Skip stub entries in default exports

README.md

@@ -154,6 +154,8 @@ PYTHONPATH=src .venv/bin/python -m citegeist --db library.sqlite3 export --outpu
 
 For a fuller option-by-option CLI cookbook, see [examples/cli/README.md](./examples/cli/README.md).
 
+Broad BibTeX exports skip DOI-only placeholder records such as `Referenced work N` by default. Use `--include-stubs` on `export` or `export-topic` if you want those entries included anyway.
+
 For live-source development, prefer fixture-backed or cache-backed source clients so resolver and expansion work can be exercised repeatedly without re-hitting upstream APIs on every run.
 
 ## Example Application

examples/cli/README.md

@@ -129,6 +129,12 @@ Write BibTeX to a file:
 .venv/bin/python -m citegeist --db library.sqlite3 export --output artificial-life.bib
 ```
 
+Include DOI-only placeholder records in a broad export:
+
+```bash
+.venv/bin/python -m citegeist --db library.sqlite3 export --include-stubs --output artificial-life.bib
+```
+
 ## Review And Clean Metadata
 
 Purpose: inspect merge conflicts, apply corrections, and enrich incomplete records.
@@ -393,6 +399,12 @@ Write the topic slice to a file:
 .venv/bin/python -m citegeist --db library.sqlite3 export-topic artificial-life --output artificial-life-topic.bib
 ```
 
+Include DOI-only placeholder records in the topic export:
+
+```bash
+.venv/bin/python -m citegeist --db library.sqlite3 export-topic artificial-life --include-stubs --output artificial-life-topic.bib
+```
+
 ### Bootstrap
 
 Seed from a BibTeX file:

src/citegeist/cli.py

@@ -43,6 +43,11 @@ def build_parser() -> argparse.ArgumentParser:
     export_parser = subparsers.add_parser("export", help="Export entries as BibTeX")
     export_parser.add_argument("citation_keys", nargs="*", help="Optional citation keys to export")
     export_parser.add_argument("--output", help="Write BibTeX to a file instead of stdout")
+    export_parser.add_argument(
+        "--include-stubs",
+        action="store_true",
+        help="Include DOI-only placeholder records in broad exports",
+    )
 
     status_parser = subparsers.add_parser("set-status", help="Set the review status for one entry")
     status_parser.add_argument("citation_key", help="Citation key to update")
@@ -494,6 +499,11 @@ def build_parser() -> argparse.ArgumentParser:
     )
     export_topic_parser.add_argument("topic_slug", help="Topic slug to export")
     export_topic_parser.add_argument("--output", help="Write BibTeX to a file instead of stdout")
+    export_topic_parser.add_argument(
+        "--include-stubs",
+        action="store_true",
+        help="Include DOI-only placeholder records in the topic export",
+    )
 
     return parser
 
@@ -511,7 +521,7 @@ def main(argv: list[str] | None = None) -> int:
         if args.command == "show":
             return _run_show(store, args.citation_key, args.limit, args.provenance, args.conflicts)
         if args.command == "export":
-            return _run_export(store, args.citation_keys, args.output)
+            return _run_export(store, args.citation_keys, args.output, args.include_stubs)
         if args.command == "set-status":
             return _run_set_status(store, args.citation_key, args.review_status)
         if args.command == "resolve-conflicts":
@@ -660,7 +670,7 @@ def main(argv: list[str] | None = None) -> int:
         if args.command == "topic-entries":
             return _run_topic_entries(store, args.topic_slug, args.limit)
         if args.command == "export-topic":
-            return _run_export_topic(store, args.topic_slug, args.output)
+            return _run_export_topic(store, args.topic_slug, args.output, args.include_stubs)
     finally:
         store.close()
 
@@ -715,8 +725,14 @@ def _run_show(
     return 0
 
 
-def _run_export(store: BibliographyStore, citation_keys: list[str], output: str | None) -> int:
-    rendered = store.export_bibtex(citation_keys or None)
+def _run_export(
+    store: BibliographyStore,
+    citation_keys: list[str],
+    output: str | None,
+    include_stubs: bool,
+) -> int:
+    explicit_keys = citation_keys or None
+    rendered = store.export_bibtex(explicit_keys, include_stubs=include_stubs or explicit_keys is not None)
     if output:
         Path(output).write_text(rendered + ("\n" if rendered else ""), encoding="utf-8")
     else:
@@ -1731,13 +1747,13 @@ def _run_topic_entries(store: BibliographyStore, topic_slug: str, limit: int) ->
     return 0
 
 
-def _run_export_topic(store: BibliographyStore, topic_slug: str, output: str | None) -> int:
+def _run_export_topic(store: BibliographyStore, topic_slug: str, output: str | None, include_stubs: bool) -> int:
     topic = store.get_topic(topic_slug)
     if topic is None:
         print(f"Topic not found: {topic_slug}", file=sys.stderr)
         return 1
     citation_keys = [row["citation_key"] for row in store.list_topic_entries(topic_slug, limit=100000)]
-    rendered = store.export_bibtex(citation_keys)
+    rendered = store.export_bibtex(citation_keys, include_stubs=include_stubs)
     if output:
         Path(output).write_text(rendered + ("\n" if rendered else ""), encoding="utf-8")
     else:

src/citegeist/storage.py

@@ -1010,7 +1010,10 @@ class BibliographyStore:
             return None
         return render_bibtex([entry])
 
-    def export_bibtex(self, citation_keys: list[str] | None = None) -> str:
+    def export_bibtex(self, citation_keys: list[str] | None = None, include_stubs: bool | None = None) -> str:
+        explicit_keys = citation_keys is not None
+        if include_stubs is None:
+            include_stubs = explicit_keys
         if citation_keys is None:
             rows = self.connection.execute(
                 "SELECT citation_key FROM entries ORDER BY COALESCE(year, ''), citation_key"
@@ -1022,6 +1025,8 @@ class BibliographyStore:
         for citation_key in citation_keys:
             entry = self._load_bib_entry(citation_key)
             if entry is not None:
+                if not include_stubs and self._is_export_stub(entry):
+                    continue
                 entries.append(entry)
         if not entries:
             return ""
@@ -1091,6 +1096,22 @@ class BibliographyStore:
             fields=dict(fields),
         )
 
+    def _is_export_stub(self, entry: BibEntry) -> bool:
+        title = " ".join(entry.fields.get("title", "").split()).strip().lower()
+        doi = " ".join(entry.fields.get("doi", "").split()).strip()
+        url = " ".join(entry.fields.get("url", "").split()).strip()
+        has_author = bool(" ".join(entry.fields.get("author", "").split()).strip())
+        has_abstract = bool(" ".join(entry.fields.get("abstract", "").split()).strip())
+        has_journal = bool(" ".join(entry.fields.get("journal", "").split()).strip())
+        has_booktitle = bool(" ".join(entry.fields.get("booktitle", "").split()).strip())
+        if not doi:
+            return False
+        if title and not (title.startswith("referenced work ") or title.startswith("untitled")):
+            return False
+        return not any((has_author, has_abstract, has_journal, has_booktitle)) and (
+            not url or url.startswith("https://doi.org/")
+        )
+
     def _load_creator_names(self, citation_key: str, role: str) -> list[str]:
         rows = self.connection.execute(
             """

tests/test_cli.py

@@ -74,6 +74,42 @@ def test_cli_ingest_show_search_and_export(tmp_path: Path):
     assert "@article{smith2024graphs," in exported
 
 
+def test_cli_export_skips_stub_entries_by_default_but_can_include_them(tmp_path: Path):
+    bib_path = tmp_path / "input.bib"
+    bib_path.write_text(
+        """
+@misc{stubdoi,
+  title = {Referenced work 6},
+  doi = {10.1200/JCO.2002.04.117},
+  url = {https://doi.org/10.1200/JCO.2002.04.117}
+}
+
+@article{realentry,
+  author = {Smith, Jane},
+  title = {Real Entry},
+  year = {2024},
+  doi = {10.1000/real}
+}
+""",
+        encoding="utf-8",
+    )
+
+    assert run_cli(tmp_path, "ingest", str(bib_path)).returncode == 0
+
+    default_export = run_cli(tmp_path, "export")
+    assert default_export.returncode == 0
+    assert "@article{realentry," in default_export.stdout
+    assert "@misc{stubdoi," not in default_export.stdout
+
+    explicit_export = run_cli(tmp_path, "export", "stubdoi")
+    assert explicit_export.returncode == 0
+    assert "@misc{stubdoi," in explicit_export.stdout
+
+    include_export = run_cli(tmp_path, "export", "--include-stubs")
+    assert include_export.returncode == 0
+    assert "@misc{stubdoi," in include_export.stdout
+
+
 def test_cli_provenance_and_status_updates(tmp_path: Path):
     bib_path = tmp_path / "input.bib"
     bib_path.write_text(SAMPLE_BIB, encoding="utf-8")
@@ -1140,6 +1176,52 @@ def test_cli_export_topic(tmp_path: Path):
     assert "@article{seed2024," in exported
 
 
+def test_cli_export_topic_skips_stub_entries_by_default(tmp_path: Path):
+    bib_path = tmp_path / "input.bib"
+    bib_path.write_text(
+        """
+@misc{stubdoi,
+  title = {Referenced work 6},
+  doi = {10.1200/JCO.2002.04.117},
+  url = {https://doi.org/10.1200/JCO.2002.04.117}
+}
+
+@article{seed2024,
+  author = {Seed, Alice},
+  title = {Seed Paper},
+  year = {2024}
+}
+""",
+        encoding="utf-8",
+    )
+    assert run_cli(tmp_path, "ingest", str(bib_path)).returncode == 0
+
+    from citegeist.storage import BibliographyStore
+
+    database = tmp_path / "library.sqlite3"
+    store = BibliographyStore(database)
+    try:
+        for citation_key in ("stubdoi", "seed2024"):
+            store.add_entry_topic(
+                citation_key,
+                topic_slug="graph-methods",
+                topic_name="Graph Methods",
+                source_label="topic-seed",
+            )
+        store.connection.commit()
+    finally:
+        store.close()
+
+    default_export = run_cli(tmp_path, "export-topic", "graph-methods")
+    assert default_export.returncode == 0
+    assert "@article{seed2024," in default_export.stdout
+    assert "@misc{stubdoi," not in default_export.stdout
+
+    include_export = run_cli(tmp_path, "export-topic", "graph-methods", "--include-stubs")
+    assert include_export.returncode == 0
+    assert "@misc{stubdoi," in include_export.stdout
+
+
 def test_cli_search_can_filter_by_topic(tmp_path: Path):
     bib_path = tmp_path / "input.bib"
     bib_path.write_text(

tests/test_storage.py

@@ -69,6 +69,39 @@ def test_store_exports_bibtex_from_normalized_rows():
         store.close()
 
 
+def test_store_export_skips_doi_only_stub_by_default():
+    store = BibliographyStore()
+    try:
+        store.ingest_bibtex(
+            """
+@misc{stubdoi,
+  title = {Referenced work 6},
+  doi = {10.1200/JCO.2002.04.117},
+  url = {https://doi.org/10.1200/JCO.2002.04.117}
+}
+
+@article{realentry,
+  author = {Smith, Jane},
+  title = {Real Entry},
+  year = {2024},
+  doi = {10.1000/real}
+}
+"""
+        )
+
+        exported = store.export_bibtex()
+        assert "@article{realentry," in exported
+        assert "@misc{stubdoi," not in exported
+
+        explicit = store.export_bibtex(["stubdoi"])
+        assert "@misc{stubdoi," in explicit
+
+        with_stubs = store.export_bibtex(include_stubs=True)
+        assert "@misc{stubdoi," in with_stubs
+    finally:
+        store.close()
+
+
 def test_store_records_provenance_and_review_status():
     store = BibliographyStore()
     try: