Ensure app.config.config_file is an absolute path #8836
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Both fails caused by error in test implementation. Fixing it... [Update: fixed.] |
Also, add integration tests for base config dirs. NOTE: this is a rebased commit that contains a fix to a previously failed commit: - the expected value of config_dir is calculated separately; - the default value of data_dir is not testable in this context and is marked accordingly.
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jmchilton
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Oct 23, 2019
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Also, added integration tests for base config dirs. (I'll add all other config options that are paths in a follow-up)
RATIONALE:
If
galaxy.ymlexists, thenconfig.config_fileis an ABSOLUTE path. Because__find_config_files()inutil/propertiesusesos.getcwd()to build a list of directories - and that results in an absolute path.(see https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/properties.py#L56)
If
galaxy.ymldoes NOT exist (testing is one use case), thenconfig.config_fileis set to a RELATIVE path. Because it uses the value of__file__inglobal_confdictionary passed inkwargsand set in the galaxy-main script. (see https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/__init__.py#L113)As a result, the value of
config.config_dirwill be relative OR absolute (os.path.dirname()ofconfig_file) (https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/__init__.py#L124)And that leads to config files (initially) being resolved to a relative OR an absolute path.
It is all fixed in the end in
_parse_config_file_options()where everything is resolved w.r.t.config.root(so with an absolute path, the path is left as is, but with a relative path, it is resolved w.r.t root). However, because conceptually it doesn't feel right (I think, in the end,config_fileshould be relative OR absolute, regardless of what file was loaded and how it was discovered); and because it causes problems during testing (when galaxy is run without a preset config file, so all config properties containing paths to config files become relative), ensuringconfig_fileis always an absolute path, seems the logical choice. I've consulted with @natefoo on this.(marking this a bug; although it's not quite a bug: it's resolved in the end, but it shouldn't have to be).