Mercurial > repos > ggricourt > data_manager_bigg

annotate data_manager/bigg_model_sbml_fetcher.py @ 5:5e6f76507721 draft

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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
author ggricourt
date Thu, 24 Feb 2022 10:56:46 +0000
parents 2f837e65b33c
children 65589e7476b6
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262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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1 import argparse
5
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2 import ast
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3 import json
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4 import os
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5 import sys
5
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6 import time
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7 try:
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8 # For Python 3.0 and later
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9 from urllib.request import Request, urlopen
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10 except ImportError:
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11 # Fall back to Python 2 imports
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12 from urllib2 import Request, urlopen
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13
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15 MODEL_URL = 'http://bigg.ucsd.edu/static/models/'
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16 MODEL_DETAIL_URL = 'http://bigg.ucsd.edu/api/v2/models/'
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0
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18
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19 def url_download(url, path):
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20 try:
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21 with urlopen(Request(url)) as fod:
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22 with open(path, 'wb') as dst:
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23 while True:
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24 chunk = fod.read(2**10)
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25 if chunk:
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26 dst.write(chunk)
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27 else:
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28 break
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29 except Exception as e:
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30 sys.exit(str(e))
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33 def url_json(url):
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34 data = {}
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35 try:
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36 with urlopen(Request(url)) as fod:
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37 data = fod.read().encode('utf-8')
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38 data = ast.literal_evals(data)
0
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39 except Exception as e:
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40 sys.exit(str(e))
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41 return data
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42
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43
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44 def get_model_organism(model_id):
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45 data = url_json(MODEL_DETAIL_URL + model_id)
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46 org = data.get('organism', 'undefined')
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47 res = "(%s) %s" (model_id, org)
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48 return res
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49
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50
5
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51 def download_entries(model_ids, workdir):
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52 for model_id in model_ids:
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53 model_filename = model_id + '.xml'
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54 path = os.path.abspath(os.path.join(workdir, model_filename))
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55
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56 url_download(MODEL_DETAIL_URL + model_filename, path)
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57 data_manager_entry = {}
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58 data_manager_entry['value'] = model_id
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59 data_manager_entry['name'] = get_model_organism(model_id)
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60 data_manager_entry['path'] = path
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61
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62 # Make sure that less than 10 requests per second, as required by host (http://bigg.ucsd.edu/data_access)
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63 time.sleep(1)
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64 yield data_manager_entry
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65
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66
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67 if __name__ == '__main__':
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68 parser = argparse.ArgumentParser()
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69 pinput = parser.add_mutually_exclusive_group(required=True)
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70 pinput.add_argument('--model-id', help='Model BIGG id')
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71 pinput.add_argument('--model-all', action='store_true', help='Download all models')
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72 parser.add_argument('--out-file', help='JSON output file')
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73 args = parser.parse_args()
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74
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75 # Init.
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76 data_manager_json = {'data_tables': {}}
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77 with open(args.out_file) as fh:
0
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78 params = json.load(fh)
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79
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80 workdir = params['output_data'][0]['extra_files_path']
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81 os.makedirs(workdir)
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82
5
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83 model_ids = []
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84 if args.model_id:
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85 model_ids.append(args.model_id)
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86 else:
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87 data = url_json(MODEL_DETAIL_URL)
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88 for result in data.get("results", []):
5e6f76507721 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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89 model_ids.append(result.get("bigg_id"))
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90
5
5e6f76507721 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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91 entries = list(download_entries(model_ids, workdir))
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262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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92
5
5e6f76507721 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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93 # Write data.
5e6f76507721 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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94 data_manager_json['data_tables']['bigg_model_sbml'] = entries
5e6f76507721 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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95 with open(args.out_file, 'w') as fh:
5e6f76507721 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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96 json.dump(data_manager_json, fh, sort_keys=True)