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1 import argparse
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2 import json
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3 import os
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4 import sys
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5 try:
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6 # For Python 3.0 and later
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7 from urllib.request import Request, urlopen
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8 except ImportError:
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9 # Fall back to Python 2 imports
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10 from urllib2 import Request, urlopen
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11
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12
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13 def url_download(url, workdir):
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14 file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
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15 src = None
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16 dst = None
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17 try:
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18 req = Request(url)
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19 src = urlopen(req)
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20 with open(file_path, 'w') as dst:
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21 while True:
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22 chunk = src.read(2**10)
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23 if chunk:
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24 dst.write(chunk)
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25 else:
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26 break
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27 except Exception as e:
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28 sys.exit(str(e))
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29 finally:
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30 if src:
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31 src.close()
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32 return file_path
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33
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34
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35 def download(dbkey, name, url, out_file):
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36
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37 with open(out_file) as fh:
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38 params = json.loads(fh.read())
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39
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40 workdir = params['output_data'][0]['extra_files_path']
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41 os.makedirs(workdir)
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42 file_path = url_download(url, workdir)
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43 entry_name = os.path.basename(file_path)
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44
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45 data_manager_json = {"data_tables": {}}
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46 data_manager_entry = {}
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47 data_manager_entry['value'] = dbkey
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48 data_manager_entry['name'] = entry_name
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49 data_manager_entry['path'] = file_path
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50 data_manager_entry['description'] = "Genbank file for %s" % name
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51 data_manager_json["data_tables"]["vsnp_genbank"] = data_manager_entry
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52
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53 with open(out_file, 'w') as fh:
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54 fh.write(json.dumps(data_manager_json, sort_keys=True))
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55
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56
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57 parser = argparse.ArgumentParser()
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58
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59 parser.add_argument('--dbkey', dest='dbkey', help='Genome reference dbkey')
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60 parser.add_argument('--name', dest='name', help='Reference display name')
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61 parser.add_argument('--url', dest='url', help='URL to download Genbank file')
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62 parser.add_argument('--out_file', dest='out_file', help='JSON output file')
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63
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64 args = parser.parse_args()
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65
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66 download(args.dbkey, args.name, args.url, args.out_file)
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