Mercurial > repos > iuc > data_manager_nextclade

annotate data_manager/nextclade_dm.py @ 1:8b7bb3c635b1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 0617f25cbfdca61240f16b85ae21f3cd46b1a44e
author iuc
date Sat, 06 Aug 2022 15:43:32 +0000
parents 6e64cb3d2b1d
children
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6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
iuc
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1 #!/usr/bin/env python
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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2
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3 import argparse
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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4 import datetime
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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5 import json
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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6 import operator
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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7 import pathlib
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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8 import subprocess
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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9 import sys
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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10 from typing import List
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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11
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12
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13 def parse_date(d: str) -> datetime.datetime:
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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14 # Parses the publication date from the nextclade release tags or user input into a datetime object.
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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15 date = None
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16 try:
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17 date = datetime.datetime.strptime(d, "%Y-%m-%dT%H:%M:%SZ")
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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18 except ValueError:
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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19 date = datetime.datetime.strptime(d, "%Y-%m-%d")
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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20 return date
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21
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22
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23 def entry_to_tag(entry: dict) -> str:
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24 return (
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25 entry["attributes"]["name"]["value"] + "_" + entry["attributes"]["tag"]["value"]
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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26 )
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27
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28
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29 def get_database_list() -> List[dict]:
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30 list_cmd = [
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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31 "nextclade",
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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32 "dataset",
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33 "list",
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34 "--json",
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35 "--include-old",
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36 "--include-incompatible",
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37 ]
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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38 list_proc = subprocess.run(list_cmd, capture_output=True, check=True)
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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39 database_list = json.loads(list_proc.stdout)
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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40 entry_list = []
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41 for db_entry in database_list:
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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42 attributes = db_entry["attributes"]
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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43 entry = {
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44 "value": entry_to_tag(db_entry),
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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45 "database_name": attributes["name"]["value"],
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46 "description": attributes["name"]["valueFriendly"],
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47 "date": datetime.datetime.fromisoformat(
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48 attributes["tag"]["value"].replace("Z", "")
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49 ),
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50 "tag": attributes["tag"]["value"],
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51 "min_nextclade_version": db_entry["compatibility"]["nextcladeCli"]["min"],
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52 }
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53 entry_list.append(entry)
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54 return entry_list
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55
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56
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57 def filter_by_date(
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58 existing_release_tags: List[str],
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59 name: str,
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60 releases: list,
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61 start_date: datetime.datetime = None,
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62 end_date: datetime.datetime = None,
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63 ) -> List[dict]:
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64 ret = []
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65 for release in releases:
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66 if (
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67 release["database_name"] != name
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68 or release["value"] in existing_release_tags
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69 ):
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70 continue
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71 if start_date and release["date"] < start_date:
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72 break
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73 if not end_date or release["date"] <= end_date:
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74 ret.append(release)
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75
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76 return ret
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77
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78
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79 def download_and_unpack(name: str, release: str, output_directory: str) -> pathlib.Path:
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80 download_cmd = [
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81 "nextclade",
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82 "dataset",
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83 "get",
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84 "--name",
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85 name,
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86 "--tag",
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87 release,
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88 "--output-dir",
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89 ]
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90 output_path = pathlib.Path(output_directory) / (
6e64cb3d2b1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_nextclade commit 3d6dabd066dcbe31cfa38fbfac340e253d8a984d
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91 name + "_" + release.replace(":", "-")
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92 )
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93 download_cmd.append(str(output_path))
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94 subprocess.run(download_cmd, check=True)
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95 return output_path
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96
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97
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98 def comma_split(args: str) -> List[str]:
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99 return args.split(",")
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100
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101
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102 if __name__ == "__main__":
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103
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104 parser = argparse.ArgumentParser()
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105 parser.add_argument("--testmode", default=False, action="store_true")
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106 parser.add_argument("--latest", default=False, action="store_true")
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107 parser.add_argument("--start_date", type=parse_date)
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108 parser.add_argument("--end_date", type=parse_date)
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109 parser.add_argument("--known_revisions", type=comma_split)
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110 parser.add_argument("--datasets", type=comma_split, default=["sars-cov-2"])
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111 parser.add_argument("datatable_name", default="nextclade")
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112 parser.add_argument("galaxy_config")
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113 args = parser.parse_args()
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114
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115 # known-revisions is populated from the Galaxy data table by the wrapper
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116 if args.known_revisions is not None:
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117 existing_release_tags = set(args.known_revisions)
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118 else:
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119 existing_release_tags = set()
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120
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121 releases_available = get_database_list()
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122 if args.testmode:
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123 releases = []
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124 for name in args.datasets:
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125 releases.extend(
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126 filter_by_date(
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127 [],
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128 name,
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129 releases_available,
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130 start_date=args.start_date,
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131 end_date=args.end_date,
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132 )
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133 )
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134 for release in releases:
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135 print(
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136 release["value"],
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137 release["description"],
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138 release["date"].isoformat(),
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139 release["min_nextclade_version"],
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140 )
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141 sys.exit(0)
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142
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143 with open(args.galaxy_config) as fh:
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144 config = json.load(fh)
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145
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146 output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
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147
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148 data_manager_dict = {"data_tables": {args.datatable_name: []}}
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149
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150 releases = []
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151 if args.latest:
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152 for dataset in args.datasets:
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153 for release in releases_available:
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154 if release["database_name"] == dataset:
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155 if release["value"] not in existing_release_tags:
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156 # add the latest release for this dataset, but only if we don't already have it
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157 releases.append(release)
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diff changeset
158 break
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159 else:
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160 for dataset in args.datasets:
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161 releases_for_ds = filter_by_date(
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162 existing_release_tags,
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163 dataset,
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164 releases_available,
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165 start_date=args.start_date,
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166 end_date=args.end_date,
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167 )
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168 releases.extend(releases_for_ds)
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169
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170 for release in releases:
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171 fname = download_and_unpack(
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172 release["database_name"], release["tag"], output_directory
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173 )
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174 if fname is not None:
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175 data_manager_dict["data_tables"][args.datatable_name].append(
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176 {
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177 "value": release["value"],
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178 "database_name": release["database_name"],
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179 "description": release["description"],
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180 "min_nextclade_version": release["min_nextclade_version"],
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181 "date": release["date"].isoformat(), # ISO 8601 is easily sortable
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182 "path": str(output_directory / fname),
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183 }
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184 )
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185 data_manager_dict["data_tables"][args.datatable_name].sort(
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186 key=operator.itemgetter("value"), reverse=True
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187 )
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188 with open(args.galaxy_config, "w") as fh:
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189 json.dump(data_manager_dict, fh, indent=2, sort_keys=True)