Skip to content

Add ADR for: Internal identifiers SHOULD NOT be prefixed #42

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 9 commits into from
Jul 27, 2023

Conversation

nsheff
Copy link
Member

@nsheff nsheff commented Jan 11, 2023

Resolves half of #37

@nsheff nsheff changed the title add ADR for no internal prefixes Add ADR for: Interal identifiers SHOULD NOT be prefixed Jan 25, 2023
@nsheff nsheff changed the title Add ADR for: Interal identifiers SHOULD NOT be prefixed Add ADR for: Internal identifiers SHOULD NOT be prefixed Jan 25, 2023
@nsheff
Copy link
Member Author

nsheff commented Jan 25, 2023

In discussion today we came up with 2 suggestions:

  1. "external" can mean 2 things: A) content provided to us; B) the way our identifiers are used externally. Should be clarified.
  2. We need more explicit direction on how/when content provided to us should be prefixed.

Also, need a bit more discussion on this. What will happen with refget identifiers?

Copy link
Collaborator

@sveinugu sveinugu left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I am happy with the part of the ADR that refer to internal identifiers, however I think it is premature to approve the part on external without knowing the conclusion of a) whether refget digests must be prefixed or not, and b) any top-level decision on GA4GH CURIE namespacing.

If for instance it is decided to use the same namespace for seqcol and refget identifiers, I would argue
that the refget identifiers should NOT be prefixed inside a seqcol (as the namespace would is the default one).

In addition one could also add an explicit requirement that values that are defined as CURIEs (in the schema?) from other namespace MUST include the namespace prefix.

@nsheff
Copy link
Member Author

nsheff commented Jul 12, 2023

decision: sequences should not be prefixed with ga4gh:, but they should be prefixed with SQ.

@nsheff nsheff changed the base branch from master to dev July 26, 2023 12:35
@nsheff
Copy link
Member Author

nsheff commented Jul 26, 2023

Ok, I added this statement:

More specifically, for refget, there are two types of prefix: the namespace prefix (ga4gh:) and type type prefix (SQ.). Right now, the refget server requires you to have the type prefix to request a lookup; the refget protocol declares that this type prefix is part of the identifier. However, the ga4gh: prefix is more of a namespace prefix and is not required, and therefore not considered part of the identifier. Therefore, the seqcol sequence values would include the SQ. but not the ga4gh:.

Is that correct?

@nsheff nsheff merged commit 046b56f into dev Jul 27, 2023
@nsheff nsheff deleted the internal-prefix branch July 27, 2023 11:38
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants