526 lines
16 KiB
Python
526 lines
16 KiB
Python
from citegeist import BibliographyStore, parse_bibtex
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SAMPLE_BIB = """
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@article{smith2024graphs,
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author = {Smith, Jane and Doe, Alex},
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title = {Graph-first bibliography augmentation},
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year = {2024},
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doi = {10.1000/graph.2024.1},
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abstract = {We study citation graphs for literature discovery.},
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references = {miller2023search}
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}
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@inproceedings{miller2023search,
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author = {Miller, Sam},
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title = {Semantic search for research corpora},
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year = {2023},
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abstract = {Dense retrieval improves recall for academic search.}
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}
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"""
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def test_parse_bibtex_extracts_entries_and_fields():
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entries = parse_bibtex(SAMPLE_BIB)
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assert [entry.citation_key for entry in entries] == ["smith2024graphs", "miller2023search"]
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assert entries[0].fields["title"] == "Graph-first bibliography augmentation"
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assert entries[0].fields["references"] == "miller2023search"
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def test_store_ingests_entries_relations_and_search_text():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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SAMPLE_BIB,
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fulltext_by_key={
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"smith2024graphs": "This paper links citation graphs with semantic search over abstracts."
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},
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)
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entry = store.get_entry("smith2024graphs")
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assert entry is not None
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assert entry["doi"] == "10.1000/graph.2024.1"
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assert store.get_relations("smith2024graphs") == ["miller2023search"]
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results = store.search_text("semantic")
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assert [row["citation_key"] for row in results][:2] == [
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"miller2023search",
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"smith2024graphs",
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]
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finally:
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store.close()
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def test_store_exports_bibtex_from_normalized_rows():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(SAMPLE_BIB)
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exported = store.export_bibtex()
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parsed = {entry.citation_key: entry for entry in parse_bibtex(exported)}
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assert "@article{smith2024graphs," in exported
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assert "@inproceedings{miller2023search," in exported
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assert parsed["smith2024graphs"].fields["author"] == "Smith, Jane and Doe, Alex"
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assert parsed["smith2024graphs"].fields["references"] == "miller2023search"
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finally:
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store.close()
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def test_store_export_skips_doi_only_stub_by_default():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@misc{stubdoi,
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title = {Referenced work 6},
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doi = {10.1200/JCO.2002.04.117},
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url = {https://doi.org/10.1200/JCO.2002.04.117}
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}
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@article{realentry,
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author = {Smith, Jane},
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title = {Real Entry},
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year = {2024},
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doi = {10.1000/real}
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}
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"""
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)
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exported = store.export_bibtex()
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assert "@article{realentry," in exported
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assert "@misc{stubdoi," not in exported
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explicit = store.export_bibtex(["stubdoi"])
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assert "@misc{stubdoi," in explicit
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with_stubs = store.export_bibtex(include_stubs=True)
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assert "@misc{stubdoi," in with_stubs
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finally:
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store.close()
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def test_store_records_provenance_and_review_status():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(SAMPLE_BIB, source_label="fixtures/sample.bib", review_status="draft")
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entry = store.get_entry("smith2024graphs")
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assert entry is not None
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assert entry["review_status"] == "draft"
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provenance = store.get_field_provenance("smith2024graphs")
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assert provenance
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assert provenance[0]["source_type"] == "bibtex"
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assert provenance[0]["source_label"] == "fixtures/sample.bib"
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assert store.set_entry_status("smith2024graphs", "reviewed") is True
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updated = store.get_entry("smith2024graphs")
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assert updated is not None
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assert updated["review_status"] == "reviewed"
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finally:
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store.close()
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def test_store_traverses_graph_and_surfaces_missing_targets():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@article{seed2024,
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author = {Seed, Alice},
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title = {Seed Paper},
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year = {2024},
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references = {known2023, missing2022}
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}
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@article{known2023,
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author = {Known, Bob},
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title = {Known Paper},
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year = {2023},
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references = {leaf2021}
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}
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@article{leaf2021,
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author = {Leaf, Carol},
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title = {Leaf Paper},
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year = {2021}
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}
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""",
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review_status="reviewed",
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)
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rows = store.traverse_graph(["seed2024"], relation_types=["cites"], max_depth=2)
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assert [row["target_citation_key"] for row in rows] == [
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"known2023",
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"missing2022",
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"leaf2021",
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]
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assert rows[1]["target_exists"] is False
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assert rows[2]["depth"] == 2
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finally:
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store.close()
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def test_store_records_and_updates_field_conflicts():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@article{seed2024,
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author = {Seed, Alice},
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title = {Seed Paper},
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year = {2024}
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}
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"""
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)
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ok = store.record_conflicts(
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"seed2024",
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[
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{
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"field_name": "title",
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"current_value": "Seed Paper",
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"proposed_value": "Resolved Seed Paper",
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}
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],
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source_type="resolver",
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source_label="crossref:doi:10.1000/seed",
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)
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assert ok is True
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conflicts = store.get_field_conflicts("seed2024")
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assert conflicts[0]["field_name"] == "title"
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assert conflicts[0]["status"] == "open"
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assert store.set_conflict_status("seed2024", "title", "accepted") == 1
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updated = store.get_field_conflicts("seed2024", status="accepted")
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assert len(updated) == 1
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finally:
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store.close()
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def test_store_can_apply_latest_conflict_value():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@article{seed2024,
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author = {Seed, Alice},
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title = {Seed Paper},
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year = {2024}
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}
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"""
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)
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store.record_conflicts(
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"seed2024",
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[
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{
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"field_name": "title",
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"current_value": "Seed Paper",
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"proposed_value": "Resolved Seed Paper",
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}
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],
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source_type="resolver",
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source_label="crossref:doi:10.1000/seed",
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)
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assert store.apply_conflict_value("seed2024", "title") is True
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entry = store.get_entry("seed2024")
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assert entry is not None
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assert entry["title"] == "Resolved Seed Paper"
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accepted = store.get_field_conflicts("seed2024", status="accepted")
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assert len(accepted) == 1
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finally:
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store.close()
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def test_store_supports_entry_topic_membership():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@article{seed2024,
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author = {Seed, Alice},
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title = {Seed Paper},
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year = {2024}
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}
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"""
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)
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assert store.add_entry_topic(
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"seed2024",
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topic_slug="graph-methods",
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topic_name="Graph Methods",
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source_type="talkorigins",
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source_url="https://example.org/topics/graph-methods",
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source_label="topic-seed",
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) is True
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assert store.add_entry_topic(
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"seed2024",
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topic_slug="semantic-search",
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topic_name="Semantic Search",
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source_type="talkorigins",
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source_url="https://example.org/topics/semantic-search",
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source_label="topic-seed",
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) is True
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entry = store.get_entry("seed2024")
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assert entry is not None
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assert [topic["slug"] for topic in entry["topics"]] == ["graph-methods", "semantic-search"]
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topics = store.list_topics()
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assert [topic["slug"] for topic in topics] == ["graph-methods", "semantic-search"]
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assert topics[0]["entry_count"] == 1
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topic = store.get_topic("graph-methods")
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assert topic is not None
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assert topic["name"] == "Graph Methods"
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assert topic["expansion_phrase"] is None
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topic_entries = store.list_topic_entries("graph-methods")
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assert topic_entries[0]["citation_key"] == "seed2024"
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finally:
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store.close()
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def test_store_can_set_topic_expansion_phrase():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@article{seed2024,
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author = {Seed, Alice},
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title = {Seed Paper},
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year = {2024}
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}
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"""
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)
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store.add_entry_topic(
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"seed2024",
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topic_slug="graph-methods",
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topic_name="Graph Methods",
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source_type="talkorigins",
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source_url="https://example.org/topics/graph-methods",
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source_label="topic-seed",
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)
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assert store.set_topic_expansion_phrase("graph-methods", "graph networks biology") is True
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topic = store.get_topic("graph-methods")
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assert topic is not None
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assert topic["expansion_phrase"] == "graph networks biology"
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assert topic["phrase_review_status"] == "unreviewed"
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topics = store.list_topics()
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assert topics[0]["expansion_phrase"] == "graph networks biology"
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finally:
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store.close()
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def test_store_lists_stub_resolution_candidates():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@misc{stubdoi,
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title = {Referenced work 6},
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doi = {10.1200/JCO.2002.04.117},
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url = {https://doi.org/10.1200/JCO.2002.04.117}
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}
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@article{complete,
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author = {Smith, Jane},
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title = {Complete Record},
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year = {2024},
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doi = {10.1000/complete}
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}
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"""
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)
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store.add_entry_topic(
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"stubdoi",
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topic_slug="artificial-life",
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topic_name="Artificial life",
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source_label="test",
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)
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candidates = store.list_resolution_candidates(limit=10, doi_only=True, stub_only=True)
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assert [row["citation_key"] for row in candidates] == ["stubdoi"]
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topic_candidates = store.list_resolution_candidates(
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limit=10,
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doi_only=True,
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stub_only=True,
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topic_slug="artificial-life",
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)
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assert [row["citation_key"] for row in topic_candidates] == ["stubdoi"]
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finally:
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store.close()
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def test_store_can_list_all_misc_resolution_candidates():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@misc{miscwithtitle,
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author = {Doe, Alex},
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title = {Avida Conference Record},
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year = {2005},
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doi = {10.1117/12.512613}
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}
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@article{complete,
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author = {Smith, Jane},
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title = {Complete Record},
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year = {2024},
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doi = {10.1000/complete}
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}
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"""
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)
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candidates = store.list_resolution_candidates(limit=10, doi_only=True, misc_only=True)
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assert [row["citation_key"] for row in candidates] == ["miscwithtitle"]
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finally:
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store.close()
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def test_store_can_stage_and_review_topic_phrase_suggestion():
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store = BibliographyStore()
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try:
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store.ensure_topic("graph-methods", "Graph Methods")
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assert store.stage_topic_phrase_suggestion(
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"graph-methods",
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"graph networks biology",
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review_notes="generated from local titles",
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) is True
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staged = store.get_topic("graph-methods")
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assert staged is not None
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assert staged["suggested_phrase"] == "graph networks biology"
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assert staged["expansion_phrase"] is None
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assert staged["phrase_review_status"] == "pending"
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assert staged["phrase_review_notes"] == "generated from local titles"
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assert store.review_topic_phrase_suggestion(
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"graph-methods",
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"accepted",
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review_notes="looks good",
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) is True
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reviewed = store.get_topic("graph-methods")
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assert reviewed is not None
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assert reviewed["suggested_phrase"] is None
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assert reviewed["expansion_phrase"] == "graph networks biology"
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assert reviewed["phrase_review_status"] == "accepted"
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assert reviewed["phrase_review_notes"] == "looks good"
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finally:
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store.close()
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def test_store_can_filter_topics_by_phrase_review_status():
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store = BibliographyStore()
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try:
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store.ensure_topic("graph-methods", "Graph Methods")
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store.ensure_topic("abiogenesis", "Abiogenesis")
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store.stage_topic_phrase_suggestion("graph-methods", "graph networks biology")
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store.stage_topic_phrase_suggestion("abiogenesis", "abiogenesis life origin")
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store.review_topic_phrase_suggestion("abiogenesis", "accepted")
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pending_topics = store.list_topics(phrase_review_status="pending")
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accepted_topics = store.list_topics(phrase_review_status="accepted")
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assert [topic["slug"] for topic in pending_topics] == ["graph-methods"]
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assert [topic["slug"] for topic in accepted_topics] == ["abiogenesis"]
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finally:
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store.close()
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def test_store_can_list_topic_phrase_reviews():
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store = BibliographyStore()
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try:
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store.ensure_topic("graph-methods", "Graph Methods")
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store.ensure_topic("abiogenesis", "Abiogenesis")
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store.ensure_topic("plain-topic", "Plain Topic")
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store.stage_topic_phrase_suggestion("graph-methods", "graph networks biology")
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store.stage_topic_phrase_suggestion("abiogenesis", "abiogenesis life origin")
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store.review_topic_phrase_suggestion("abiogenesis", "accepted")
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reviews = store.list_topic_phrase_reviews()
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pending_reviews = store.list_topic_phrase_reviews(phrase_review_status="pending")
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assert [review["slug"] for review in reviews] == ["graph-methods"]
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assert reviews[0]["suggested_phrase"] == "graph networks biology"
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assert reviews[0]["phrase_review_status"] == "pending"
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assert [review["slug"] for review in pending_reviews] == ["graph-methods"]
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finally:
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store.close()
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def test_store_rejected_topic_phrase_stays_in_review_queue():
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store = BibliographyStore()
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try:
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store.ensure_topic("graph-methods", "Graph Methods")
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store.stage_topic_phrase_suggestion("graph-methods", "graph networks biology")
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assert store.review_topic_phrase_suggestion(
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"graph-methods",
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"rejected",
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review_notes="too broad",
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) is True
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topic = store.get_topic("graph-methods")
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assert topic is not None
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assert topic["suggested_phrase"] == "graph networks biology"
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assert topic["expansion_phrase"] is None
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assert topic["phrase_review_status"] == "rejected"
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reviews = store.list_topic_phrase_reviews()
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assert [review["slug"] for review in reviews] == ["graph-methods"]
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assert reviews[0]["phrase_review_status"] == "rejected"
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finally:
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store.close()
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def test_store_search_text_can_filter_by_topic():
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store = BibliographyStore()
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try:
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store.ingest_bibtex(
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"""
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@article{seed2024,
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author = {Seed, Alice},
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title = {Graph Methods for Biology},
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year = {2024},
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abstract = {A graph methods paper.}
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}
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@article{other2023,
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author = {Other, Bob},
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title = {Graph Methods for Chemistry},
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year = {2023},
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abstract = {Another graph methods paper.}
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}
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"""
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)
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store.add_entry_topic(
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"seed2024",
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topic_slug="biology",
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topic_name="Biology",
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source_type="talkorigins",
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source_url="https://example.org/topics/biology",
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source_label="topic-seed",
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)
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store.add_entry_topic(
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"other2023",
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topic_slug="chemistry",
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topic_name="Chemistry",
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source_type="talkorigins",
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source_url="https://example.org/topics/chemistry",
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source_label="topic-seed",
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)
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store.connection.commit()
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results = store.search_text("graph", topic_slug="biology")
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assert [row["citation_key"] for row in results] == ["seed2024"]
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finally:
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store.close()
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