Repository navigation
feat(catalog): support catalog schema 3 (technology vocabulary ids, vendor, variant, technology.json) - #72
Merged
Merged
Conversation
…endor, variant, technology.json) SUPPORTED_CATALOG_SCHEMA is 3. A schema-3 catalog's technology is the vocabulary id, with a required vendor and a nullable variant; assay stays as the legacy label. Catalog.technologies() loads the release's technology.json beside the catalog and refuses a newer schema major. A catalog that declares no version still loads as legacy. The test fixture is hub #406's dry-run vocab/technology.json.
Documentation build overview
3 files changed± genindex.html± reference/catalog-columns.html± reference/generated/sddb.Catalog.html |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #72 +/- ##
==========================================
+ Coverage 94.72% 94.84% +0.11%
==========================================
Files 22 22
Lines 2313 2326 +13
==========================================
+ Hits 2191 2206 +15
+ Misses 122 120 -2 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The client now reads catalogs with schema version 3, the format the hub's technology-vocabulary work (T111) will publish.
SUPPORTED_CATALOG_SCHEMAgoes from 2 to 3. A catalog declaring version 4 or higher in its parquetsddb_release_infois refused with an upgrade hint. A catalog that declares no version still loads as legacy, as before.vendor, the vendor id, which a schema-3 catalog must have; andvariant, the technology's variant id or null. In a schema-3 catalog,technologyholds the vocabulary id (e.g.10x_visium), andassaystays as the legacy label.vendorandvariantare also facets.Catalog.technologies(), which loads the release'stechnology.jsonfrom besidecatalog.parquet(cached like the other assets). It returns the vendors, technologies with their variants, readouts andlegacy_assaylabels. A file with a newer schema major is refused.Tests (
tests/test_catalog_metadata.py):vendoris refused.technology.jsondeclaring schema 4.0.0 is refused.The fixture
tests/data/technology_v3.jsonis the hub's committed dry-run vocabulary. The full suite passes (451 passed;test_docs_statsneeds sphinx and was not run locally).The hub's client pin gets bumped past this PR before the first schema-3 cut is published.