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Reported issues for endnote-mcp

Pod holds 5 of 5 GitHub reports that passed its relevance review. This can include external user reports, maintainer-confirmed bugs, and concrete feature gaps. Treat them as evidence to inspect, not a count of distinct defects.

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Most discussed

Problem with embed

Thanks for developing this - it is exactly what I was hoping would arrive!!! I have done the update to the latest version this morning (yikes to that error), and decided to update to the semantic search however on embed I get the following:

Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in run_code File "C:\Users\willi.local\bin\endnote-mcp.exe_main.py", line 10, in sys.exit(main())…

Read the thread · 2026-02-26 · closed · external user · 4 comments

Setup fails

Hello again! I just got a new computer (macbook) and was trying to install the MCP again but it will not go beyond the PDF source folder request... it just lets you keep inputing letters but ignore Enter so does not move on. Any ideas? thank you. See below - it just stops responding to Enter and lets you type more and more text.

Thank you - I am finding it really useful on my other machine!

Will.

EndNote MCP — Setup Wizard Connect your reference library to Claude

Step 1: EndNote XML…

Read the thread · 2026-06-06 · closed · external user · 3 comments

Index <research-notes> and <notes> fields from the EndNote XML export

Summary

EndNote exports user-written notes in the XML, but they don't appear to reach the SQLite index, so they can't be searched or returned. Since these fields hold the user's own summaries and judgments — the one thing not already recoverable from the abstract or PDF — indexing them would add a lot for a small change.

What I observed

EndNote 22.3 exports both fields with well-formed content, wrapped in the same <style> tags as title and abstract:

<notes><style…

[Read the thread](https://github.com/gokmengokhan/endnote-mcp/issues/5) · 2026-09-03 · closed · external user · 2 comments

### UnicodeEncodeError on Traditional Chinese Windows (cp950) during indexing

Hi, thank you for building endnote-mcp.

I’m using endnote-mcp on Traditional Chinese Windows.

The MCP server starts successfully and connects normally, but during indexing / rebuild operations I get this error:

UnicodeEncodeError: 'cp950' codec can't encode character '\u2713'

It seems related to the Windows Traditional Chinese console/code page environment.

The server can start and connect, but longer operations may fail or time out after this encoding-related issue.

Would you be able to…

[Read the thread](https://github.com/gokmengokhan/endnote-mcp/issues/2) · 2026-04-18 · closed · external user · 1 comment

### Concurrent tool calls crash with sqlite3.ProgrammingError (thread-affinity violation)

### Summary

Any two `endnote-mcp` MCP tool calls that execute concurrently (not sequentially) fail with a `sqlite3.ProgrammingError` about cross-thread SQLite object use. This is independent of query content — plain, previously-working queries (`"habituation"`, `"reward"`, `"alpha"`) fail exactly the same way as queries with punctuation.

### What I observed

Using the MCP tools from a client that batches independent tool calls together (so they run concurrently), calls to `search_references`,…

[Read the thread](https://github.com/gokmengokhan/endnote-mcp/issues/7) · 2026-09-25 · open · external user · 0 comments

## Most recent

The remaining reports are on [the project's issue tracker](https://github.com/gokmengokhan/endnote-mcp/issues).