1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9300f9bd7ba1/ Changeset: 9300f9bd7ba1 User: natefoo Date: 2014-09-17 19:23:51+00:00 Summary: With the exception of shed_*.xml configs, which are still instantiated from their samples by common_startup.sh, reverse the stream polarity and prefer the config/ version of config files, since their existence suggests the administrator took an intentional action to create them. Note that none of this magical detection applies unless you leave the options in galaxy.ini that set the paths to these configs commented/unset. Credit to John for the suggestion. Affected #: 2 files diff -r 69bb888b05cd2cbb0f553fe7f2b7c24d05e6ac97 -r 9300f9bd7ba1b791b97e91fd1db75fc88280f013 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -378,24 +378,34 @@ Backwards compatibility for config files moved to the config/ dir. """ defaults = dict( - data_manager_config_file = [ 'data_manager_conf.xml', 'config/data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ], - datatypes_config_file = [ 'datatypes_conf.xml', 'config/datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], - external_service_type_config_file = [ 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample', 'config/external_service_types_conf.xml.sample' ], - job_config_file = [ 'job_conf.xml', 'config/job_conf.xml' ], - job_metrics_config_file = [ 'job_metrics_conf.xml', 'config/job_metrics_conf.xml' ], - dependency_resolvers_config_file = [ 'dependency_resolvers_conf.xml', 'config/dependency_resolvers_conf.xml' ], - job_resource_params_file = [ 'job_resource_params_conf.xml', 'config/job_resource_params_conf.xml' ], + data_manager_config_file = [ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ], + datatypes_config_file = [ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], + external_service_type_config_file = [ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ], + job_config_file = [ 'config/job_conf.xml', 'job_conf.xml' ], + job_metrics_config_file = [ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml' ], + dependency_resolvers_config_file = [ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ], + job_resource_params_file = [ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], - object_store_config_file = [ 'object_store_conf.xml', 'config/object_store_conf.xml' ], - openid_config_file = [ 'openid_conf.xml', 'config/openid_conf.xml' 'config/openid_conf.xml.sample' ], + object_store_config_file = [ 'config/object_store_conf.xml', 'object_store_conf.xml' ], + openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml' 'config/openid_conf.xml.sample' ], shed_data_manager_config_file = [ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], - tool_sheds_config_file = [ 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], + tool_sheds_config_file = [ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], ) listify_defaults = dict( - tool_data_table_config_path = [ 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], - tool_config_file = [ 'tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml,config/shed_tool_conf.xml', 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] + tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + # rationale: + # [0]: user has explicitly created config/tool_conf.xml but did not + # move their existing shed_tool_conf.xml, don't use + # config/shed_tool_conf.xml, which is probably the empty + # version copied from the sample, or else their shed tools + # will disappear + # [1]: user has created config/tool_conf.xml and, having passed + # [0], probably moved their shed_tool_conf.xml as well + # [2]: user has done nothing, use the old files + # [3]: fresh install + tool_config_file = [ 'config/tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml,config/shed_tool_conf.xml', 'tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] ) for var, defaults in defaults.items(): diff -r 69bb888b05cd2cbb0f553fe7f2b7c24d05e6ac97 -r 9300f9bd7ba1b791b97e91fd1db75fc88280f013 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -139,12 +139,12 @@ def __parse_config_file_options( self, kwargs ): defaults = dict( - datatypes_config_file = [ 'datatypes_conf.xml', 'config/datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], + datatypes_config_file = [ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], ) listify_defaults = dict( - tool_data_table_config_path = [ 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], ) for var, defaults in defaults.items(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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