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The goal of this issue is to migrate namespaces to those used in identifiers.org. Those namespaces will become the standard in seqrepo. The namespaces are:
NCBI → refseq (for most accessions)
Ensembl → ensembl
LRG → lrg
Implementation options:
Abrupt db migration. Migrate namespaces in database in-place without a transition and release. Clients using old namespaces would break.
Use optional API translation to transition. Use three releases in which the new namespaces are is 1) optional w/default off (no behavior change), 2) optional w/default on, 3) updated in db and API translation is removed.
Automatic translation. In the first release (e.g., 0.5.7), add obligatory translation from new to old namespaces. Storing aliases would continue to use the old namespace. Finding would use translate new namespaces to old. Fetching alias records would add synthetic record for the new namespace. In a subsequent release (e.g., 0.6) invert the previous translation.
Option 3 seem pretty clearly the superior choice: it's easier to understand, requires less communication, and obviates client switches.
Translate from NCBI to refseq
Translate Ensembl to ensembl
Translate LRG to lrg
The text was updated successfully, but these errors were encountered:
The goal of this issue is to migrate namespaces to those used in identifiers.org. Those namespaces will become the standard in seqrepo. The namespaces are:
NCBI
→refseq
(for most accessions)Ensembl
→ensembl
LRG
→lrg
Implementation options:
Option 3 seem pretty clearly the superior choice: it's easier to understand, requires less communication, and obviates client switches.
NCBI
torefseq
Ensembl
toensembl
LRG
tolrg
The text was updated successfully, but these errors were encountered: