Mercurial > repos > iuc > data_manager_pharokka

annotate data_manager/data_manager_fetch_pharokka_db.py @ 1:bba8135dc024 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
author iuc
date Sun, 06 Aug 2023 10:10:51 +0000
parents 3b3daabcc63e
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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1 #!/usr/bin/env python
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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3 import argparse
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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4 import json
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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5 import os
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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6 import subprocess
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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7 import sys
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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8 from datetime import datetime
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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11 def main():
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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12 # Parse Command Line
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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13 parser = argparse.ArgumentParser(description="Create data manager JSON.")
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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14 parser.add_argument("--out", dest="output", action="store", help="JSON filename")
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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15 parser.add_argument("--version", dest="version", action="store", help="Version of the DB")
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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16 parser.add_argument(
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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17 "--test",
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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18 action="store_true",
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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19 help="option to test the script with an lighted database",
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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20 )
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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22 args = parser.parse_args()
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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24 # the output file of a DM is a json containing args that can be used by the DM
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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25 # most tools mainly use these args to find the extra_files_path for the DM, which can be used
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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26 # to store the DB data
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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27 with open(args.output) as fh:
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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28 params = json.load(fh)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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30 workdir = params["output_data"][0]["extra_files_path"]
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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31 os.mkdir(workdir)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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33 time = datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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34 db_value = "db_from_{0}".format(time)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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35 db_path = os.path.join(workdir, db_value)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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37 # create DB
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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38 if args.test: # the test only checks that the pharokka download script is available and copies the test DB
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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40 # check if install_databases.py is there
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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41 command_args = ["install_databases.py", "-h"]
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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42 proc = subprocess.Popen(args=command_args, shell=False)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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43 return_code = proc.wait()
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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44 if return_code:
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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45 print("Error downloading Pharokka database.", file=sys.stderr)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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46 sys.exit(return_code)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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47
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48 # copy the test DB
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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49 test_db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "subset_pharokka_db")
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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50 command_args = ["cp", "-r", test_db_path, db_path]
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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51 else:
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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52 command_args = ["install_databases.py", "-o", db_path]
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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54 proc = subprocess.Popen(args=command_args, shell=False)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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55 return_code = proc.wait()
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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56 if return_code:
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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57 print("Error downloading Pharokka database.", file=sys.stderr)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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58 sys.exit(return_code)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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60 # Update Data Manager JSON and write to file
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61 data_manager_entry = {
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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62 "data_tables": {
1
bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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63 "pharokka_db_versioned": {
0
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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64 "value": db_value,
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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65 "dbkey": db_value,
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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66 "version": args.version,
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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67 "name": f"Pharokka DB version {args.version} downloaded at {datetime.now()}",
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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68 "path": db_path,
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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69 }
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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70 }
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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71 }
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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72
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73 with open(os.path.join(args.output), "w+") as fh:
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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74 json.dump(data_manager_entry, fh, sort_keys=True)
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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75
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76
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77 if __name__ == "__main__":
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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78 main()