- Move tool_config_file out of parse_config_file_options
- Use path_resolves_to in schema
- Correct schema default (remove 'config/' prefix)
- Remove reference to tool_config_file_set, use config.is_set() instead
- Get rid of parse_config_file_options and _parse_config_file_options
- Run make config-rebuild
- Automate handling of cases where a config option's value is a list and
we may need to select one or all list items, depending on file
existance (including added sample files)
- Add unit tests for the above
- Move tool_data_table_config_path out of parse_config_file_options
- Use path_resolves_to in schema
- Correct schema default (remove 'config/' prefix)
- Test driver: make paths absolute before passing them to galaxy: this
prevents incorrect path resolving (see comment in driver_util.py)
- Refactor post-processing of config paths after they have been
resolved.
- Run make config-rebuild
- Move option out of parse_config_file_options
- Use path_resolves_to in schema
- Correct schema default (remove 'config/' prefix)
- Run make config-rebuild
- Handle path resolving of values that are lists of paths
- Automate handling of cases where we add sample config files to defaults
and pick one existing file or sample file
- Add unit tests for handling of the above
- Adjust existsitn unit tests
- Move option out of parse_config_file_options
- Run make config-rebuild
Purpose: let the config system load this just like any other path to a config file.
Update comment in sample file
Enable unit test
Run make config-rebuild.
Purpose:
1) Let the config system load this just like any other path to a config file.
2) Fix: the sample config file mentions setting this config option in galaxy.yml.
Also:
- Run make config-rebuild
- Enable unit test
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
- Get rid of config.oidc_backends_config property; use schema property
instead (oidc_backends_config_file)
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
- Get rid of config.oidc_config property; use schema property
instead (oidc_config_file)
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild (previous changes rebuilt)
- Replace call to appconfig.data_manager_config_file_set with
appconfig.is_set('data_manager_config_file')
- Modify test driver_utils: make the path to the sample config file
absolute: resolving that path w.r.t to root in the config module was a
bug and is fixed now. Thus, if a relative path is supplied, the config
module will resolve it w.r.t config_dir - as per schema. Passing the
file used for testing, therefore, must be an absolute path, since it
is located under 'test/', not 'config/'.
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. managed_config_dir)
- Run make config-rebuild (previous changes rebuilt)
- Replace call to appconfig.shed_tool_data_table_config with
appconfig.is_set('shed_tool_data_table_config')
- Modify test driver_utils: do not add option to mock config if default
is None: this value will overwrite the schema default, even if set to
None - thus causing an error when galaxy tries to parse the file
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. managed_config_dir)
- Run make config-rebuild (previous changes rebuilt)
- Replace call to appconfig.shed_tool_config_file_set with
appconfig.is_set('shed_tool_config_file')
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Replace call to appconfig.workflow_schedulers_config_file_set with
appconfig.is_set('workflow_schedulers_config_file')
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Replace call to appconfig.user_preferences_extra_conf_path_set with
appconfig.is_set('user_preferences_extra_conf_path')
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. managed_config_dir)
- Run make config-rebuild
- Replace call to appconfig.shed_data_manager_config_file_set with
appconfig.is_set('shed_data_manager_config_file')
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. managed_config_dir)
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild
Process like any other config option:
- Remove from list of defaults in parse_config_options()
- Add path_resolves_to to schema (resolves w.r.t. config_dir)
- Run make config-rebuild (previous changes rebuilt)
- Replace call to appconfig.auth_config_file_set with
appconfig.is_set('auth_config_file')
Nolan Woods