feat(collections): add created_at and updated_at timestamps to collections and variants tables by fhennig · Pull Request #1119 · GenSpectrum/dashboards

fhennig · 2026-03-26T12:43:14Z

resolves #1113

Summary

Add created_at and updated_at fields to collections and variants; they behave as you'd expect.

Example timestamp: 2026-03-26T12:59:18.027Z - uses millisecond precision.

Adds tests to see that updating works, and that you can't manually set the dates.

Jackson is now configured to always fail parsing on unknown properties.

Example API response object

  {
    "id": 1,
    "name": "Covid: Alpha & Beta comparison",
    "ownedBy": "foobar",
    "organism": "covid",
    "description": "Comparing Alpha and Beta variant trajectories",
    "variants": [
      {
        "type": "query",
        "id": 1,
        "collectionId": 1,
        "name": "Alpha (B.1.1.7)",
        "description": "Alpha lineage globally",
        "countQuery": "pangoLineage=B.1.1.7*",
        "coverageQuery": null,
        "createdAt": "2026-03-26T11:31:23.404Z",
        "updatedAt": "2026-03-26T11:31:23.404Z"
      },
      {
        "type": "query",
        "id": 2,
        "collectionId": 1,
        "name": "Beta (B.1.351)",
        "description": "Beta lineage globally",
        "countQuery": "pangoLineage=B.1.351*",
        "coverageQuery": null,
        "createdAt": "2026-03-26T11:31:23.404Z",
        "updatedAt": "2026-03-26T11:31:23.404Z"
      }
    ],
    "createdAt": "2026-03-26T11:31:23.404Z",
    "updatedAt": "2026-03-26T11:31:23.404Z"
  }

PR Checklist

All necessary documentation has been adapted.
The implemented feature is covered by an appropriate test.

Co-Authored-By: Claude Sonnet 4.6 noreply@anthropic.com

…tions and variants tables Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

vercel · 2026-03-26T12:43:19Z

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Project	Deployment	Actions	Updated (UTC)
dashboards	Ready	Preview, Comment	Mar 26, 2026 1:09pm

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…alization Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…ion mismatches Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Copilot

Pull request overview

Adds server-managed createdAt/updatedAt timestamps to collections and variants, persists them in Postgres, and exposes them via the API. This addresses issue #1113 by making timestamps available to API consumers and ensuring updatedAt changes on updates.

Changes:

Add created_at / updated_at columns to collections_table and variants_table via a new DB migration.
Plumb timestamps through Exposed entities/model logic into the Collection and Variant API responses, and update timestamps on writes.
Add tests around timestamp presence/update behavior and rejecting client attempts to set timestamp fields; configure Jackson to fail on unknown properties.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsPutTest.kt	Adds update-time assertions and 400 tests when timestamps are provided in update bodies.
backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsPostTest.kt	Adds creation-time assertions and 400 tests when timestamps are provided in create bodies.
backend/src/main/resources/db/migration/V1.2__add_timestamps_to_collections_and_variants.sql	Adds timestamp columns + defaults for collections and variants tables.
backend/src/main/resources/application.properties	Enables global Jackson “fail on unknown properties”.
backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/VariantTable.kt	Adds timestamp columns to the Exposed table/entity + maps them to API variants.
backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionTable.kt	Adds timestamp columns to the Exposed table/entity + maps them to API collections.
backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt	Sets timestamps on create/update and updates `updatedAt` on collection/variant changes.
backend/src/main/kotlin/org/genspectrum/dashboardsbackend/config/InstantSerializer.kt	Adds Jackson (de)serialization for `kotlinx.datetime.Instant`.
backend/src/main/kotlin/org/genspectrum/dashboardsbackend/api/Variant.kt	Exposes `createdAt`/`updatedAt` on API variants.
backend/src/main/kotlin/org/genspectrum/dashboardsbackend/api/Collection.kt	Exposes `createdAt`/`updatedAt` on API collections.
backend/build.gradle.kts	Adds `exposed-kotlin-datetime` dependency for timestamp column support.

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Copilot · 2026-03-31T08:09:31Z

backend/src/main/resources/db/migration/V1.2__add_timestamps_to_collections_and_variants.sql

+ALTER TABLE collections_table
+    ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),
+    ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);
+
+-- Variants
+ALTER TABLE variants_table
+    ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),
+    ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);


The column defaults use timezone('UTC', CURRENT_TIMESTAMP), which is not a constant default in Postgres and can trigger a full table rewrite/long lock on large tables when adding the column. It also preserves microsecond precision, which may conflict with the “millisecond precision” guarantee mentioned in the PR. Consider a safer migration pattern (add nullable column, backfill with date_trunc('milliseconds', ...), then set NOT NULL + default), or at least truncate the default to milliseconds.

Suggested change

ALTER TABLE collections_table

ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),

ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);

-- Variants

ALTER TABLE variants_table

ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),

ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);

-- Step 1: add nullable columns without defaults to avoid table rewrite

ALTER TABLE collections_table

ADD COLUMN created_at timestamp without time zone,

ADD COLUMN updated_at timestamp without time zone;

-- Step 2: backfill existing rows with millisecond-precision UTC timestamps

UPDATE collections_table

SET created_at = date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP)),

updated_at = date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP))

WHERE created_at IS NULL

OR updated_at IS NULL;

-- Step 3: enforce NOT NULL and set millisecond-precision defaults

ALTER TABLE collections_table

ALTER COLUMN created_at SET NOT NULL,

ALTER COLUMN created_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP)),

ALTER COLUMN updated_at SET NOT NULL,

ALTER COLUMN updated_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP));

-- Variants

-- Step 1: add nullable columns without defaults to avoid table rewrite

ALTER TABLE variants_table

ADD COLUMN created_at timestamp without time zone,

ADD COLUMN updated_at timestamp without time zone;

-- Step 2: backfill existing rows with millisecond-precision UTC timestamps

UPDATE variants_table

SET created_at = date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP)),

updated_at = date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP))

WHERE created_at IS NULL

OR updated_at IS NULL;

-- Step 3: enforce NOT NULL and set millisecond-precision defaults

ALTER TABLE variants_table

ALTER COLUMN created_at SET NOT NULL,

ALTER COLUMN created_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP)),

ALTER COLUMN updated_at SET NOT NULL,

ALTER COLUMN updated_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP));

Copilot · 2026-03-31T08:09:31Z

backend/src/main/resources/db/migration/V1.2__add_timestamps_to_collections_and_variants.sql

+    ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),
+    ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);
+
+-- Variants
+ALTER TABLE variants_table
+    ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),
+    ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);


Same concern as the collections table: adding NOT NULL columns with a non-constant CURRENT_TIMESTAMP-based default can rewrite/lock the table and yields microsecond precision. Consider backfilling and then applying a milliseconds-truncated default to avoid operational risk and ensure consistent timestamp precision.

Suggested change

ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),

ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);

-- Variants

ALTER TABLE variants_table

ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),

ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);

ADD COLUMN created_at timestamp without time zone,

ADD COLUMN updated_at timestamp without time zone;

-- Backfill existing collections with millisecond-truncated UTC timestamps

UPDATE collections_table

SET created_at = COALESCE(created_at, date_trunc('milliseconds', timezone('UTC', now()))),

updated_at = COALESCE(updated_at, date_trunc('milliseconds', timezone('UTC', now())));

-- Enforce NOT NULL and set millisecond-truncated UTC defaults for collections

ALTER TABLE collections_table

ALTER COLUMN created_at SET NOT NULL,

ALTER COLUMN created_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', now())),

ALTER COLUMN updated_at SET NOT NULL,

ALTER COLUMN updated_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', now()));

-- Variants

ALTER TABLE variants_table

ADD COLUMN created_at timestamp without time zone,

ADD COLUMN updated_at timestamp without time zone;

-- Backfill existing variants with millisecond-truncated UTC timestamps

UPDATE variants_table

SET created_at = COALESCE(created_at, date_trunc('milliseconds', timezone('UTC', now()))),

updated_at = COALESCE(updated_at, date_trunc('milliseconds', timezone('UTC', now())));

-- Enforce NOT NULL and set millisecond-truncated UTC defaults for variants

ALTER TABLE variants_table

ALTER COLUMN created_at SET NOT NULL,

ALTER COLUMN created_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', now())),

ALTER COLUMN updated_at SET NOT NULL,

ALTER COLUMN updated_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', now()));

backend/src/main/resources/application.properties

fengelniederhammer · 2026-03-31T08:09:24Z

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt

+import kotlinx.datetime.Clock
+import kotlinx.datetime.Instant


My IDE claims that these are deprecated and we should use this instead:

Suggested change

import kotlinx.datetime.Clock

import kotlinx.datetime.Instant

import kotlin.time.Clock

import kotlin.time.Instant

Ah, I see, Exposed still needs it...

backend/src/main/resources/application.properties

fengelniederhammer · 2026-03-31T08:19:20Z

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt

+    private fun createVariantEntity(collectionEntity: CollectionEntity, variantRequest: VariantRequest): VariantEntity {
+        val now = now()


I wonder whether this method should maybe rather accept a now argument from the caller?

feat(collections): add created_at and updated_at timestamps to collec…

fe06c31

…tions and variants tables Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

feat(collections): expose createdAt and updatedAt in API responses

e213524

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

fhennig force-pushed the collections-with-dates branch from d06249d to e213524 Compare March 26, 2026 12:44

vercel bot deployed to Preview March 26, 2026 12:44 View deployment

test(collections): add timestamp tests and fix Jackson Instant deseri…

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…alization Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

vercel bot deployed to Preview March 26, 2026 12:50 View deployment

test(collections): reject client-provided timestamp fields with 400

0799bbe

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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fhennig self-assigned this Mar 26, 2026

fhennig requested a review from fengelniederhammer March 26, 2026 13:00

fix(collections): truncate timestamps to milliseconds to avoid precis…

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…ion mismatches Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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feat(collections): add created_at and updated_at timestamps to collections and variants tables#1119

feat(collections): add created_at and updated_at timestamps to collections and variants tables#1119
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-ALTER TABLE collections_table
-    ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),
-    ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);
--- Variants
-ALTER TABLE variants_table
-    ADD COLUMN created_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP),
-    ADD COLUMN updated_at timestamp without time zone NOT NULL DEFAULT timezone('UTC', CURRENT_TIMESTAMP);
+-- Step 1: add nullable columns without defaults to avoid table rewrite
+ALTER TABLE collections_table
+    ADD COLUMN created_at timestamp without time zone,
+    ADD COLUMN updated_at timestamp without time zone;
+-- Step 2: backfill existing rows with millisecond-precision UTC timestamps
+UPDATE collections_table
+SET created_at = date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP)),
+    updated_at = date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP))
+WHERE created_at IS NULL
+   OR updated_at IS NULL;
+-- Step 3: enforce NOT NULL and set millisecond-precision defaults
+ALTER TABLE collections_table
+    ALTER COLUMN created_at SET NOT NULL,
+    ALTER COLUMN created_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP)),
+    ALTER COLUMN updated_at SET NOT NULL,
+    ALTER COLUMN updated_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP));
+-- Variants
+-- Step 1: add nullable columns without defaults to avoid table rewrite
+ALTER TABLE variants_table
+    ADD COLUMN created_at timestamp without time zone,
+    ADD COLUMN updated_at timestamp without time zone;
+-- Step 2: backfill existing rows with millisecond-precision UTC timestamps
+UPDATE variants_table
+SET created_at = date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP)),
+    updated_at = date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP))
+WHERE created_at IS NULL
+   OR updated_at IS NULL;
+-- Step 3: enforce NOT NULL and set millisecond-precision defaults
+ALTER TABLE variants_table
+    ALTER COLUMN created_at SET NOT NULL,
+    ALTER COLUMN created_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP)),
+    ALTER COLUMN updated_at SET NOT NULL,
+    ALTER COLUMN updated_at SET DEFAULT date_trunc('milliseconds', timezone('UTC', CURRENT_TIMESTAMP));

		import kotlinx.datetime.Clock
		import kotlinx.datetime.Instant

		private fun createVariantEntity(collectionEntity: CollectionEntity, variantRequest: VariantRequest): VariantEntity {
		val now = now()

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Summary

Example API response object

PR Checklist

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fhennig commented Mar 26, 2026 •

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