feat: amend new fields to interval schema by project-defiant · Pull Request #317 · opentargets/platform-api

project-defiant · 2026-02-02T10:07:38Z

Context

This PR adds the new fields

biosampleFromSourceId
qualityControls

to the Intervals dataset.

Copilot

Pull request overview

This pull request adds two new fields to the Interval schema to enhance genomic interval data representation: biosampleFromSourceId to capture the original biosample identifier from data sources, and qualityControls to store quality control flags.

Changes:

Added biosampleFromSourceId field to store the original biosample identifier as defined by datasource providers
Added qualityControls field to track quality control flags for interval data
Updated both the entity model and GraphQL schema definitions to maintain consistency

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
app/models/entities/Intervals.scala	Added two new required fields to the Interval case class: biosampleFromSourceId (String) and qualityControls (Vector[String])
app/models/gql/Objects.scala	Added corresponding GraphQL DocumentField definitions for the new fields with appropriate descriptions

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app/models/gql/Objects.scala

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

app/models/entities/Intervals.scala

Copilot

Pull request overview

Copilot reviewed 6 out of 6 changed files in this pull request and generated 8 comments.

Comments suppressed due to low confidence (1)

app/models/entities/EnhancerToGene.scala:27

The PR description states this change only adds two new fields (biosampleFromSourceId and qualityControls) to the Intervals dataset. However, the actual changes include a significant refactoring that renames "Interval" to "EnhancerToGene" throughout the codebase. This is a breaking API change that should be clearly documented in the PR description. If this refactoring is intentional, please update the PR description to reflect the full scope of changes. If it's unintentional, consider splitting the new field additions from the renaming refactoring into separate PRs.

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Copilot · 2026-02-13T14:43:03Z

app/models/entities/Configuration.scala

  case class ClickhouseSettings(
      defaultDatabaseName: String,
-      intervals: DbTableSettings,
+      enhancerToGene: DbTableSettings,


This configuration field rename from "intervals" to "enhancerToGene" will require updating any existing application.conf files in production environments. This should be documented in the PR description or migration guide, along with any necessary database table renaming if the table name changed from "intervals" to "enhancer_to_gene".

Copilot · 2026-02-13T14:43:04Z

app/models/db/IntervalsQuery.scala

+case class EnhancerToGeneQuery(chromosome: String,
+                               start: Int,
+                               end: Int,
+                               tableName: String,
+                               offset: Int,
+                               size: Int
 ) extends Queryable


The file name "IntervalsQuery.scala" does not match the renamed case class "EnhancerToGeneQuery". Following the established codebase convention where query files are named after their contained case classes (e.g., TargetsQuery.scala contains TargetsQuery, QW2V.scala contains QW2V), this file should be renamed to "EnhancerToGeneQuery.scala".

Copilot · 2026-02-13T14:43:04Z

app/models/Backend.scala

+    val tableName = getTableWithPrefixOrDefault(defaultOTSettings.clickhouse.enhancerToGene.name)
    val page = pagination.getOrElse(Pagination.mkDefault).offsetLimit
-    val intervalsQuery = IntervalsQuery(
+    val intervalsQuery = EnhancerToGeneQuery(


The variable name "intervalsQuery" is inconsistent with the renamed case class "EnhancerToGeneQuery". For better code clarity and consistency with the refactoring, this variable should be renamed to "enhancerToGeneQuery".

Copilot · 2026-02-13T14:43:04Z

app/models/Backend.scala

@@ -998,11 +998,11 @@ class Backend @Inject() (implicit
    logger.info(s"Total intervals found: $total")


The log message "Total intervals found" uses outdated terminology. It should be updated to reflect the new naming convention, such as "Total enhancer to gene mappings found" or similar, to be consistent with the refactoring throughout the codebase.

Suggested change

logger.info(s"Total intervals found: $total")

logger.info(s"Total enhancer to gene mappings found: $total")

Copilot · 2026-02-13T14:43:04Z

app/models/Backend.scala

-          .executeQuery[Interval, Query](intervalsQuery.query)
-          .map(intervals => Intervals(total, intervals))
+          .executeQuery[EnhancerToGene, Query](intervalsQuery.query)
+          .map(intervals => EnhancerToGenes(total, intervals))


The lambda parameter "intervals" should be renamed to "enhancerToGenes" to be consistent with the refactoring and to better reflect what the data represents. This improves code readability and maintains naming consistency throughout the method.

Suggested change

.map(intervals => EnhancerToGenes(total, intervals))

.map(enhancerToGenes => EnhancerToGenes(total, enhancerToGenes))

Copilot · 2026-02-13T14:43:05Z

app/models/gql/Objects.scala

+          "enhancerToGenes",
+          enhancerToGenesImp,
          description = Some(
            "Regulatory enhancer/promoter regions to gene (target) predictions overlapping with this variant's location. These intervals link regulatory regions to target genes based on experimental data for specific tissues or cell types."


The description still uses the old terminology "These intervals link" instead of reflecting the new naming convention. Consider updating to be more consistent with the refactoring, such as "These enhancer-to-gene mappings link" or keeping "intervals" as a more general descriptive term while using "enhancerToGenes" for the field name. The current mix may cause confusion.

Suggested change

"Regulatory enhancer/promoter regions to gene (target) predictions overlapping with this variant's location. These intervals link regulatory regions to target genes based on experimental data for specific tissues or cell types."

"Enhancer-to-gene mappings that link regulatory enhancer/promoter regions to target genes when they overlap this variant's location. These predictions are derived from experimental data for specific tissues or cell types."

Copilot · 2026-02-13T14:43:05Z

app/models/gql/Objects.scala

@@ -1491,6 +1491,10 @@ object Objects extends OTLogging {
      ),
      DocumentField("studyId", "Identifier of the study providing the experimental data"),
      DocumentField("biosampleName", "Name of the biosample where the interval was identified"),


The field description for "biosampleName" still refers to "interval" in the phrase "where the interval was identified". For consistency with the refactoring, this should be updated to refer to "regulatory region" or "enhancer/promoter region" instead of "interval".

Suggested change

DocumentField("biosampleName", "Name of the biosample where the interval was identified"),

DocumentField("biosampleName",

"Name of the biosample where the regulatory region was identified"

),

Copilot · 2026-02-13T14:43:05Z

app/models/gql/Objects.scala

+                                       ctx.value.position,
+                                       ctx.value.position,
+                                       ctx.arg(pageArg)
            )


This PR introduces a breaking API change by renaming the GraphQL field from "intervals" to "enhancerToGenes". This will break existing GraphQL queries that use the old field name. Consider: 1) Providing a deprecation period where both field names are supported, or 2) Documenting this as a breaking change in the PR description with migration instructions for API consumers, or 3) Bumping the API version if applicable.

Suggested change

)

)

),

Field(

"intervals",

enhancerToGenesImp,

description = Some(

"Deprecated: use `enhancerToGenes` instead. Regulatory enhancer/promoter regions to gene (target) predictions overlapping with this variant's location."

),

arguments = pageArg :: Nil,

complexity = Some(complexityCalculator(pageArg)),

deprecationReason = Some("Use `enhancerToGenes` instead."),

resolve = ctx =>

ctx.ctx.getEnhancerToGenes(ctx.value.chromosome,

ctx.value.position,

ctx.value.position,

ctx.arg(pageArg)

)

feat: amend new fields to interval schema

c49fe51

project-defiant requested a review from Copilot February 2, 2026 10:07

Copilot started reviewing on behalf of project-defiant February 2, 2026 10:08 View session

Copilot AI reviewed Feb 2, 2026

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app/models/gql/Objects.scala Outdated Show resolved Hide resolved

chore: typo

6f941f0

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

project-defiant marked this pull request as ready for review February 2, 2026 10:30

project-defiant linked an issue Feb 2, 2026 that may be closed by this pull request

enhancer_to_gene update: schemas, widget and L2G opentargets/issues#4274

Open

2 tasks

feat: make fields optional

6168676

project-defiant requested a review from jdhayhurst February 2, 2026 10:45

feat: update interval start and end to long type

b54ac2a

jdhayhurst requested changes Feb 12, 2026

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app/models/entities/Intervals.scala Outdated Show resolved Hide resolved

chore: rename interval query

3e7332a

project-defiant requested review from Copilot and jdhayhurst February 13, 2026 14:34

Copilot started reviewing on behalf of project-defiant February 13, 2026 14:34 View session

Copilot AI reviewed Feb 13, 2026

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feat: amend new fields to interval schema#317

feat: amend new fields to interval schema#317
project-defiant wants to merge 5 commits intomasterfrom
interval-qc-update

project-defiant commented Feb 2, 2026 •

edited

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		@@ -998,11 +998,11 @@ class Backend @Inject() (implicit
		logger.info(s"Total intervals found: $total")

	logger.info(s"Total intervals found: $total")
	logger.info(s"Total enhancer to gene mappings found: $total")

	.map(intervals => EnhancerToGenes(total, intervals))
	.map(enhancerToGenes => EnhancerToGenes(total, enhancerToGenes))

	"Regulatory enhancer/promoter regions to gene (target) predictions overlapping with this variant's location. These intervals link regulatory regions to target genes based on experimental data for specific tissues or cell types."
	"Enhancer-to-gene mappings that link regulatory enhancer/promoter regions to target genes when they overlap this variant's location. These predictions are derived from experimental data for specific tissues or cell types."

-            )
+            )
+        ),
+        Field(
+          "intervals",
+          enhancerToGenesImp,
+          description = Some(
+            "Deprecated: use `enhancerToGenes` instead. Regulatory enhancer/promoter regions to gene (target) predictions overlapping with this variant's location."
+          ),
+          arguments = pageArg :: Nil,
+          complexity = Some(complexityCalculator(pageArg)),
+          deprecationReason = Some("Use `enhancerToGenes` instead."),
+          resolve = ctx =>
+            ctx.ctx.getEnhancerToGenes(ctx.value.chromosome,
+                                       ctx.value.position,
+                                       ctx.value.position,
+                                       ctx.arg(pageArg)
+            )

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project-defiant commented Feb 2, 2026 •

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