annotate data_manager/bigg_model_sbml_fetcher.py @ 2:2be543b08426 draft

"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit ca4bd5776dd6d4dc8493544f123ef09496902981"
author ggricourt
date Wed, 23 Feb 2022 16:09:22 +0000
parents 5068c6484606
children 2f837e65b33c
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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
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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2 import json
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3 import os
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4 import sys
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5 try:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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6 # For Python 3.0 and later
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7 from urllib.request import Request, urlopen
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8 except ImportError:
262b8d79bc08 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"
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9 # Fall back to Python 2 imports
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10 from urllib2 import Request, urlopen
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11
1
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12 BASE_URL = 'http://bigg.ucsd.edu/static/models'
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13 ID2ORG = {
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14 "iCN718": "Acinetobacter baumannii AYE",
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15 "iYO844": "Bacillus subtilis subsp. subtilis str. 168",
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16 "iRC1080": "Chlamydomonas reinhardtii",
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17 "iCN900": "Clostridioides difficile 630",
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18 "iHN637": "Clostridium ljungdahlii DSM 13528",
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19 "iCHOv1_DG44": "Cricetulus griseus",
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20 "iCHOv1": "Cricetulus griseus",
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21 "iAF1260b": "Escherichia coli str. K-12 substr. MG1655",
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22 "iAF1260": "Escherichia coli str. K-12 substr. MG1655",
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23 "iML1515": "Escherichia coli str. K-12 substr. MG1655",
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24 "iJO1366": "Escherichia coli str. K-12 substr. MG1655",
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25 "iJR904": "Escherichia coli str. K-12 substr. MG1655",
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26 "e_coli_core": "Escherichia coli str. K-12 substr. MG1655",
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27 "iAF987": "Geobacter metallireducens GS-15",
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28 "iIT341": "Helicobacter pylori 26695",
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29 "iAT_PLT_636": "Homo sapiens",
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30 "Recon3D": "Homo sapiens",
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31 "iAB_RBC_283": "Homo sapiens",
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32 "RECON1": "Homo sapiens",
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33 "iYL1228": "Klebsiella pneumoniae subsp. pneumoniae MGH 78578",
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34 "iNF517": "Lactococcus lactis subsp. cremoris MG1363",
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35 "iAF692": "Methanosarcina barkeri str. Fusaro",
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36 "iMM1415": "Mus musculus",
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37 "iNJ661": "Mycobacterium tuberculosis H37Rv",
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38 "iEK1008": "Mycobacterium tuberculosis H37Rv",
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39 "iLB1027_lipid": "Phaeodactylum tricornutum CCAP 1055/1",
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40 "iAM_Pb448": "Plasmodium berghei",
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41 "iAM_Pc455": "Plasmodium cynomolgi strain B",
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42 "iAM_Pf480": "Plasmodium falciparum 3D7",
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43 "iAM_Pk459": "Plasmodium knowlesi strain H",
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44 "iAM_Pv461": "Plasmodium vivax Sal-1",
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45 "iJN746": "Pseudomonas putida KT2440",
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46 "iJN1463": "Pseudomonas putida KT2440",
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47 "iND750": "Saccharomyces cerevisiae S288C",
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48 "iMM904": "Saccharomyces cerevisiae S288C",
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49 "STM_v1_0": "Salmonella enterica subsp. enterica serovar Typhimurium str. LT2",
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50 "iYS1720": "Salmonella pan-reactome",
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51 "iSB619": "Staphylococcus aureus subsp. aureus N315",
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52 "iYS854": "Staphylococcus aureus subsp. aureus USA300_TCH1516",
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53 "iJB785": "Synechococcus elongatus PCC 7942",
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54 "iJN678": "Synechocystis sp. PCC 6803",
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55 "iSynCJ816": "Synechocystis sp. PCC 6803",
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56 "iLJ478": "Thermotoga maritima MSB8",
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57 "iIS312": "Trypanosoma cruzi Dm28c",
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58 "iIS312_Trypomastigote": "Trypanosoma cruzi Dm28c",
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59 "iIS312_Epimastigote": "Trypanosoma cruzi Dm28c",
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60 "iIS312_Amastigote": "Trypanosoma cruzi Dm28c"
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61 }
0
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62
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63 def url_download(url, workdir):
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64 file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
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65 src = None
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66 dst = None
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67 try:
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68 req = Request(url)
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69 src = urlopen(req)
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70 with open(file_path, 'wb') as dst:
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71 while True:
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72 chunk = src.read(2**10)
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73 if chunk:
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74 dst.write(chunk)
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75 else:
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76 break
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77 except Exception as e:
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78 sys.exit(str(e))
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79 finally:
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80 if src:
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81 src.close()
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82 return file_path
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83
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84
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85 def download(model_id, out_file):
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86
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87 with open(out_file) as fh:
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88 params = json.load(fh)
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89
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90 workdir = params['output_data'][0]['extra_files_path']
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91 os.makedirs(workdir)
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92
1
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93 data_manager_json = {'data_tables': {}}
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94 file_path = url_download(BASE_URL + '/' + model_id + '.xml', workdir)
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95
0
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96 data_manager_entry = {}
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97 data_manager_entry['value'] = model_id
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98 data_manager_entry['name'] = MODELID2ORG.get(model_id, 'undefined')
0
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99 data_manager_entry['path'] = file_path
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100
1
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101 data_manager_json['data_tables']['bigg_model_sbml'] = data_manager_entry
0
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102 with open(out_file, 'w') as fh:
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103 json.dump(data_manager_json, fh, sort_keys=True)
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104
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105
1
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106 if __name__ == '__main__':
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107 parser = argparse.ArgumentParser()
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108 parser.add_argument('--model-id', help='Model BIGG id')
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109 parser.add_argument('--out-file', help='JSON output file')
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110 args = parser.parse_args()
0
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111
2
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112 download(args.model_id, args.out_file)