Mercurial > repos > stevecassidy > alveoimport

annotate alveo_get_primary_text.py @ 16:fd22df0c6d9b draft

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planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit f2432aaedd36ae7662873623d8861d0982dffdd2-dirty
author stevecassidy
date Sun, 03 Dec 2017 18:21:20 -0500
parents 3fd0f8f1f3ce
children
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1 from __future__ import print_function
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2 import argparse
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3 import pyalveo
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4 import sys
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5 import os
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7 from util import API_URL, read_item_list
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10 def parser():
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11 parser = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List")
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12 parser.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
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13 parser.add_argument('--item_list', required=True, action="store", type=str, help="File containing list of item URLs")
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14 parser.add_argument('--output_path', required=True, action="store", type=str, help="Path to output file")
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15 return parser.parse_args()
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18 # this file name pattern allows galaxy to discover the dataset designation and type
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19 FNPAT = "%(designation)s_%(ext)s"
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22 def galaxy_name(fname, ext):
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23 """construct a filename suitable for Galaxy dataset discovery"""
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25 fname = FNPAT % {'designation': fname, 'ext': ext}
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27 return fname
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30 def download_text(item_list, output_path):
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31 """
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32 Downloads primary text from a list of items to the directory specified by output_path.
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34 :type item_list: ItemGroup
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35 :param item_list: item list to download
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37 :type output_path: String
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38 :param output_path: directory to download to the documents to
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39 """
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40 if not os.path.exists(output_path):
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41 os.makedirs(output_path)
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43 downloaded = []
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45 items = item_list.get_all()
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46 for item in items:
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47 md = item.metadata()
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48 fname = os.path.join(output_path, galaxy_name(md['alveo:metadata']['dcterms:identifier'], 'txt'))
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49 content = item.get_primary_text()
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50 if content is not None:
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51 with open(fname, 'w') as out:
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52 out.write(content.decode('utf-8'))
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54 return downloaded
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57 def main():
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58 args = parser()
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59 try:
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60 api_key = open(args.api_key, 'r').read().strip()
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61 client = pyalveo.Client(api_url=API_URL, api_key=api_key, use_cache=False)
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62 item_list = read_item_list(args.item_list, client)
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63 download_text(item_list, args.output_path)
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64 except pyalveo.APIError as e:
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65 print("ERROR: " + str(e), file=sys.stderr)
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66 sys.exit(1)
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67
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69 if __name__ == '__main__':
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70 main()