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https://github.com/galaxyproject/galaxy.git
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Remove the sharing of toolbox in GRT
This has been broken for a while and was never super useful data to obtain. Fixes #6534
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+3
-19
@@ -26,25 +26,18 @@ sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml
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default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml'))
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def _init(args, need_app=False):
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def _init(args):
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properties = app_properties_from_args(args)
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config = galaxy.config.Configuration(**properties)
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object_store = build_object_store_from_config(config)
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if not config.database_connection:
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logging.warning("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml")
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if need_app:
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config_file = config_file_from_args(args)
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app = galaxy.app.UniverseApplication(global_conf={'__file__': config_file, 'here': os.getcwd()})
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else:
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app = None
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model = galaxy.config.init_models_from_config(config, object_store=object_store)
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return (
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model,
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object_store,
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config,
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app
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)
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@@ -172,7 +165,7 @@ def main(argv):
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last_job_sent = -1
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annotate('galaxy_init', 'Loading Galaxy...')
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model, object_store, gxconfig, app = _init(args, need_app=config['grt']['share_toolbox'])
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model, object_store, gxconfig = _init(args)
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# Galaxy overrides our logging level.
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logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
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@@ -409,16 +402,8 @@ def main(argv):
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# Now serialize the individual report data.
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with open(REPORT_BASE + '.json', 'w') as handle:
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if config['grt']['share_toolbox']:
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toolbox = [
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(tool.id, tool.name, tool.version, tool.tool_shed, tool.repository_id, tool.repository_name)
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for tool_id, tool in app.toolbox._tools_by_id.items()
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]
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else:
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toolbox = None
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json.dump({
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"version": 1,
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"version": 2,
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"galaxy_version": gxconfig.version_major,
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"generated": REPORT_IDENTIFIER,
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"report_hash": "sha256:" + sha,
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@@ -430,7 +415,6 @@ def main(argv):
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"total": sa_session.query(model.User.id).count(),
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},
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"jobs": job_state_data,
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"tools": toolbox
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}, handle)
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# Write our checkpoint file so we know where to start next time.
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@@ -8,14 +8,6 @@ grt:
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# willing and able to contribute your data publicly.
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url: https://telescope.galaxyproject.org/grt-admin/
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# Are you willing to share your toolbox? I.e. what tools are installed.
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# If your instance is public, this can help us direct users to your
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# instance. If you elect to not send your entire toolbox, we will still
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# (necessarily) receive a list of tools that have been run, just not the
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# complete list. WARNING: This may not work on production instances, currently.
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share_toolbox: False
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sanitization:
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# Blacklist the entire tool from appearing
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tools:
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