Mercurial > repos > ggricourt > data_manager_bigg
annotate data_manager/bigg_model_sbml_fetcher.py @ 10:a9f72fd191b5 draft
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
author | ggricourt |
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date | Thu, 24 Feb 2022 12:05:43 +0000 |
parents | e2f2977b1675 |
children | 2bb0d8ca1710 |
rev | line source |
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0
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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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"
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4 import sys |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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5 import time |
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262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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6 try: |
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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7 # 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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8 from urllib.request import Request, urlopen |
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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9 except ImportError: |
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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10 # Fall back to Python 2 imports |
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
parents:
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11 from urllib2 import Request, urlopen |
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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12 |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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13 |
10
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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14 MODEL_URL = "http://bigg.ucsd.edu/static/models/" |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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15 MODEL_DETAIL_URL = "http://bigg.ucsd.edu/api/v2/models/" |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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16 |
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262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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17 |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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18 def url_download(url, path): |
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262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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19 try: |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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20 with urlopen(Request(url)) as fod: |
10
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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21 with open(path, "wb") as dst: |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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22 while True: |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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23 chunk = fod.read(2**10) |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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24 if chunk: |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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25 dst.write(chunk) |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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26 else: |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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27 break |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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28 except Exception as e: |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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29 sys.exit(str(e)) |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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30 |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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31 |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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32 def url_json(url): |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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33 data = {} |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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34 try: |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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35 with urlopen(Request(url)) as fod: |
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a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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36 data = fod.read().decode("utf-8") |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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37 data = json.loads(data) |
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262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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38 except Exception as e: |
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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39 sys.exit(str(e)) |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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40 return data |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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41 |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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42 |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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43 def get_model_organism(model_id): |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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44 data = url_json(MODEL_DETAIL_URL + model_id) |
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a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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45 org = data.get("organism", "") |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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46 if org is None: |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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47 org = "" |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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48 res = "%s - %s" % (model_id, org) |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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49 return res |
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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"
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51 |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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52 def download_entries(model_ids, workdir): |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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53 for model_id in model_ids: |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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54 model_filename = model_id + ".xml" |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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55 path = os.path.abspath(os.path.join(workdir, model_filename)) |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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56 |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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57 url_download(MODEL_URL + model_filename, path) |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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58 data_manager_entry = {} |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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59 data_manager_entry["value"] = model_id |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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60 data_manager_entry["name"] = get_model_organism(model_id) |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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61 data_manager_entry["path"] = path |
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262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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62 |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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63 # Make sure that less than 10 requests per second, as required by host (http://bigg.ucsd.edu/data_access) |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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64 time.sleep(1) |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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65 yield data_manager_entry |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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66 |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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67 |
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68 if __name__ == "__main__": |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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69 parser = argparse.ArgumentParser() |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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70 pinput = parser.add_mutually_exclusive_group(required=True) |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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71 pinput.add_argument("--model-id", help="Model BIGG id") |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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72 pinput.add_argument("--model-all", action="store_true", help="Download all models") |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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73 parser.add_argument("--out-file", help="JSON output file") |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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74 args = parser.parse_args() |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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75 |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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76 # Init. |
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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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77 data_manager_json = {"data_tables": {}} |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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78 with open(args.out_file) as fh: |
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262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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79 params = json.load(fh) |
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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80 |
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a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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81 workdir = params["output_data"][0]["extra_files_path"] |
0
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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82 os.makedirs(workdir) |
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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83 |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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84 model_ids = [] |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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85 if args.model_id: |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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86 model_ids.append(args.model_id) |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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87 else: |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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88 data = url_json(MODEL_DETAIL_URL) |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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89 for result in data.get("results", []): |
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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90 model_ids.append(result.get("bigg_id")) |
0
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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91 |
5
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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92 entries = list(download_entries(model_ids, workdir)) |
0
262b8d79bc08
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
ggricourt
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93 |
5
5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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94 # Write data. |
10
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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95 data_manager_json["data_tables"]["bigg_model_sbml"] = entries |
a9f72fd191b5
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
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96 with open(args.out_file, "w") as fh: |
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5e6f76507721
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 47caed1dd87e80ae226fabb584e9d63d7c86a436-dirty"
ggricourt
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97 json.dump(data_manager_json, fh, sort_keys=True) |