Mercurial > repos > stevecassidy > alveoimport
annotate alveo_get_primary_text.py @ 14:a38315ecf593 draft
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author | stevecassidy |
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date | Wed, 01 Nov 2017 01:18:15 -0400 |
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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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6 |
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7 from util import API_URL, read_item_list |
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8 |
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9 |
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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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16 |
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17 |
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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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20 |
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21 |
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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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24 |
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25 fname = FNPAT % {'designation': fname, 'ext': ext} |
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26 |
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27 return fname |
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28 |
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29 |
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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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33 |
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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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36 |
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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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42 |
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43 downloaded = [] |
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44 |
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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) |
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53 |
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54 return downloaded |
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55 |
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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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68 |
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69 if __name__ == '__main__': |
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70 main() |