Mercurial > repos > stevecassidy > alveoimport

annotate alveo_get_primary_text.py @ 7:5a8d9ddabec4 draft

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planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
author stevecassidy
date Wed, 12 Oct 2016 17:06:33 -0400
parents 3a9f20428cff
children 2f4907372748
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1 from __future__ import print_function
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2 import json
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3 import argparse
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4 import pyalveo
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5 import sys
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6 import os
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7 from fnmatch import fnmatch
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8
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9 API_URL = 'https://app.alveo.edu.au' # TODO: export constants to a separate module
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10
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11 def parser():
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12 parser = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List")
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13 parser.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
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14 parser.add_argument('--item_list_url', required=True, action="store", type=str, help="Item List to download")
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15 parser.add_argument('--output_path', required=True, action="store", type=str, help="Path to output file")
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16 return parser.parse_args()
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17
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18 def get_item_list(api_key, item_list_url):
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19 client = pyalveo.Client(api_key=api_key, api_url=API_URL, use_cache=False)
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20 return client.get_item_list(item_list_url)
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21
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22 # this file name pattern allows galaxy to discover the dataset designation and type
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23 FNPAT = "%(designation)s_%(ext)s"
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24
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25 def galaxy_name(fname, ext):
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26 """construct a filename suitable for Galaxy dataset discovery"""
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27
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28 fname = FNPAT % {'designation': fname, 'ext': ext}
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29
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30 return fname
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31 import pprint
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32 def download_documents(item_list, output_path):
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33 """
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34 Downloads a list of documents to the directory specificed by output_path.
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35
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36 :type documents: list of pyalveo.Document
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37 :param documents: Documents to download
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38
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39 :type output_path: String
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40 :param output_path: directory to download to the documents to
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41 """
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42 if not os.path.exists(output_path):
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43 os.makedirs(output_path)
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44
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45 downloaded = []
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47 items = item_list.get_all()
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48 filtered_documents = []
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49 for item in items:
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50 md = item.metadata()
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51 fname = os.path.join(output_path, galaxy_name(md['alveo:metadata']['dc:identifier'], 'txt'))
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52 content = item.get_primary_text()
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53 if not content == None:
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54 with open(fname, 'w') as out:
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55 out.write(content)
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56
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57 return downloaded
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58
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59 def main():
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60 args = parser()
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61 try:
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62 api_key = open(args.api_key, 'r').read().strip()
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63 item_list = get_item_list(api_key, args.item_list_url)
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64 downloaded = download_documents(item_list, args.output_path)
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65 # write out a list of downloaded files as a result?
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66 except pyalveo.APIError as e:
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67 print("ERROR: " + str(e), file=sys.stderr)
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68 sys.exit(1)
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69
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70 if __name__ == '__main__':
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71 main()