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microbiomedata / nmdc-server

Data portal client and server for NMDC.
https://data.microbiomedata.org
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use tagged version of nmdc-ontology #1183

Closed aclum closed 4 months ago

aclum commented 5 months ago

Placeholder for updating to a tagged release version of nmdc-ontology. Changes in main in nmdc-ontology recently broke data portal ingest (b/c of Cyclic graph) so this is a good time to update it.

Realvant code https://github.com/microbiomedata/nmdc-server/blob/f6bfe8f0f24c4dd1dd036e866a126be2ced1ef43/nmdc_server/ingest/envo.py#L16

aclum commented 5 months ago

cc @turbomam let us know when you have a tagged nmdc-ontology release that resolves the cyclical graph issue.

turbomam commented 5 months ago

https://raw.githubusercontent.com/microbiomedata/nmdc-ontology/2024-02-16/nmdco-classes.json

ssarrafan commented 5 months ago

@aclum should this be in the current sprint? Who owns this issue?

ssarrafan commented 5 months ago

@mbthornton-lbl @naglepuff is this something you are currently working on?

aclum commented 5 months ago

This should be a ticket for Mike or Mary

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aclum commented 5 months ago

It should be a straightforward swap so seemed okay to have in this sprint. If not, next sprint is fine too.

On Wednesday, April 3, 2024, ssarrafan @.***> wrote:

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ssarrafan commented 5 months ago

@naglepuff @marySalvi I'm assigning this to you in case one of you has time to do this week.

ssarrafan commented 5 months ago

@marySalvi said she is looking into this one. I'll remove Mike from this ticket.

marySalvi commented 5 months ago

@turbomam @aclum Do we want to always use the latest release or do we want to 'pin' to a specific release? Pinning would require manual updating but potentially less friction for testing different releases

turbomam commented 5 months ago

I defer to @aclum

I am doing active development in the main branch. I'm pretty careful about what I merge, but I haven't been doing an ingest each time. So a pinned release would be safer.

aclum commented 5 months ago

The request is for a pinned release. We haven't been doing this and it broke ingest a few weeks ago. The nmdc-server code and therefore ingest will be more stable. I'd like updating the pinned version to be part of the monthly release cycle. That is, if Mark has a new version there would be a nmdc-server ticket to update the nmdc-ontology version, ideally at least a week before the monthly production release so we could test ingest and the data portal interface on dev. cc @shreddd @pkalita-lbl