#VFB-233 - Refactor Neuroglass state management and viewer configuration

[jrmartin]

Changes Neuroglassviewer component to match design described on VFB-232. The changes enable dynamic construction of Neuroglass viewer state based on loaded VFB instances selected from the Layers Component. The Neuroglassviewer will display in a layer each of the selected instances toggled from the Layers Component, as well as delete and show/hide instances as selected from Layers Component. Allows updating the VFB data server as a configuration instead of hardcoding location.

Variables added to the Codefresh for storing these configuration values:

[Copilot]

Pull request overview

Refactors the Virtual Fly Brain frontend’s Neuroglass integration to dynamically generate Neuroglancer viewer state from loaded instances, support layout selection via Redux + ?layout=..., and make the Neuroglass datasource configurable at build/deploy time.

Changes:

• Replaced static Neuroglass state mappings with a buildNeuroglassState builder + shared shader/datasource config.
• Added neuroglassView to Redux, plus middleware to read/write the layout URL parameter.
• Introduced Docker/CI build args intended to configure Neuroglass datasource protocol/base URL.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
deployment/codefresh-dev.yaml	Passes Neuroglass datasource build args into the image build step.
applications/virtual-fly-brain/Dockerfile	Adds build args and exports datasource config during the Vite build.
applications/virtual-fly-brain/frontend/src/utils/neuroglassStateConfig.js	Implements dynamic viewer state builder, datasource URL builder, shader, and layout resolver.
applications/virtual-fly-brain/frontend/src/utils/neuroglassActions.js	Removes legacy state lookup helpers tied to static mappings.
applications/virtual-fly-brain/frontend/src/utils/constants.js	Defines known layouts, defaults, and URL parameter name.
applications/virtual-fly-brain/frontend/src/reducers/middleware/urlUpdaterMiddleware.js	Syncs ?layout into Redux on first load and writes it back on state change.
applications/virtual-fly-brain/frontend/src/reducers/actions/types/GlobalTypes.js	Adds SET_NEUROGLASS_VIEW action type.
applications/virtual-fly-brain/frontend/src/reducers/actions/globals.js	Adds setNeuroglassView action creator.
applications/virtual-fly-brain/frontend/src/reducers/GlobalReducer.js	Stores neuroglassView in global reducer state.
applications/virtual-fly-brain/frontend/src/components/NeuroglassViewer.jsx	Switches viewer to builder-based state, responsive layout selection, and debounced iframe reload.

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[Copilot]

Pull request overview

Refactors the Neuroglass viewer integration to dynamically build Neuroglancer viewer state from loaded VFB instances, add Redux/URL-driven layout selection, and make the Neuroglass datasource configurable via build/deploy-time variables.

Changes:

• Replaced hardcoded Neuroglass state mappings with a dynamic buildNeuroglassState builder and shared datasource/shader config.
• Added neuroglassView to global Redux state and synchronized it with the URL ?layout parameter via middleware.
• Plumbed NEUROGLASS_DATA_PROTOCOL / NEUROGLASS_DATA_BASE_URL through build/deploy config and Vite defines.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
deployment/codefresh-dev.yaml	Passes Neuroglass datasource variables into the build pipeline.
applications/virtual-fly-brain/frontend/vite.config.js	Injects Neuroglass datasource env into the frontend build (and logs build config).
applications/virtual-fly-brain/frontend/src/utils/neuroglassStateConfig.js	Implements dynamic Neuroglass state generation and layout resolution.
applications/virtual-fly-brain/frontend/src/utils/neuroglassActions.js	Removes legacy state lookup utilities tied to static state maps.
applications/virtual-fly-brain/frontend/src/utils/constants.js	Adds known layouts and layout URL param/defaults.
applications/virtual-fly-brain/frontend/src/reducers/middleware/urlUpdaterMiddleware.js	Reads/writes ?layout and syncs it with Redux state.
applications/virtual-fly-brain/frontend/src/reducers/actions/types/GlobalTypes.js	Adds SET_NEUROGLASS_VIEW action type.
applications/virtual-fly-brain/frontend/src/reducers/actions/globals.js	Adds setNeuroglassView action creator.
applications/virtual-fly-brain/frontend/src/reducers/GlobalReducer.js	Stores neuroglassView in global state.
applications/virtual-fly-brain/frontend/src/components/NeuroglassViewer.jsx	Rebuilds iframe state dynamically, supports layout switching, and debounces reloads.
applications/virtual-fly-brain/Dockerfile	Exposes Neuroglass datasource build args and exports them for the Vite build.

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[Copilot]

Pull request overview

Refactors the Neuroglass viewer integration to dynamically build Neuroglancer state from the currently loaded VFB instances and adds configurable Neuroglass datasource settings (protocol/base URL), plus URL/Redux syncing for viewer layout selection.

Changes:

• Replaced static Neuroglass state presets with dynamic state generation (buildNeuroglassState) and layout resolution (resolveNeuroglassLayout).
• Added Neuroglass datasource configuration via environment variables and propagated them through Vite build configuration and the Docker build.
• Introduced globalInfo.neuroglassView in Redux and middleware syncing of ?layout= between URL and store.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
deployment/codefresh-dev.yaml	Passes Neuroglass datasource env vars into Codefresh build context.
applications/virtual-fly-brain/frontend/vite.config.js	Inlines Neuroglass config into the frontend bundle via define and logs build config.
applications/virtual-fly-brain/frontend/src/utils/neuroglassStateConfig.js	Implements dynamic layer/state generation and configurable datasource URL building.
applications/virtual-fly-brain/frontend/src/utils/neuroglassActions.js	Removes legacy helpers tied to static Neuroglass state maps.
applications/virtual-fly-brain/frontend/src/utils/constants.js	Adds known Neuroglass layout constants and URL param key.
applications/virtual-fly-brain/frontend/src/reducers/middleware/urlUpdaterMiddleware.js	Syncs layout URL param into Redux and updates URL when view changes.
applications/virtual-fly-brain/frontend/src/reducers/actions/types/GlobalTypes.js	Adds a new global action type for Neuroglass view updates.
applications/virtual-fly-brain/frontend/src/reducers/actions/globals.js	Adds setNeuroglassView(view) action creator.
applications/virtual-fly-brain/frontend/src/reducers/GlobalReducer.js	Stores neuroglassView in global Redux state.
applications/virtual-fly-brain/frontend/src/components/queryBuilder/FullscreenSlider.jsx	Removes a file-level eslint disable comment.
applications/virtual-fly-brain/frontend/src/components/configuration/VFBToolbar/vfbtoolbarHTML.jsx	Removes a file-level eslint disable comment.
applications/virtual-fly-brain/frontend/src/components/NeuroglassViewer.jsx	Refactors viewer to use dynamic state/layout and debounced iframe src updates.
applications/virtual-fly-brain/Dockerfile	Wires Neuroglass datasource vars into the Vite build step.

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[Copilot]

Pull request overview

This PR refactors the Neuroglass viewer integration to dynamically generate Neuroglancer state from currently loaded VFB instances, and makes the Neuroglass datasource/viewer endpoints configurable via build-time environment variables. It also introduces Redux + URL synchronization for selecting the Neuroglass layout.

Changes:

• Build Neuroglass viewer state dynamically from allLoadedInstances (layers, colors, visibility) and resolve layout based on URL/Redux + mobile/desktop.
• Add NEUROGLASS_DATA_PROTOCOL, NEUROGLASS_DATA_BASE_URL, and NEUROGLASS_URL configuration plumbing through Codefresh, Docker build, and Vite define.
• Add globalInfo.neuroglassView Redux state and middleware support to sync ?layout= between URL and Redux.

Reviewed changes

Copilot reviewed 11 out of 13 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
deployment/codefresh-dev.yaml	Pass Neuroglass-related build args into the app image build step.
applications/virtual-fly-brain/frontend/vite.config.js	Load + inject Neuroglass env vars into import.meta.env.* via Vite define.
applications/virtual-fly-brain/frontend/src/utils/neuroglassStateConfig.js	Replace static state maps with datasource config, layout resolution, and dynamic state/layer builders.
applications/virtual-fly-brain/frontend/src/utils/neuroglassActions.js	Remove legacy helpers tied to static Neuroglass state maps.
applications/virtual-fly-brain/frontend/src/utils/constants.js	Add known Neuroglass layouts + URL param + defaults.
applications/virtual-fly-brain/frontend/src/reducers/middleware/urlUpdaterMiddleware.js	Read/write ?layout= and sync it to/from Redux.
applications/virtual-fly-brain/frontend/src/reducers/actions/types/GlobalTypes.js	Add SET_NEUROGLASS_VIEW action type.
applications/virtual-fly-brain/frontend/src/reducers/actions/globals.js	Add setNeuroglassView(view) action creator.
applications/virtual-fly-brain/frontend/src/reducers/GlobalReducer.js	Store neuroglassView in global reducer state.
applications/virtual-fly-brain/frontend/src/components/queryBuilder/FullscreenSlider.jsx	Remove file-level eslint disable comment.
applications/virtual-fly-brain/frontend/src/components/configuration/VFBToolbar/vfbtoolbarHTML.jsx	Remove file-level eslint disable comment.
applications/virtual-fly-brain/frontend/src/components/NeuroglassViewer.jsx	Rebuild iframe URL from dynamic state, add debounced updates, and handle mobile/desktop layout selection.
applications/virtual-fly-brain/Dockerfile	Export Neuroglass build-time env vars into the Vite build step.

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