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[FIX] Enable graph setup to run on stack restart #57

Merged
merged 7 commits into from
May 16, 2024
Merged

[FIX] Enable graph setup to run on stack restart #57

merged 7 commits into from
May 16, 2024

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surchs
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@surchs surchs commented May 14, 2024 •
edited by alyssadai
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Changes proposed in this pull request:

  • fix the wait statement in the setup script so that it
    • works on the second run (when we will already have a repository created)
    • works once we have enabled password security for the repository endpoint
  • replace the bind-mount for the graph data with a docker volume

Checklist

This section is for the PR reviewer

  • PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines 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 added 4 commits May 13, 2024 20:11
@surchs
[FIX] Look for any repositories
7229f63 
previously we expected an empty array here,
but really we only care that any array is returned.
Because this signifies that the graph is ready to
talk to us
@surchs
[FIX] Enable auth for the repository check
dbc2178 
From the second time we'll run this check it will have to be
with username and password auth
@surchs
[ENH] Clean out graph data before reupload
2f64814
@surchs
[ENH] Replace local graph data with volume
59cb11f 
Addresses #55
surchs added a commit to neurobagel/documentation that referenced this pull request May 14, 2024
@surchs
[REF] Update the graph reset docs to reflect volumes
e64a912 
Related to neurobagel/recipes#57
@surchs surchs mentioned this pull request May 14, 2024
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@alyssadai alyssadai self-requested a review May 15, 2024 15:47
alyssadai
alyssadai requested changes May 15, 2024
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Thanks @surchs!

I think the main change needed is the addition of an if block to skip the GraphDB server setup steps when there are databases already in GraphDB.

@surchs surchs requested a review from alyssadai May 15, 2024 21:32
alyssadai
alyssadai approved these changes May 16, 2024
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I think this looks good to me. Thanks @surchs ! 🧑‍🍳

@surchs surchs merged commit 089f3cd into main May 16, 2024
@surchs surchs deleted the issue54 branch May 16, 2024 16:05
@alyssadai alyssadai added pr-patch Incremental feature improvement, will increment patch version when merged (0.0.+1) pr-bug-fix Bug fix, will increment patch version when merged (0.0.+1) and removed pr-bug-fix Bug fix, will increment patch version when merged (0.0.+1) pr-patch Incremental feature improvement, will increment patch version when merged (0.0.+1) labels Aug 7, 2024
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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
@surchs surchs mentioned this pull request Sep 11, 2024
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