Mercurial > repos > ggricourt > data_manager_bigg

annotate data_manager/bigg_model_sbml_fetcher.py @ 0:262b8d79bc08 draft

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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
author ggricourt
date Wed, 23 Feb 2022 14:33:49 +0000
parents
children 5068c6484606
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
parents:
diff changeset
1 import argparse
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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2 import json
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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3 import os
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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4 import sys
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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5 try:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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6 # For Python 3.0 and later
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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7 from urllib.request import Request, urlopen
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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8 except ImportError:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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9 # Fall back to Python 2 imports
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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10 from urllib2 import Request, urlopen
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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11
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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12
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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13 def url_download(url, workdir):
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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14 file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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15 src = None
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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16 dst = None
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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17 try:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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18 req = Request(url)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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19 src = urlopen(req)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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20 with open(file_path, 'wb') as dst:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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21 while True:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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22 chunk = src.read(2**10)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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23 if chunk:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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24 dst.write(chunk)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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25 else:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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26 break
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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27 except Exception as e:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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28 sys.exit(str(e))
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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29 finally:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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30 if src:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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31 src.close()
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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32 return file_path
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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33
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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34
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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35 def download(model_id, out_file):
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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36
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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37 with open(out_file) as fh:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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38 params = json.load(fh)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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39
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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40 workdir = params['output_data'][0]['extra_files_path']
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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41 os.makedirs(workdir)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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42 file_path = url_download('http://bigg.ucsd.edu/static/models/%s.xml' % (model_id,), workdir)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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43 entry_name = os.path.basename(file_path)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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44
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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45 data_manager_json = {"data_tables": {}}
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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46 data_manager_entry = {}
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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47 data_manager_entry['value'] = model_id
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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48 data_manager_entry['name'] = entry_name
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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49 data_manager_entry['path'] = file_path
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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50
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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51 with open(out_file, 'w') as fh:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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52 json.dump(data_manager_json, fh, sort_keys=True)
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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53
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54
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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55 parser = argparse.ArgumentParser()
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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56
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57 parser.add_argument('--model-id', help='Model id')
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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58 parser.add_argument('--out-file', help='JSON output file')
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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59
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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60 args = parser.parse_args()
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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61
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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62 download(args.model_id, args.out_file)