mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 02:21:32 +08:00
Nicola Soranzo
a2018a5e60
but allow `dict()` calls that make use of keyword arguments (e.g., `dict(a=1, b=2)`).
81 lines
2.6 KiB
Python
Executable File
81 lines
2.6 KiB
Python
Executable File
#!/usr/bin/env python
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import argparse
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import shutil
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from datetime import datetime
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from lxml import etree
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desc = """
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Fix shed_data_manager_conf.xml
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Modifies the guid and version attribute of data_manager tags:
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- the version in the guid (text after the last slash) is replaced
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by the data manager tool version
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- the version attribute is set to the data manager tool version
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By default only data managers with duplicated guid are modified
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and version attributes are not added if absent.
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A copy of the original file with a time stamp appended to the name
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is created.
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Note, if there are versions of the data manager tool that have the
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same version there will still be DMs with duplicated guids. These
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need to be corrected manually.
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"""
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parser = argparse.ArgumentParser(description=desc)
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parser.add_argument(
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"shed_data_manager_conf",
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metavar="CONFIG_FILE",
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type=str,
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default="config/shed_data_manager_conf.xml",
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help="an integer for the accumulator",
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)
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parser.add_argument(
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"--all-entries", action="store_true", help="modify all entries (default only those with duplicated guid)"
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)
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parser.add_argument("--add-version", action="store_true", help="also add version attribute if absent")
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parser.add_argument("--dry-run", action="store_true", help="do not write resulting config file")
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args = parser.parse_args()
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with open(args.shed_data_manager_conf) as fh:
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tree = etree.parse(args.shed_data_manager_conf)
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root = tree.getroot()
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guid_mapping = {}
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for dm in root.iter("data_manager"):
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guid = dm.attrib["guid"]
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if guid not in guid_mapping:
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guid_mapping[guid] = [dm]
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else:
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guid_mapping[guid].append(dm)
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for guid in guid_mapping:
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if len(guid_mapping[guid]) > 1:
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print(f"{guid} found {len(guid_mapping[guid])}x")
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elif not args.all_entries:
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continue
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for dm in guid_mapping[guid]:
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tool_version = dm.find("./tool/version")
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tool_version = tool_version.text
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new_guid = f"{guid[:guid.rfind('/')]}/{tool_version}"
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dm.attrib["guid"] = new_guid
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print(f"changing guid: {guid} -> {new_guid}")
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if "version" in dm.attrib:
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print(f"changing version: {dm.attrib['version']} -> {tool_version}")
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dm.attrib["version"] = tool_version
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elif args.add_version:
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print(f"adding version: {tool_version}")
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dm.attrib["version"] = tool_version
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if not args.dry_run:
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nfn = args.shed_data_manager_conf + datetime.now().isoformat()
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print(f"save copy at {nfn}")
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shutil.copyfile(args.shed_data_manager_conf, nfn)
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print(f"saving {args.shed_data_manager_conf}")
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tree.write(args.shed_data_manager_conf)
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