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added 2 commits
February 10, 2026 12:56
…owed for things like copy/pasting in the chatbot panel
…gs model while reindexing everything. Also added a keyword search fallback and made the documentation more relevant for users asking for help navigating the UI. Set a limit for number of search documentation calls
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I vote @samcraftt review cuz he has worked more recently with the agent implementation... |
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Pull request overview
This PR improves the in-app chatbot’s retrieval quality and grounding by reindexing documentation with a stronger embedding model + chunking, adding a keyword-search fallback, and tightening prompt/tooling rules to reduce hallucinations. It also expands file-management capabilities in the UI/backend (mount/unmount project directories, image previews, OS “reveal in folder”) and updates the chatbot’s documentation corpus to be end-user page guides rather than source-file summaries.
Changes:
- Rebuild RAG indexing (chunked documents, new embedding model), add keyword fallback, and cap documentation tool calls per user question.
- Replace code-oriented “file summaries” with end-user-focused page/workflow documentation used by the chatbot.
- Add File Manager mounting/unmounting + preview endpoints and corresponding UI/Electron integrations; adjust workflow selection modal behavior.
Reviewed changes
Copilot reviewed 53 out of 55 changed files in this pull request and generated 12 comments.
Show a summary per file
| File | Description |
|---|---|
| server_api/main.py | Uses a reset callback from build_chain() before chat queries/clears (replacing prior memory clearing behavior). |
| server_api/chatbot/update_faiss.py | Reindexes docs with chunking and a new embeddings model; saves updated FAISS index. |
| server_api/chatbot/chatbot.py | Updates prompts/routing rules, limits doc search calls, adds keyword fallback, changes embedding model default, and returns a reset function. |
| server_api/chatbot/faiss_index/index.pkl | Updated/added serialized FAISS docstore artifact committed to repo. |
| server_api/auth/router.py | Adds file preview endpoint, mount/unmount project directory endpoints, and safer recursive delete behavior. |
| server_api/auth/models.py | Adds MountDirectoryRequest schema for mount endpoint. |
| client/src/views/Views.js | Removes workflow preference persistence/polling and defaults workflow selector modal to open on startup. |
| client/src/views/FilesManager.js | Adds mounted project UX (mount/unmount, reveal-in-folder, mounted badges), image thumbnails via preview endpoint, and properties enhancements. |
| client/src/components/UnifiedFileInput.js | Simplifies browse flow to use mounted-storage picker (removes source selection modal). |
| client/src/components/FileTreeSidebar.js | Improves tree rendering/ellipsis styling for long names. |
| client/src/components/FilePickerModal.js | Adds upload-from-local, image-only filtering, and thumbnail previews in picker. |
| client/main.js | Adds standard Edit menu roles (cut/copy/paste/etc.) and IPC handler to reveal files in OS file explorer. |
| server_api/chatbot/file_summaries/views/ehtool/UnifiedImageEditor.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/ProofreadingEditor.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/ProgressTracker.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/LayerGrid.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/DetectionWorkflow.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/DatasetLoader.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ehtool/ClassificationPanel.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/WormErrorHandling.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/Visualization.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/Views.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ProofReading.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/Monitoring.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ModelTraining.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/ModelInference.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/FilesManager.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/views/EHTool.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/main.md | Removed legacy server main summary from RAG corpus. |
| server_api/chatbot/file_summaries/contexts/YamlContext.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/contexts/GlobalContext.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/YamlFileUploader.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/YamlFileEditor.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/WorkflowSelector.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/UnifiedFileInput.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/SynapseList.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/ProofreadingControls.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/NeuroglancerViewer.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/InputSelector.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/FileTreeSidebar.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/FilePickerModal.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/Configurator.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/components/Chatbot.md | Removed legacy code-oriented summary (replaced by end-user docs). |
| server_api/chatbot/file_summaries/api.md | Removed legacy API-client summary from RAG corpus. |
| server_api/chatbot/file_summaries/App.md | Removed legacy app root summary from RAG corpus. |
| server_api/chatbot/file_summaries/GettingStarted.md | Adds end-user “Getting Started” guide for overall app navigation. |
| server_api/chatbot/file_summaries/FileManager.md | Adds end-user File Manager workflow guide. |
| server_api/chatbot/file_summaries/Visualization.md | Adds end-user Visualization (Neuroglancer) workflow guide. |
| server_api/chatbot/file_summaries/ModelTraining.md | Adds end-user Model Training wizard/workflow guide. |
| server_api/chatbot/file_summaries/ModelInference.md | Adds end-user Model Inference wizard/workflow guide. |
| server_api/chatbot/file_summaries/Monitoring.md | Adds end-user TensorBoard Monitoring guide. |
| server_api/chatbot/file_summaries/Proofreading.md | Adds end-user SynAnno proofreading guide. |
| server_api/chatbot/file_summaries/ErrorHandlingTool.md | Adds end-user Error Handling Tool (EHT) workflow guide. |
| server_api/chatbot/file_summaries/WormErrorHandling.md | Adds end-user Worm Error Handling page guide. |
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Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
[WIP] Update based on feedback for chatbot improvement PR
Co-authored-by: zhangdjr <123129802+zhangdjr@users.noreply.github.com>
…nother-one [WIP] Update to improve chatbot functionality based on feedback
…gain Add input validation to /chat/query endpoint
samcraftt
reviewed
Feb 10, 2026
server_api/auth/router.py
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| oauth2_scheme = OAuth2PasswordBearer(tokenUrl="token", auto_error=False) | ||
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| # Mount operation guardrails to prevent self-DoS |
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These changes seem unrelated to the chatbot and have to do with the file management functionality, right? If so, why are they necessary? @akgohain any thoughts on this since you were doing file management?
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I concur.....I'll pull in a bit and see if it's just an extra guardrail (then sure...fine) or if it's breaking
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It was something suggested by copilot during review, I think we could still move on without it but it's still good to have. Let me know what you think
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I'd say it's best to move on without these specific changes for now. If we didn't realize we needed them no need to fix what's not broken. We can always apply the file management-related changes in a later PR if we realize they're necessary.
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Ok I can remove those then
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Ok I reverted router.py back to what it was before.
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Also, you can follow the formatting steps in |
samcraftt
approved these changes
Feb 12, 2026
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Fixed the issue with crappy RAG retrievals by using a better embeddings model while reindexing everything. Also added a keyword search fallback and made the documentation more relevant for users asking for help navigating the UI. Set a limit for number of search documentation calls. Improved Chatbot prompts to reduce hallucination tendencies. Also allowed for things like copy/pasting in the chatbot panel