Mercurial > repos > bgruening > data_manager_motus

annotate data_manager/data_manager_fetch_motus_db.py @ 1:ed9fc4e56553 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit 6ae189ed2bd62ea78fceb19d0d38ea4658b029e2
author bgruening
date Sat, 08 Feb 2025 20:40:31 +0000
parents 73c0eff7246d
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73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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1 #!/usr/bin/env python
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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2
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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3 import argparse
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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4 import json
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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5 import os
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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6 import shutil
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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7 import subprocess
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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8 import sys
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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9 import tarfile
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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10 from datetime import datetime
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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11
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12 import wget
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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14 version_mapping = {
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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15 "3.1.0": "https://zenodo.org/records/7778108/files/db_mOTU_v3.1.0.tar.gz",
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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16 "3.0.1": "https://zenodo.org/records/5140350/files/db_mOTU_v3.0.1.tar.gz",
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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17 "3.0.0": "https://zenodo.org/records/5012106/files/db_mOTU_v3.0.0.tar.gz",
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18 }
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21 def download_untar_store(url, tmp_path, dest_path):
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22 """
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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23 Download a tar.gz file containing one folder,
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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24 extract that folder and move the content inside dest_path
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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25 """
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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27 extract_path = os.path.join(tmp_path, "extract")
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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29 os.makedirs(tmp_path, exist_ok=True)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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31 # download data
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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32 filename = wget.download(url, out=tmp_path)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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33 tarfile_path = os.path.join(tmp_path, filename)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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34 tar = tarfile.open(tarfile_path)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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35 tar.extractall(extract_path)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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37 if len(list(os.listdir(extract_path))) > 1:
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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38 print("More then one folder in zipped file, aborting !")
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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39 else:
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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40 for folder in os.listdir(extract_path):
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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41 folder_path = os.path.join(extract_path, folder)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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42
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43 print(f"Copy data to {dest_path}")
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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44 shutil.copytree(folder_path, dest_path)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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45 print("Done !")
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47 shutil.rmtree(tmp_path)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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49
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50 def main():
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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51 # Parse Command Line
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52 parser = argparse.ArgumentParser(description="Create data manager JSON.")
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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53 parser.add_argument("--out", dest="output", action="store", help="JSON filename")
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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54 parser.add_argument(
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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55 "--version", dest="version", action="store", help="Version of the DB"
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56 )
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57 parser.add_argument(
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58 "--test",
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59 action="store_true",
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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60 help="option to test the script with an lighted database",
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61 )
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62
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63 args = parser.parse_args()
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64
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65 # the output file of a DM is a json containing args that can be used by the DM
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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66 # most tools mainly use these args to find the extra_files_path for the DM, which can be used
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67 # to store the DB data
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68 with open(args.output) as fh:
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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69 params = json.load(fh)
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70
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71 workdir = params["output_data"][0]["extra_files_path"]
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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72 os.mkdir(workdir)
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73
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74 time = datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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75 db_value = "db_from_{0}".format(time)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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76 db_path = os.path.join(workdir, db_value)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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77 tmp_path = os.path.join(workdir, "tmp")
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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78 url = version_mapping[args.version]
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79
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80 # create DB
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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81 if args.test: # the test only checks that the pharokka download script is available
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82
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83 # check if link is there
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84 command_args = ["wget", "--spider", url]
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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85 proc = subprocess.Popen(args=command_args, shell=False)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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86 return_code = proc.wait()
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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87 if return_code:
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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88 print("Error downloading motus database.", file=sys.stderr)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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89 sys.exit(return_code)
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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90
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91 # copy the test DB
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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92 # TODO ones available: https://github.com/motu-tool/mOTUs/issues/121
73c0eff7246d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14
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93 test_db_path = os.path.join(
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94 os.path.dirname(os.path.realpath(__file__)), "motus_test_DB_non_functional"
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95 )
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96 command_args = ["cp", "-r", test_db_path, db_path]
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97 proc = subprocess.Popen(args=command_args, shell=False)
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98 return_code = proc.wait()
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99 if return_code:
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100 print("Error copying motus database.", file=sys.stderr)
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101 sys.exit(return_code)
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102
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103 else:
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104
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105 # download data
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106 download_untar_store(url, tmp_path, db_path)
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107
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108 # Update Data Manager JSON and write to file
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109 data_manager_entry = {
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110 "data_tables": {
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111 "motus_db_versioned": {
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112 "value": db_value,
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113 "version": args.version,
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114 "name": f"mOTUs DB version {args.version} downloaded at {datetime.now()}",
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115 "path": db_path,
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116 }
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117 }
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118 }
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119
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120 with open(os.path.join(args.output), "w+") as fh:
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121 json.dump(data_manager_entry, fh, sort_keys=True)
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122
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123
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124 if __name__ == "__main__":
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125 main()