fix: fix build speed (#1021)

[frano-m]

Closes #1021.

This pull request refactors the way genome/assembly entities are handled throughout the workflow input configuration codebase. It standardizes the genome type to a single Assembly type, replacing previous usages of BRCDataCatalogGenome and GA2AssemblyEntity. Additionally, it introduces a new workflows entity loading and querying system, centralizing API calls and entity storage for assemblies and workflows.

Type Standardization and Refactoring:

• Replaces all usages of BRCDataCatalogGenome and GA2AssemblyEntity with the new unified Assembly type in hooks, components, and type definitions such as useUCSCFiles, useRequirementsMatches, and related props and utility functions. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]

Workflows Entity Loading System:

• Adds a new entity loading and querying system under app/services/workflows, including utilities to load, store, and retrieve assemblies and workflows from API endpoints, with centralized state management. [1] [2] [3] [4] [5] [6] [7] [8]

Component and Utility Updates:

• Updates imports and props in workflow input configuration components to use the new Assembly type and the refactored entity types, ensuring consistency across the codebase. [1] [2] [3]

These changes improve type safety, code maintainability, and centralize entity management for assemblies and workflows, making future enhancements and debugging easier.

[Copilot]

Pull request overview

This pull request refactors entity loading to improve build performance by moving genome/assembly resolution from build-time to runtime. It introduces a centralized in-memory entity management system and standardizes the genome type to a single Assembly type union.

• Implements a new runtime entity loading system with store, query, loader, and hooks to fetch and cache assemblies and workflows from JSON API endpoints
• Simplifies getStaticProps to only return route parameters, eliminating expensive build-time entity fetching and validation
• Unifies BRCDataCatalogGenome and GA2AssemblyEntity types under a single Assembly type alias throughout the codebase

Reviewed changes

Copilot reviewed 29 out of 30 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
app/services/workflows/store.ts	Introduces in-memory maps to store entities by type and by ID
app/services/workflows/query.ts	Provides getter functions to retrieve entities from the store with error handling
app/services/workflows/loader.ts	Implements fetch logic to load entities and workflows from API endpoints into the store
app/services/workflows/entities.ts	Exports typed getter functions for assemblies and workflows
app/services/workflows/hooks/UseEntities/hook.ts	Custom hook to load entities on app initialization
app/services/workflows/hooks/UseEntities/utils.ts	Singleton pattern to ensure entities load only once
app/services/workflows/routes.ts	Defines API endpoint constants for assemblies and workflows
app/services/workflows/types.ts	Type definitions for entity routes
pages/_app.tsx	Integrates entity loading hook to populate store before rendering
pages/data/[entityListType]/[entityId]/[trsId]/index.tsx	Simplifies getStaticProps by removing build-time entity resolution
app/views/WorkflowInputsView/workflowInputsView.tsx	Refactored to fetch entities at runtime using new getter functions
app/views/WorkflowInputsView/types.ts	Defines unified Assembly type alias
app/components/Entity/components/ConfigureWorkflowInputs/**/*.ts	Updated type references from specific genome types to Assembly
scripts/sync-api-brc-analytics.sh	Script to copy catalog JSONs to public API directory for brc-analytics
scripts/sync-api-ga2.sh	Script to copy catalog JSONs to public API directory for ga2
package.json	Updated build and dev scripts to run sync-api scripts before Next.js commands
.gitignore	Excludes generated /public/api directory from version control
tests/services/workflows.store.test.ts	Test coverage for entity store operations
tests/services/workflows.query.test.ts	Test coverage for entity query functions
tests/services/workflows.loader.test.ts	Test coverage for entity loading logic with fetch mocking

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[Copilot]

Pull request overview

Copilot reviewed 29 out of 30 changed files in this pull request and generated 4 comments.

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[hunterckx]

I've approved this but I think @NoopDog wanted to review the API path before merging?