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1 import os
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2 import sys
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3 import json
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4 import argparse
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5 import requests
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6 from requests.exceptions import ContentDecodingError
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7
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8
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9 def url_download(url):
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10 """Attempt to download gene annotation file from a given url
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11 :param url: full url to gene annotation file
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12 :type url: str.
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13 :returns: name of downloaded gene annotation file
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14 :raises: ContentDecodingError, IOError
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15 """
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16 response = requests.get(url=url, stream=True)
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17
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18 # Generate file_name
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19 file_name = response.url.split("/")[-1]
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20
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21 block_size = 10 * 1024 * 1024 # 10MB chunked download
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22 with open(file_name, 'w+') as f:
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23 try:
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24 # Good to note here that requests' iter_content() will
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25 # automatically handle decoding "gzip" and "deflate" encoding
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26 # formats
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27 for buf in response.iter_content(block_size):
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28 f.write(buf)
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29 except (ContentDecodingError, IOError) as e:
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30 sys.stderr.write("Error occured downloading reference file: %s"
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31 % e)
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32 os.remove(file_name)
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33
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34 return file_name
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35
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36
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37 def main():
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38
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39 # Generate and parse command line args
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40 parser = argparse.ArgumentParser(description='Create data manager JSON.')
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41 parser.add_argument('--out', dest='output', action='store',
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42 help='JSON filename')
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43 parser.add_argument('--name', dest='name', action='store',
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42
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44 default=None, help='Data table entry unique ID'
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40
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45 )
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46 parser.add_argument('--url', dest='url', action='store',
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47 help='Url to download gtf file from')
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48
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49 args = parser.parse_args()
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50
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51 work_dir = os.getcwd()
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52
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53 # Attempt to download gene annotation file from given url
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54 gene_annotation_file_name = url_download(args.url)
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55
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42
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56 name = str(args.name)
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57
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58 if not name:
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59 name = gene_annotation_file_name.split(".")[0]
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60
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40
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61 # Update Data Manager JSON and write to file
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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 'value': gene_annotation_file_name.split(".")[0],
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41
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66 'dbkey': gene_annotation_file_name.split(".")[0],
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67 'name': name,
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68 'path': gene_annotation_file_name
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69 }
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70 }
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71 }
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72
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73 with open(os.path.join(args.output), "w+") as f:
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74 f.write(json.dumps(data_manager_entry))
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75
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76 if __name__ == '__main__':
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77 main()
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