research-hub-pipeline 0.26.0

Zotero -> Obsidian -> NotebookLM research pipeline

research-hub-pipeline

Zotero -> Obsidian -> NotebookLM research pipeline. Search, verify, save, organize, and upload academic papers -> all from the terminal.

Install

pip install research-hub-pipeline
# With NotebookLM browser automation:
pip install research-hub-pipeline[playwright]
playwright install chromium

research-hub requires Python 3.10 or newer. Install the playwright extra only if you plan to use NotebookLM login, upload, or generation.

Two personas, one tool

research-hub supports two workflows out of the box:

Researcher (default)

pip install research-hub-pipeline[playwright]
research-hub init                  # interactive: vault + Zotero + library id
research-hub doctor                # 7-check health diagnostic
research-hub add 10.1234/example   # one-shot fetch + ingest
research-hub notebooklm upload --cluster my-topic

You get: Zotero items with full citation metadata + Obsidian research notes + NotebookLM upload + AI suggestions + BibTeX export.

Data analyst (no Zotero)

pip install research-hub-pipeline[playwright]
research-hub init --persona analyst   # skips Zotero prompts
research-hub doctor                    # Zotero checks marked "skipped"
research-hub add 10.1234/example       # writes to Obsidian only
research-hub notebooklm upload --cluster my-topic

You get: Obsidian-only knowledge base + NotebookLM upload + AI suggestions. No Zotero account required. Perfect for industry research, white papers, and technical documentation.

Quick start

1. Run the first-time setup wizard:

   research-hub init
   

   This creates your config file, vault folders, and optional Zotero settings.

2. Verify the installation:

   research-hub doctor
   

   The health check reports config, vault paths, Zotero credentials, dedup index status, Chrome availability, and NotebookLM session state.

3. Search for papers and verify DOIs while printing results:

   research-hub search "graph neural networks" --verify
   

4. Ask for cluster and related-paper suggestions for a DOI:

   research-hub suggest 10.1145/3448016.3452841 --json
   

5. Ingest papers into your Zotero + Obsidian workflow:

   research-hub ingest --cluster my-cluster
   

6. Upload a prepared cluster to NotebookLM:

   research-hub notebooklm upload --cluster my-cluster
   

7. Export a citation when you need it:

   research-hub cite 10.1145/3448016.3452841 --format bibtex
   

If you are starting from scratch, a common first session is:

research-hub init
research-hub doctor
research-hub clusters new --query "graph neural networks" --slug my-cluster
research-hub search "graph neural networks" --verify
research-hub ingest --cluster my-cluster
research-hub notebooklm login --cdp
research-hub notebooklm upload --cluster my-cluster

Features

The CLI is organized around a paper workflow: find papers, verify identifiers, save notes, keep clusters aligned, and push selected clusters into NotebookLM.

Stage	Command	Description
Search	search	Query Semantic Scholar for new papers by keyword
Verify	verify --doi / verify --arxiv / verify --paper	Check that a DOI, arXiv ID, or fuzzy title match resolves
Save	run / ingest	Run the ingestion pipeline and write Zotero + Obsidian outputs
Organize	clusters new / clusters list / clusters show / clusters bind	Create, inspect, and bind topic clusters
Suggest	suggest <id> [--json]	Recommend a cluster and related existing papers
Sync	sync status / sync reconcile	Detect and reconcile Zotero -> Obsidian drift
Upload	notebooklm upload	Upload bundle sources to NotebookLM using a saved browser session
Generate	notebooklm generate --type brief	Trigger NotebookLM artifact generation
Cite	cite <id> --format bibtex	Export BibTeX, BibLaTeX, RIS, or CSL-JSON
Maintain	index / status / cleanup / synthesize	Rebuild indexes, check progress, deduplicate hub pages, generate synthesis pages
Setup	init / doctor	Create config and validate the local environment

Search and verify

Use search to discover candidate papers before adding anything to your vault:

research-hub search "retrieval augmented generation" --limit 10

Add --verify when you want each DOI checked against doi.org before it is printed:

research-hub search "retrieval augmented generation" --limit 10 --verify

Use verify directly when you already know the identifier:

research-hub verify --doi 10.48550/arXiv.1706.03762
research-hub verify --arxiv 1706.03762
research-hub verify --paper "Attention Is All You Need" --paper-year 2017
research-hub verify --paper "Attention Is All You Need" --paper-author Vaswani

Run ingestion

run and ingest both execute the pipeline. Use --dry-run when you want to validate config and inputs without writing anything:

research-hub ingest --cluster my-cluster --dry-run
research-hub ingest --cluster my-cluster --query "retrieval augmented generation"
research-hub run --cluster my-cluster --query "retrieval augmented generation"

Verification is enabled by default for run and ingest. Skip DOI or arXiv checks only when you want faster batch work:

research-hub ingest --cluster my-cluster --no-verify

Organize by cluster

Clusters give the rest of the workflow a stable slug for folders, Zotero collections, and NotebookLM notebooks:

research-hub clusters new --query "retrieval augmented generation" --name "RAG" --slug rag
research-hub clusters list
research-hub clusters show rag
research-hub clusters bind rag --zotero ABCD1234 --obsidian rag --notebooklm "RAG Notebook"

Get suggestions before saving

suggest accepts a DOI, arXiv ID, or quoted title and scores both cluster matches and related existing notes:

research-hub suggest 10.48550/arXiv.1706.03762
research-hub suggest 1706.03762 --top 8
research-hub suggest "Attention Is All You Need" --json

This is the fastest way to decide whether a new paper belongs in an existing cluster before you ingest it.

Track status and repair drift

Use status for reading progress, sync status for cross-system drift, and sync reconcile to create missing Obsidian notes from Zotero:

research-hub status
research-hub status --cluster rag
research-hub sync status
research-hub sync status --cluster rag
research-hub sync reconcile --cluster rag --dry-run
research-hub sync reconcile --cluster rag --execute

Export citations

cite can export one paper by DOI or filename stem, or an entire cluster:

research-hub cite 10.48550/arXiv.1706.03762 --format bibtex
research-hub cite 10.48550/arXiv.1706.03762 --format ris
research-hub cite --cluster rag --format biblatex --out rag.bib

Supported output formats are bibtex, biblatex, ris, and csljson.

Maintain the vault

These commands help keep the local knowledge base consistent:

research-hub index
research-hub cleanup --dry-run
research-hub cleanup
research-hub synthesize
research-hub synthesize --cluster rag --graph-colors
research-hub migrate-yaml --dry-run
research-hub migrate-yaml --assign-cluster rag --folder raw --force

index rebuilds the dedup index from Zotero and Obsidian. cleanup removes duplicate wiki links in hub pages. synthesize writes cluster summary pages. migrate-yaml patches older notes to the current YAML layout.

NotebookLM workflow

NotebookLM commands are separate because they require browser automation:

research-hub notebooklm login --cdp
research-hub notebooklm bundle --cluster rag
research-hub notebooklm upload --cluster rag --dry-run
research-hub notebooklm upload --cluster rag
research-hub notebooklm generate --cluster rag --type brief
research-hub notebooklm generate --cluster rag --type all

Use --headless for unattended runs or --visible when you want to watch the browser. generate --type supports brief, audio, mind-map, video, and all.

Configuration

research-hub init writes a JSON config file automatically. By default the config file lives at ~/.config/research-hub/config.json on Linux and macOS, or %APPDATA%/research-hub/config.json on Windows.

If you want to point the CLI at a different file, set RESEARCH_HUB_CONFIG.

The vault root comes from config field knowledge_base.root or from RESEARCH_HUB_ROOT. If neither is set, the default root is ~/knowledge-base.

Useful path overrides:

• RESEARCH_HUB_RAW
• RESEARCH_HUB_HUB
• RESEARCH_HUB_PROJECTS
• RESEARCH_HUB_LOGS
• RESEARCH_HUB_GRAPH

Zotero credentials can come from config or environment variables:

• ZOTERO_API_KEY
• ZOTERO_LIBRARY_ID
• ZOTERO_LIBRARY_TYPE
• RESEARCH_HUB_DEFAULT_COLLECTION

The typical vault layout created by research-hub init is:

<vault>/
  raw/
  hub/
  logs/
  .research_hub/

After setup, research-hub doctor is the fastest way to confirm the config file, vault, Zotero credentials, dedup index, Chrome, and saved NotebookLM session all look valid.

NotebookLM integration

NotebookLM support uses a Chrome DevTools Protocol attach flow rather than a Playwright-launched browser, which avoids the Google bot check that blocks normal automated logins. Install Chrome, run research-hub notebooklm login --cdp once, then use notebooklm bundle, notebooklm upload, and notebooklm generate for cluster-level workflows. Full setup, troubleshooting, and selector maintenance notes are in docs/notebooklm.md.

For developers

If you are working from a clone instead of installing from PyPI:

git clone https://github.com/WenyuChiou/research-hub.git
cd research-hub
pip install -e '.[dev,playwright]'
python -m pytest -q

Useful developer checks:

research-hub --help
research-hub doctor
research-hub search "test query" --limit 3

The package entry point is research-hub, while the PyPI package name is research-hub-pipeline.

License

MIT. See LICENSE.