feat(pmid): retrieve PublicationTypeList from PubMed metadata

[caufieldjh]

Closes #56.

Retrieves PubMed's PublicationTypeList — the MeSH publication-type descriptors that classify a source (e.g. "Case Reports", "Clinical Trial", "Review"; full list at https://www.nlm.nih.gov/mesh/pubtypes.html) — and surfaces it end-to-end.

Changes

• ReferenceContent gains a publication_types: Optional[list[str]] field, the single carrier for citation metadata.
• PMIDSource now fetches the article XML once and parses both MeSH terms and publication types from it, avoiding a second NCBI round-trip. Split into _fetch_pubmed_xml (fetch) plus pure parsers _parse_mesh_terms / _parse_publication_types.
• Persisted to and reloaded from the disk-cache YAML frontmatter (round-trips through the cache).
• Exposed in lookup json / yaml / text output.

Example

A real lookup of PMID:33301246 (the BNT162b2 trial paper) now caches:

publication_types:
- "Clinical Trial, Phase II"
- "Clinical Trial, Phase III"
- Journal Article
- Multicenter Study
- Randomized Controlled Trial
- "Research Support, Non-U.S. Gov't"

Notes

• Values are preserved verbatim from PubMed, including the generic Journal Article type that tags nearly every record — not filtered, since it's a legitimate value downstream consumers may want.

Testing

Tests written first (TDD), following the repo's mocked-Entrez pattern: XML parse (present/absent), fetch() population with mocked Entrez.efetch, disk-cache round-trip, plus doctests on the parsers. Verified live against PMID:33301246.

Full just test green: 619 passed, mypy clean, ruff clean.

🤖 Generated with Claude Code

[claude]

Claude finished @caufieldjh's task in 1m 39s —— View job

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PR Review: PublicationTypeList from PubMed metadata

• Read changed files
• Review code quality & best practices
• Check for bugs / edge cases
• Assess test coverage
• Post review

Overall this is a clean, well-scoped change. It follows the repo's TDD conventions, adds real (mocked-Entrez) tests plus doctests, threads the new field consistently through model → source → cache → CLI, and the docstrings are genuinely helpful. Nice work. A few notes below, none blocking.

👍 Strengths

• TDD + doctests on both parsers (_parse_mesh_terms, _parse_publication_types) — matches CLAUDE.md guidance.
• Good refactor: splitting fetch (_fetch_pubmed_xml) from pure parsing makes the parsers trivially unit-testable without mocking Entrez, and folding MeSH + pub-types into one XML fetch removes a redundant NCBI round-trip.
• End-to-end threading is complete and symmetric with the existing keywords handling (model default None, cache save/load, json/yaml/text output).
• find_all("PublicationType") is correctly scoped to type_list rather than the whole document, and the walrus filter drops empty values.

🔧 Minor suggestions (non-blocking)

1. Redundant self-assignment in cache load — reference_fetcher.py:638-644

publication_types = frontmatter.get("publication_types")
if publication_types and isinstance(publication_types, list):
    publication_types = publication_types   # no-op branch
elif publication_types:
    publication_types = [publication_types]
else:
    publication_types = None

The publication_types = publication_types branch is a no-op. This is a faithful copy of the existing authors/keywords blocks just above (lines 622-636), so it's consistent with current style — but all three could collapse to a small helper, e.g.:

def _as_optional_list(value):
    if not value:
        return None
    return value if isinstance(value, list) else [value]

Worth doing only if you want to tidy the trio together; otherwise consistency is a fine reason to leave it.

2. Still two efetch calls per PMID — pmid.py:140-141
_fetch_abstract (rettype="abstract", text) and _fetch_pubmed_xml (rettype="xml") are separate calls, each with its own rate_limit_delay sleep. The article XML already contains the abstract, so in principle both could come from the single XML fetch. This is a pre-existing pattern (the abstract was always fetched separately) and the formatted text abstract is convenient, so it's reasonable to defer — just flagging it as the natural next optimization now that the XML is already in hand.

3. Test gap: empty PublicationTypeList — test_sources.py
test_parse_publication_types_absent covers the missing-element path, but not an element that's present-but-empty (<PublicationTypeList></PublicationTypeList>), which exercises the return types if types else None branch. A one-line case would close that. Same untested branch exists for _parse_mesh_terms.

Bugs / security / performance

No correctness bugs spotted. No security concerns (read-only parsing of NCBI XML, values preserved verbatim). Performance is neutral-to-slightly-better (one fewer XML fetch than before). The is not None handling for None article XML is correct.

Test coverage is solid for the happy paths and the round-trip; the only real gap is the empty-list edge case above.

[caufieldjh]

Thanks for the review! Addressed in 9caecc9:

Note 1 (redundant self-assignment) — collapsed the authors / keywords / publication_types frontmatter blocks into a shared _as_optional_list staticmethod (with a doctest). The no-op branches are gone and all three are consistent.

Note 3 (empty-list edge case) — added test_parse_publication_types_empty_list and test_parse_mesh_terms_empty_list, both exercising the present-but-empty element path (return x if x else None).

Note 2 (still two efetch calls) — deferring for now. The rettype="abstract"&retmode="text" fetch returns a fuller human-formatted citation block than the raw AbstractText XML nodes, and that text is what feeds supporting-text validation. There's no test currently pinning the abstract format, so folding it into the XML fetch is a behavior change rather than a mechanical cleanup — better as its own PR with a format-equivalence test. Flagging as follow-up, as you noted it's deferrable.

just test green: 621 passed, mypy + ruff clean.

[claude]

Claude finished @caufieldjh's task in 1m 14s —— View job

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Follow-up review — fixes in 9caecc9 ✅

I re-reviewed the commit that addressed my earlier notes. All three items are handled correctly.

• Read the follow-up commit (9caecc9)
• Verify review notes were addressed correctly
• Check new helper + tests for bugs/edge cases
• Post review

Note 1 — list-coercion helper ✅

_as_optional_list (reference_fetcher.py:600) cleanly collapses the three duplicated authors / keywords / publication_types blocks, no-op branches gone. Behavior is equivalent to the originals: the old code used if value and isinstance(value, list), so an empty list [] was falsy and fell through to None — the new if not value: return None preserves that exactly, and also folds in the empty-string / empty-list cases. The doctest covers list / scalar / None. Good.

Note 3 — empty-element edge cases ✅

test_parse_publication_types_empty_list and test_parse_mesh_terms_empty_list correctly target the intended branch: soup.find("...") on a present-but-empty element returns a truthy Tag, so it passes the if not ...: return None guard, then find_all yields nothing → the return x if x else None branch fires. This is genuinely the previously-untested path, not a duplicate of the _absent case.

Note 2 — single-fetch optimization

Reasonable deferral, and the reasoning in the commit message is sound: the rettype="abstract"&retmode="text" block is a richer human-formatted citation than raw AbstractText nodes and feeds supporting-text validation, so folding it into the XML fetch is a behavior change needing a format-equivalence test — better as its own PR. Agreed it's a follow-up, not a blocker.

Minor nit (non-blocking)

_as_optional_list is annotated Optional[list] rather than Optional[list[str]]. It's a generic coercion helper so the bare list is defensible, and mypy is clean — leaving it is fine.

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Nothing outstanding on my end. The change is complete, consistent, and the edge cases my earlier review flagged are now covered. LGTM 🚀

Note: I couldn't run the test suite here (test execution wasn't permitted in this job), so I'm relying on the reported just test green (621 passed, mypy + ruff clean) plus static analysis of the diff.