Fix refdata path convention: version is the refdata version, not the tool version

Per Gavin: same refdata can serve multiple tool versions, and CTS already
tracks (image, refdata) compatibility at registration time. Path versioning
should reflect the refdata itself, not what reads it.

Updated paths:
- kofam: use KEGG download date (2025-04-30)
- bakta: use Bakta DB schema version (v6.0)

Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>

Author: jplfaria

README.md

@@ -77,9 +77,15 @@ Things waiting on someone else. Update as items move.
 
 ### Pending CTS admin (Gavin) registrations
 
-Refdata path convention (Gavin's): `cts-refdata/{toolname}/{tool_version}/{filename}`
+Refdata path convention: `cts-refdata/{toolname}/{refdata_version}/{filename}`
+
+The path version is the **refdata version**, not the tool version. The same refdata can serve multiple tool versions; CTS tracks (image, refdata) compatibility at registration time.
 
 | Tool | Move from | Move to | Image |
 |------|-----------|---------|-------|
-| kofamscan | `cts/io/jplfaria/refdata_staging/kofam/kofam_refdata.tar.gz` (~1.5GB) | `cts-refdata/kofam/1.3.0/kofam_refdata.tar.gz` | `ghcr.io/kbaseincubator/cdm_kofamscan:0.1.0@sha256:d6b20eccf4c6bf1b095e530844a8b04dbae5fca85daf0c9b2bdffb0cf10a9a42` |
-| bakta | `cts/io/jplfaria/refdata_staging/bakta/bakta_db.tar.gz` (~30GB) | `cts-refdata/bakta/1.12.0/bakta_db.tar.gz` | `ghcr.io/kbaseincubator/cdm_bakta:0.1.0@sha256:6de4c51cadd75bc6a1d9f6e6b05716ecfdcfa63510b82459477ff757200d8d06` |
+| kofamscan | `cts/io/jplfaria/refdata_staging/kofam/kofam_refdata.tar.gz` (~1.5GB) | `cts-refdata/kofam/2025-04-30/kofam_refdata.tar.gz` | `ghcr.io/kbaseincubator/cdm_kofamscan:0.1.0@sha256:d6b20eccf4c6bf1b095e530844a8b04dbae5fca85daf0c9b2bdffb0cf10a9a42` |
+| bakta | `cts/io/jplfaria/refdata_staging/bakta/bakta_db.tar.gz` (~30GB) | `cts-refdata/bakta/v6.0/bakta_db.tar.gz` | `ghcr.io/kbaseincubator/cdm_bakta:0.1.0@sha256:6de4c51cadd75bc6a1d9f6e6b05716ecfdcfa63510b82459477ff757200d8d06` |
+
+Refdata version notes:
+- **kofam** uses the date pulled from KEGG FTP (KEGG does not publish formal version numbers for the kofam dump).
+- **bakta** uses the published DB schema version (v6.0, Feb 2025), which is what Bakta 1.12.0 expects.

docs/pattern.md

@@ -255,7 +255,7 @@ importer_meta:
 | Make GHCR package public | José (GitHub settings) |
 | Register image in CTS | Gavin only (`full_admin`) |
 | Register refdata in CTS | Gavin only |
-| Refdata path convention | `cts-refdata/{toolname}/{tool_version}/{filename}` (Gavin's convention, e.g. `cts-refdata/checkm2/1.1.0/uniref100.KO.1.dmnd.gz`) |
+| Refdata path convention | `cts-refdata/{toolname}/{refdata_version}/{filename}` — version in the path is the **refdata** version, not the tool version. Same refdata can serve multiple tool versions; CTS tracks (image, refdata) compatibility at registration. For tools without formal refdata versions (e.g. KEGG kofam dumps), use the date pulled from upstream as the version stamp. |
 | Submit jobs | José (needs `kbase_staff` role) |
 | Write to `cts/io/` | José |
 | Merge importer PRs | Gavin |