739 lines
20 KiB
Markdown
739 lines
20 KiB
Markdown
# CLI Examples
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This guide gives example invocations for the `citegeist` CLI, including the major option combinations for each command.
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Where a topic is named, this guide uses:
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- topic phrase: `artificial life`
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- topic slug: `artificial-life`
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- topic name: `Artificial life`
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Assume:
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```bash
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cd citegeist
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export PYTHONPATH=src
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```
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## Setup
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Purpose: point commands at the right database before doing anything else.
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### Global Option
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Use a non-default database path:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 topics
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```
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## Build And Inspect A Library
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Purpose: ingest records, search them, inspect them, and export them.
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### Ingest
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Basic ingest:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 ingest references.bib
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```
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Set initial review status:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 ingest references.bib --status reviewed
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```
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Set a provenance label:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 ingest references.bib --source-label "examples/artificial-life/references.bib"
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```
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Use both ingest options together:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 ingest references.bib --status draft --source-label "manual-import:artificial-life"
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```
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### Search
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Basic search:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 search "artificial life"
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```
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Limit the number of matches:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 search "artificial life" --limit 5
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```
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Restrict search to one topic slice:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 search "artificial life" --topic artificial-life
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```
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### Show
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Show one entry:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 show langton1989artificial1
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```
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List entries:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 show --limit 10
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```
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Include provenance:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 show langton1989artificial1 --provenance
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```
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Include conflicts:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 show langton1989artificial1 --conflicts
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```
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Use both:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 show langton1989artificial1 --provenance --conflicts
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```
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### Export
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Export the whole library:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 export
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```
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Export selected citation keys:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 export langton1989artificial1 bedau2003artificial2
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```
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Write BibTeX to a file:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 export --output artificial-life.bib
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```
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Include DOI-only placeholder records in a broad export:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 export --include-stubs --output artificial-life.bib
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```
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## Review And Clean Metadata
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Purpose: inspect merge conflicts, apply corrections, and enrich incomplete records.
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### Entry Review
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Set review status:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 set-status langton1989artificial1 reviewed
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```
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Resolve field conflicts:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 resolve-conflicts langton1989artificial1 title accepted
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```
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Reject a conflict instead:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 resolve-conflicts langton1989artificial1 title rejected
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```
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Apply the latest proposed conflict value:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 apply-conflict langton1989artificial1 title
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```
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### Extract
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Extract draft BibTeX from plaintext:
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```bash
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.venv/bin/python -m citegeist extract references.txt
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```
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Write extracted BibTeX to a file:
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```bash
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.venv/bin/python -m citegeist extract references.txt --output extracted-artificial-life.bib
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```
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Extraction notes from messy legacy corpora:
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- use the full raw reference line as the repair source when the first parse leaves a truncated venue stub;
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- split title from publication data at likely sentence boundaries before falling back to keyword markers, so titles containing words like `report` are not cut early;
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- keep refreshed local BibTeX for unresolved entries so parser improvements can propagate even when no remote metadata source yields a match.
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### Resolve
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Resolve one or more entries against remote metadata:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 resolve langton1989artificial1 bedau2003artificial2
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```
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Preview DOI-bearing placeholder records before enriching them:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --preview --limit 25
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```
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Enrich DOI-bearing placeholder records inside one topic slice:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --topic artificial-life --limit 25
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```
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Preview all current `@misc` entries with DOIs, not just placeholder-like stubs:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --all-misc --preview --limit 25
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```
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Re-enrich all current `@misc` entries with DOIs:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --all-misc --limit 25
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```
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When Crossref expansion only yields an unstructured citation blob without a DOI, citegeist now skips materializing that discovery instead of storing it as a weak `@misc` entry. Cleaner fallback cases that infer a more specific type, such as proceedings-like titles, are still admitted. Thesis and dissertation citation blobs are also normalized more aggressively so fallback `@phdthesis` entries keep the work title instead of the entire ProQuest-style citation string.
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OpenAlex expansion now applies the same kind of admission control before writing or previewing discoveries. DOI-backed discoveries prefer DOI-based citation keys, noisy webpage/export abstracts are dropped, generic venue-title stubs are rejected, and weak DOI-less article records that merely shadow an existing book/chapter/dissertation title in your store are suppressed instead of being materialized as parallel duplicates. Both OpenAlex and Crossref discovery also normalize some malformed upstream author strings so records like `J., Fogel L.` are stored in stable BibTeX form as `Fogel, L. J.`.
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## Explore Citation Graphs
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Purpose: traverse citation edges, export graph data, and render quick visualizations.
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### Graph Traversal
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Basic traversal:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 graph langton1989artificial1
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```
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Use multiple relation filters:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 graph langton1989artificial1 --relation cites --relation cited_by
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```
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Set traversal depth:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 graph langton1989artificial1 --depth 2
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```
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Filter by target review status:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 graph langton1989artificial1 --review-status reviewed
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```
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Show only unresolved targets:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 graph langton1989artificial1 --missing-only
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```
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Render DOT instead of traversal rows:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 graph langton1989artificial1 --format dot
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```
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Render node/edge JSON for visualization:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 graph langton1989artificial1 --format json-graph
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```
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Write graph output to a file:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 graph langton1989artificial1 --depth 2 --format dot --output artificial-life.dot
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```
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### Graph Viewer
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Render a standalone HTML page from a `json-graph` export:
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```bash
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.venv/bin/python -m citegeist graph-view artificial-life.json --output artificial-life.html
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```
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Set the HTML page title:
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```bash
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.venv/bin/python -m citegeist graph-view artificial-life.json --output artificial-life.html --title "Artificial Life Graph"
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```
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### Graph Expansion
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Expand from one or more seed entries:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand langton1989artificial1
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```
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Choose the graph expansion source:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand langton1989artificial1 --source openalex
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```
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Choose relation direction:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand langton1989artificial1 --source openalex --relation cited_by
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```
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Limit discoveries per seed:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand langton1989artificial1 --source openalex --limit 10
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```
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### JabRef Round Trip
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Use JabRef as the main editor and CiteGeist as the enrichment pass:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 sync-jabref my-library.bib --output my-library.enriched.bib
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```
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Skip resolver calls if you only want a normalized import/export pass:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 sync-jabref my-library.bib --output my-library.enriched.bib --no-resolve
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```
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Write back to the same file and include CiteGeist review cues as BibTeX sidecar fields for JabRef:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 sync-jabref my-library.bib --in-place --annotate-review
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```
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## Build A Topic-Centered Bibliography
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Purpose: create, expand, inspect, and export a topic slice such as `artificial life`.
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### Topic Expansion
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Basic topic expansion from stored topic metadata:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand-topic artificial-life
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```
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Override the topic phrase:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand-topic artificial-life --topic-phrase "artificial life alife artificial organisms"
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```
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Choose graph expansion source and relation:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand-topic artificial-life --source openalex --relation cited_by
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```
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Note: graph expansion currently supports `openalex` and `crossref`. Metadata resolution, verification, and bootstrap topic seeding also use `datacite` and `pubmed`.
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Control seed and discovery limits:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand-topic artificial-life --seed-limit 10 --per-seed-limit 5
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```
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Restrict to trusted seed entries:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand-topic artificial-life --seed-key langton1989artificial1 --seed-key bedau2003artificial2
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```
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Raise or lower the topic assignment threshold:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand-topic artificial-life --min-relevance 0.3
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```
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Preview without writing:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 expand-topic artificial-life --preview
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```
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### Topic Phrase Storage
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Set a stored topic phrase:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 set-topic-phrase artificial-life "artificial life alife artificial organisms complex systems evolution simulation"
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```
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Clear a stored topic phrase:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 set-topic-phrase artificial-life --clear
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```
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### Topic Inspection
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List topics:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 topics
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```
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Limit topic rows:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 topics --limit 20
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```
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Filter topics by phrase review status:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 topics --phrase-review-status pending
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```
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List entries for a topic:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 topic-entries artificial-life
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```
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Limit topic entries:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 topic-entries artificial-life --limit 25
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```
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Export one topic slice as BibTeX:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 export-topic artificial-life
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```
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Write the topic slice to a file:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 export-topic artificial-life --output artificial-life-topic.bib
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```
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Include DOI-only placeholder records in the topic export:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 export-topic artificial-life --include-stubs --output artificial-life-topic.bib
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```
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### Bootstrap
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Seed from a BibTeX file:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap --seed-bib artificial-life.bib
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```
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Seed from a topic phrase alone:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap --topic "artificial life"
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```
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Use both a seed `.bib` and a topic phrase:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap --seed-bib artificial-life.bib --topic "artificial life"
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```
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Store topic metadata while bootstrapping:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 \
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bootstrap \
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--topic "artificial life" \
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--topic-slug artificial-life \
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--topic-name "Artificial life" \
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--store-topic-phrase "artificial life alife artificial organisms complex systems evolution simulation"
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```
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Control topic-search candidate count:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap --topic "artificial life" --topic-limit 10
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```
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Control how many topic candidates are actually committed:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap --topic "artificial life" --topic-commit-limit 5
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```
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Disable immediate expansion:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap --topic "artificial life" --no-expand
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```
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Preview without writing:
|
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|
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap --topic "artificial life" --preview
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```
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|
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Set review status for imported entries:
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|
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap --topic "artificial life" --status reviewed
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```
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### Batch Bootstrap
|
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Run a JSON batch file:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 bootstrap-batch artificial-life.json
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```
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### Topic Phrase Review Workflow
|
||
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Apply topic phrases directly:
|
||
|
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 apply-topic-phrases topic-phrases.json
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```
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Stage topic phrase suggestions:
|
||
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 stage-topic-phrases topic-phrases.json
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```
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Review one staged phrase:
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||
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 review-topic-phrase artificial-life accepted
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```
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Add notes while reviewing:
|
||
|
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 review-topic-phrase artificial-life accepted --notes "good fit for topic expansion"
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```
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Override the accepted phrase while reviewing:
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 review-topic-phrase artificial-life accepted --phrase "artificial life alife artificial organisms autonomous agents"
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```
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Apply review decisions in bulk:
|
||
|
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 review-topic-phrases topic-phrase-review.json
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```
|
||
|
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List staged phrase reviews:
|
||
|
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 topic-phrase-reviews
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||
```
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||
|
||
Filter review rows by status:
|
||
|
||
```bash
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.venv/bin/python -m citegeist --db library.sqlite3 topic-phrase-reviews --phrase-review-status pending
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```
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|
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Export an editable review template:
|
||
|
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```bash
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.venv/bin/python -m citegeist --db library.sqlite3 export-topic-phrase-reviews
|
||
```
|
||
|
||
Limit exported review rows:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 export-topic-phrase-reviews --limit 10
|
||
```
|
||
|
||
Filter exported rows by status:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 export-topic-phrase-reviews --phrase-review-status rejected
|
||
```
|
||
|
||
Write the review template to a file:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 export-topic-phrase-reviews --output topic-phrase-review.json
|
||
```
|
||
|
||
## Harvest External Repositories
|
||
|
||
Purpose: inspect and harvest OAI-PMH repositories into the library.
|
||
|
||
### OAI-PMH Harvesting
|
||
|
||
Inspect a repository:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist discover-oai https://example.edu/oai
|
||
```
|
||
|
||
Harvest with default metadata prefix:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 harvest-oai https://example.edu/oai
|
||
```
|
||
|
||
Use an alternate metadata prefix:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 harvest-oai https://example.edu/oai --metadata-prefix mods
|
||
```
|
||
|
||
Restrict to a set:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 harvest-oai https://example.edu/oai --set artificial-life
|
||
```
|
||
|
||
Harvest a date range:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 harvest-oai https://example.edu/oai --from 2024-01-01 --until 2024-12-31
|
||
```
|
||
|
||
Limit harvested records and set review status:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 harvest-oai https://example.edu/oai --limit 10 --status draft
|
||
```
|
||
|
||
## Work Through Example Corpora
|
||
|
||
Purpose: run the repo’s example workflows without treating them as the core product surface.
|
||
|
||
### TalkOrigins Example Commands
|
||
|
||
Scrape the example corpus:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist example-talkorigins-scrape talkorigins-out
|
||
```
|
||
|
||
Override the source URL:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist example-talkorigins-scrape talkorigins-out --base-url https://www.talkorigins.org/origins/biblio/
|
||
```
|
||
|
||
Limit topics and entries:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist example-talkorigins-scrape talkorigins-out --limit-topics 5 --limit-entries-per-topic 20
|
||
```
|
||
|
||
Resolve seeds, ingest immediately, and keep expansion disabled:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db library.sqlite3 example-talkorigins-scrape talkorigins-out --resolve-seeds --ingest --no-expand
|
||
```
|
||
|
||
Disable snapshot reuse:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist example-talkorigins-scrape talkorigins-out --no-resume
|
||
```
|
||
|
||
Control generated bootstrap defaults:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist example-talkorigins-scrape talkorigins-out --topic-limit 10 --topic-commit-limit 5 --status draft
|
||
```
|
||
|
||
Validate the generated manifest:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist example-talkorigins-validate talkorigins-out/talkorigins_manifest.json
|
||
```
|
||
|
||
Suggest phrases from the corpus:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist example-talkorigins-suggest-phrases talkorigins-out/talkorigins_manifest.json --topic abiogenesis --limit 10 --output topic-phrases.json
|
||
```
|
||
|
||
Inspect duplicate clusters:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist example-talkorigins-duplicates talkorigins-out/talkorigins_manifest.json --limit 20 --min-count 2 --match origin --topic abiogenesis --preview --weak-only
|
||
```
|
||
|
||
Ingest the reconstructed corpus:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db talkorigins.sqlite3 example-talkorigins-ingest talkorigins-out/talkorigins_manifest.json --status draft
|
||
```
|
||
|
||
Disable deduplication during example ingest:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db talkorigins.sqlite3 example-talkorigins-ingest talkorigins-out/talkorigins_manifest.json --no-dedupe
|
||
```
|
||
|
||
Enrich weak canonical entries:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db talkorigins.sqlite3 example-talkorigins-enrich talkorigins-out/talkorigins_manifest.json --limit 20 --min-count 2 --match origin --topic abiogenesis --status enriched
|
||
```
|
||
|
||
Apply enrichment and allow unsafe search matches for experiments:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db talkorigins-copy.sqlite3 example-talkorigins-enrich talkorigins-out/talkorigins_manifest.json --apply --allow-unsafe-search-matches
|
||
```
|
||
|
||
Export a review artifact:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db talkorigins.sqlite3 example-talkorigins-review talkorigins-out/talkorigins_manifest.json --limit 20 --min-count 2 --match origin --topic abiogenesis --output talkorigins-review.json
|
||
```
|
||
|
||
Apply curated corrections:
|
||
|
||
```bash
|
||
.venv/bin/python -m citegeist --db talkorigins.sqlite3 example-talkorigins-apply-corrections talkorigins-out/talkorigins_manifest.json talkorigins-corrections.json --status reviewed
|
||
```
|
||
|
||
## Notes
|
||
|
||
- Some commands depend on live source access.
|
||
- For topic-oriented examples, use preview mode before committing changes when possible.
|
||
- The older TalkOrigins alias commands remain available, but the example-prefixed names are the preferred surface.
|
||
- For extraction work on OCR-heavy or legacy references, keep regression fixtures for abbreviation-heavy venues such as `Proc.`, `Occas. Pap.`, and `Comm. Rept.` because those are easy places for title/venue splits to go wrong.
|