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[ENH] Add configuration files and templates for different deployment flavours #2

Merged
merged 7 commits into from
Dec 6, 2023
Merged

[ENH] Add configuration files and templates for different deployment flavours #2

merged 7 commits into from
Dec 6, 2023

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alyssadai
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@alyssadai alyssadai commented Dec 5, 2023 •
edited by surchs
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Changes proposed in this pull request:

  • Subdirectories created with relevant config files for 3 deployment flavours for 1) setting up local federation (f-API + query tool), 2) setting up a local node (n-API + graph), and 3) setting up a local node with a query tool automatically deployed (n-API, graph, query tool)
  • The template .env file for 2) is taken from the API repo, but has the variables relevant for communication with a local query tool commented out (the docker-compose.yml similarly has the query service removed)
  • Added basic usage instructions in README

Checklist

  • PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see https://neurobagel.org/contributing/pull_requests for more info)
  • PR links to GitHub issue with mention Closes #XXXX
  • Tests pass
  • Checks pass

For new features:

  • Tests have been added

For bug fixes:

  • There is at least one test that would fail under the original bug conditions.

@surchs surchs self-requested a review December 5, 2023 19:03
surchs
surchs reviewed Dec 5, 2023
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Thanks @alyssadai for setting this up. I think this will be super useful and a nice way to get started.

One thing that I noticed while trying these files out is that having to copy/rename files is a bit tedious compared to being able to immediately going docker compose up. I know we want people to look at these and configure them, but if we can make this runnable out of the box, it'll be very useful even for ourselves. And if I mess up my local file, git is always there to bring me back to a safe version.

I left a couple of comments on the files themselves as well.

README.md Outdated Show resolved Hide resolved
README.md Outdated Show resolved Hide resolved
local_federation/template.env Outdated Show resolved Hide resolved
local_node/template.env Outdated Show resolved Hide resolved
local_node_with_query_tool/template.env Outdated Show resolved Hide resolved
local_node/docker-compose.yml Outdated Show resolved Hide resolved
local_node_with_query_tool/docker-compose.yml Outdated Show resolved Hide resolved
surchs
surchs approved these changes Dec 5, 2023
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Thanks @alyssadai. Looks good 🧑‍🍳

scripts/add_data_to_graph.sh
Comment on lines +53 to +54
printf '\t%s\n' "--use-graphdb-syntax, --no-use-graphdb-syntax: Whether or not to use GraphDB API endpoints to update the specified graph database. If off, assumes the graph database is a Stardog database. (off by default)"
}
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now that everything is graphDB, we should also make graphDB the default here. Maybe for a future PR and only docs for now?

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Good idea! Will address in:

@alyssadai alyssadai mentioned this pull request Dec 6, 2023
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@alyssadai alyssadai merged commit fef3c0b into main Dec 6, 2023
@alyssadai alyssadai deleted the add-config-files branch December 19, 2023 01:25
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neurobagel-bot bot commented Aug 7, 2024

🚀 PR was released in v0.0.1 🚀

@neurobagel-bot neurobagel-bot bot added the released This issue/pull request has been released. label Aug 7, 2024
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@surchs surchs surchs approved these changes

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Store all Compose files and configs in one place
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@alyssadai @surchs