Mercurial > repos > iuc > data_manager_cat

annotate data_manager/data_manager_cat.py @ 2:472dabcb03bf draft default tip

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planemo upload commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:36:10 +0000
parents 74af283d8ebd
children
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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3
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4 import argparse
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5 import json
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6 import os.path
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7 import subprocess
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8 import sys
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9 import tarfile
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10 import tempfile
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11 import zipfile
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12 try:
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13 # For Python 3.0 and later
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14 from urllib.request import urlopen
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15 except ImportError:
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16 # Fall back to Python 2 imports
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17 from urllib2 import urlopen
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18
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19
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20 def url_download(url, workdir):
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21 file_path = os.path.join(workdir, 'download.dat')
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22 src = None
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23 dst = None
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24 try:
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25 src = urlopen(url)
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26 with open(file_path, 'wb') as dst:
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27 while True:
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28 chunk = src.read(2**10)
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29 if chunk:
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30 dst.write(chunk)
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31 else:
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32 break
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33 finally:
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34 if src:
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35 src.close()
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36 if tarfile.is_tarfile(file_path):
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37 fh = tarfile.open(file_path, 'r:*')
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38 elif zipfile.is_zipfile(file_path):
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39 fh = zipfile.ZipFile(file_path, 'r')
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40 else:
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41 return
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42 fh.extractall(workdir)
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43 os.remove(file_path)
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44
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45
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46 def cat_prepare(install_dir, db_dir=None, tax_dir=None):
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47 if db_dir and tax_dir:
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48 cmd = ['CAT', 'prepare', '--existing', '-d', db_dir, '-t', tax_dir]
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49 else:
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50 cmd = ['CAT', 'prepare', '--fresh', '-q']
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51 cmd_stdout = tempfile.NamedTemporaryFile()
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52 cmd_stderr = tempfile.NamedTemporaryFile()
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53 return_code = subprocess.call(cmd, shell=False, cwd=install_dir,
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54 stdout=cmd_stdout, stderr=cmd_stderr)
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55 if return_code:
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56 msg = "stdout:\n%s\nstderr:\n%s" % (cmd_stdout.read(),
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57 cmd_stderr.read())
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58 cmd_stdout.close()
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59 cmd_stderr.close()
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60 raise Exception('Error: (%s), returncode=%s %s'
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61 % (' '.join(cmd), return_code, msg))
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62
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63
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64 def main():
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65 parser = argparse.ArgumentParser()
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66 parser.add_argument('--config_file', required=True)
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67 parser.add_argument('--install_path', default=None)
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68 parser.add_argument('--db_url', default=None)
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69 parser.add_argument('--database_folder', default=None)
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70 parser.add_argument('--taxonomy_folder', default=None)
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71 args = parser.parse_args()
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72
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73 cat_path = None
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74 cat_db = None
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75 tax_db = None
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76 if args.database_folder and args.taxonomy_folder:
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77 cat_path = os.path.dirname(args.database_folder)
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78 cat_db = os.path.basename(args.database_folder)
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79 tax_db = os.path.basename(args.taxonomy_folder)
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80 cat_prepare(os.getcwd(),
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81 db_dir=args.database_folder,
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82 tax_dir=args.taxonomy_folder)
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83 elif not args.install_path:
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84 sys.exit(1)
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85 else:
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86 if not os.path.exists(args.install_path):
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87 os.makedirs(args.install_path)
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88 if args.db_url:
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89 url_download(args.db_url, args.install_path)
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90 else:
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91 cat_prepare(args.install_path)
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92 for root, dirs, _ in os.walk(args.install_path):
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93 for dname in dirs:
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94 if dname.endswith('CAT_database'):
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95 cat_db = dname
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96 elif dname.endswith('taxonomy'):
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97 tax_db = dname
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98 if cat_db and tax_db:
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99 cat_path = root
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100 break
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101 cat_dir = os.path.basename(cat_path)
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102 dm_dict = {}
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103 dm_dict['data_tables'] = dm_dict.get('data_tables', {})
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104 data_table = 'cat_database'
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105 dm_dict['data_tables'][data_table]\
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106 = dm_dict['data_tables'].get(data_table, [])
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107 data_table_entry = dict(value=cat_dir, name=cat_dir,
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108 database_folder=os.path.join(cat_dir, cat_db),
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109 taxonomy_folder=os.path.join(cat_dir, tax_db))
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110 dm_dict['data_tables'][data_table].append(data_table_entry)
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111 # save info to json file
1
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112 with open(args.config_file, 'w') as fh:
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113 json.dump(dm_dict, fh, sort_keys=True)
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114
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115
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116 if __name__ == "__main__":
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117 main()