mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nicola Soranzo
d1bc98dfcb
Remove some debugging prints. Fix import order. Consolidate exception logging in ToolShed database migrations.
32 lines
1.6 KiB
Python
32 lines
1.6 KiB
Python
"""
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This script will start up its own web application which includes a ToolMigrationManager (~/lib/galaxy/tool_shed/tool_migration_manager.py).
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For each tool discovered missing, the tool shed repository that contains it will be installed on disk and a new entry will be
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created for it in the migrated_tools_conf.xml file. These entries will be made so that the tool panel will be displayed the same
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as it was before the tools were eliminated from the Galaxy distribution. The ToolMigrationManager will properly handle entries in
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migrated_tools_conf.xml for tools outside tool panel sections as well as tools inside tool panel sections, depending upon the
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layout of the local tool_conf.xml file. Entries will not be created in migrated_tools_conf.xml for tools included in the tool
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shed repository but not defined in tool_conf.xml.
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"""
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from __future__ import print_function
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import os
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import sys
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
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from tool_shed.galaxy_install.migrate.common import MigrateToolsApplication
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app = MigrateToolsApplication(sys.argv[1])
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non_shed_tool_confs = app.tool_migration_manager.proprietary_tool_confs
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if len(non_shed_tool_confs) == 1:
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plural = ''
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file_names = non_shed_tool_confs[0]
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else:
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plural = 's'
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file_names = ', '.join(non_shed_tool_confs)
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msg = "\nThe installation process is finished. All tools associated with this migration that were defined in your file%s named\n" % plural
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msg += "%s, have been removed. You may now start your Galaxy server.\n" % file_names
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print(msg)
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app.shutdown()
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sys.exit(0)
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