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OpenTreeOfLife / opentree

Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo.
http://tree.opentreeoflife.org/
BSD 2-Clause "Simplified" License
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Remove some outdated cruft from deployment scripts #417

Open jimallman opened 10 years ago

jimallman commented 10 years ago

Some of the deployment scripts have outdated material in them that may lead to confusion or mysterious bugs, based on simple typos in a server-config file. Examples:

It looks like the old OPENTREE_NEO4J_HOST variable is expected by the push.sh script. If not set explicitly, it's assumed to be $OPENTREE_HOST. Ultimately, this is passed to variable NEO4J_HOST and used in calls to setup/install-web2py-apps.sh, where it does... nothing, apparently, beyond appearing in a misleading log message.

I also see some places where we set default base URLs for APIs that almost certainly will fail. These should be updated, or we should insist that the server-config file define these base URLs explicitly.

jimallman commented 10 years ago

Regarding default API base URLs, @jar398 suggests:

it might be better if there were no defaults, and presence of a definition was checked at the points where it was needed.

The old system assumes that all APIs are likely on a single server (and that $OPENTREE_NEO4J_HOST was defined), both of which are questionable assumptions. Instead, individual components should check just before using one of these variables, and complain if it’s not defined.