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1 import os
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2 import sys
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3 import uuid
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4 import json
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0
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5 import argparse
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6 import datetime
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7
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7 import requests
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8 from requests.exceptions import ContentDecodingError
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9
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10 parser = argparse.ArgumentParser(description='Create data manager json.')
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7
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11 parser.add_argument('--out',
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12 dest='output',
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13 action='store',
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14 help='JSON filename',
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15 default="gene_annotation.json"
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16 )
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17 parser.add_argument('--name',
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18 dest='name',
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19 action='store',
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20 default=uuid.uuid4(),
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21 help='Data table entry unique ID'
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22 )
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23 parser.add_argument('--url',
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24 dest='url',
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25 action='store',
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26 help='Download URL',
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27 default="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf")
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0
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28
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29 args = parser.parse_args()
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30
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7
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31
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32 def url_download(url, name, workdir):
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33 # Create path if it doesn't exist
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34 if not os.path.exists(workdir):
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35 os.makedirs(workdir)
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36
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37 response = requests.get(url=url, stream=True)
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38
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39 # Create path that we will write the file to
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40 file_path = os.path.join(workdir, 'download_{}.dat'.format(name))
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41
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42 block_size = 10 * 1024 * 1024 # 10MB chunked download
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43 with open(file_path, 'w+') as f:
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44 try:
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45 for buf in response.iter_content(block_size):
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46 f.write(buf)
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47 except (ContentDecodingError, IOError) as e:
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48 sys.stderr.write("Error occured downloading reference file: %s"
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49 % e)
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50 os.remove(file_path)
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51
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52 return file_path
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0
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53
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54
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55 def main(args):
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56 workdir = os.path.join(os.getcwd(), 'gene_annotation')
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7
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57
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58 # Attempt to download gene annotation file from given url
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59 gene_annotation_file_path = url_download(args.url, args.name, workdir)
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60
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61 # Update Data Manager Json and write out
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62 data_manager_entry = {
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63 'data_tables': {
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64 'gene_annotation': {
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65 'date': str(datetime.datetime.now()),
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66 'name': str(args.name),
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67 'path': gene_annotation_file_path
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68 }
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69 }
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70 }
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71
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72 with open(os.path.join(workdir, args.output), "w+") as f:
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73 f.write(json.dumps(data_manager_entry))
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0
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74
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75 if __name__ == '__main__':
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7
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76 main(args)
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