Add misc re-enrichment mode

README.md

@@ -134,6 +134,7 @@ PYTHONPATH=src .venv/bin/python -m citegeist --db library.sqlite3 bootstrap --to
 PYTHONPATH=src .venv/bin/python -m citegeist extract references.txt --output draft.bib
 PYTHONPATH=src .venv/bin/python -m citegeist --db library.sqlite3 resolve smith2024graphs
 PYTHONPATH=src .venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --preview --limit 25
+PYTHONPATH=src .venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --all-misc --limit 25
 PYTHONPATH=src .venv/bin/python -m citegeist --db library.sqlite3 topics
 PYTHONPATH=src .venv/bin/python -m citegeist --db library.sqlite3 topic-entries abiogenesis
 PYTHONPATH=src .venv/bin/python -m citegeist --db library.sqlite3 export-topic abiogenesis --output abiogenesis.bib

examples/cli/README.md

@@ -199,6 +199,18 @@ Enrich DOI-bearing placeholder records inside one topic slice:
 .venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --topic artificial-life --limit 25
 ```
 
+Preview all current `@misc` entries with DOIs, not just placeholder-like stubs:
+
+```bash
+.venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --all-misc --preview --limit 25
+```
+
+Re-enrich all current `@misc` entries with DOIs:
+
+```bash
+.venv/bin/python -m citegeist --db library.sqlite3 resolve-stubs --doi-only --all-misc --limit 25
+```
+
 ## Explore Citation Graphs
 
 Purpose: traverse citation edges, export graph data, and render quick visualizations.

src/citegeist/cli.py

@@ -82,6 +82,11 @@ def build_parser() -> argparse.ArgumentParser:
         action="store_true",
         help="Only consider candidates that already have a DOI",
     )
+    resolve_stubs_parser.add_argument(
+        "--all-misc",
+        action="store_true",
+        help="Consider all stored @misc entries instead of only placeholder-like stub records",
+    )
     resolve_stubs_parser.add_argument(
         "--topic",
         help="Optional topic slug to limit candidate selection",
@@ -533,7 +538,7 @@ def main(argv: list[str] | None = None) -> int:
         if args.command == "resolve":
             return _run_resolve(store, args.citation_keys)
         if args.command == "resolve-stubs":
-            return _run_resolve_stubs(store, args.limit, args.doi_only, args.topic, args.preview)
+            return _run_resolve_stubs(store, args.limit, args.doi_only, args.all_misc, args.topic, args.preview)
         if args.command == "graph":
             return _run_graph(
                 store,
@@ -824,13 +829,15 @@ def _run_resolve_stubs(
     store: BibliographyStore,
     limit: int,
     doi_only: bool,
+    all_misc: bool,
     topic_slug: str | None,
     preview: bool,
 ) -> int:
     candidates = store.list_resolution_candidates(
         limit=limit,
         doi_only=doi_only,
-        stub_only=True,
+        stub_only=not all_misc,
+        misc_only=all_misc,
         topic_slug=topic_slug,
     )
     if preview:

src/citegeist/resolve.py

@@ -292,7 +292,7 @@ def merge_entries_with_conflicts(base: BibEntry, resolved: BibEntry) -> tuple[Bi
             merged_fields[key] = value
     return (
         BibEntry(
-            entry_type=base.entry_type or resolved.entry_type,
+            entry_type=_merged_entry_type(base.entry_type, resolved.entry_type),
             citation_key=base.citation_key,
             fields=merged_fields,
         ),
@@ -310,6 +310,12 @@ def _is_placeholder_value(field_name: str, value: str) -> bool:
     return False
 
 
+def _merged_entry_type(base_entry_type: str, resolved_entry_type: str) -> str:
+    if base_entry_type == "misc" and resolved_entry_type and resolved_entry_type != "misc":
+        return resolved_entry_type
+    return base_entry_type or resolved_entry_type
+
+
 def _crossref_message_to_entry(message: dict) -> BibEntry:
     entry_type = _crossref_type_to_bibtype(message.get("type", "article"))
     title_values = message.get("title", [])

src/citegeist/storage.py

@@ -472,6 +472,7 @@ class BibliographyStore:
         limit: int = 50,
         doi_only: bool = False,
         stub_only: bool = False,
+        misc_only: bool = False,
         topic_slug: str | None = None,
     ) -> list[dict[str, object]]:
         clauses: list[str] = []
@@ -489,6 +490,9 @@ class BibliographyStore:
         if doi_only:
             clauses.append("e.doi IS NOT NULL AND TRIM(e.doi) <> ''")
 
+        if misc_only:
+            clauses.append("e.entry_type = 'misc'")
+
         if stub_only:
             clauses.append(
                 """

tests/test_cli.py

@@ -218,6 +218,34 @@ def test_cli_resolve_stubs_preview_lists_doi_stub_candidates(tmp_path: Path):
     assert payload[0]["title"] == "Referenced work 6"
 
 
+def test_cli_resolve_stubs_preview_can_target_all_misc_entries(tmp_path: Path):
+    bib_path = tmp_path / "input.bib"
+    bib_path.write_text(
+        """
+@misc{miscwithtitle,
+  author = {Doe, Alex},
+  title = {Avida Conference Record},
+  year = {2005},
+  doi = {10.1117/12.512613}
+}
+
+@article{complete,
+  author = {Smith, Jane},
+  title = {Complete Record},
+  year = {2024},
+  doi = {10.1000/complete}
+}
+""",
+        encoding="utf-8",
+    )
+    assert run_cli(tmp_path, "ingest", str(bib_path)).returncode == 0
+
+    result = run_cli(tmp_path, "resolve-stubs", "--doi-only", "--all-misc", "--preview", "--limit", "10")
+    assert result.returncode == 0
+    payload = json.loads(result.stdout)
+    assert [row["citation_key"] for row in payload] == ["miscwithtitle"]
+
+
 def test_cli_resolve_stubs_enriches_matching_candidates(tmp_path: Path):
     bib_path = tmp_path / "input.bib"
     bib_path.write_text(
@@ -271,6 +299,63 @@ def test_cli_resolve_stubs_enriches_matching_candidates(tmp_path: Path):
     assert payload["review_status"] == "enriched"
 
 
+def test_cli_resolve_stubs_can_enrich_all_misc_entries(tmp_path: Path):
+    bib_path = tmp_path / "input.bib"
+    bib_path.write_text(
+        """
+@misc{miscwithtitle,
+  author = {Doe, Alex},
+  title = {Avida Conference Record},
+  year = {2005},
+  doi = {10.1117/12.512613}
+}
+""",
+        encoding="utf-8",
+    )
+    assert run_cli(tmp_path, "ingest", str(bib_path)).returncode == 0
+
+    from citegeist.bibtex import BibEntry
+    from citegeist.resolve import Resolution
+
+    database = tmp_path / "library.sqlite3"
+
+    with patch("citegeist.cli.MetadataResolver.resolve_entry") as mocked_resolve:
+        mocked_resolve.return_value = Resolution(
+            entry=BibEntry(
+                entry_type="inproceedings",
+                citation_key="resolvedkey",
+                fields={
+                    "author": "Koza, J. R.",
+                    "title": "Genetic Programming IV: Routine Human-Competitive Machine Intelligence",
+                    "year": "2005",
+                    "booktitle": "Genetic and Evolutionary Computation Conference",
+                    "doi": "10.1117/12.512613",
+                },
+            ),
+            source_type="resolver",
+            source_label="crossref:doi:10.1117/12.512613",
+        )
+        exit_code = main(
+            [
+                "--db",
+                str(database),
+                "resolve-stubs",
+                "--doi-only",
+                "--all-misc",
+                "--limit",
+                "10",
+            ]
+        )
+
+    assert exit_code == 0
+    show = run_cli(tmp_path, "show", "--conflicts", "miscwithtitle")
+    payload = json.loads(show.stdout)
+    assert payload["entry_type"] == "inproceedings"
+    assert payload["title"] == "Avida Conference Record"
+    assert payload["booktitle"] == "Genetic and Evolutionary Computation Conference"
+    assert "title" in {item["field_name"] for item in payload["field_conflicts"]}
+
+
 def test_cli_resolve_conflicts_updates_status(tmp_path: Path):
     bib_path = tmp_path / "input.bib"
     bib_path.write_text(

tests/test_resolve.py

@@ -128,6 +128,30 @@ def test_merge_entries_replaces_placeholder_titles_without_conflict():
     assert conflicts == []
 
 
+def test_merge_entries_upgrades_misc_type_when_resolver_has_better_type():
+    base = BibEntry(
+        entry_type="misc",
+        citation_key="miscwithtitle",
+        fields={"title": "Avida Conference Record", "doi": "10.1117/12.512613"},
+    )
+    resolved = BibEntry(
+        entry_type="inproceedings",
+        citation_key="resolved",
+        fields={"title": "Genetic Programming IV", "booktitle": "GECCO"},
+    )
+
+    merged, conflicts = merge_entries_with_conflicts(base, resolved)
+
+    assert merged.entry_type == "inproceedings"
+    assert conflicts == [
+        {
+            "field_name": "title",
+            "current_value": "Avida Conference Record",
+            "proposed_value": "Genetic Programming IV",
+        }
+    ]
+
+
 def test_resolver_tries_doi_before_dblp():
     resolver = MetadataResolver()
     calls: list[tuple[str, str]] = []

tests/test_storage.py

@@ -354,6 +354,33 @@ def test_store_lists_stub_resolution_candidates():
         store.close()
 
 
+def test_store_can_list_all_misc_resolution_candidates():
+    store = BibliographyStore()
+    try:
+        store.ingest_bibtex(
+            """
+@misc{miscwithtitle,
+  author = {Doe, Alex},
+  title = {Avida Conference Record},
+  year = {2005},
+  doi = {10.1117/12.512613}
+}
+
+@article{complete,
+  author = {Smith, Jane},
+  title = {Complete Record},
+  year = {2024},
+  doi = {10.1000/complete}
+}
+"""
+        )
+
+        candidates = store.list_resolution_candidates(limit=10, doi_only=True, misc_only=True)
+        assert [row["citation_key"] for row in candidates] == ["miscwithtitle"]
+    finally:
+        store.close()
+
+
 def test_store_can_stage_and_review_topic_phrase_suggestion():
     store = BibliographyStore()
     try: