args()
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17
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18 def url_download(url, workdir):
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19 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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20 if not os.path.exists(workdir):
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21 os.makedirs(workdir)
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22 src = None
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23 dst = None
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24 try:
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25 req = urllib2.Request(url)
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26 src = urllib2.urlopen(req)
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27 dst = open(file_path, 'wb')
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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28 while True:
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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29 chunk = src.read(2**10)
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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30 if chunk:
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31 dst.write(chunk)
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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32 else:
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33 break
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34 except Exception, e:
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 print >>sys.stderr, str(e)
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 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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37 if src:
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38 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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39 if dst:
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40 dst.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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41 if tarfile.is_tarfile(file_path):
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42 fh = tarfile.open(file_path, 'r:*')
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43 elif zipfile.is_zipfile(file_path):
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44 fh = zipfile.ZipFile(file_path, 'r')
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45 else:
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46 return
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47 fh.extractall(workdir)
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48 os.remove(file_path)
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49
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50
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51 def main(args):
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52 workdir = os.path.join(os.getcwd(), 'taxonomy')
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53 url_download(args.url, workdir)
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54 data_manager_entry = {}
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55 data_manager_entry['value'] = args.name.lower()
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56 data_manager_entry['name'] = args.name
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57 data_manager_entry['path'] = '.'
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58 data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry))
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59 params = json.loads(open(args.output).read())
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60 target_directory = params['output_data'][0]['extra_files_path']
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61 os.mkdir(target_directory)
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62 output_path = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy'))
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63 for filename in os.listdir(workdir):
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64 shutil.move(os.path.join(output_path, filename), target_directory)
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65 file(args.output, 'w').write(json.dumps(data_manager_json))
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66
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67 if __name__ == '__main__':
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68 main(args)